Nanoporous anodic aluminum oxide with a long-range order and tunable cell sizes by phosphoric acid anodization on pre-patterned substrates

PubMed Central

Surawathanawises, Krissada; Cheng, Xuanhong

2014-01-01

Nanoporous anodic aluminum oxide (AAO) has been explored for various applications due to its regular cell arrangement and relatively easy fabrication processes. However, conventional two-step anodization based on self-organization only allows the fabrication of a few discrete cell sizes and formation of small domains of hexagonally packed pores. Recent efforts to pre-pattern aluminum followed with anodization significantly improve the regularity and available pore geometries in AAO, while systematic study of the anodization condition, especially the impact of acid composition on pore formation guided by nanoindentation is still lacking. In this work, we pre-patterned aluminium thin films using ordered monolayers of silica beads and formed porous AAO in a single-step anodization in phosphoric acid. Controllable cell sizes ranging from 280 nm to 760 nm were obtained, matching the diameters of the silica nanobead molds used. This range of cell size is significantly greater than what has been reported for AAO formed in phosphoric acid in the literature. In addition, the relationships between the acid concentration, cell size, pore size, anodization voltage and film growth rate were studied quantitatively. The results are consistent with the theory of oxide formation through an electrochemical reaction. Not only does this study provide useful operational conditions of nanoindentation induced anodization in phosphoric acid, it also generates significant information for fundamental understanding of AAO formation. PMID:24535886

Pore Effect on the Occurrence and Formation of Gas Hydrate in Permafrost of Qilian Mountain, Qinghai-Tibet Plateau, China

NASA Astrophysics Data System (ADS)

Gao, H.; Lu, H.; Lu, Z.

2014-12-01

Gas hydrates were found in the permafrost of Qilian Mountain, Qinghai- Tibet Plateau, China in 2008. It has been found that gas hydrates occur in Jurassic sedimentary rocks, and the hydrated gases are mainly thermogenic. Different from the gas hydrates existing in loose sands in Mallik, Mackenzie Delta, Canada and North Slope, Alaska, USA, the gas hydrates in Qilian Mountain occurred in hard rocks. For understanding the occurrence and formation mechanism of gas hydrate in hard rcok, extensive experimental investigations have been conducted to study the pore features and hydrate formation in the rocks recovered from the hydrate layers in Qilian Mountain. The structures of sedimentary rock were observed by high-resolution X-ray CT, and pore size distribution of a rock specimen was measured with the mercury-injection method. Methane hydrate was synthesized in water-saturated rocks, and the saturations of hydrate in sedimentary rocks of various types were estimated from the amount of gas released from certain volume of rock. X-ray CT observation revealed that fractures were developed in the rocks associated with faults, while those away from faults were generally with massive structure. The mercury-injection analysis of pore features found that the porosities of the hydrate-existing rocks were generally less than 3%, and the pore sizes were generally smaller than 100 nm. The synthesizing experiments found that the saturation of methane hydrate were generally lower than 6% of pore space in rocks, but up to 16% when fractures developed. The low hydrate saturation in Qilian sedimentary rocks has been found mainly due to the small pore size of rock. The low hydrate saturation in the rocks might be the reason for the failure of regional seismic and logging detections of gas hydrates in Qilian Mountain.

Pore dynamics in lipid membranes

NASA Astrophysics Data System (ADS)

Gozen, I.; Dommersnes, P.

2014-09-01

Transient circular pores can open in plasma membrane of cells due to mechanical stress, and failure to repair such pores lead to cell death. Similar pores in the form of defects also exist among smectic membranes, such as in myelin sheaths or mitochondrial membranes. The formation and growth of membrane defects are associated with diseases, for example multiple sclerosis. A deeper understanding of membrane pore dynamics can provide a more refined picture of membrane integrity-related disease development, and possibly also treatment options and strategies. Pore dynamics is also of great importance regarding healthcare applications such as drug delivery, gene or as recently been implied, cancer therapy. The dynamics of pores significantly differ in stacks which are confined in 2D compared to those in cells or vesicles. In this short review, we will summarize the dynamics of different types of pores that can be observed in biological membranes, which include circular transient, fusion and hemi-fusion pores. We will dedicate a section to floral and fractal pores which were discovered a few years ago and have highly peculiar characteristics. Finally, we will discuss the repair mechanisms of large area pores in conjunction with the current cell membrane repair hypotheses.

Investigating Hydrophilic Pores in Model Lipid Bilayers using Molecular Simulations: Correlating Bilayer Properties with Pore Formation Thermodynamics

PubMed Central

Hu, Yuan; Sinha, Sudipta Kumar

2015-01-01

Cell-penetrating and antimicrobial peptides show remarkable ability to translocate across physiological membranes. Along with factors such as electric potential induced-perturbations of membrane structure and surface tension effects, experiments invoke pore-like membrane configurations during the solute transfer process into vesicles and cells. The initiation and formation of pores are associated with a non-trivial free energy cost, thus necessitating consideration of the factors associated with pore formation and attendant free energetics. Due to experimental and modeling challenges related to the long timescales of the translocation process, we use umbrella-sampling molecular dynamics simulations with a lipid-density based order parameter to investigate membrane pore-formation free energy employing Martini coarse-grained models. We investigate structure and thermodynamic features of the pore in 18 lipids spanning a range of head-groups, charge states, acyl chain lengths and saturation. We probe the dependence of pore-formation barriers on area per lipid, lipid bilayer thickness, membrane bending rigidities in three different lipid classes. The pore formation free energy in pure bilayers and peptide translocating scenarios are significantly coupled with bilayer thickness. Thicker bilayers require more reversible work to create pores. Pore formation free energy is higher in peptide-lipid systems relative to the peptide-free lipid systems due to penalties to maintain solvation of charged hydrophilic solutes within the membrane environment. PMID:25614183

Localized fluid discharge in subduction zones: Insights from tension veins around an ancient megasplay fault (Nobeoka Thrust, SW Japan)

NASA Astrophysics Data System (ADS)

Otsubo, M.; Hardebeck, J.; Miyakawa, A.; Yamaguchi, A.; Kimura, G.

2017-12-01

Fluid-rock interactions along seismogenic faults are of great importance to understand fault mechanics. The fluid loss by the formation of mode I cracks (tension cracks) increases the fault strength and creates drainage asperities along the plate interface (Sibson, 2013, Tectonophysics). The Nobeoka Thrust, in southwestern Japan, is an on-land example of an ancient megasplay fault and provides an excellent record of deformation and fluid flow at seismogenic depths of a subduction zone (Kondo et al., 2005, Tectonics). We focus on (1) Pore fluid pressure loss, (2) Amount of fault strength recovery, and (3) Fluid circulation by the formation of mode I cracks in the post-seismic period around the fault zone of the Nobeoka Thrust. Many quartz veins that filled mode I crack at the coastal outcrops suggest a normal faulting stress regime after faulting of the Nobeoka Thrust (Otsubo et al., 2016, Island Arc). We estimated the decrease of the pore fluid pressure by the formation of the mode I cracks around the Nobeoka Thrust in the post-seismic period. When the pore fluid pressure exceeds σ3, veins filling mode I cracks are constructed (Jolly and Sanderson, 1997, Jour. Struct. Geol.). We call the pore fluid pressure that exceeds σ3 "pore fluid over pressure". The differential stress in the post-seismic period and the driving pore fluid pressure ratio P* (P* = (Pf - σ3) / (σ1 - σ3), Pf: pore fluid pressure) are parameters to estimate the pore fluid over pressure. In the case of the Nobeoka Thrust (P* = 0.4, Otsubo et al., 2016, Island Arc), the pore fluid over pressure is up to 20 MPa (assuming tensile strength = 10 MPa). 20 MPa is equivalent to <10% of the total pore fluid pressure around the Nobeoka Thrust (depth = 10 km, density = 2.7 kg/m3). When the pore fluid pressure decreases by 4%, the normalized pore pressure ratio λ* (λ* = (Pf - Ph) / (Pl - Ph), Pl: lithostatic pressure; Ph: hydrostatic pressure) changes from 0.95 to 0.86. In the case of the Nobeoka Thrust, the fault strength can increase by up to 10 MPa (assuming frictional coefficient = 0.6). 10 MPa is almost equivalent to the stress drop values in large trench type earthquakes. Hence, we suggest that the fluid loss caused by the formation of mode I cracks in the post-seismic period may play an important role by increasing frictional strength along the megasplay fault.

Molecular Dynamics Simulations of the Permeation of Bisphenol A and Pore Formation in a Lipid Membrane

NASA Astrophysics Data System (ADS)

Chen, Liang; Chen, Junlang; Zhou, Guoquan; Wang, Yu; Xu, Can; Wang, Xiaogang

2016-09-01

Bisphenol A (BPA) is particularly considered as one of the most suspicious endocrine disruptors. Exposure to BPA may bring about possible human toxicities, such as cancerous tumors, birth defects and neoteny. One of the key issues to understand its toxicities is how BPA enters cells. In this paper, we perform molecular dynamics simulations to explore the interactions between BPA and a phospholipid membrane (dipalmitoylphosphatidylcholine, DPPC bilayer). The simulation results show that BPA can easily enter the membrane from the aqueous phase. With the increasing concentrations of BPA in the membrane, BPA tends to aggregate and form into cluster. Meanwhile, several DPPC lipids are pulled out from each leaflet and adsorbed on the cluster surface, leading to pore formation. Detailed observations indicate that the lipid extraction results mainly from the dispersion interactions between BPA cluster and lipid tails, as well as weak electrostatic attractions between lipid headgroups and the two hydroxyl groups on BPA. The lipid extraction and pore formation may cause cell membrane damage and are of great importance to uncover BPA’s cytotoxicity.

Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics.

PubMed

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

2015-06-23

Cell-penetrating and antimicrobial peptides show a remarkable ability to translocate across physiological membranes. Along with factors such as electric-potential-induced perturbations of membrane structure and surface tension effects, experiments invoke porelike membrane configurations during the solute transfer process into vesicles and cells. The initiation and formation of pores are associated with a nontrivial free-energy cost, thus necessitating a consideration of the factors associated with pore formation and the attendant free energies. Because of experimental and modeling challenges related to the long time scales of the translocation process, we use umbrella sampling molecular dynamics simulations with a lipid-density-based order parameter to investigate membrane-pore-formation free energy employing Martini coarse-grained models. We investigate structure and thermodynamic features of the pore in 18 lipids spanning a range of headgroups, charge states, acyl chain lengths, and saturation. We probe the dependence of pore-formation barriers on the area per lipid, lipid bilayer thickness, and membrane bending rigidities in three different lipid classes. The pore-formation free energy in pure bilayers and peptide translocating scenarios are significantly coupled with bilayer thickness. Thicker bilayers require more reversible work to create pores. The pore-formation free energy is higher in peptide-lipid systems than in peptide-free lipid systems due to penalties to maintain the solvation of charged hydrophilic solutes within the membrane environment.

Giant MACPF/CDC pore forming toxins: A class of their own.

PubMed

Reboul, Cyril F; Whisstock, James C; Dunstone, Michelle A

2016-03-01

Pore Forming Toxins (PFTs) represent a key mechanism for permitting the passage of proteins and small molecules across the lipid membrane. These proteins are typically produced as soluble monomers that self-assemble into ring-like oligomeric structures on the membrane surface. Following such assembly PFTs undergo a remarkable conformational change to insert into the lipid membrane. While many different protein families have independently evolved such ability, members of the Membrane Attack Complex PerForin/Cholesterol Dependent Cytolysin (MACPF/CDC) superfamily form distinctive giant β-barrel pores comprised of up to 50 monomers and up to 300Å in diameter. In this review we focus on recent advances in understanding the structure of these giant MACPF/CDC pores as well as the underlying molecular mechanisms leading to their formation. Commonalities and evolved variations of the pore forming mechanism across the superfamily are discussed. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale. Copyright © 2015 Elsevier B.V. All rights reserved.

Combined Neutron and X-Ray Radiographic/Tomographic Analysis of Dissolution Limestones under Acidic Conditions

NASA Astrophysics Data System (ADS)

Anovitz, L. M.; Cole, D. R.; Hussey, D. S.; LaManna, J.; Swift, A.; Jacobson, D. L.

2016-12-01

Carbon dioxide capture and sequestration in deep geological formations is an important option for reducing greenhouse gas emissions. While the importance of porosity and pore-evolution has long been recognized, the evolution of porosity and permeability in reactive carbonates exposed to CO2-loaded brines is not well constrained. A typical pH range for CO2-acidified brine is 3 to 4.5 depending on alkalinity. This represents a substantial perturbation of typical brines that range from pH 6 to 8. The key questions include how accessible are the pores to fluid transport and how does the pore network evolve as the matrix reacts with the acidic solution? Limestones and dolostones contain nano- to macroscale porosity comprised of cracks, grain boundaries, fluid inclusions, single pores, vugs and networks of pores of random shapes and orientations. Accessible, interconnected pores may act as pore throats, constraining overall flow and are the most likely locations for extensive rock alteration. Neutron imaging is well suited to interrogation of fluid flow in porous media. Because of the large scattering cross section of hydrogen it can be used to directly image water or hydrocarbons without an added contrast medium that might modify interfacial tension and fluid/fluid interactions. In order to understand the reaction of acidified fluids we used simultaneous neutron and X-ray tomography to study the uptake and reaction of water and an acidic fluid (pH 1 HCl) with two types of Indiana limestone, one with a permeability of 2-4 mD, and the other 70 mD. One set of experiments explored capillary uptake in a dry core. These documented rapid uptake and CO2 bubble formation at the inlet. A second set introduced at a constant forced flow rate of 10 ml/min. Both core types exhibited wormhole formation, but the low perm limestone wormhole consisted of one well-delineated channel with a few side "tributaries," whereas the high perm core exhibited a more diffuse array of channels. Post-flow neutron and X-ray tomography showed that grain boundaries and other initial parts of the porous network play an important role in controlling the dissolution process. Neutron radiography and tomography have the potential to significantly advance our understanding of fluid flow and reactive behavior relevant to a wide variety of subsurface applications.

Pore Formation During Solidification of Aluminum: Reconciliation of Experimental Observations, Modeling Assumptions, and Classical Nucleation Theory

NASA Astrophysics Data System (ADS)

Yousefian, Pedram; Tiryakioğlu, Murat

2018-02-01

An in-depth discussion of pore formation is presented in this paper by first reinterpreting in situ observations reported in the literature as well as assumptions commonly made to model pore formation in aluminum castings. The physics of pore formation is reviewed through theoretical fracture pressure calculations based on classical nucleation theory for homogeneous and heterogeneous nucleation, with and without dissolved gas, i.e., hydrogen. Based on the fracture pressure for aluminum, critical pore size and the corresponding probability of vacancies clustering to form that size have been calculated using thermodynamic data reported in the literature. Calculations show that it is impossible for a pore to nucleate either homogeneously or heterogeneously in aluminum, even with dissolved hydrogen. The formation of pores in aluminum castings can only be explained by inflation of entrained surface oxide films (bifilms) under reduced pressure and/or with dissolved gas, which involves only growth, avoiding any nucleation problem. This mechanism is consistent with the reinterpretations of in situ observations as well as the assumptions made in the literature to model pore formation.

Microfluidic Experiments Studying Pore Scale Interactions of Microbes and Geochemistry

NASA Astrophysics Data System (ADS)

Chen, M.; Kocar, B. D.

2016-12-01

Understanding how physical phenomena, chemical reactions, and microbial behavior interact at the pore-scale is crucial to understanding larger scale trends in groundwater chemistry. Recent studies illustrate the utility of microfluidic devices for illuminating pore-scale physical-biogeochemical processes and their control(s) on the cycling of iron, uranium, and other important elements 1-3. These experimental systems are ideal for examining geochemical reactions mediated by microbes, which include processes governed by complex biological phenomenon (e.g. biofilm formation, etc.)4. We present results of microfluidic experiments using a model metal reducing bacteria and varying pore geometries, exploring the limitations of the microorganisms' ability to access tight pore spaces, and examining coupled biogeochemical-physical controls on the cycling of redox sensitive metals. Experimental results will provide an enhanced understanding of coupled physical-biogeochemical processes transpiring at the pore-scale, and will constrain and compliment continuum models used to predict and describe the subsurface cycling of redox-sensitive elements5. 1. Vrionis, H. A. et al. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71, 6308-6318 (2005). 2. Pearce, C. I. et al. Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions. Environ. Sci. Technol. 46, 7992-8000 (2012). 3. Zhang, C., Liu, C. & Shi, Z. Micromodel investigation of transport effect on the kinetics of reductive dissolution of hematite. Environ. Sci. Technol. 47, 4131-4139 (2013). 4. Ginn, T. R. et al. Processes in microbial transport in the natural subsurface. Adv. Water Resour. 25, 1017-1042 (2002). 5. Scheibe, T. D. et al. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb. Biotechnol. 2, 274-286 (2009).

Nucleation in mesoscopic systems under transient conditions: Peptide-induced pore formation in vesicles

NASA Astrophysics Data System (ADS)

Zhdanov, Vladimir P.; Höök, Fredrik

2013-04-01

Attachment of lytic peptides to the lipid membrane of virions or bacteria is often accompanied by their aggregation and pore formation, resulting eventually in membrane rupture and pathogen neutralization. The membrane rupture may occur gradually via formation of many pores or abruptly after the formation of the first pore. In academic studies, this process is observed during interaction of peptides with lipid vesicles. We present an analytical model and the corresponding Monte Carlo simulations focused on the pore formation in such situations. Specifically, we calculate the time of the first nucleation-limited pore-formation event and show the distribution of this time in the regime when the fluctuations of the number of peptides attached to a vesicle are appreciable. The results obtained are used to clarify the mechanism of the pore formation and membrane destabilization observed recently during interaction of highly active α-helical peptide with sub-100-nm lipid vesicles that mimic enveloped viruses with nanoscale membrane curvature. The model proposed and the analysis presented are generic and may be applicable to other meso- and nanosystems.

Seismic attributes and advanced computer algorithm to predict formation pore pressure: Qalibah formation of Northwest Saudi Arabia

NASA Astrophysics Data System (ADS)

Nour, Abdoulshakour M.

Oil and gas exploration professionals have long recognized the importance of predicting pore pressure before drilling wells. Pre-drill pore pressure estimation not only helps with drilling wells safely but also aids in the determination of formation fluids migration and seal integrity. With respect to the hydrocarbon reservoirs, the appropriate drilling mud weight is directly related to the estimated pore pressure in the formation. If the mud weight is lower than the formation pressure, a blowout may occur, and conversely, if it is higher than the formation pressure, the formation may suffer irreparable damage due to the invasion of drilling fluids into the formation. A simple definition of pore pressure is the pressure of the pore fluids in excess of the hydrostatic pressure. In this thesis, I investigated the utility of advance computer algorithm called Support Vector Machine (SVM) to learn the pattern of high pore pressure regime, using seismic attributes such as Instantaneous phase, t*Attenuation, Cosine of Phase, Vp/Vs ratio, P-Impedance, Reflection Acoustic Impedance, Dominant frequency and one well attribute (Mud-Weigh) as the learning dataset. I applied this technique to the over pressured Qalibah formation of Northwest Saudi Arabia. The results of my research revealed that in the Qalibah formation of Northwest Saudi Arabia, the pore pressure trend can be predicted using SVM with seismic and well attributes as the learning dataset. I was able to show the pore pressure trend at any given point within the geographical extent of the 3D seismic data from which the seismic attributes were derived. In addition, my results surprisingly showed the subtle variation of pressure within the thick succession of shale units of the Qalibah formation.

Influence of Solutocapillary Convection on Macrovoid Defect Formation in Polymeric Membranes

NASA Technical Reports Server (NTRS)

Greenberg, Alan R.; Krantz, William B.; Todd, Paul

2003-01-01

The focus of this research project involved the dry-cast process for polymeric membrane formation, whereby evaporation of solvent from an initially homogeneous polymer/solvent/ nonsolvent solution results in phase separation and the formation of polymer-rich and polymer-lean phases. Under certain conditions the polymer-lean phase gives rise to very large and usually undesirable, tear-drop-shaped pores (size approx. 10 - 50 microns) termed macrovoids (MVs). Although in many cases the presence of MV pores has deleterious effects on membrane performance, there are a number of innovative applications where the presence of such pores is highly desirable. Although researchers have proposed a variety of mechanisms for MV formation over the past three decades, two main hypotheses are currently favored: one asserts that MV growth can be attributed solely to diffusion (the diffusive growth hypothesis), whereas the other states that solutocapillary convection (the SC hypothesis) at the MV interface contributes to growth. The overall goal of this research was to obtain a more comprehensive understanding of the fundamental mechanism of MV growth. This research incorporates a coupled modeling and experimental approach to test a solutocapillary convection hypothesis for the growth of macrovoid pores in polymeric membranes. Specifically, we utilized a modification of the first principles model developed by two of the PIs (ARG and WBK) for dry-cast CA membranes. For the experimental component, two separate and mutually complementary approaches were used to study MV growth. In the first, membranes cast in a zero-g environment aboard the NASA KC-135 aircraft were compared with those cast on the ground to assess the effect of the buoyancy force on membrane morphology and MV size and shape. In the second approach, videomicroscopy flow visualization (VMFV) was utilized to observe MV formation and growth in real time and to assess the effect of surface tension on the MV growth dynamics. As a result of these fundamental studies, our research group advanced a new hypothesis for MV pore development in polymeric membranes.

PdHx entrapped in covalent triazine framework modulates selectivity in glycerol oxidation [Modulation of palladium activity and stability by a covalent triazine framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chan-Thaw, Carine E.; Villa, Alberto; Wang, Di

The confinement of a Pd nanoparticle within a nitrogen-containing covalent triazine framework (CTF) material was investigated to understand if the highly tunable CTF chemistry mediates the Pd catalytic properties through an ensemble effect with the CTF nitrogen atoms or a confinement effect within the CTF pores. The results surprisingly demonstrate that the CTF stabilizes the formation of 2.6 nm PdHx particles within the pores. These PdHx particles are very active for the liquid phase oxidation of glycerol due to the in situ formation of H2O2 which catalytically promotes the initial C-C cleavage. In addition the confined particles are stable overmore » many catalytic cycles whereas nanoparticles trapped outside of the pores loose activity rapidly. These results indicate that there is the potential to tune the CTF chemistry to significantly modify the chemistry of the catalytic metals.« less

PdHx entrapped in covalent triazine framework modulates selectivity in glycerol oxidation [Modulation of palladium activity and stability by a covalent triazine framework

DOE PAGES

Chan-Thaw, Carine E.; Villa, Alberto; Wang, Di; ...

2015-06-25

The confinement of a Pd nanoparticle within a nitrogen-containing covalent triazine framework (CTF) material was investigated to understand if the highly tunable CTF chemistry mediates the Pd catalytic properties through an ensemble effect with the CTF nitrogen atoms or a confinement effect within the CTF pores. The results surprisingly demonstrate that the CTF stabilizes the formation of 2.6 nm PdHx particles within the pores. These PdHx particles are very active for the liquid phase oxidation of glycerol due to the in situ formation of H2O2 which catalytically promotes the initial C-C cleavage. In addition the confined particles are stable overmore » many catalytic cycles whereas nanoparticles trapped outside of the pores loose activity rapidly. These results indicate that there is the potential to tune the CTF chemistry to significantly modify the chemistry of the catalytic metals.« less

Studying of shale organic matter structure and pore space transformations during hydrocarbon generation

NASA Astrophysics Data System (ADS)

Giliazetdinova, Dina; Korost, Dmitry; Gerke, Kirill

2016-04-01

Due to the increased interest in the study of the structure, composition, and oil and gas potential of unconventional hydrocarbon resources, investigations of the transformation of the pore space of rocks and organic matter alterations during the generation of hydrocarbon fluids are getting attention again. Due to the conventional hydrocarbon resources decreasing, there will be a necessity to develop new unconventional hydrocarbon resources. Study of the conditions and processes of hydrocarbon generation, formation and transformation of the pore space in these rocks is pivotal to understand the mechanisms of oil formation and determine the optimal and cost effective ways for their industrial exploration. In this study, we focus on organic matter structure and its interaction with the pore space of shales during hydrocarbon generation and report some new results. Collected rock samples from Domanic horizon of South-Tatar arch were heated in the pyrolyzer to temperatures closely corresponding to different catagenesis stages. X-ray microtomography method and SEM were used to monitor changes in the morphology of the pore space and organic matter structure within studied shale rocks. By routine measurements we made sure that all samples (10 in total) had similar composition of organic and mineral phases. All samples in the collection were grouped according to initial structure and amount of organics and processed separately to: 1) study the influence of organic matter content on the changing morphology of the rock under thermal effects; 2) study the effect of initial structure on the primary migration processes for samples with similar organic matter content. An additional experiment was conducted to study the dynamics of changes in the structure of the pore space and prove the validity of our approach. At each stage of heating the morphology of altered rocks was characterized by formation of new pores and channels connecting primary voids. However, it was noted that the samples with a relatively low content of the organic matter had less changes in pore space morphology, in contrast to rocks with a high organic content. Second part of the study also revealed significant differences in resulting pore structures depending on initial structure of the unaltered rocks and connectivity of original organics. Significant changes in the structure of the pore space were observed during the sequential heating in the range from 260 C to 430 C, which corresponds to the most intense stage of the hydrocarbons formation. This work was partially supported by RSF grant 14-17-00658.

Size Dependent Pore Formation in Germanium Nanowires Undergoing Reversible Delithiation Observed by In Situ TEM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Xiaotang; He, Yang; Mao, Scott X.

Germanium (Ge) nanowires coated with an amorphous silicon (Si) shell undergoing lithiation and delithiation were studied using in situ transmission electron microscopy (TEM). Delithiation creates pores in nanowires with diameters larger than ~25 nm, but not in smaller diameter nanowires. The formation of pores in Ge nanowires undergoing delithiation has been observed before in in situ TEM experiments, but there has been no indication that a critical diameter exists below which pores do not form. Pore formation occurs as a result of fast lithium diffusion compared to vacancy migration. We propose that a short diffusion path for vacancies to themore » nanowire surface plays a role in limiting pore formation even when lithium diffusion is fast.« less

Characterization of Unconventional Reservoirs: CO2 Induced Petrophysics

NASA Astrophysics Data System (ADS)

Verba, C.; Goral, J.; Washburn, A.; Crandall, D.; Moore, J.

2017-12-01

As concerns about human-driven CO2 emissions grow, it is critical to develop economically and environmentally effective strategies to mitigate impacts associated with fossil energy. Geologic carbon storage (GCS) is a potentially promising technique which involves the injection of captured CO2 into subsurface formations. Unconventional shale formations are attractive targets for GCS while concurrently improving gas recovery. However, shales are inherently heterogeneous, and minor differences can impact the ability of the shale to effectively adsorb and store CO2. Understanding GCS capacity from such endemic heterogeneities is further complicated by the complex geochemical processes which can dynamically alter shale petrophysics. We investigated the size distribution, connectivity, and type (intraparticle, interparticle, and organic) of pores in shale; the mineralogy of cores from unconventional shale (e.g. Bakken); and the changes to these properties under simulated GCS conditions. Electron microscopy and dual beam focused ion beam scanning electron microscopy were used to reconstruct 2D/3D digital matrix and pore structures. Comparison of pre and post-reacted samples gives insights into CO2-shale interactions - such as the mechanism of CO2 sorption in shales- intended for enhanced oil recovery and GCS initiatives. These comparisons also show how geochemical processes proceed differently across shales based on their initial diagenesis. Results show that most shale pore sizes fall within meso-macro pore classification (> 2 nm), but have variable porosity and organic content. The formation of secondary minerals (calcite, gypsum, and halite) may play a role in the infilling of fractures and pore spaces in the shale, which may reduce permeability and inhibit the flow of fluids.

Evolution of dealloying induced strain in nanoporous gold crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen-Wiegart, Yu-chen Karen; Harder, Ross; Dunand, David C.

For this paper, we studied the evolution of dealloying-induced strain along the {111} in a Ag-Au nano-crystal in situ, during formation of nanoporous gold at the initial stage of dealloying using Bragg coherent x-ray diffractive imaging. The maximum strain magnitude in the crystal doubled in 10 s of dealloying. Although formation of nano-pores just began at the surface, the greatest strain is located 60-80 nm deep within the crystal. Dealloying induced a compressive strain in this region, indicating volume shrinkage occurred during pore formation. The crystal interior showed a small tensile strain, which can be explained by 'pulling' of themore » dealloyed region by the non-dealloyed region during volume reduction. A surface strain relaxation developed, attributed to atomic rearrangement during dealloying. This clearer understanding of the role of strain in the initial stages of formation of nanoporous gold by dealloying can be exploited for development of new sensors, battery electrodes, and materials for catalysis.« less

Evolution of dealloying induced strain in nanoporous gold crystals

DOE PAGES

Chen-Wiegart, Yu-chen Karen; Harder, Ross; Dunand, David C.; ...

2017-04-10

For this paper, we studied the evolution of dealloying-induced strain along the {111} in a Ag-Au nano-crystal in situ, during formation of nanoporous gold at the initial stage of dealloying using Bragg coherent x-ray diffractive imaging. The maximum strain magnitude in the crystal doubled in 10 s of dealloying. Although formation of nano-pores just began at the surface, the greatest strain is located 60-80 nm deep within the crystal. Dealloying induced a compressive strain in this region, indicating volume shrinkage occurred during pore formation. The crystal interior showed a small tensile strain, which can be explained by 'pulling' of themore » dealloyed region by the non-dealloyed region during volume reduction. A surface strain relaxation developed, attributed to atomic rearrangement during dealloying. This clearer understanding of the role of strain in the initial stages of formation of nanoporous gold by dealloying can be exploited for development of new sensors, battery electrodes, and materials for catalysis.« less

Dissolution Front Instabilities in Reacting Porous Media

NASA Astrophysics Data System (ADS)

Raoof, Amir; Spiers, Chris; Hassanizadeh, Majid

2013-04-01

The main objective of this research is to gain a better understanding of the relation between regime of reaction and dissolution front instability, leading to formation of channels or wormholes. Potential applications are geological sequestration of CO2 and acid-gas injection during enhanced oil recovery. The microscopic pore space is modeled using a multi-directional pore network, allowing for a distribution of pore coordination number, together with distribution of pore sizes. In order to simulate transport of multi-component chemical species, mass balance equations are solved within each element of the network (i.e., pore body and pore throat). We have considered advective and diffusive transport processes within the pore spaces together with multi-component chemical reactions, including both equilibrium and kinetic reactions. Using dimensionless scaling groups (such as Damköhler number and Péclet-Damköhler number) we characterized the dissolution front behavior, and by averaging over the network domain we calculated the evolution of porosity and permeability as well as flux-averaged concentration breakthrough curves. We obtain constitutive relations linking porosity and permeability, under conditions relevant to geological storage of CO2. Effect of distribution of reactive minerals is also evaluated and regime of reaction is shown to play a key role.

A Comparative Study of N2O Formation during the Selective Catalytic Reduction of NOx with NH3 on Zeolite Supported Cu Catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Hai-Ying; Wei, Zhehao; Kollar, Marton

A comparative study was carried out on a small-pore CHA.Cu and a large-pore BEA.Cu zeolite catalyst to understand the lower N2O formation on small-pore zeolite supported Cu catalysts in the selective catalytic reduction (SCR) of NOx with NH3. On both catalysts, the N2O yield increases with an increase in the NO2/NOx ratios of the feed gas, suggesting N2O formation via the decomposition of NH4NO3. Temperature-programmed desorption experiments reveal that NH4NO3 is more stable on CHA.Cu than on BEA.Cu. In situ FTIR spectra following stepwise (NO2 + O2) and (15NO + NH3 + O2) adsorption and reaction, and product distribution analysismore » using isotope-labelled reactants, unambiguously prove that surface nitrate groups are essential for the formation of NH4NO3. Furthermore, CHA.Cu is shown to be considerably less active than BEA.Cu in catalyzing NO oxidation and the subsequent formation of surface nitrate groups. Both factors, i.e., (1) the higher thermal stability of NH4NO3 on CHA.Cu, and (2) the lower activity for this catalyst to catalyze NO oxidation and the subsequent formation of surface nitrates, likely contribute to the higher SCR selectivity with less N2O formation on this catalyst as compared to BEA.Cu. The latter is determined as the primary reason since surface nitrates are the source that leads to the formation of NH4NO3 on the catalysts.« less

Micromechanics of cataclastic pore collapse in limestone

NASA Astrophysics Data System (ADS)

Zhu, Wei; Baud, Patrick; Wong, Teng-Fong

2010-04-01

The analysis of compactant failure in carbonate formations hinges upon a fundamental understanding of the mechanics of inelastic compaction. Microstructural observations indicate that pore collapse in a limestone initiates at the larger pores, and microcracking dominates the deformation in the periphery of a collapsed pore. To capture these micromechanical processes, we developed a model treating the limestone as a dual porosity medium, with the total porosity partitioned between macroporosity and microporosity. The representative volume element is made up of a large pore which is surrounded by an effective medium containing the microporosity. Cataclastic yielding of this effective medium obeys the Mohr-Coulomb or Drucker-Prager criterion, with failure parameters dependent on porosity and pore size. An analytic approximation was derived for the unconfined compressive strength associated with failure due to the propagation and coalescence of pore-emanated cracks. For hydrostatic loading, identical theoretical results for the pore collapse pressure were obtained using the Mohr-Coulomb or Drucker-Prager criterion. For nonhydrostatic loading, the stress state at the onset of shear-enhanced compaction was predicted to fall on a linear cap according to the Mohr-Coulomb criterion. In contrast, nonlinear caps in qualitative agreement with laboratory data were predicted using the Drucker-Prager criterion. Our micromechanical model implies that the effective medium is significantly stronger and relatively pressure-insensitive in comparison to the bulk sample.

Mechanics of water pore formation in lipid membrane under electric field

NASA Astrophysics Data System (ADS)

Bu, Bing; Li, Dechang; Diao, Jiajie; Ji, Baohua

2017-04-01

Transmembrane water pores are crucial for substance transport through cell membranes via membrane fusion, such as in neural communication. However, the molecular mechanism of water pore formation is not clear. In this study, we apply all-atom molecular dynamics and bias-exchange metadynamics simulations to study the process of water pore formation under an electric field. We show that water molecules can enter a membrane under an electric field and form a water pore of a few nanometers in diameter. These water molecules disturb the interactions between lipid head groups and the ordered arrangement of lipids. Following the movement of water molecules, the lipid head groups are rotated and driven into the hydrophobic region of the membrane. The reorientated lipid head groups inside the membrane form a hydrophilic surface of the water pore. This study reveals the atomic details of how an electric field influences the movement of water molecules and lipid head groups, resulting in water pore formation.

Crystal structure of listeriolysin O reveals molecular details of oligomerization and pore formation

NASA Astrophysics Data System (ADS)

Köster, Stefan; van Pee, Katharina; Hudel, Martina; Leustik, Martin; Rhinow, Daniel; Kühlbrandt, Werner; Chakraborty, Trinad; Yildiz, Özkan

2014-04-01

Listeriolysin O (LLO) is an essential virulence factor of Listeria monocytogenes that causes listeriosis. Listeria monocytogenes owes its ability to live within cells to the pH- and temperature-dependent pore-forming activity of LLO, which is unique among cholesterol-dependent cytolysins. LLO enables the bacteria to cross the phagosomal membrane and is also involved in activation of cellular processes, including the modulation of gene expression or intracellular Ca2+ oscillations. Neither the pore-forming mechanism nor the mechanisms triggering the signalling processes in the host cell are known in detail. Here, we report the crystal structure of LLO, in which we identified regions important for oligomerization and pore formation. Mutants were characterized by determining their haemolytic and Ca2+ uptake activity. We analysed the pore formation of LLO and its variants on erythrocyte ghosts by electron microscopy and show that pore formation requires precise interface interactions during toxin oligomerization on the membrane.

Anomalous mobility of highly charged particles in pores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qiu, Yinghua; Yang, Crystal; Hinkle, Preston

2015-07-16

Single micropores in resistive-pulse technique were used to understand a complex dependence of particle mobility on its surface charge density. We show that the mobility of highly charged carboxylated particles decreases with the increase of the solution pH due to an interplay of three effects: (i) ion condensation, (ii) formation of an asymmetric electrical double layer around the particle, and (iii) electroosmotic flow induced by the charges on the pore walls and the particle surfaces. The results are important for applying resistive-pulse technique to determine surface charge density and zeta potential of the particles. As a result, the experiments alsomore » indicate the presence of condensed ions, which contribute to the measured current if a sufficiently high electric field is applied across the pore.« less

Optimization of hybrid laser arc welding of 42CrMo steel to suppress pore formation

NASA Astrophysics Data System (ADS)

Zhang, Yan; Chen, Genyu; Mao, Shuai; Zhou, Cong; Chen, Fei

2017-06-01

The hybrid laser arc welding (HLAW) of 42CrMo quenched and tempered steel was conducted. The effect of the processing parameters, such as the relative positions of the laser and the arc, the shielding gas flow rate, the defocusing distance, the laser power, the wire feed rate and the welding speed, on the pore formation was analyzed, the morphological characteristics of the pores were analyzed using scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS). The results showed that the majority of the pores were invasive. The pores formed at the leading a laser (LA) welding process were fewer than those at the leading a arc (AL) welding process. Increasing the shielding gas flow rate could also facilitate the reduction of pores. The laser power and the welding speed were two key process parameters to reduce the pores. The flow of the molten pool, the weld cooling rate and the pore escaping rate as a result of different parameters could all affect pore formation. An ideal pore-free weld was obtained for the optimal welding process parameters.

Regularities of Filamentary Channels Formation During Formation of Nanostructured Non-Metallic Inorganic Coatings in Microplasma Galvanostatic Mode in Solutions

NASA Astrophysics Data System (ADS)

Mamaev, A. I.; Mamaeva, V. A.; Kolenchin, N. F.; Chubenko, A. K.; Kovalskaya, Ya. B.; Konstantinova, T. A.; Dolgova, Yu. N.; Beletskaya, E. Yu.

2016-04-01

This paper presents the theoretical models describing the growth of filamentary channels of nanostructured non-metallic coatings formed by anodizing and microplasma oxidation. The authors identified dependences of the number of pores on the coating thickness. The paper presents graphic dependences of the number of filamentary channels on the process time and the coating thickness. These dependences allow calculating through and surface porosity, and in cases, when the pores are filled with functional material, they allow calculating the concentration distribution of this functional material throughout the coating thickness. The theoretical models enhance our understanding of the nature of anode processes and can be used to describe and forecast the growth and filling of porous coatings, so they can also be used to create functional and bioactive materials.

Inhibited phase behavior of gas hydrates in graphene oxide: influences of surface and geometric constraints.

PubMed

Kim, Daeok; Kim, Dae Woo; Lim, Hyung-Kyu; Jeon, Jiwon; Kim, Hyungjun; Jung, Hee-Tae; Lee, Huen

2014-11-07

Porous materials have provided us unprecedented opportunities to develop emerging technologies such as molecular storage systems and separation mechanisms. Pores have also been used as supports to contain gas hydrates for the application in gas treatments. Necessarily, an exact understanding of the properties of gas hydrates in confining pores is important. Here, we investigated the formation of CO2, CH4 and N2 hydrates in non-interlamellar voids in graphene oxide (GO), and their thermodynamic behaviors. For that, low temperature XRD and P-T traces were conducted to analyze the water structure and confirm hydrate formation, respectively, in GO after its exposure to gaseous molecules. Confinement and strong interaction of water with the hydrophilic surface of graphene oxide reduce water activity, which leads to the inhibited phase behavior of gas hydrates.

Effect of flow on bacterial transport and biofilm formation in saturated porous media

NASA Astrophysics Data System (ADS)

Rusconi, R.

2016-12-01

Understanding the transport of bacteria in saturated porous media is crucial for many applications ranging from the management of pumping wells subject to bio-clogging to the design of new bioremediation schemes for subsurface contamination. However, little is known about the spatial distribution of bacteria at the pore scale, particularly when small-scale heterogeneities - always present even in seemingly homogeneous aquifers - lead to preferential pathways for groundwater flow. In particular, the coupling of flow and motility has recently been shown to strongly affect bacterial transport1, and this leads us to predict that subsurface flow may strongly affect the dispersal of bacteria and the formation of biofilms in saturated aquifers. I present here microfluidic experiments combined with numerical simulations to show how the topological features of the flow correlate with bacterial concentration and promote the attachment of bacteria to specific regions of the pore network, which will ultimately influence the formations of biofilms. These results highlight the intimate link between small-scale biological processes and transport in porous media.

Two innovative pore pressure calculation methods for shallow deep-water formations

NASA Astrophysics Data System (ADS)

Deng, Song; Fan, Honghai; Liu, Yuhan; He, Yanfeng; Zhang, Shifeng; Yang, Jing; Fu, Lipei

2017-11-01

There are many geological hazards in shallow formations associated with oil and gas exploration and development in deep-water settings. Abnormal pore pressure can lead to water flow and gas and gas hydrate accumulations, which may affect drilling safety. Therefore, it is of great importance to accurately predict pore pressure in shallow deep-water formations. Experience over previous decades has shown, however, that there are not appropriate pressure calculation methods for these shallow formations. Pore pressure change is reflected closely in log data, particularly for mudstone formations. In this paper, pore pressure calculations for shallow formations are highlighted, and two concrete methods using log data are presented. The first method is modified from an E. Philips test in which a linear-exponential overburden pressure model is used. The second method is a new pore pressure method based on P-wave velocity that accounts for the effect of shallow gas and shallow water flow. Afterwards, the two methods are validated using case studies from two wells in the Yingqiong basin. Calculated results are compared with those obtained by the Eaton method, which demonstrates that the multi-regression method is more suitable for quick prediction of geological hazards in shallow layers.

Evaluation of the influence of sulfur-based functional groups on the embedding of silver nanoparticles into the pores of MCM-41

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oliveira, Roselaine da S.; Camilo, Fernanda F.; Bizeto, Marcos A., E-mail: mabizeto@unifesp.br

The incorporation of noble metals in the pores of mesoporous silicas might produce materials with interesting catalytic and sensing capabilities, but the proper control of pore filling and the avoidance of nanoparticles migration to outside the pores are processes not yet completely understood. In this work, we evaluated the role of –SH and –SO{sub 3}H groups post-grafted into MCM-41 on the production of silver nanoparticles by using 1-butanol as reducing agent. Thiol groups were the most efficient on promoting the formation of nanoparticles within the pores. Conversely, sulfonic groups establish electrostatic interactions with silver cations that preclude the formation ofmore » nanoparticle in yields comparable to thiol groups. MCM-41 without functional groups did not have good affinity to silver and the nanoparticles are produced outside the pores. This study showed the importance on selecting an adequate surface functional group in order to obtain silver nanoparticles filling the pores of MCM-41. - Graphical abstract: Silver nanoparticles formation inside the pores of sulfur-groups functionalized mesoporous silica. - Highlights: • Silver nanoparticles formation inside the pores of mesoporous silica. • n-butanol as reducing agent of impregnated silver cations. • Tuning the silica surface properties by grafting sulfur-based functional groups. • Influence on the loading and distribution of the nanoparticles through the pores.« less

Characterization of porosity in sulfide ore minerals: A USANS/SANS study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, F.; Zhao, J.; Etschmann, B. E.

Porosity plays a key role in the formation and alteration of sulfide ore minerals, yet our knowledge of the nature and formation of the residual pores is very limited. Herein, we report the application of ultra-small-angle neutron scattering and small-angle neutron scattering (USANS/SANS) to assess the porosity in five natural sulfide minerals (violarite, marcasite, pyrite, chalcopyrite, and bornite) possibly formed by hydrothermal mineral replacement reactions and two synthetic sulfide minerals (violarite and marcasite) prepared experimentally by mimicking natural hydrothermal conditions. USANS/SANS data showed very different pore size distributions for these minerals. Natural violarite and marcasite tend to possess less poresmore » in the small size range (<100 nm) compared with their synthetic counterparts. This phenomenon is consistent with a higher degree of pore healing or diagenetic compaction experienced by the natural violarite and marcasite. Surprisingly, nanometer-sized (<20 nm) pores were revealed for a natural pyrite cube from La Rioga, Spain, and the sample has a pore volume fraction of ~7.7%. Both chalcopyrite and bornite from the massive sulfide assemblage of the Olympic Dam deposit in Roxby Downs, South Australia, were found to be porous with a similar pore volume fraction (~15%), but chalcopyrite tends to have a higher proportion of nanometer-size pores centered at ~4 nm while bornite tends to have a broader pore size distribution. The specific surface area is generally low for these minerals ranging from 0.94 to 6.28 m2/g, and the surfaces are generally rough as surface fractal behavior was observed for all these minerals. This investigation has demonstrated that USANS/SANS is a very useful tool for analyzing porosity in ore minerals. We believe that with this quantified porosity information a deeper understanding of the complex fluid flow behavior within the porous minerals can be expected.« less

Pore-throat radius and tortuosity estimation from formation resistivity data for tight-gas sandstone reservoirs

NASA Astrophysics Data System (ADS)

Ziarani, Ali S.; Aguilera, Roberto

2012-08-01

A new model is proposed for estimation of pore-throat aperture size from formation resistivity factor and permeability data. The model is validated with data from the Mesaverde sandstone using brine salinities ranging from 20,000 to 200,000 ppm. The data analyzed includes various basins such as Green River, Piceance, Sand Wash, Powder River, Uinta, Washakie and Wind River, available in the literature. For pore-throat radii analysis the methodology involves the use of log-log plots of pore-throat radius versus the product of formation resistivity factor and permeability (rT = a(FK)b + c). The model fits over 280 samples from the Mesaverde formation with coefficients of determination varying between 0.95 and 0.99 depending primarily on the type of model used for pore throat radius calculation. The brine salinity has some minor effects on the results. The model can provide better estimates of pore-throat radii if it is calibrated with experimental techniques such as mercury porosimetry. The results show pore-throat radii varying between 0.001 and 5 μm for the Mesaverde tight sandstone; however, most of the samples fall in a range between 0.01 and 1 μm. For tortuosity analysis, the calculation involves the use of product of formation factor and porosity data. Results indicate that the estimated tortuosity values range mainly between 1 and 5. For samples with lower porosities (< 5%), tortuosity values show a wider scatter (between 1 and 8); whereas for samples with larger porosities (> 15%), the scattering in tortuosity decreases significantly. In general, for tortuosity calculation in tight gas sandstone formations, a square root model with a parameter (bf) representing various types of connecting pores, i.e., sheet-like and tubular pores, is recommended.

Detecting Pore Fluid Pressure Changes by Using the Vp/Vs Ratio

NASA Astrophysics Data System (ADS)

Vanorio, T.; Mavko, G.

2006-12-01

A central problem in studies aimed at predicting the dynamic behavior of faults is monitoring and quantifying fluid changes in areas prone to overpressure. Experimental and modeling studies show the Vp/Vs ratio to be a good determinant of the saturation state of a rock formation as well as of its inner pore pressure condition. Dectecting pore pressure changes depends, among other causes, on the reliability of laboratory data to calibrate the in-situ measured velocities. Ideally, laboratory experiments performed under controlled conditions would identify the fundamental mechanisms responsible for changes in the measured acoustic properties. However, technical limitations in the laboratory together with the assumptions driving the experimental and modeling approaches rise spouriuos mechanisms which hinder our present understanding of the actual role of high pore pressure on the elastic and poroelastic parameters. Critical issues unclude: a) the frequencies used in the laboratory are responsible for high-frequency fluid effects which induce velocity dispersion. As a result, both the effective stress parameter and velocities (and their pressure-dependence) estimated from high- frequency ultrasonic data are different from those applicable to crustal low frequency wave propagation; b) laboratory measurements made at dry, drained conditions are assumed to mimic those in gas pressured rocks. However, in dry, drained conditions, no pore pressure is exerted in the pore space, and the pore gas is infinitely compressible; c) when using room-dry, drained measurements as the baseline to model pressured rock formations, the unloading path (i.e. decreasing confining pressure) is supposed to mimic the inflationary path due to pore pressure increase. Doing so, it is assumed that the amount of crack opening due to pore pressure is equal to that of crack closure caused by the overburden stress and thus, the effective stress coefficient is implicitely assumed equal to 1. To minimize the assumptions and limitations described above, we designed a laboratory experiment which used gas as pore fluid medium. Experimental results show that in gas-pressured saturated rocks the Vp/Vs ratio, while remaining lower than values reported for liquid saturation conditions, increases with decreasing differential pressure, similarly to the trend observed in liquid saturated rocks.

Visualization and measurement of CO2 flooding in an artificial porous structure using micromodels

NASA Astrophysics Data System (ADS)

Park, Bogyeong; Wang, Sookyun; Um, Jeong-Gi; Lee, Minhee; Kim, Seon-Ok

2015-04-01

Geological CO2 sequestration is one of the most important technologies to mitigate greenhouse gas emission into the atmosphere by isolating great volumes of CO2 in deep geological formations. This novel storage option for CO2 involves injecting supercritical CO2 into porous formations saturated with pore fluid such as brine and initiate CO2 flooding with immiscible displacement. Despite of significant effects on macroscopic migration and distribution of injected CO2, however, only a limited information is available on wettability in microscopic scCO2-brine-mineral systems. In this study, a micromodel had been developed to improve our understanding of how CO2 flooding and residual characteristics of pore water are affected by the wettability in scCO2-water-glass bead systems. The micromodel (a transparent pore structure made of 1 mm diameter glass beads between two glass plates) in a high-pressure cell provided the opportunity to visualize spread of supercritical CO2 and displacement of pore water in high pressure and high temperature conditions. CO2 flooding followed by fingering migration and dewatering followed by formation of residual water were observed through a imaging system with a microscope. Measurement of contact angles of droplets of residual water on and between glass beads in a micromodel were conducted to estimate differential pressure between wetting and nonwetting fluids in a scCO2-water-glass bead system. The experimental observation results could provide important fundamental informations on capillary characteristics of reservoirs and caprocks for geological CO2 sequestration.

Visualization of CO2 flooding in an artificial porous structure using micromodels

NASA Astrophysics Data System (ADS)

Park, B.; Wang, S.; Lee, M.; Um, J. G.

2014-12-01

Geological CO2 sequestration is one of the most important technologies to mitigate greenhouse gas emission into the atmosphere by isolating great volumes of CO2 in deep geological formations. This novel storage option for CO2 involves injecting supercritical CO2 into porous formations saturated with pore fluid such as brine and initiate CO2 flooding with immiscible displacement. Despite of significant effects on macroscopic migration and distribution of injected CO2, however, only a limited information is available on wettability in microscopic scCO2-brine-mineral systems. In this study, a micromodel had been developed to improve our understanding of how CO2 flooding and residual characteristics of pore water are affected by the wettability in scCO2-water-glass bead systems. The micromodel (a transparent pore structure made of 0.5 mm diameter glass beads between two glass plates) in a high-pressure cell provided the opportunity to visualize spread of supercritical CO2 and displacement of pore water in high pressure and high temperature conditions. CO2 flooding followed by fingering migration and dewatering followed by formation of residual water were observed through a imaging system with a microscope. Measurement of contact angles of droplets of residual water on and between glass beads in a micromodel were conducted to estimate differential pressure between wetting and nonwetting fluids in a scCO2-water-glass bead system. The experimental observation results could provide important fundamental informations on capillary characteristics of reservoirs and caprocks for geological CO2 sequestration.

Control and formation mechanism of extended nanochannel geometry in colloidal mesoporous silica particles.

PubMed

Sokolov, I; Kalaparthi, V; Volkov, D O; Palantavida, S; Mordvinova, N E; Lebedev, O I; Owens, J

2017-01-04

A large class of colloidal multi-micron mesoporous silica particles have well-defined cylindrical nanopores, nanochannels which self-assembled in the templated sol-gel process. These particles are of broad interest in photonics, for timed drug release, enzyme stabilization, separation and filtration technologies, catalysis, etc. Although the pore geometry and mechanism of pore formation of such particles has been widely investigated at the nanoscale, their pore geometry and its formation mechanism at a larger (extended) scale is still under debate. The extended geometry of nanochannels is paramount for all aforementioned applications because it defines accessibility of nanochannels, and subsequently, kinetics of interaction of the nanochannel content with the particle surrounding. Here we present both experimental and theoretical investigation of the extended geometry and its formation mechanism in colloidal multi-micron mesoporous silica particles. We demonstrate that disordered (and consequently, well accessible) nanochannels in the initially formed colloidal particles gradually align and form extended self-sealed channels. This knowledge allows to control the percentage of disordered versus self-sealed nanochannels, which defines accessibility of nanochannels in such particles. We further show that the observed aligning the channels is in agreement with theory; it is thermodynamically favored as it decreases the Gibbs free energy of the particles. Besides the practical use of the obtained results, developing a fundamental understanding of the mechanisms of morphogenesis of complex geometry of nanopores will open doors to efficient and controllable synthesis that will, in turn, further fuel the practical utilization of these particles.

An analysis of electrical conductivity model in saturated porous media

NASA Astrophysics Data System (ADS)

Cai, J.; Wei, W.; Qin, X.; Hu, X.

2017-12-01

Electrical conductivity of saturated porous media has numerous applications in many fields. In recent years, the number of theoretical methods to model electrical conductivity of complex porous media has dramatically increased. Nevertheless, the process of modeling the spatial conductivity distributed function continues to present challenges when these models used in reservoirs, particularly in porous media with strongly heterogeneous pore-space distributions. Many experiments show a more complex distribution of electrical conductivity data than the predictions derived from the experiential model. Studies have observed anomalously-high electrical conductivity of some low-porosity (tight) formations compared to more- porous reservoir rocks, which indicates current flow in porous media is complex and difficult to predict. Moreover, the change of electrical conductivity depends not only on the pore volume fraction but also on several geometric properties of the more extensive pore network, including pore interconnection and tortuosity. In our understanding of electrical conductivity models in porous media, we study the applicability of several well-known methods/theories to electrical characteristics of porous rocks as a function of pore volume, tortuosity and interconnection, to estimate electrical conductivity based on the micro-geometrical properties of rocks. We analyze the state of the art of scientific knowledge and practice for modeling porous structural systems, with the purpose of identifying current limitations and defining a blueprint for future modeling advances. We compare conceptual descriptions of electrical current flow processes in pore space considering several distinct modeling approaches. Approaches to obtaining more reasonable electrical conductivity models are discussed. Experiments suggest more complex relationships between electrical conductivity and porosity than experiential models, particularly in low-porosity formations. However, the available theoretical models combined with simulations do provide insight to how microscale physics affects macroscale electrical conductivity in porous media.

Root induced changes of effective 1D hydraulic properties in a soil column.

PubMed

Scholl, P; Leitner, D; Kammerer, G; Loiskandl, W; Kaul, H-P; Bodner, G

Roots are essential drivers of soil structure and pore formation. This study aimed at quantifying root induced changes of the pore size distribution (PSD). The focus was on the extent of clogging vs. formation of pores during active root growth. Parameters of Kosugi's lognormal PSD model were determined by inverse estimation in a column experiment with two cover crops (mustard, rye) and an unplanted control. Pore dynamics were described using a convection-dispersion like pore evolution model. Rooted treatments showed a wider range of pore radii with increasing volumes of large macropores >500 μm and micropores <2.5 μm, while fine macropores, mesopores and larger micropores decreased. The non-rooted control showed narrowing of the PSD and reduced porosity over all radius classes. The pore evolution model accurately described root induced changes, while structure degradation in the non-rooted control was not captured properly. Our study demonstrated significant short term root effects with heterogenization of the pore system as dominant process of root induced structure formation. Pore clogging is suggested as a partial cause for reduced pore volume. The important change in micro- and large macropores however indicates that multiple mechanic and biochemical processes are involved in root-pore interactions.

Nano-Pore Size Analysis by SAXS Method of Cementitious Mortars Undergoing Delayed Ettringite Formation

NASA Astrophysics Data System (ADS)

Shekar, Yamini

This research investigates the nano-scale pore structure of cementitious mortars undergoing delayed ettringite formation (DEF) using small angle x-ray scattering (SAXS). DEF has been known to cause expansion and cracking during later ages (around 4000 days) in concrete that has been heat cured at temperatures of 70°C or above. Though DEF normally occurs in heat cured concrete, mass cured concrete can also experience DEF. Large crystalline pressures result in smaller pore sizes. The objectives of this research are: (1) to investigate why some samples expand early than later expansion, (2) to evaluate the effects of curing conditions and pore size distributions at high temperatures, and (3) to assess the evolution of the pore size distributions over time. The most important outcome of the research is the pore sizes obtained from SAXS were used in the development of a 3-stage model. From the data obtained, the pore sizes increase in stage 1 due to initial ettringite formation and in turn filling up the smallest pores. Once the critical pore size threshold is reached (around 20nm) stage 2 is formed due to cracking which tends to decrease in the pore sizes. Finally, in stage 3, the cracking continues, therefore increasing in the pore size.

Electrical Conductive Mechanism of Gas Hydrate-Bearing Reservoirs in the Permafrost Region of Qilian Mountain

NASA Astrophysics Data System (ADS)

Peng, C.; Zou, C.; Tang, Y.; Liu, A.; Hu, X.

2017-12-01

In the Qilian Mountain, gas hydrates not only occur in pore spaces of sandstones, but also fill in fractures of mudstones. This leads to the difficulty in identification and evaluation of gas hydrate reservoir from resistivity and velocity logs. Understanding electrical conductive mechanism is the basis for log interpretation. However, the research is insufficient in this area. We have collected well logs from 30 wells in this area. Well logs and rock samples from DK-9, DK-11 and DK-12 wells were used in this study. The experiments including SEM, thin section, NMR, XRD, synthesis of gas hydrate in consolidated rock cores under low temperature and measurement of their resistivity and others were performed for understanding the effects of pore structure, rock composition, temperature and gas hydrate on conductivity. The results show that the porosity of reservoir of pore filling type is less than 10% and its clay mineral content is high. As good conductive passages, fractures can reduce resistivity of water-saturated rock. If fractures in the mudstone are filled by calcite, resistivity increases significantly. The resistivity of water-saturated rock at 2°C is twice of that at 18°C. The gas hydrate formation process in the sandstone was studied by resistivity recorded in real time. In the early stage of gas hydrate formation, the increase of residual water salinity may lead to the decrease of resistivity. In the late stage of gas hydrate formation, the continuity decrease of water leads to continuity increase of resistivity. In summary, fractures, rock composition, temperature and gas hydrate are important factors influencing resistivity of formation. This study is helpful for more accurate evaluation of gas hydrate from resistivity log. Acknowledgment: We acknowledge the financial support of the National Special Program for Gas Hydrate Exploration and Test-production (GZH201400302).

Pore shape of honeycomb-patterned films: modulation and interfacial behavior.

PubMed

Wan, Ling-Shu; Ke, Bei-Bei; Zhang, Jing; Xu, Zhi-Kang

2012-01-12

The control of the pore size of honeycomb-patterned films has been more or less involved in most work on the topic of breath figures. Modulation of the pore shape was largely ignored, although it is important to applications in replica molding, filtration, particle assembly, and cell culture. This article reports a tunable pore shape for patterned films prepared from commercially available polystyrene (PS). We investigated the effects of solvents including tetrahydrofuran (THF) and chloroform (CF) and hydrophilic additives including poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA), poly(ethylene glycol) (PEG), and poly(N-vinyl pyrrolidone) (PVP). Water droplets on/in the polymer solutions were observed and analyzed for simulating the formation and stabilization of breath figures. Interfacial tensions of the studied systems were measured and considered as a main factor to modulate the pore shape. Results indicate that the pores gradually change from near-spherical to ellipsoidal with the increase of additive content when using CF as the solvent; however, only ellipsoidal pores are formed from the THF solution. It is demonstrated that the aggregation of the additives at the water/polymer solution interface is more efficient in the THF solution than that in the CF solution. This aggregation decreases the interfacial tension, stabilizes the condensed water droplets, and shapes the pores of the films. The results may facilitate our understanding of the dynamic breath figure process and provide a new pathway to prepare patterned films with different pore structures.

Improved dual-porosity models for petrophysical analysis of vuggy reservoirs

NASA Astrophysics Data System (ADS)

Wang, Haitao

2017-08-01

A new vug interconnection, isolated vug (IVG), was investigated through resistivity modeling and the dual-porosity model for connected vug (CVG) vuggy reservoirs was tested. The vuggy models were built by pore-scale modeling, and their electrical resistivity was calculated by the finite difference method. For CVG vuggy reservoirs, the CVG reduced formation factors and increased the porosity exponents, and the existing dual-porosity model failed to match these results. Based on the existing dual-porosity model, a conceptual dual-porosity model for CVG was developed by introducing a decoupled term to reduce the resistivity of the model. For IVG vuggy reservoirs, IVG increased the formation factors and porosity exponents. The existing dual-porosity model succeeded due to accurate calculation of the formation factors of the deformed interparticle porous media caused by the insertion of the IVG. Based on the existing dual-porosity model, a new porosity model for IVG vuggy reservoirs was developed by simultaneously recalculating the formation factors of the altered interparticle pore-scale models. The formation factors and porosity exponents from the improved and extended dual-porosity models for CVG and IVG vuggy reservoirs well matched the simulated formation factors and porosity exponents. This work is helpful for understanding the influence of connected and disconnected vugs on resistivity factors—an issue of particular importance in carbonates.

Assembly of streptolysin O pores assessed by quartz crystal microbalance and atomic force microscopy provides evidence for the formation of anchored but incomplete oligomers.

PubMed

Stewart, Sarah E; D'Angelo, Michael E; Paintavigna, Stefania; Tabor, Rico F; Martin, Lisandra L; Bird, Phillip I

2015-01-01

Streptolysin O (SLO) is a bacterial pore forming protein that is part of the cholesterol dependent cytolysin (CDC) family. We have used quartz crystal microbalance with dissipation monitoring (QCM-D) to examine SLO membrane binding and pore formation. In this system, SLO binds tightly to cholesterol-containing membranes, and assembles into partial and complete pores confirmed by atomic force microscopy. SLO binds to the lipid bilayer at a single rate consistent with the Langmuir isotherm model of adsorption. Changes in dissipation illustrate that SLO alters the viscoelastic properties of the bilayer during pore formation, but there is no loss of material from the bilayer as reported for small membrane-penetrating peptides. SLO mutants were used to further dissect the assembly and insertion processes by QCM-D. This shows the signature of SLO in QCM-D changes when pore formation is inhibited, and that bound and inserted SLO forms can be distinguished. Furthermore a pre-pore locked SLO mutant binds reversibly to lipid, suggesting that the partially complete wtSLO forms observed by AFM are anchored to the membrane. Copyright © 2014 Elsevier B.V. All rights reserved.

Dynamin-related protein-1 controls fusion pore dynamics during platelet granule exocytosis.

PubMed

Koseoglu, Secil; Dilks, James R; Peters, Christian G; Fitch-Tewfik, Jennifer L; Fadel, Nathalie A; Jasuja, Reema; Italiano, Joseph E; Haynes, Christy L; Flaumenhaft, Robert

2013-03-01

Platelet granule exocytosis serves a central role in hemostasis and thrombosis. Recently, single-cell amperometry has shown that platelet membrane fusion during granule exocytosis results in the formation of a fusion pore that subsequently expands to enable the extrusion of granule contents. However, the molecular mechanisms that control platelet fusion pore expansion and collapse are not known. We identified dynamin-related protein-1 (Drp1) in platelets and found that an inhibitor of Drp1, mdivi-1, blocked exocytosis of both platelet dense and α-granules. We used single-cell amperometry to monitor serotonin release from individual dense granules and, thereby, measured the effect of Drp1 inhibition on fusion pore dynamics. Inhibition of Drp1 increased spike width and decreased prespike foot events, indicating that Drp1 influences fusion pore formation and expansion. Platelet-mediated thrombus formation in vivo after laser-induced injury of mouse cremaster arterioles was impaired after infusion of mdivi-1. These results demonstrate that inhibition of Drp1 disrupts platelet fusion pore dynamics and indicate that Drp1 can be targeted to control thrombus formation in vivo.

Soil fungi colony growth and community dynamics

NASA Astrophysics Data System (ADS)

Falconer, Ruth E.; Kravchenko, Alexandra; Otten, Wilfred

2010-05-01

Fungi are a major player in soil functioning, they contribute to soil structure formation and shaping of plant communities through their role in nutrient cycling, pathogenesis and symbiosis. Theoretical approaches which have emerged over the years and improved considerably our understanding of above ground plant communities are still lacking below ground. A theoretical framework is needed, such that links soil physics, fungal biology and mathematical biology in order to understand fungal community dynamics and diversity in undisturbed soils. Such a framework is essential if we are to understand how environmental change or soil manipulation impacts biodiversity. Different land use and management practices significantly affect soil environmental characteristics crucial for fungal communities by contributing different quantities and qualities of biomass inputs, generating different levels of soil disturbance, influencing soil temperature and moisture regimes, and affecting structure and geometry of soil pore space. Differences in pore structures generated by long-term differences in land use and management are reflected in notable changes in soil physical and hydraulic properties, including soil porosity, hydraulic conductivity and water retention (Brye and Pirani, 2005). Changes in numbers, shapes, and distributions of soil macropores have been often observed (e.g., Pachepsky et al., 1996; Giménez et al., 1997; Udawatta et al., 2008). However, specific implications of these differences in pore structure and geometries for ability of pathogenic as well as non-pathogenic fungi to colonize soil have not yet been addressed. Recent advances in computed tomography and microscopy facilitate detailed examination of the inner pore structures of undisturbed soil samples as well as visualization of fungal mycelia. Such tools together with modelling generate a new level of understanding of the mechanisms governing fungal behaviour at microscopic scales, and for the first time allow us to examine species interactions in a 3D soil environment.

Assessing the role of clay authigenesis in the seawater potassium cycle: A paired K and Mg isotope study of deep-sea pore fluids

NASA Astrophysics Data System (ADS)

Santiago Ramos, D. P.; Higgins, J. A.

2017-12-01

In situ formation of clays (clay authigenesis) in marine sediments and altered oceanic crust is an important sink of a number of seawater cations. In particular, clay authigenesis is a major, and yet unconstrained, flux in the global seawater potassium cycle. Potassium is the fourth most abundant cation in the ocean, which constitutes an isotopically enriched K reservoir (δ41K 0‰) compared to the solid Earth (δ41K -0.5‰). Understanding what processes control this isotopic offset is the main goal of this study. Here we use a multi-collector inductively coupled plasma mass spectrometer (MC-ICP-MS) to measure the K and Mg isotope ratios (41K/39K and 26Mg/24Mg) of deep-sea pore fluids in order to assess the effects of clay formation in the K isotope composition of seawater. Mg isotopes are used as an independent proxy for clay formation, since marine authigenic clays are isotopically distinct from their detrital counterpart, an abundant component of marine sediments. Our study sites (ODP/IODP 1052, U1378, U1395, U1403) vary in location, lithology, age and sedimentation rates; however, pore-fluids from all sites show decreasing K concentrations with depth, suggesting potassium uptake into the sediments. We find that although K concentration trends are similar across all sites, measured δ41K values vary significantly. Results from 1-D diffusion-advection-reaction models suggest that these differences in isotopic profiles arise from a complex interplay between sedimentation rate and K isotopic fractionation during clay formation, aqueous K diffusion and ion exchange reactions. Further, model simulations yield fractionation factors between 0.9980 and 1.0000 for clay formation in deep-sea sediments. Despite the minor contribution of these deep-sea pore-fluids as sinks of seawater K, the processes responsible for K isotope fractionation in our study sites (clay formation and aqueous K diffusion) are also observed at shallow marine systems (major K sinks) and are thus likely responsible for setting the K isotopic composition of seawater.

Mesoscopic Ni particles and nanowires by pulsed electrodeposition into porous Si

NASA Astrophysics Data System (ADS)

Michelakaki, E.; Valalaki, K.; G. Nassiopoulou, A.

2013-04-01

We report in this article on the formation of mesoscopic Ni particles and filling of continuous Ni nanowires into porous Si layers of thickness in the range of 0.5-4 μm with anisotropic vertical pores of average diameter in the range of 30-45 nm using pulsed electrodeposition from a Ni salt solution. The effect of pulse duration, number of pulses, and total process time on pore filling was investigated for porous Si with different porosities and porous Si layer thicknesses in the above thickness range. Scanning and transmission electron microscopy were used to characterize the samples. It was found that pore filling starts with Ni nucleation and nanoparticle formation at different points of the pore walls along the whole pore length and continues with nanoparticle coalescence to form continuous Ni nanowires that completely fill the pores. The mechanism involved in pore filling is particle nucleation and diffusion-controlled growth of Ni nanoparticles that coalesce to nanowires. From the beginning of the process, a metal film starts to form on the porous Si surface, and its thickness increases with increasing the process time. However, the presence of this film does not impede further pore filling and nanowire formation into the pores. This supports further the diffusion-controlled growth mechanism. Finally, it was demonstrated that full pore filling and continuous Ni nanowire formation were also achieved under direct current electrodeposition, and the results are quite similar to those obtained with pulsed electrodeposition when the same total deposition time is used in both cases.

Disturbances to metal partitioning during toxicity testing of iron(II)-rich estuarine pore waters and whole sediments.

PubMed

Simpson, Stuart L; Batley, Graeme E

2003-02-01

Metal partitioning is altered when suboxic estuarine sediments containing Fe(II)-rich pore waters are disturbed during collection, preparation, and toxicity testing. Experiments with model Fe(II)-rich pore waters demonstrated the rates at which adsorptive losses of Cd, Cu, Ni, Mn, Pb, and Zn occur upon exposure to air. Experiments with Zn-contaminated estuarine sediments demonstrated large and often unpredictable changes to metal partitioning during sediment storage, removal of organisms, and homogenization before testing. Small modifications to conditions, such as aeration of overlying waters, caused large changes to the metal partitioning. Disturbances caused by sediment collection required many weeks for reestablishment of equilibrium. Bioturbation by benthic organisms led to oxidation of pore-water Fe(II) and lower Zn fluxes because of the formation of Fe hydroxide precipitates that adsorb pore-water Zn. For five weeks after the addition of organisms to sediments, Zn fluxes increased slowly as the organisms established themselves in the sediments, indicating that the establishment of equilibrium was not rapid. The results are discussed in terms of the dynamic nature of suboxic, Fe(II)-rich estuarine sediments, how organisms perturb their environment, and the importance of understanding chemistry in toxicity testing with whole sediments or pore water. Recommendations are provided for the handling of sediments for toxicity testing.

Simulations of skin barrier function: free energies of hydrophobic and hydrophilic transmembrane pores in ceramide bilayers.

PubMed

Notman, Rebecca; Anwar, Jamshed; Briels, W J; Noro, Massimo G; den Otter, Wouter K

2008-11-15

Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel phase and in the DMSO-induced fluidized state. Our simulations show that the fluid phase bilayers form archetypal water-filled hydrophilic pores similar to those observed in phospholipid bilayers. In contrast, the rigid gel-phase bilayers develop hydrophobic pores. At the relatively small pore diameters studied here, the hydrophobic pores are empty rather than filled with bulk water, suggesting that they do not compromise the barrier function of ceramide membranes. A phenomenological analysis suggests that these vapor pores are stable, below a critical radius, because the penalty of creating water-vapor and tail-vapor interfaces is lower than that of directly exposing the strongly hydrophobic tails to water. The PMCF free energy profile of the vapor pore supports this analysis. The simulations indicate that high DMSO concentrations drastically impair the barrier function of the skin by strongly reducing the free energy required for pore opening.

Simulations of Skin Barrier Function: Free Energies of Hydrophobic and Hydrophilic Transmembrane Pores in Ceramide Bilayers

PubMed Central

Notman, Rebecca; Anwar, Jamshed; Briels, W. J.; Noro, Massimo G.; den Otter, Wouter K.

2008-01-01

Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel phase and in the DMSO-induced fluidized state. Our simulations show that the fluid phase bilayers form archetypal water-filled hydrophilic pores similar to those observed in phospholipid bilayers. In contrast, the rigid gel-phase bilayers develop hydrophobic pores. At the relatively small pore diameters studied here, the hydrophobic pores are empty rather than filled with bulk water, suggesting that they do not compromise the barrier function of ceramide membranes. A phenomenological analysis suggests that these vapor pores are stable, below a critical radius, because the penalty of creating water-vapor and tail-vapor interfaces is lower than that of directly exposing the strongly hydrophobic tails to water. The PMCF free energy profile of the vapor pore supports this analysis. The simulations indicate that high DMSO concentrations drastically impair the barrier function of the skin by strongly reducing the free energy required for pore opening. PMID:18708461

Modelling in conventional electroporation for model cell with organelles using COMSOL Multiphysics

NASA Astrophysics Data System (ADS)

Sulaeman, M. Y.; Widita, R.

2016-03-01

Conventional electroporation is a formation of pores in the membrane cell due to the external electric field applied to the cell. The purpose of creating pores in the cell using conventional electroporation are to increase the effectiveness of chemotherapy (electrochemotherapy) and to kill cancer tissue using irreversible electroporation. Modeling of electroporation phenomenon on a model cell had been done by using software COMSOL Multiphysics 4.3b with the applied external electric field with intensity at 1.1 kV/cm to find transmembrane voltage and pore density. It can be concluded from the results of potential distribution and transmembrane voltage, it show that pores formation only occurs in the membrane cells and it could not penetrate into inside the model cell so there is not pores formation in its organells.

Variations of permeability and pore size distribution of porous media with pressure.

PubMed

Chen, Quan; Kinzelbach, Wolfgang; Ye, Chaohui; Yue, Yong

2002-01-01

Porosity and permeability of porous and fractured geological media decrease with the exploitation of formation fluids such as petroleum, natural gas, or ground water. This may result in ground subsidence and a decrease of recovery of petroleum, natural gas, or ground water. Therefore, an evaluation of the behavior of permeability and porosity under formation fluid pressure changes is important to petroleum and ground water industries. This study for the first time establishes a method, which allows for the measurement of permeability, porosity, and pore size distribution of cores simultaneously. From the observation of the pore size distribution by low-field nuclear magnetic resonance (NMR) relaxation time spectrometry the mechanisms of pressure-dependent porosity and permeability change can be derived. This information cannot be obtained by traditional methods. As the large-size pores or fractures contribute significantly to the permeability, their change consequently leads to a large permeability change. The contribution of fractures to permeability is even larger than that of pores. Thus, the permeability of the cores with fractures decreased more than that of cores without fractures during formation pressure decrease. Furthermore, it did not recover during formation pressure increase. It can be concluded that in fractures, mainly plastic deformation takes place, while matrix pores mainly show elastic deformation. Therefore, it is very important to keep an appropriate formation fluid pressure during the exploitation of ground water and petroleum in a fractured formation.

The effects of Fe-oxidizing microorganisms on post-biostimulation permeability reduction and oxidative processes at the Rifle IFRC site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chan, Clara Sze-Yue

2015-07-02

Fe oxidation and biomineral formation is important in aquifers because the highly-reactive oxides can control the mobility of nutrients (e.g. phosphate, C) and metals (e.g. arsenic, uranium). Mineral formation also has the potential to affect hydrology, depending on the volume and distribution in pore spaces. In this exploratory study, we sought to understand how microbial Fe-oxidizers and their biominerals affect, and are affected by groundwater flow. As part of work at the Rifle aquifer in Colorado, we initially hypothesized that Fe-oxidizers were contributing to aquifer clogging problems associated with enhanced bioremediation. To demonstrate the presence of Fe-oxidizers in the Riflemore » aquifer, we enriched FeOM from groundwater samples, and isolated two novel chemolithotrophic, microaerophilic Fe-oxidizing Betaproteobacteria, Hydrogenophaga sp. P101 and Curvibacter sp. CD03. To image cells and biominerals in the context of pores, we developed a “micro-aquifer,” a sand-filled flow-through culture chamber that allows for imaging of sediment pore space with multiphoton confocal microscopy. Fe oxide biofilms formed on sand grains, demonstrating that FeOM produce Fe oxide sand coatings. Fe coatings are common on aquifer sands, and tend to sequester contaminants; however, it has never previously been shown that microbes are responsible for their formation. In contrast to our original hypothesis, the biominerals did not clog the mini-aquifer. Instead, Fe biofilm distribution was dynamic: they grew as coatings, then periodically sloughed off sand grains, with some flocs later caught in pore throats. This has implications for physical hydrology, including pore scale architecture, and element transport. The sloughing of coatings likely prevents the biominerals from clogging wells and aquifers, at least initially. Although attached biomineral coatings sequester Fe-associated elements (e.g. P, As, C, U), when biominerals detach, these elements are transported as particles through the aquifer. Our work shows that microbial mineralization impacts in aquifers are dynamic, and that the fate and transport of biomineral-associated elements depend not only on geochemical conditions, but also physical pore-scale processes.« less

A new method of evaluating tight gas sands pore structure from nuclear magnetic resonance (NMR) logs

NASA Astrophysics Data System (ADS)

Xiao, Liang; Mao, Zhi-qiang; Xie, Xiu-hong

2016-04-01

Tight gas sands always display such characteristics of ultra-low porosity, permeability, high irreducible water, low resistivity contrast, complicated pore structure and strong heterogeneity, these make that the conventional methods are invalid. Many effective gas bearing formations are considered as dry zones or water saturated layers, and cannot be identified and exploited. To improve tight gas sands evaluation, the best method is quantitative characterizing rock pore structure. The mercury injection capillary pressure (MICP) curves are advantageous in predicting formation pore structure. However, the MICP experimental measurements are limited due to the environment and economy factors, this leads formation pore structure cannot be consecutively evaluated. Nuclear magnetic resonance (NMR) logs are considered to be promising in evaluating rock pore structure. Generally, to consecutively quantitatively evaluate tight gas sands pore structure, the best method is constructing pseudo Pc curves from NMR logs. In this paper, based on the analysis of lab experimental results for 20 core samples, which were drilled from tight gas sandstone reservoirs of Sichuan basin, and simultaneously applied for lab MICP and NMR measurements, the relationships of piecewise power function between nuclear magnetic resonance (NMR) transverse relaxation T2 time and pore-throat radius Rc are established. A novel method, which is used to transform NMR reverse cumulative curve as pseudo capillary pressure (Pc) curve is proposed, and the corresponding model is established based on formation classification. By using this model, formation pseudo Pc curves can be consecutively synthesized. The pore throat radius distribution, and pore structure evaluation parameters, such as the average pore throat radius (Rm), the threshold pressure (Pd), the maximum pore throat radius (Rmax) and so on, can also be precisely extracted. After this method is extended into field applications, several tight gas sandstone reservoirs are processed, and the predicted results are compared with core derived results. Good consistency between evaluated results with core derived results illustrates the dependability of the proposed method. Comparing with the previous methods, this presented model is much more theoretical, and the applicability is much improved. Combining with the evaluated results, our target tight gas sands are well evaluated, and many potential gas-bearing layers are effectively identified.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, Chan Yi, E-mail: vicchanyiwei@hotmail.com; Ongkudon, Clarence M., E-mail: clarence@ums.edu.my; Kansil, Tamar, E-mail: tamarkansil87@gmail.com

Modern day synthesis protocols of methacrylate monolithic polymer adsorbent are based on existing polymerization blueprint without a thorough understanding of the dynamics of pore structure and formation. This has resulted in unproductiveness of polymer adsorbent consequently affecting purity and recovery of final product, productivity, retention time and cost effectiveness of the whole process. The problems magnified in monolith scaling-up where internal heat buildup resulting from external heating and high exothermic polymerization reaction was reflected in cracking of the adsorbent. We believe that through careful and precise control of the polymerization kinetics and parameters, it is possible to prepare macroporous methacrylatemore » monolithic adsorbents with controlled pore structures despite being carried out in an unstirred mould. This research involved the study of the effect of scaling-up on pore morphology of monolith, in other words, porous polymethacrylate adsorbents that were prepared via bulk free radical polymerization process by imaging the porous morphology of polymethacrylate with scanning electron microscope.« less

Virial series expansion and Monte Carlo studies of equation of state for hard spheres in narrow cylindrical pores

NASA Astrophysics Data System (ADS)

Mon, K. K.

2018-05-01

In this paper, the virial series expansion and constant pressure Monte Carlo method are used to study the longitudinal pressure equation of state for hard spheres in narrow cylindrical pores. We invoke dimensional reduction and map the model into an effective one-dimensional fluid model with interacting internal degrees of freedom. The one-dimensional model is extensive. The Euler relation holds, and longitudinal pressure can be probed with the standard virial series expansion method. Virial coefficients B2 and B3 were obtained analytically, and numerical quadrature was used for B4. A range of narrow pore widths (2 Rp) , Rp<(√{3 }+2 ) /4 =0.9330 ... (in units of the hard sphere diameter) was used, corresponding to fluids in the important single-file formations. We have also computed the virial pressure series coefficients B2', B3', and B4' to compare a truncated virial pressure series equation of state with accurate constant pressure Monte Carlo data. We find very good agreement for a wide range of pressures for narrow pores. These results contribute toward increasing the rather limited understanding of virial coefficients and the equation of state of hard sphere fluids in narrow cylindrical pores.

Pore-level mechanics of foam generation and coalescence in the presence of oil.

PubMed

Almajid, Muhammad M; Kovscek, Anthony R

2016-07-01

The stability of foam in porous media is extremely important for realizing the advantages of foamed gas on gas mobility reduction. Foam texture (i.e., bubbles per volume of gas) achieved is dictated by foam generation and coalescence processes occurring at the pore-level. For foam injection to be widely applied during gas injection projects, we need to understand these pore-scale events that lead to foam stability/instability so that they are modeled accurately. Foam flow has been studied for decades, but most efforts focused on studying foam generation and coalescence in the absence of oil. Here, the extensive existing literature is reviewed and analyzed to identify open questions. Then, we use etched-silicon micromodels to observe foam generation and coalescence processes at the pore-level. Special emphasis is placed on foam coalescence in the presence of oil. For the first time, lamella pinch-off as described by Myers and Radke [40] is observed in porous media and documented. Additionally, a new mechanism coined "hindered generation" is found. Hindered generation refers to the role oil plays in preventing the successful formation of a lamella following snap-off near a pore throat. Copyright © 2015 Elsevier B.V. All rights reserved.

Multiphysics Simulations of Hot-Spot Initiation in Shocked Insensitive High-Explosive

NASA Astrophysics Data System (ADS)

Najjar, Fady; Howard, W. M.; Fried, L. E.

2010-11-01

Solid plastic-bonded high-explosive materials consist of crystals with micron-sized pores embedded. Under mechanical or thermal insults, these voids increase the ease of shock initiation by generating high-temperature regions during their collapse that might lead to ignition. Understanding the mechanisms of hot-spot initiation has significant research interest due to safety, reliability and development of new insensitive munitions. Multi-dimensional high-resolution meso-scale simulations are performed using the multiphysics software, ALE3D, to understand the hot-spot initiation. The Cheetah code is coupled to ALE3D, creating multi-dimensional sparse tables for the HE properties. The reaction rates were obtained from MD Quantum computations. Our current predictions showcase several interesting features regarding hot spot dynamics including the formation of a "secondary" jet. We will discuss the results obtained with hydro-thermo-chemical processes leading to ignition growth for various pore sizes and different shock pressures.

NSF- and SNARE-mediated membrane fusion is required for nuclear envelope formation and completion of nuclear pore complex assembly in Xenopus laevis egg extracts.

PubMed

Baur, Tina; Ramadan, Kristijan; Schlundt, Andreas; Kartenbeck, Jürgen; Meyer, Hemmo H

2007-08-15

Despite the progress in understanding nuclear envelope (NE) reformation after mitosis, it has remained unclear what drives the required membrane fusion and how exactly this is coordinated with nuclear pore complex (NPC) assembly. Here, we show that, like other intracellular fusion reactions, NE fusion in Xenopus laevis egg extracts is mediated by SNARE proteins that require activation by NSF. Antibodies against Xenopus NSF, depletion of NSF or the dominant-negative NSF(E329Q) variant specifically inhibited NE formation. Staging experiments further revealed that NSF was required until sealing of the envelope was completed. Moreover, excess exogenous alpha-SNAP that blocks SNARE function prevented membrane fusion and caused accumulation of non-flattened vesicles on the chromatin surface. Under these conditions, the nucleoporins Nup107 and gp210 were fully recruited, whereas assembly of FxFG-repeat-containing nucleoporins was blocked. Together, we define NSF- and SNARE-mediated membrane fusion events as essential steps during NE formation downstream of Nup107 recruitment, and upstream of membrane flattening and completion of NPC assembly.

Understanding Potassium Isotope Fractionation During Authigenic Clay Formation in Pore-fluid Systems: Implications for the δ41K of Seawater

NASA Astrophysics Data System (ADS)

Santiago Ramos, D. P.; Higgins, J. A.

2015-12-01

Improvements in analytical precision on the latest generation multi-collector inductively coupled plasma mass spectrometers (MC-ICP-MS) have revealed a ~2‰ range in the ratios of stable potassium isotopes (41K/39K) in terrestrial materials (Morgan et al., in prep). Preliminary measurements of δ41K values indicate that seawater and silicate rocks are isotopically distinct reservoirs, with seawater having a δ41K value that is ~0.5‰ heavier than the silicate average (-0.5‰; Morgan et al., in prep). The heavy δ41K character of seawater might be related to 1) an isotopically enriched input flux (rivers and high-temperature hydrothermal reactions); or 2) a 41K-depleted sink associated with authigenic clay formation during low-temperature alteration of volcanic rocks. Here we present measurements of the δ41K values of pore-fluids from ODP site 1052 in order to constrain potassium isotope fractionation during secondary clay formation. We find that δ41K values and K concentrations both decline systematically with depth. Results from 1-D diffusion-advection-reaction modeling of potassium concentrations and isotopic compositions indicate that fractionation of K isotopes during diffusion (Bourg et al., 2010) can explain all of the change in δ41K values of the pore-fluid with depth. Although the size of the K sink at site 1052 is a trivial fraction of the global K sink in clay minerals, our results suggest that diffusive fractionation of K isotopes in shallow pore-fluids may be, in part, responsible for the elevated δ41K value of seawater.

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane.

PubMed

Zhang, Mingzhen; Zheng, Jie; Nussinov, Ruth; Ma, Buyong

2016-09-15

Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane

NASA Astrophysics Data System (ADS)

Zhang, Mingzhen; Zheng, Jie; Nussinov, Ruth; Ma, Buyong

2016-09-01

Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.

Characteristics and origin of the relatively high-quality tight reservoir in the Silurian Xiaoheba Formation in the southeastern Sichuan Basin

PubMed Central

Gong, Xiaoxing; Shi, Zejin; Wang, Yong; Tian, Yaming; Li, Wenjie; Liu, Lei

2017-01-01

A mature understanding of the sandstone gas reservoir in the Xiaoheba Formation in the southeastern Sichuan Basin remains lacking. To assess the reservoir characteristics and the origin of the high-quality reservoir in the Xiaoheba Formation, this paper uses systematic field investigations, physical property analysis, thin section identification, scanning electron microscopy and electron microprobe methods. The results indicate that the Xiaoheba sandstone is an ultra-tight and ultra-low permeability reservoir, with an average porosity of 2.97% and an average permeability of 0.56×10−3 μm2. This promising reservoir is mainly distributed in the Lengshuixi and Shuangliuba regions and the latter has a relatively high-quality reservoir with an average porosity of 5.28% and average permeability of 0.53×10−3 μm2. The reservoir space comprises secondary intergranular dissolved pores, moldic pores and fractures. Microfacies, feldspar dissolution and fracture connectivity control the quality of this reservoir. The relatively weak compaction and cementation in the interbedded delta front distal bar and interdistributary bay microfacies indirectly protected the primary intergranular pores and enhanced late-stage dissolution. Late-stage potassium feldspar dissolution was controlled by the early-stage organic acid dissolution intensity and the distance from the hydrocarbon generation center. Early-stage fractures acted as pathways for organic acid migration and were therefore important factors in the formation of the reservoir. Based on these observations, the area to the west of the Shuangliuba and Lengshuixi regions has potential for gas exploration. PMID:28686735

Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

NASA Astrophysics Data System (ADS)

Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

2016-11-01

Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures--formed by a single sequence--may be a key feature in preventing bacterial resistance and could explain why sequence-function relationships in AMPs remain elusive.

Blanching of paint and varnish layers in easel paintings: contribution to the understanding of the alteration

NASA Astrophysics Data System (ADS)

Genty-Vincent, Anaïs; Eveno, Myriam; Nowik, Witold; Bastian, Gilles; Ravaud, Elisabeth; Cabillic, Isabelle; Uziel, Jacques; Lubin-Germain, Nadège; Menu, Michel

2015-11-01

The blanching of easel paintings can affect the varnish layer and also the paint layer with a blurring effect. The understanding of the physicochemical and optical phenomena involved in the whitening process remains an important challenge for the painting conservation. A set of ca. 50 microsamples from French, Flemish, and Italian blanched oil paintings, from sixteenth to nineteenth century, have been collected for in deep investigations. In parallel, the reproduction of the alteration was achieved by preparing some paint layers according to historical treatises and altering them in a climatic chamber in a humid environment or directly by immersing in ultrapure water. The observation of raw samples with a field-emission gun scanning electron microscope revealed for the first time that the altered layers have an unexpected highly porous structure with a pore size ranging from ca. 40 nm to 2 μm. The formation mechanism of these pores should mostly be physical as the supplementary analyses (Fourier transform infrared spectroscopy, gas chromatography-mass spectrometry) do not reveal any noticeable molecular modification. Considering the tiny size of the pores, the alteration can be explained by the Rayleigh or Mie light scattering.

Fluid source inferred from strontium isotopes in pore fluid and carbonate recovered during Expedition 337 off Shimokita, Japan

NASA Astrophysics Data System (ADS)

Hong, W.; Moen, N.; Haley, B. A.

2013-12-01

IODP Expedition 337 was designed to understand the relationship between a deep-buried (2000 meters below seafloor) hydrocarbon reservoir off the Shimokita peninsula (Japan), and the microbial community that this carbon reservoir sustains at such depth. Understanding sources and pathways of flow of fluids that carry hydrocarbons, nutrients, and other reduced components is of particular interest to fulfilling the expedition objectives, since this migrating fluid supports microbial activity not only of the deep-seated communities but also to the shallow-dwelling organisms. To this aim, the concentration and isotopic signature of Sr can be valuable due to that it is relatively free from biogenic influence and pristine in terms of drill fluid contamination. From the pore water Sr profile, concentration gradually increases from 1500 to 2400 mbsf. The depth where highest Sr concentration is observed corresponds to the depths where couple layers of carbonate were observed. Such profile suggests an upward-migrating fluid carries Sr from those deep-seated carbonate layers (>2400 mbsf) to shallower sediments. To confirm this inference, pore water, in-situ formation fluid, and carbonate samples were analyzed for Sr isotopes to investigate the fluid source.

Laser-induced micropore formation and modification of cartilage structure in osteoarthritis healing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobol, Emil; Baum, Olga; Shekhter, Anatoly

Pores are vital for functioning of avascular tissues. Laser-induced pores play an important role in the process of cartilage regeneration. The aim of any treatment for osteoarthritis is to repair hyaline-type cartilage. The aims of this study are to answer two questions: (1) How do laser-assisted pores affect the cartilaginous cells to synthesize hyaline cartilage (HC)? and (2) How can the size distribution of pores arising in the course of laser radiation be controlled? We have shown that in cartilage, the pores arise predominately near chondrocytes, which promote nutrition of cells and signal molecular transfer that activates regeneration of cartilage.more » In vivo laser treatment of damaged cartilage of miniature pig joints provides cellular transformation and formation of HC. We propose a simple model of pore formation in biopolymers that paves the way for going beyond the trial-anderror approach when choosing an optimal laser treatment regime. Our findings support the approach toward laser healing of osteoarthritis.« less

Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process

NASA Astrophysics Data System (ADS)

Iacovache, Ioan; de Carlo, Sacha; Cirauqui, Nuria; Dal Peraro, Matteo; van der Goot, F. Gisou; Zuber, Benoît

2016-07-01

Owing to their pathogenical role and unique ability to exist both as soluble proteins and transmembrane complexes, pore-forming toxins (PFTs) have been a focus of microbiologists and structural biologists for decades. PFTs are generally secreted as water-soluble monomers and subsequently bind the membrane of target cells. Then, they assemble into circular oligomers, which undergo conformational changes that allow membrane insertion leading to pore formation and potentially cell death. Aerolysin, produced by the human pathogen Aeromonas hydrophila, is the founding member of a major PFT family found throughout all kingdoms of life. We report cryo-electron microscopy structures of three conformational intermediates and of the final aerolysin pore, jointly providing insight into the conformational changes that allow pore formation. Moreover, the structures reveal a protein fold consisting of two concentric β-barrels, tightly kept together by hydrophobic interactions. This fold suggests a basis for the prion-like ultrastability of aerolysin pore and its stoichiometry.

Laser-induced micropore formation and modification of cartilage structure in osteoarthritis healing.

PubMed

Sobol, Emil; Baum, Olga; Shekhter, Anatoly; Wachsmann-Hogiu, Sebastian; Shnirelman, Alexander; Alexandrovskaya, Yulia; Sadovskyy, Ivan; Vinokur, Valerii

2017-09-01

Pores are vital for functioning of avascular tissues. Laser-induced pores play an important role in the process of cartilage regeneration. The aim of any treatment for osteoarthritis is to repair hyaline-type cartilage. The aims of this study are to answer two questions: (1) How do laser-assisted pores affect the cartilaginous cells to synthesize hyaline cartilage (HC)? and (2) How can the size distribution of pores arising in the course of laser radiation be controlled? We have shown that in cartilage, the pores arise predominately near chondrocytes, which promote nutrition of cells and signal molecular transfer that activates regeneration of cartilage. In vivo laser treatment of damaged cartilage of miniature pig joints provides cellular transformation and formation of HC. We propose a simple model of pore formation in biopolymers that paves the way for going beyond the trial-and-error approach when choosing an optimal laser treatment regime. Our findings support the approach toward laser healing of osteoarthritis.

Laser-induced micropore formation and modification of cartilage structure in osteoarthritis healing

NASA Astrophysics Data System (ADS)

Sobol, Emil; Baum, Olga; Shekhter, Anatoly; Wachsmann-Hogiu, Sebastian; Shnirelman, Alexander; Alexandrovskaya, Yulia; Sadovskyy, Ivan; Vinokur, Valerii

2017-09-01

Pores are vital for functioning of avascular tissues. Laser-induced pores play an important role in the process of cartilage regeneration. The aim of any treatment for osteoarthritis is to repair hyaline-type cartilage. The aims of this study are to answer two questions: (1) How do laser-assisted pores affect the cartilaginous cells to synthesize hyaline cartilage (HC)? and (2) How can the size distribution of pores arising in the course of laser radiation be controlled? We have shown that in cartilage, the pores arise predominately near chondrocytes, which promote nutrition of cells and signal molecular transfer that activates regeneration of cartilage. In vivo laser treatment of damaged cartilage of miniature pig joints provides cellular transformation and formation of HC. We propose a simple model of pore formation in biopolymers that paves the way for going beyond the trial-and-error approach when choosing an optimal laser treatment regime. Our findings support the approach toward laser healing of osteoarthritis.

The assembly dynamics of the cytolytic pore toxin ClyA

PubMed Central

Benke, Stephan; Roderer, Daniel; Wunderlich, Bengt; Nettels, Daniel; Glockshuber, Rudi; Schuler, Benjamin

2015-01-01

Pore-forming toxins are protein assemblies used by many organisms to disrupt the membranes of target cells. They are expressed as soluble monomers that assemble spontaneously into multimeric pores. However, owing to their complexity, the assembly processes have not been resolved in detail for any pore-forming toxin. To determine the assembly mechanism for the ring-shaped, homododecameric pore of the bacterial cytolytic toxin ClyA, we collected a diverse set of kinetic data using single-molecule spectroscopy and complementary techniques on timescales from milliseconds to hours, and from picomolar to micromolar ClyA concentrations. The entire range of experimental results can be explained quantitatively by a surprisingly simple mechanism. First, addition of the detergent n-dodecyl-β-D-maltopyranoside to the soluble monomers triggers the formation of assembly-competent toxin subunits, accompanied by the transient formation of a molten-globule-like intermediate. Then, all sterically compatible oligomers contribute to assembly, which greatly enhances the efficiency of pore formation compared with simple monomer addition. PMID:25652783

Methane gas hydrate effect on sediment acoustic and strength properties

USGS Publications Warehouse

Winters, W.J.; Waite, W.F.; Mason, D.H.; Gilbert, L.Y.; Pecher, I.A.

2007-01-01

To improve our understanding of the interaction of methane gas hydrate with host sediment, we studied: (1) the effects of gas hydrate and ice on acoustic velocity in different sediment types, (2) effect of different hydrate formation mechanisms on measured acoustic properties (3) dependence of shear strength on pore space contents, and (4) pore pressure effects during undrained shear.A wide range in acoustic p-wave velocities (Vp) were measured in coarse-grained sediment for different pore space occupants. Vp ranged from less than 1 km/s for gas-charged sediment to 1.77–1.94 km/s for water-saturated sediment, 2.91–4.00 km/s for sediment with varying degrees of hydrate saturation, and 3.88–4.33 km/s for frozen sediment. Vp measured in fine-grained sediment containing gas hydrate was substantially lower (1.97 km/s). Acoustic models based on measured Vp indicate that hydrate which formed in high gas flux environments can cement coarse-grained sediment, whereas hydrate formed from methane dissolved in the pore fluid may not.The presence of gas hydrate and other solid pore-filling material, such as ice, increased the sediment shear strength. The magnitude of that increase is related to the amount of hydrate in the pore space and cementation characteristics between the hydrate and sediment grains. We have found, that for consolidation stresses associated with the upper several hundred meters of sub-bottom depth, pore pressures decreased during shear in coarse-grained sediment containing gas hydrate, whereas pore pressure in fine-grained sediment typically increased during shear. The presence of free gas in pore spaces damped pore pressure response during shear and reduced the strengthening effect of gas hydrate in sands.

Effects of Pore Size on the Osteoconductivity and Mechanical Properties of Calcium Phosphate Cement in a Rabbit Model.

PubMed

Zhao, Yi-Nan; Fan, Jun-Jun; Li, Zhi-Quan; Liu, Yan-Wu; Wu, Yao-Ping; Liu, Jian

2017-02-01

Calcium phosphate cement (CPC) porous scaffold is widely used as a suitable bone substitute to repair bone defect, but the optimal pore size is unclear yet. The current study aimed to evaluate the effect of different pore sizes on the processing of bone formation in repairing segmental bone defect of rabbits using CPC porous scaffolds. Three kinds of CPC porous scaffolds with 5 mm diameters and 12 mm length were prepared with the same porosity but different pore sizes (Group A: 200-300 µm, Group B: 300-450 µm, Group C: 450-600 µm, respectively). Twelve millimeter segmental bone defects were created in the middle of the radius bone and filled with different kinds of CPC cylindrical scaffolds. After 4, 12, and 24 weeks, alkaline phosphatase (ALP), histological assessment, and mechanical properties evaluation were performed in all three groups. After 4 weeks, ALP activity increased in all groups but was highest in Group A with smallest pore size. The new bone formation within the scaffolds was not obvious in all groups. After 12 weeks, the new bone formation within the scaffolds was obvious in each group and highest in Group A. At 24 weeks, no significant difference in new bone formation was observed among different groups. Besides the osteoconductive effect, Group A with smallest pore size also had the best mechanical properties in vivo at 12 weeks. We demonstrate that pore size has a significant effect on the osteoconductivity and mechanical properties of calcium phosphate cement porous scaffold in vivo. Small pore size favors the bone formation in the early stage and may be more suitable for repairing segmental bone defect in vivo. © 2016 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Gradual pore formation in natural origin scaffolds throughout subcutaneous implantation

PubMed Central

Martins, Ana M.; Kretlow, James D.; Costa-Pinto, Ana R.; Malafaya, Patrícia B.; Fernandes, Emanuel M.; Neves, Nuno M.; Alves, Catarina M.; Mikos, Antonios G.; Kasper, F. Kurtis; Reis, Rui L.

2012-01-01

The present study employed a rat subcutaneous implantation model to investigate gradual in situ pore formation in a self-regulating degradable chitosan-based material, which comprises lysozyme incorporated into biomimetic calcium phosphate (CaP) coatings at the surface in order to control the scaffold degradation and subsequent pore formation. Specifically, the in vivo degradation of the scaffolds, the in situ pore formation and the tissue response were investigated. Chitosan or chitosan/starch scaffolds were studied with and without a CaP coating in the presence or absence of lysozyme for a total of 6 experimental groups. Twenty-four scaffolds per group were implanted, and eight scaffolds were retrieved at each of three time points (3, 6 and 12 weeks). Harvested samples were analyzed for weight loss, micro-computed tomography, and histological analysis. All scaffolds showed pronounced weight loss and pore formation as a function of time. The highest weight loss was 29.8 ± 1.5%, obtained at week 12 for CaP chitosan/starch scaffolds with lysozyme incorporated. Moreover, all experimental groups showed a significant increase in porosity after 12 weeks. At all time points no adverse tissue reaction was observed, and as degradation increased, histological analysis showed cellular ingrowth throughout the implants. Using this innovative methodology, the ability to gradually generate pores in situ was clearly demonstrated in vivo. PMID:22213676

a Fractal Permeability Model Coupling Boundary-Layer Effect for Tight Oil Reservoirs

NASA Astrophysics Data System (ADS)

Wang, Fuyong; Liu, Zhichao; Jiao, Liang; Wang, Congle; Guo, Hu

A fractal permeability model coupling non-flowing boundary-layer effect for tight oil reservoirs was proposed. Firstly, pore structures of tight formations were characterized with fractal theory. Then, with the empirical equation of boundary-layer thickness, Hagen-Poiseuille equation and fractal theory, a fractal torturous capillary tube model coupled with boundary-layer effect was developed, and verified with experimental data. Finally, the parameters influencing effective liquid permeability were quantitatively investigated. The research results show that effective liquid permeability of tight formations is not only decided by pore structures, but also affected by boundary-layer distributions, and effective liquid permeability is the function of fluid type, fluid viscosity, pressure gradient, fractal dimension, tortuosity fractal dimension, minimum pore radius and maximum pore radius. For the tight formations dominated with nanoscale pores, boundary-layer effect can significantly reduce effective liquid permeability, especially under low pressure gradient.

Effect of Fe- and Si-Enriched Secondary Precipitates and Surface Roughness on Pore Formation on Aluminum Plate Surfaces During Anodizing

NASA Astrophysics Data System (ADS)

Zhu, Yuanzhi; Wang, Shizhi; Yang, Qingda; Zhou, Feng

2014-09-01

Two twin roll casts (TRCs) and one hot rolled (HR) AA 1235 aluminum alloy plates with different microstructures are prepared. The plates were electrolyzed in a 1.2 wt% HCl solution with a voltage of 21 V and a current of 1.9 mA. The shape, size, and number of pores formed on the surfaces of these plates were analyzed and correlated with the microstructures of the plates. It is found that pores are easier to form on the alloy plates containing subgrains with a lower dislocation density inside the subgrains, rather than along the grain boundaries. Furthermore, Fe- and Si-enriched particles in the AA1235 aluminum alloys lead to the formation of pores on the surface during electrolyzing; the average precipitate sizes of 4, 3.5, and 2 μm in Alloy 1#, Alloy 2# and Alloy 3# result in the average pore sizes of 3.78, 2.76, and 1.9 μm on the surfaces of the three alloys, respectively; The G.P zone in the alloy also facilitates the surface pore formation. High-surface roughness enhances the possibility of entrapping more lubricants into the plate surface, which eventually blocks the formation of the pores on the surface of the aluminum plates in the following electrolyzing process.

Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers.

PubMed

Bennett, W F Drew; Hong, Chun Kit; Wang, Yi; Tieleman, D Peter

2016-09-13

Due to antimicrobial resistance, the development of new drugs to combat bacterial and fungal infections is an important area of research. Nature uses short, charged, and amphipathic peptides for antimicrobial defense, many of which disrupt the lipid membrane in addition to other possible targets inside the cell. Computer simulations have revealed atomistic details for the interactions of antimicrobial peptides and cell-penetrating peptides with lipid bilayers. Strong interactions between the polar interface and the charged peptides can induce bilayer deformations - including membrane rupture and peptide stabilization of a hydrophilic pore. Here, we performed microsecond-long simulations of the antimicrobial peptide CM15 in a POPC bilayer expecting to observe pore formation (based on previous molecular dynamics simulations). We show that caution is needed when interpreting results of equilibrium peptide-membrane simulations, given the length of time single trajectories can dwell in local energy minima for 100's of ns to microseconds. While we did record significant membrane perturbations from the CM15 peptide, pores were not observed. We explain this discrepancy by computing the free energy for pore formation with different force fields. Our results show a large difference in the free energy barrier (ca. 40 kJ/mol) against pore formation predicted by the different force fields that would result in orders of magnitude differences in the simulation time required to observe spontaneous pore formation. This explains why previous simulations using the Berger lipid parameters reported pores induced by charged peptides, while with CHARMM based models pores were not observed in our long time-scale simulations. We reconcile some of the differences in the distance dependent free energies by shifting the free energy profiles to account for thickness differences between force fields. The shifted curves show that all the models describe small defects in lipid bilayers in a consistent manner, suggesting a common physical basis.

Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor

PubMed Central

Sarker, Muzaddid; de Antueno, Roberto; Langelaan, David N.; Parmar, Hiren B.; Shin, Kyungsoo; Rainey, Jan K.; Duncan, Roy

2015-01-01

Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS) in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST) protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS) but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation. PMID:26061049

Relationship between mineralogy and porosity in seals relevant to geologic CO2 Sequestration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swift, Alexander; Anovitz, Lawrence; Sheets, Julia

2014-01-01

Porosity and permeability are key petrophysical variables that link the thermal, hydrological, geochemical, and geomechanical properties of subsurface formations. The size, shape, distribution, and connectivity of rock pores dictate how fluids migrate into and through micro- and nano-environments, then wet and react with accessible solids. Three representative samples of cap rock from the Eau Claire Formation, the prospective sealing unit that overlies the Mount Simon Sandstone, a potential CO 2 storage formation, were interrogated with an array of complementary methods. neutron scattering, backscattered-electron imaging, energydispersive spectroscopy, and mercury porosimetry. Results are presented that detail variations between lithologic types in totalmore » and connected nano- to microporosity across more than five orders of magnitude. Pore types are identified and then characterized according to presence in each rock type, relative abundance, and surface area of adjacent minerals, pore and pore-throat diameters, and degree of connectivity. We observe a bimodal distribution of porosity as a function of both pore diameter and pore-throat diameter. The contribution of pores at the nano- and microscales to the total and the connected porosity is a distinguishing feature of each lithology observed. Pore:pore-throat ratios at each of these two scales diverge markedly, being almost unity at the nanoscale regime (dominated by illitic clay and micas), and varying by one and a half orders of magnitude at the microscale within a clastic mudstone.« less

Dependence of cell adhesion on extracellular matrix materials formed on pore bridge boundaries by nanopore opening and closing geometry.

PubMed

Kim, Sueon; Han, Dong Yeol; Chen, Zhenzhong; Lee, Won Gu

2018-04-30

In this study, we report experimental results for characterization of the growth and formation of pore bridge materials that modified the adhesion structures of cells cultured on nanomembranes with opening and closing geometry. To perform the proof-of-concept experiments, we fabricated two types of anodized alumina oxide substrates with single-sided opening (i.e., one side open, but closed at the other side) and double-sided opening (i.e., both sides open). In our experiment, we compared the densities of pores formed and of bridge materials which differently act as connective proteins depending on the size of pores. The results show that the pore opening geometry can be used to promote the net contact force between pores, resulting in the growth and formation of pore bridge materials before and after cell culture. The results also imply that the bridge materials can be used to attract the structural protrusion of filopodia that can promote the adhesion of cell-to-cell and cell-to-pore bridge. It is observed that the shape and size of cellular structures of filopodia depend on the presence of pore bridge materials. Overall, this observation brought us a significant clue that cells cultured on nanopore substrates would change the adhesion property depending on not only the formation of nanopores formed on the surface of topological substrates, but also that of pore bridge materials by its morphological growth.

Quantification of subsurface pore pressure through IODP drilling

NASA Astrophysics Data System (ADS)

Saffer, D. M.; Flemings, P. B.

2010-12-01

It is critical to understand the magnitude and distribution of subsurface pore fluid pressure: it controls effective stress and thus mechanical strength, slope stability, and sediment compaction. Elevated pore pressures also drive fluid flows that serve as agents of mass, solute, and heat fluxes. The Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) have provided important avenues to quantify pore pressure in a range of geologic and tectonic settings. These approaches include 1) analysis of continuous downhole logs and shipboard physical properties data to infer compaction state and in situ pressure and stress, 2) laboratory consolidation testing of core samples collected by drilling, 3) direct downhole measurements using pore pressure probes, 3) pore pressure and stress measurements using downhole tools that can be deployed in wide diameter pipe recently acquired for riser drilling, and 4) long-term monitoring of formation pore pressure in sealed boreholes within hydraulically isolated intervals. Here, we summarize key advances in quantification of subsurface pore pressure rooted in scientific drilling, highlighting with examples from subduction zones, the Gulf of Mexico, and the New Jersey continental shelf. At the Nankai, Costa Rican, and Barbados subduction zones, consolidation testing of cores samples, combined with analysis of physical properties data, indicates that even within a few km landward of the trench, pore pressures in and below plate boundary décollement zones reach a significant fraction of the lithostatic load (λ*=0.25-0.91). These results document a viable and quantifiable mechanism to explain the mechanical weakness of subduction décollements, and are corroborated by a small number of direct measurements in sealed boreholes and by inferences from seismic reflection data. Recent downhole measurements conducted during riser drilling using the modular formation dynamics tester wireline tool (MDT) in a forearc basin ~50 km from the trench document hydrostatic pore pressures in the basin fill down to ~1500 mbsf, and illustrate a promising technique for obtaining pore pressure and stress magnitude. In the Gulf of Mexico, we used pore pressure penetrometers to measure severe overpressures (λ*=0.7); a comprehensive program of consolidation testing on recovered core samples confirms elevated pore pressures due to rapid sedimentation, reflecting disequilibrium compaction. Similarly, along the New Jersey continental shelf, analysis of porosity data from downhole logs and augmented by geotechnical testing of cores demonstrates elevated pore pressures in the shallow subsurface. In both offshore New Jersey and the Gulf of Mexico, integration of direct measurements, geotechnical testing, and hydrodynamic modeling illustrate how flow is focused along permeable layers to reduce effective stress and drive submarine landslides. In sum, pore pressure observations made through the ODP and IODP provide insight into how pore pressure controls the large-scale form of passive and active continental margins, how submarine landslides form, and provide strategies for engineering deep boreholes.

The Pore Formation and Mobility Investigation: A Case Study for Conducting Research on the International Space Station in Support of Exploration

NASA Technical Reports Server (NTRS)

Grugel, R. N.; Luz, P.; Smith, G. A.; Spivey, R.; Mingo, C.; Jeter, L.; Volz, M. P.

2005-01-01

The Pore Formation and Mobility Investigation (PFMI) is being conducted in the Microgravity Science Glovebox (MSG) aboard the International Space Station (ISS) with the goal of understanding bubble generation and interactions during controlled directional solidification processing. Through the course of the experiments, beginning in September 2002, a number of key factors pertinent to solidification processing of materials in a microgravity environment have been directly observed, measured, and modeled. Though most experiments ran uninterrupted, on four separate occasions malfunctions to the PFMI hardware and software were experienced that required crew intervention, including in-space repair. Fortunately, each repair attempt was successful and restored the PFMI apparatus to a fully functional condition. Based on PFMI results and lessons learned, the intent of this presentation is to draw attention to the role ISS experiments/hardware can play in providing insight to potential fabrication processing techniques and repair scenarios that might arise during long duration space transport and/or on the lunar/Mars surface.

The Pore Formation and Mobility Investigation: A Summary of Conducted Research on the International Space Station

NASA Technical Reports Server (NTRS)

Grugel, R. N.; Luz, P.; Smith, G. A.; Spivey, R.; Jeter, L.; Volz, M. P.; Anilkumar, A.

2006-01-01

The Pore Formation and Mobility Investigation (PFMI) is being conducted in the Microgravity Science Glovebox (MSG) aboard the International Space Station (ISS) with the goal of understanding bubble generation and interactions during controlled directional solidification processing. Through the course of the experiments, beginning in September 2002, a number of key factors pertinent to solidification processing of materials in a microgravity environment have been directly observed, measured, and modeled. Though most experiments ran uninterrupted, on four separate occasions malfunctions to the PFMI hardware and software were experienced that required crew intervention, including in-space repair. Fortunately, each repair attempt was successful and restored the PFMI apparatus to a fully functional condition. Based on PFMI results and lessons learned, the intent of this presentation is to draw attention to the role ISS experiments/hardware can play in providing insight to potential fabrication processing techniques and repair scenarios that might arise during long duration space transport and/or on the lunar/Mars surface.

Pore Formation and Mobility Investigation (PFMI): Concept, Hardware Development, and Initial Analysis of Experiments Conducted Aboard the International Space Station

NASA Technical Reports Server (NTRS)

Grugel, Richard N.

2003-01-01

Porosity in the form of "bubbles and pipes" can occur during controlled directional solidification processing of metal alloys. This is a consequence that 1) precludes obtaining any meaningful scientific results and 2) is detrimental to desired material properties. Unfortunately, several Microgravity experiments have been compromised by porosity. The intent of the PFMl investigation is to conduct a systematic effort directed towards understanding porosity formation and mobility during controlled directional solidification (DS) in a microgravity environment. PFMl uses a pure transparent material, succinonitrile (SCN), as well as SCN "alloyed" with water, in conjunction with a translating temperature gradient stage so that direct observation and recording of pore generation and mobility can be made. PFMl is investigating the role of thermocapillary forces and temperature gradients in affecting bubble dynamics as well as other solidification processes in a microgravity environment. This presentation will cover the concept, hardware development, operations, and the initial results from experiments conducted aboard the International Space Station.

Pore Formation and Mobility Investigation (PFMI): Concept, Hardware Development and Initial Analysis of Experiments

NASA Technical Reports Server (NTRS)

Grugel, Richard N.

2004-01-01

Porosity in the form of "bubbles and pipes" can occur during controlled directional solidification processing of metal alloys. This is a consequence that 1) precludes obtaining any meaningful scientific results and 2) is detrimental to desired material properties. Unfortunately, several Microgravity experiments have been compromised by porosity. The intent of the PFMI investigation is to conduct a systematic effort directed towards understanding porosity formation and mobility during controlled directional solidification (DS) in a microgravity environment. PFMI uses a pure transparent material, succinonitrile (SCN), as well as SCN "alloyed" with water, in conjunction with a translating temperature gradient stage so that direct observation and recording of pore generation and mobility can be made. PFMI is investigating the role of thermocapillary forces and temperature gradients in affecting bubble dynamics as well as other solidification processes in a microgravity Environment. This presentation will cover the concept, hardware development, operations, and the initial results from experiments conducted aboard the International Space Station. .

Experiments Conducted Aboard the International Space Station: The Pore Formation and Mobility Investigation (PFMI) and the In-Space Soldering Investigation (ISSI): A Current Study of Results

NASA Technical Reports Server (NTRS)

Grugel, R. N.; Luz, P.; Smith, G. A.; Spivey, R.; Jeter, L.; Gillies, D. C> ; Hua, F.; Anilkumar, A. V.

2006-01-01

Experiments in support of the Pore Formation and Mobility Investigation (PFMI) and the In-Space Soldering Investigation (ISSI) were conducted aboard the International Space Station (ISS) with the goal of promoting our fundamental understanding of melting dynamics , solidification phenomena, and defect generation during materials processing in a microgravity environment. Through the course of many experiments a number of observations, expected and unexpected, have been directly made. These include gradient-driven bubble migration, thermocapillary flow, and novel microstructural development. The experimental results are presented and found to be in good agreement with models pertinent to a microgravity environment. Based on the space station results, and noting the futility of duplicating them in Earth s unit-gravity environment, attention is drawn to the role ISS experimentslhardware can play to provide insight to potential materials processing techniques and/or repair scenarios that might arise during long duration space transport and/or on the lunar/Mars surface.

Fractal Nature of Porosity in Volcanic Tight Reservoirs of the Santanghu Basin and its Relationship to Pore Formation Processes

NASA Astrophysics Data System (ADS)

Wang, Weiming; Wang, Zhixuan; Chen, Xuan; Long, Fei; Lu, Shuangfang; Liu, Guohong; Tian, Weichao; Su, Yue

In this paper, in a case study of Santanghu Basin in China, the morphological characteristics and size distribution of nanoscale pores in the volcanic rocks of the Haerjiawu Formation were investigated using the results of low temperature nitrogen adsorption experiments. This research showed that within the target layer, a large number of nanoscale, eroded pores showed an “ink bottle” morphology with narrow pore mouths and wide bodies. The fractal dimension of pores increases gradually with increasing depth. Moreover, as fractal dimension increases, BET-specific surface area gradually increases, average pore diameter decreases and total pore volume gradually increases. The deeper burial of the Haerjiawu volcanic rocks in the Santanghu Basin leads to more intense erosion by organic acids derived from the basin’s source rocks. Furthermore, the internal surface roughness of these corrosion pores results in poor connectivity. As stated above, the corrosion process is directly related to the organic acids generated by the source rock of the interbedded volcanic rocks. The deeper the reservoir, the more the organic acids being released from the source rock. However, due to the fact that the Haerjiawu volcanic rocks are tight reservoirs and have complicated pore-throat systems, while organic acids dissolve unstable minerals such as feldspars which improve the effective reservoir space; the dissolution of feldspars results in the formation of new minerals, which cannot be expelled from the tight reservoirs. They are instead precipitated in the fine pore throats, thereby reducing pore connectivity, while enhancing reservoir micro-preservation conditions.

Towards the damage evaluation using Gurson-Tvergaard-Needleman (GTN) model for hot forming processes

NASA Astrophysics Data System (ADS)

Imran, Muhammad; Bambach, Markus

2018-05-01

In the production of semi-finished metal products, hot forming is used to eliminate the pores and voids from the casting process under compressive stresses and to modify the microstructure for further processing. In the case of caliber and flat rolling processes, tensile stresses occur at certain roll gap ratios which promote pore formation on nonmetallic inclusion. The formation of new pores contributes to ductile damage and reduces the load carrying capacity of the material. In the literature, the damage nucleation and growth during the hot forming process are not comprehensively described. The aim of this study is to understand the damage initiation and growth mechanism during hot forming processes. Hot tensile tests are performed at different temperatures and strain rates for 16MnCrS5 steel. To investigate the influence of geometrical variations on the damage mechanism, specimens with different stress triaxiality ratios are used. Finite element simulations using the Gurson-Tvergaard-Needleman (GTN) damage model are performed to estimate the critical void fraction for the damage initiation and the evolution of the void volume fraction. The results showed that the GTN model underestimates the softening of the material due to the independence of the temperature and the strain rate.

Evaluating the effect of lithology on porosity development in ridgetops in the Appalachian Piedmont

NASA Astrophysics Data System (ADS)

Marcon, V.; Gu, X.; Fisher, B.; Brantley, S. L.

2016-12-01

Together, chemical and physical processes transform fresh bedrock into friable weathered material. Even in systems where lithology, tectonic history, and climatic history are all known, it is challenging to predict the depth of weathering because the mechanisms that control the rate of regolith formation are not understood. In the Appalachian Piedmont, where rates of regolith formation and erosion are thought to be in a rough steady state, the depth of weathering varies with lithology. The Piedmont provides a controlled natural environment to isolate the effects of lithology on weathering processes so we can start to understand the mechanisms that initiate and drive weathering. Weathering is deepest over feldspathic rocks (schist/granite) with regolith 20-30m thick and thinnest over mafic and ultramafic rocks (diabase/serpentinite) with regolith <5m thick (Pavich et al., 1989). We are exploring both chemical and physical controls on weathering. For example, when regolith thickness is plotted versus fracture toughness of each lithology, regolith thickness generally increases with decreasing fracture toughness. However, serpentinite, a rheologically weak rock, does not follow this trend with thin soils. To understand this observation, physical weathering parameters (porosity, connectivity, and surface area) were evaluated using neutron scattering on Piedmont rocks at different degrees of weathering. Samples of both weathered diabase and serpentinite are dominated by small pores (<0.1micron), whereas pores in schist are characteristically larger (1-10microns). As serpentinite weathers, porosity is created by serpentinization reactions and lost from collapse during weathering. Serpentinite consists of easily weathered hydrous minerals with little quartz. Comparatively, rocks with more quartz (e.g. schist) have a supportive skeleton as the rock weathers. This quartz skeleton could prevent the collapse of pores and result in isovolumetric weathering. Non-isovolumetric weathering limits infiltration of reactive fluids deeper into the rock, minimizing regolith formation in serpentinite due to its lack of a quartz skeleton. Given this, fracture toughness may be an important parameter to consider in terms of predicting regolith thickness.

GSDMD membrane pore formation constitutes the mechanism of pyroptotic cell death.

PubMed

Sborgi, Lorenzo; Rühl, Sebastian; Mulvihill, Estefania; Pipercevic, Joka; Heilig, Rosalie; Stahlberg, Henning; Farady, Christopher J; Müller, Daniel J; Broz, Petr; Hiller, Sebastian

2016-08-15

Pyroptosis is a lytic type of cell death that is initiated by inflammatory caspases. These caspases are activated within multi-protein inflammasome complexes that assemble in response to pathogens and endogenous danger signals. Pyroptotic cell death has been proposed to proceed via the formation of a plasma membrane pore, but the underlying molecular mechanism has remained unclear. Recently, gasdermin D (GSDMD), a member of the ill-characterized gasdermin protein family, was identified as a caspase substrate and an essential mediator of pyroptosis. GSDMD is thus a candidate for pyroptotic pore formation. Here, we characterize GSDMD function in live cells and in vitro We show that the N-terminal fragment of caspase-1-cleaved GSDMD rapidly targets the membrane fraction of macrophages and that it induces the formation of a plasma membrane pore. In vitro, the N-terminal fragment of caspase-1-cleaved recombinant GSDMD tightly binds liposomes and forms large permeability pores. Visualization of liposome-inserted GSDMD at nanometer resolution by cryo-electron and atomic force microscopy shows circular pores with variable ring diameters around 20 nm. Overall, these data demonstrate that GSDMD is the direct and final executor of pyroptotic cell death. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

Amyloid pore-channel hypothesis: effect of ethanol on aggregation state using frog oocytes for an Alzheimer's disease study.

PubMed

Parodi, Jorge; Ormeño, David; Ochoa-de la Paz, Lenin D

2015-01-01

Alzheimer's disease severely compromises cognitive function. One of the mechanisms to explain the pathology of Alzheimer's disease has been the hypotheses of amyloid-pore/channel formation by complex Aβ-aggregates. Clinical studies suggested the moderate alcohol consumption can reduces probability developing neurodegenerative pathologies. A recent report explored the ability of ethanol to disrupt the generation of complex Aβ in vitro and reduce the toxicity in two cell lines. Molecular dynamics simulations were applied to understand how ethanol blocks the aggregation of amyloid. On the other hand, the in silico modeling showed ethanol effect over the dynamics assembling for complex Aβ-aggregates mediated by break the hydrosaline bridges between Asp 23 and Lys 28, was are key element for amyloid dimerization. The amyloid pore/channel hypothesis has been explored only in neuronal models, however recently experiments suggested the frog oocytes such an excellent model to explore the mechanism of the amyloid pore/channel hypothesis. So, the used of frog oocytes to explored the mechanism of amyloid aggregates is new, mainly for amyloid/pore hypothesis. Therefore, this experimental model is a powerful tool to explore the mechanism implicates in the Alzheimer's disease pathology and also suggests a model to prevent the Alzheimer's disease pathology.

From the Cover: Understanding nature's design for a nanosyringe

NASA Astrophysics Data System (ADS)

Lopez, Carlos F.; Nielsen, Steve O.; Moore, Preston B.; Klein, Michael L.

2004-03-01

Synthetic and natural peptide assemblies can possess transport or conductance activity across biomembranes through the formation of nanopores. The fundamental mechanisms of membrane insertion necessary for antimicrobial or synthetic pore formation are poorly understood. We observe a lipid-assisted mechanism for passive insertion into a model membrane from molecular dynamics simulations. The assembly used in the study, a generic nanotube functionalized with hydrophilic termini, is assisted in crossing the membrane core by transleaflet lipid flips. Lipid tails occlude a purely hydrophobic nanotube. The observed insertion mechanism requirements for hydrophobic-hydrophilic matching have implications for the design of synthetic channels and antibiotics.

A New Dual-Pore Formation Factor Model: A Percolation Network Study and Comparison to Experimental Data

NASA Astrophysics Data System (ADS)

Tang, Y. B.; Li, M.; Bernabe, Y.

2014-12-01

We modeled the electrical transport behavior of dual-pore carbonate rocks in this paper. Based on experimental data of a carbonate reservoir in China, we simply considered the low porosity samples equivalent to the matrix (micro-pore system) of the high porosity samples. For modeling the bimodal porous media, we considered that the matrix is homogeneous and interconnected. The connectivity and the pore size distribution of macro-pore system are varied randomly. Both pore systems are supposed to act electrically in parallel, connected at the nodes, where the fluid exchange takes place, an approach previously used by Bauer et al. (2012). Then, the effect of the properties of matrix, the pore size distribution and connectivity of macro-pore system on petrophysical properties of carbonates can be investigated. We simulated electrical current through networks in three-dimensional simple cubic (SC) and body-center cubic (BCC) with different coordination numbers and different pipe radius distributions of macro-pore system. Based on the simulation results, we found that the formation factor obeys a "universal" scaling relationship (i.e. independent of lattice type), 1/F∝eγz, where γ is a function of the normalized standard deviation of the pore radius distribution of macro-pore system and z is the coordination number of macro-pore system. This relationship is different from the classic "universal power law" in percolation theory. A formation factor model was inferred on the basis of the scaling relationship mentioned above and several scale-invariant quantities (such as hydraulic radius rH and throat length l of macro-pore). Several methods were developed to estimate corresponding parameters of the new model with conventional core analyses. It was satisfactorily tested against experimental data, including some published experimental data. Furthermore, the relationship between water saturation and resistivity in dual-pore carbonates was discussed based on the new model.

An emerging case for membrane pore formation as a common mechanism for the unconventional secretion of FGF2 and IL-1β.

PubMed

Brough, David; Pelegrin, Pablo; Nickel, Walter

2017-10-01

Extracellular proteins with important signalling roles in processes, such as inflammation and angiogenesis, are known to employ unconventional routes of protein secretion. Although mechanisms of unconventional protein secretion are beginning to emerge, the precise molecular details have remained elusive for the majority of cargo proteins secreted by unconventional means. Recent findings suggest that for two examples of unconventionally secreted proteins, interleukin 1β (IL-1β) and fibroblast growth factor 2 (FGF2), the common molecular principle of pore formation may be shared. Under specific experimental conditions, secretion of IL-1β and FGF2 is triggered by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 ]-dependent formation of pores across the plasma membrane. However, the underlying mechanisms are different, with FGF2 known to directly interact with PI(4,5)P 2 , whereas in the case of IL-1β secretion, it is proposed that the N-terminal fragment of gasdermin D interacts with PI(4,5)P 2 to form the pore. Thus, although implemented in different ways, these findings suggest that pore formation may be shared by the unconventional secretion mechanisms for FGF2 and IL-1β in at least some cases. In this Opinion article, we discuss the unconventional mechanisms of FGF2 and IL-1β release with a particular emphasis on recent discoveries suggesting the importance of pore formation on the plasma membrane. © 2017. Published by The Company of Biologists Ltd.

Calculating Transition Energy Barriers and Characterizing Activation States for Steps of Fusion

PubMed Central

Ryham, Rolf J.; Klotz, Thomas S.; Yao, Lihan; Cohen, Fredric S.

2016-01-01

We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm. PMID:26958888

Measuring kinetic drivers of pneumolysin pore structure.

PubMed

Gilbert, Robert J C; Sonnen, Andreas F-P

2016-05-01

Most membrane attack complex-perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins are thought to form pores in target membranes by assembling into pre-pore oligomers before undergoing a pre-pore to pore transition. Assembly during pore formation is into both full rings of subunits and incomplete rings (arcs). The balance between arcs and full rings is determined by a mechanism dependent on protein concentration in which arc pores arise due to kinetic trapping of the pre-pore forms by the depletion of free protein subunits during oligomerization. Here we describe the use of a kinetic assay to study pore formation in red blood cells by the MACPF/CDC pneumolysin from Streptococcus pneumoniae. We show that cell lysis displays two kinds of dependence on protein concentration. At lower concentrations, it is dependent on the pre-pore to pore transition of arc oligomers, which we show to be a cooperative process. At higher concentrations, it is dependent on the amount of pneumolysin bound to the membrane and reflects the affinity of the protein for its receptor, cholesterol. A lag occurs before cell lysis begins; this is dependent on oligomerization of pneumolysin. Kinetic dissection of cell lysis by pneumolysin demonstrates the capacity of MACPF/CDCs to generate pore-forming oligomeric structures of variable size with, most likely, different functional roles in biology.

Cyclic formation and dissociation of methane hydrate within partially water saturated sand

NASA Astrophysics Data System (ADS)

Kneafsey, T. J.; Nakagawa, S.

2010-12-01

For partially water-saturated sediments, laboratory experiments have shown that methane hydrate forms heterogeneously within a sample at the core scale. The heterogeneous distribution of hydrate in combination with grain-scale hydrate location (eg. grain cementing, load bearing, and pore filling), determines the overall mechanical properties of hydrate-bearing sediments including shear strength and seismic properties. For this reason, understanding the heterogeneity of hydrate-bearing sample is essential when the bulk properties of the sample are examined in the laboratory. We present a series of laboratory methane hydrate formation and dissociation experiments with concurrent x-ray CT imaging and low-frequency (near 1 kHz) seismic measurements. The seismic measurements were conducted using a new acoustic resonant bar technique called the Split Hopkinson Resonant Bar method, which allows using a small sediment core (3.75 cm diameter, 7.5 cm length). The experiment was conducted using a jacketed, pre-compacted, fine-grain silica sand sample with a 40% distilled water saturation. Under isotropic confining stress of 6.9 MPa and a temperature 4 oC, the hydrate was formed in the sample by injecting pure methane gas at 5.6 MPa. Once the hydrate formed, it was dissociated by reducing the pore pressure to 2.8 MPa. This cycle was repeated by three times (dissociation test for the third cycle was not done) to examine the resulting changes in the hydrate distribution and seismic signatures. The repeated formation of hydrate resulted in significant changes in its distribution, which resulted in differences in the overall elastic properties of the sample, determined from the seismic measurements. Interestingly, the time intervals between the dissociation and subsequent formation of hydrate affected the rate of hydrate formation, shorter intervals resulting in faster formation. This memory effect, possibly caused by the presence of residual “seed crystals” in the pore water providing nucleation points for hydrate formation, did not result in rapid formation at all locations in the sample. In spite of heterogeneity, observed seismic properties were very similar for the two measurements during dissociation.

Macroscopic tensile plasticity by scalarizating stress distribution in bulk metallic glass

PubMed Central

Gao, Meng; Dong, Jie; Huan, Yong; Wang, Yong Tian; Wang, Wei-Hua

2016-01-01

The macroscopic tensile plasticity of bulk metallic glasses (BMGs) is highly desirable for various engineering applications. However, upon yielding, plastic deformation of BMGs is highly localized into narrow shear bands and then leads to the “work softening” behaviors and subsequently catastrophic fracture, which is the major obstacle for their structural applications. Here we report that macroscopic tensile plasticity in BMG can be obtained by designing surface pore distribution using laser surface texturing. The surface pore array by design creates a complex stress field compared to the uniaxial tensile stress field of conventional glassy specimens, and the stress field scalarization induces the unusual tensile plasticity. By systematically analyzing fracture behaviors and finite element simulation, we show that the stress field scalarization can resist the main shear band propagation and promote the formation of larger plastic zones near the pores, which undertake the homogeneous tensile plasticity. These results might give enlightenment for understanding the deformation mechanism and for further improvement of the mechanical performance of metallic glasses. PMID:26902264

Cholesterol suppresses membrane leakage by decreasing water penetrability.

PubMed

Bu, Bing; Crowe, Michael; Diao, Jiajie; Ji, Baohua; Li, Dechang

2018-06-13

Membrane fusion is a fundamental biological process that lies at the heart of enveloped virus infection, synaptic signaling, intracellular vesicle trafficking, gamete fertilization, and cell-cell fusion. Membrane fusion is initiated as two apposed membranes merge to a single bilayer called a hemifusion diaphragm. It is believed that the contents of the two fusing membranes are released through a fusion pore formed at the hemifusion diaphragm, and yet another possible pathway has been proposed in which an undefined pore may form outside the hemifusion diaphragm at the apposed membranes, leading to the so-called leaky fusion. Here, we performed all-atom molecular dynamics simulations to study the evolution of the hemifusion diaphragm structure with various lipid compositions. We found that the lipid cholesterol decreased water penetrability to inhibit leakage pore formation. Biochemical leakage experiments support these simulation results. This study may shed light on the underlying mechanism of the evolution pathways of the hemifusion structure, especially the understanding of content leakage during membrane fusion.

Petrophysical Rock Typing of Unconventional Shale Plays: A Case Study for the Niobrara Formation of the Denver-Julesburg (DJ) Basin

NASA Astrophysics Data System (ADS)

Kamruzzaman, A.; Prasad, M.

2015-12-01

The hydrocarbon-rich mudstone rock layers of the Niobrara Formation were deposited in the shallow marine environment and have evolved as overmature oil- or gas-prone source and reservoir rocks. The hydrocarbon production from its low-porosity, nano-darcy permeability and interbedded chalk-marl reservoir intervals is very challenging. The post-diagenetic processes have altered the mineralogy and pore structure of its sourcing and producing rock units. A rock typing analysis in this play can help understand the reservoir heterogeneity significantly. In this study, a petrophysical rock typing workflow is presented for the Niobrara Formation by integrating experimental rock properties with geologic lithofacies classification, well log data and core study.Various Niobrara lithofacies are classified by evaluating geologic depositional history, sequence stratigraphy, mineralogy, pore structure, organic content, core texture, acoustic properties, and well log data. The experimental rock measurements are conducted on the core samples recovered from a vertical well from the Wattenberg Field of the Denver-Julesburg (DJ) Basin. Selected lithofacies are used to identify distinct petrofacies through the empirical analysis of the experimental data-set. The grouped petrofacies are observed to have unique mineralogical properties, pore characteristics, and organic contents and are labelled as discrete Niobrara rock types in the study area.Micro-textural image analysis (FESEM) is performed to qualitatively examine the pore size distribution, pore types and mineral composition in the matrix to confirm the classified rock units. The principal component analysis and the cluster analysis are carried out to establish the certainty of the selected rock types. Finally, the net-to-pay thicknesses of these rock units are compared with the cumulative production data from the field to further validate the chosen rock types.For unconventional shale plays, the rock typing information can be used to locate hydrocarbon sweetspots, facilitate the placement of the horizontal section of the wells along the sweetspots, and can augment engineers' abilities on suitable well placement considerations. It can also help enhancing the effectiveness of the hydraulic fracture stimulation and completion operation.

Membrane Pore Formation by Amyloid beta (25-35) Peptide

NASA Astrophysics Data System (ADS)

Kandel, Nabin; Tatulian, Suren

Amyloid (A β) peptide contributes to Alzheimer's disease by a yet unidentified mechanism. One of the possible mechanisms of A β toxicity is formation of pores in cellular membranes. We have characterized the formation of pores in phospholipid membranes by the Aβ25 - 35 peptide (GSNKGAIIGLM) using fluorescence, Fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) techniques. CD and FTIR identified formation of β-sheet structure upon incubation of the peptide in aqueous buffer for 2 hours. Unilamellar vesicles composed of a zwitterionic lipid, 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC), and 70 % POPC plus 30 % of an acidic lipid, 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG), are made in 30 mM CaCl2. Quin-2, a fluorophore that displays increased fluorescence upon Ca2+ binding, is added to the vesicles externally. Peptide addition results in increased Quin-2 fluorescence, which is interpreted by binding of the peptide to the vesicles, pore formation, and Ca2+ leakage. The positive and negative control measurements involve addition of a detergent, Triton X-100, which causes vesicle rupture and release of total calcium, and blank buffer, respectively.

Evolution of Micro-Pores in a Single-Crystal Nickel-Based Superalloy During Solution Heat Treatment

NASA Astrophysics Data System (ADS)

Li, Xiangwei; Wang, Li; Dong, Jiasheng; Lou, Langhong; Zhang, Jian

2017-06-01

Evolution of micro-pores in a third-generation single-crystal nickel-based superalloy during solution heat treatment at 1603 K (1330 °C) was investigated by X-ray computed tomography. 3D information including morphology, size, number, and volume fraction of micro-pores formed during solidification (S-pores) and solution (H-pores) was analyzed. The growth behaviors of both S-pores and H-pores can be related to the vacancy formation and diffusion during heat treatment.

Sea anemone actinoporins: the transition from a folded soluble state to a functionally active membrane-bound oligomeric pore.

PubMed

Alegre-Cebollada, J; Oñaderra, M; Gavilanes, J G; del Pozo, A Martínez

2007-12-01

Actinoporins are a family of 20-kDa, basic proteins isolated from sea anemones, whose activity is inhibited by preincubation with sphingomyelin. They are produced in monomeric soluble form but, when binding to the plasma membrane, they oligomerize to produce functional pores which result in cell lysis. Equinatoxin II (EqtII) from Actinia equina and Sticholysin II (StnII) from Stichodactyla helianthus are the actinoporins that have been studied in more detail. Both proteins display a beta-sandwich fold composed of 10 beta-strands flanked on each side by two short alpha-helices. Two-dimensional crystallization on lipid monolayers has allowed the determination of low-resolution models of tetrameric structures distinct from the pore. However, the actual structure of the pore is not known yet. Wild-type EqtII and StnII, as well as a nice collection of natural and artificially made variants of both proteins, have been produced in Escherichia coli and purified. Their characterization has allowed the proposal of a model for the mechanism of pore formation. Four regions of the actinoporins structure seem to play an important role. First, a phosphocholine-binding site and a cluster of exposed aromatic residues, together with a basic region, would be involved in the initial interaction with the membrane, whereas the amphipathic N-terminal region would be essential for oligomerization and pore formation. Accordingly, the model states that pore formation would proceed in at least four steps: Monomer binding to the membrane interface, assembly of four monomers, and at least two distinct conformational changes driving to the final formation of the functional pore.

Effect of pores formation process and oxygen plasma treatment to hydroxyapatite formation on bioactive PEEK prepared by incorporation of precursor of apatite.

PubMed

Yabutsuka, Takeshi; Fukushima, Keito; Hiruta, Tomoko; Takai, Shigeomi; Yao, Takeshi

2017-12-01

When bioinert substrates with fine-sized pores are immersed in a simulated body fluid (SBF) and the pH value or the temperature is increased, fine particles of calcium phosphate, which the authors denoted as 'precursor of apatite' (PrA), are formed in the pores. By this method, hydroxyapatite formation ability can be provided to various kinds of bioinert materials. In this study, the authors studied fabrication methods of bioactive PEEK by using the above-mentioned process. First, the fine-sized pores were formed on the surface of the PEEK substrate by H 2 SO 4 treatment. Next, to provide hydrophilic property to the PEEK, the surfaces of the PEEK were treated with O 2 plasma. Finally, PrA were formed in the pores by the above-mentioned process, which is denoted as 'Alkaline SBF' treatment, and the bioactive PEEK was obtained. By immersing in SBF with the physiological condition, hydroxyapatite formation was induced on the whole surface of the substrate within 1day. The formation of PrA directly contributed to hydroxyapatite formation ability. By applying the O 2 plasma treatment, hydroxyapatite formation was uniformly performed on the whole surface of the substrate. The H 2 SO 4 treatment contributed to a considerable enhancement of adhesive strength of the formed hydroxyapatite layer formed in SBF because of the increase of surface areas of the substrate. As a comparative study, the sandblasting method was applied as the pores formation process instead of the H 2 SO 4 treatment. Although hydroxyapatite formation was provided also in this case, however, the adhesion of the formed hydroxyapatite layer to the substrate was not sufficient even if the O 2 plasma treatment was conducted. This result indicates that the fine-sized pores should be formed on the whole surface of the substrate uniformly to achieve high adhesive strength of the hydroxyapatite layer. Therefore, it is considered that the H 2 SO 4 treatment before the O 2 plasma and the 'Alkaline SBF' treatment is an important factor to achieve high adhesive strength of hydroxyapatite layer to the PEEK substrate. This material is expected to be a candidate for next-generation implant materials with high bioactivity. Copyright © 2017 Elsevier B.V. All rights reserved.

Increased likelihood of induced seismicity in highly overpressured shale formations

NASA Astrophysics Data System (ADS)

Eaton, David W.; Schultz, Ryan

2018-05-01

Fluid-injection processes such as disposal of saltwater or hydraulic fracturing can induce earthquakes by increasing pore pressure and/or shear stress on faults. Natural processes, including transformation of organic material (kerogen) into hydrocarbon and cracking to produce gas, can similarly cause fluid overpressure. Here we document two examples from the Western Canada Sedimentary Basin where earthquakes induced by hydraulic fracturing are strongly clustered within areas characterized by pore-pressure gradient in excess of 15 kPa/m. Despite extensive hydraulic-fracturing activity associated with resource development, induced earthquakes are virtually absent in the Montney and Duvernay Formations elsewhere. Statistical analysis suggests a negligible probability that this spatial correlation developed by chance. This implies that, in addition to known factors such as anthropogenic pore-pressure increase and proximity to critically stressed faults, high in-situ overpressure of shale formations may also represent a controlling factor for inducing earthquakes by hydraulic fracturing. On a geological timescale, natural pore-pressure generation may lead to fault-slip episodes that regulate magnitude of formation-overpressure.

An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin.

PubMed

Wade, Kristin R; Hotze, Eileen M; Kuiper, Michael J; Morton, Craig J; Parker, Michael W; Tweten, Rodney K

2015-02-17

β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular electrostatic interaction with K336 of the adjacent monomer on completion of the prepore complex. The signal generated throughout the prepore complex by this interaction irrevocably commits it to the formation of the membrane-inserted giant β-barrel pore. This interaction supplies the free energy to overcome the energy barrier (determined here to be ∼ 19 kcal/mol) to the prepore-to-pore transition by the coordinated disruption of a critical interface within each monomer. These studies provide the first insight to our knowledge into the molecular mechanism that controls the prepore-to-pore transition for a βPFT.

An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin

PubMed Central

Wade, Kristin R.; Hotze, Eileen M.; Kuiper, Michael J.; Morton, Craig J.; Parker, Michael W.; Tweten, Rodney K.

2015-01-01

β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular electrostatic interaction with K336 of the adjacent monomer on completion of the prepore complex. The signal generated throughout the prepore complex by this interaction irrevocably commits it to the formation of the membrane-inserted giant β-barrel pore. This interaction supplies the free energy to overcome the energy barrier (determined here to be ∼19 kcal/mol) to the prepore-to-pore transition by the coordinated disruption of a critical interface within each monomer. These studies provide the first insight to our knowledge into the molecular mechanism that controls the prepore-to-pore transition for a βPFT. PMID:25646411

Free energies of stable and metastable pores in lipid membranes under tension.

PubMed

den Otter, Wouter K

2009-11-28

The free energy profile of pore formation in a lipid membrane, covering the entire range from a density fluctuation in an intact bilayer to a large tension-stabilized pore, has been calculated by molecular dynamics simulations with a coarse-grained lipid model. Several fixed elongations are used to obtain the Helmholtz free energy as a function of pore size for thermodynamically stable, metastable, and unstable pores, and the system-size dependence of these elongations is discussed. A link to the Gibbs free energy at constant tension, commonly known as the Litster model, is established by a Legendre transformation. The change of genus upon pore formation is exploited to estimate the saddle-splay modulus or Gaussian curvature modulus of the membrane leaflets. Details are provided of the simulation approach, which combines the potential of mean constraint force method with a reaction coordinate based on the local lipid density.

Low pH-Induced Pore Formation by the T Domain of Botulinum Toxin Type A is Dependent upon NaCl Concentration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lai, B.; Swaminathan, S.; Agarwal, R.

2010-07-19

Botulinum neurotoxins (BoNTs) undergo low pH-triggered membrane insertion, resulting in the translocation of their light (catalytic) chains into the cytoplasm. The T (translocation) domain of the BoNT heavy chain is believed to carry out translocation. Here, the behavior of isolated T domain from BoNT type A has been characterized, both in solution and when associated with model membranes. When BoNT T domain prepared in the detergent dodecylmaltoside was diluted into aqueous solution, it exhibited a low pH-dependent conformational change below pH 6. At low pH the T domain associated with, and formed pores within, model membrane vesicles composed of 30more » mol% dioleoylphosphatidylglycerol/70 mol% dioleoylphosphatidylcholine. Although T domain interacted with vesicles at low (50 mM) and high (400 mM) NaCl concentrations, the interaction required much less lipid at low salt. However, even at high lipid concentrations pore formation was much more pronounced at low NaCl concentrations than at high NaCl concentration. Increasing salt concentration after insertion in the presence of 50 mM NaCl did not decrease pore formation. A similar effect of NaCl concentration upon pore formation was observed in vesicles composed solely of dioleoylphosphatidylcholine, showing that the effect of NaCl did not solely involve modulation of electrostatic interactions between protein and anionic lipids. These results indicate that some feature of membrane-bound T domain tertiary structure critical for pore formation is highly dependent upon salt concentration.« less

Induction of "pore" formation in plant cell membranes by toluene.

PubMed

Lerner, H R; Ben-Bassat, D; Reinhold, L; Poljakoff-Mayber, A

1978-02-01

Treatment with aqueous toluene-ethanol has been shown to induce "pore" formation in plant cell membranes. The evidence is as follows: [List: see text]While the principal experimental material was roots of Atriplex nummularia Lindl., the fact that similar results were also observed with leaves of Pisum sativum L. and with the alga Chlorella pyrenoidosa Chik. suggests that the phenomenon is general.Although the phenomenon of pore induction is qualitatively similar to that in microorganisms, the pores induced appear to be smaller. It is proposed that induced leakage could be the basis for the development of simple and rapid methods for plant biochemical studies.

Modeling the Pore Formation Mechanism in UMo/AL Dispersion Fuel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Yeon Soo; Jamison, L.; Hofman, G.

In UMo/Al dispersion fuel meat, pores formed in the ILs or at IL-Al interfaces tend to increase in size with irradiation, potentially limiting performance of this fuel. There has been no universally accepted mechanism for the formation and growth of this type of pore. However, there is a consensus that the stress state determined by meat swelling and fission- induced creep is one of the determinants, and fission gas availability at the pore site is another. Five dispersion RERTR miniplates that have well defined irradiation conditions and PIE data were selected for examination. Meat swelling and pore volume were measuredmore » in each plate. ABAQUS finite element analysis (FEA) package was utilized to obtain the time-dependent evolution of mechanical states in the plates while matching the measured meat swelling and creep. Interpretation of these results give insights on how to model a failure function – a predictor for large pore formation – using variables such as meat swelling, interaction layer growth, stress, and creep. This model can be used for optimizing fuel design parameters to reach the desired goal: meeting high power and performance reactor demand.« less

Probing the intrinsically oil-wet surfaces of pores in North Sea chalk at subpore resolution.

PubMed

Hassenkam, T; Skovbjerg, L L; Stipp, S L S

2009-04-14

Pore surface properties control oil recovery. This is especially true for chalk reservoirs, where pores are particularly small. Wettability, the tendency for a surface to cover itself with fluid, is traditionally defined by the angle a droplet makes with a surface, but this macroscopic definition is meaningless when the particles are smaller than even the smallest droplet. Understanding surface wetting, at the pore scale, will provide clues for more effective oil recovery. We used a special mode of atomic force microscopy and a hydrophobic tip to collect matrices of 10,000 force curves over 5- x 5-mum(2) areas on internal pore surfaces and constructed maps of topography, adhesion, and elasticity. We investigated chalk samples from a water-bearing formation in the Danish North Sea oil fields that had never seen oil. Wettability and elasticity were inhomogeneous over scales of 10s of nanometers, smaller than individual chalk particles. Some areas were soft and hydrophobic, whereas others showed no correlation between hardness and adhesion. We conclude that the macroscopic parameter, "wetting," averages the nanoscopic behavior along fluid pathways, and "mixed-wet" samples have patches with vastly different properties. Development of reservoir hydrophobicity has been attributed to infiltrating oil, but these new results prove that wettability and elasticity are inherent properties of chalk. Their variability, even on single particles, must result from material originally present during sedimentation or material sorbed from the pore fluid some time later.

Probing the intrinsically oil-wet surfaces of pores in North Sea chalk at subpore resolution

PubMed Central

Hassenkam, T.; Skovbjerg, L. L.; Stipp, S. L. S.

2009-01-01

Pore surface properties control oil recovery. This is especially true for chalk reservoirs, where pores are particularly small. Wettability, the tendency for a surface to cover itself with fluid, is traditionally defined by the angle a droplet makes with a surface, but this macroscopic definition is meaningless when the particles are smaller than even the smallest droplet. Understanding surface wetting, at the pore scale, will provide clues for more effective oil recovery. We used a special mode of atomic force microscopy and a hydrophobic tip to collect matrices of 10,000 force curves over 5- × 5-μm2 areas on internal pore surfaces and constructed maps of topography, adhesion, and elasticity. We investigated chalk samples from a water-bearing formation in the Danish North Sea oil fields that had never seen oil. Wettability and elasticity were inhomogeneous over scales of 10s of nanometers, smaller than individual chalk particles. Some areas were soft and hydrophobic, whereas others showed no correlation between hardness and adhesion. We conclude that the macroscopic parameter, “wetting,” averages the nanoscopic behavior along fluid pathways, and “mixed-wet” samples have patches with vastly different properties. Development of reservoir hydrophobicity has been attributed to infiltrating oil, but these new results prove that wettability and elasticity are inherent properties of chalk. Their variability, even on single particles, must result from material originally present during sedimentation or material sorbed from the pore fluid some time later. PMID:19321418

Dynamic Pore-Scale Imaging of Reactive Transport in Heterogeneous Carbonates at Reservoir Conditions Across Multiple Dissolution Regimes

NASA Astrophysics Data System (ADS)

Menke, H. P.; Bijeljic, B.; Andrew, M. G.; Blunt, M. J.

2014-12-01

Sequestering carbon in deep geologic formations is one way of reducing anthropogenic CO2 emissions. When supercritical CO2 mixes with brine in a reservoir, the acid generated has the potential to dissolve the surrounding pore structure. However, the magnitude and type of dissolution are condition dependent. Understanding how small changes in the pore structure, chemistry, and flow properties affect dissolution is paramount for successful predictive modelling. Both 'Pink Beam' synchrotron radiation and a Micro-CT lab source are used in dynamic X-ray microtomography to investigate the pore structure changes during supercritical CO2 injection in carbonate rocks of varying heterogeneity at high temperatures and pressures and various flow-rates. Three carbonate rock types were studied, one with a homogeneous pore structure and two heterogeneous carbonates. All samples are practically pure calcium carbonate, but have widely varying rock structures. Flow-rate was varied in three successive experiments by over an order of magnitude whlie keeping all other experimental conditions constant. A 4-mm carbonate core was injected with CO2-saturated brine at 10 MPa and 50oC. Tomographic images were taken at 30-second to 20-minute time-resolutions during a 2 to 4-hour injection period. A pore network was extracted using a topological analysis of the pore space and pore-scale flow modelling was performed directly on the binarized images with connected pathways and used to track the altering velocity distributions. Significant differences in dissolution type and magnitude were found for each rock type and flowrate. At the highest flow-rates, the homogeneous carbonate was seen to have predominately uniform dissolution with minor dissolution rate differences between the pores and pore throats. Alternatively, the heterogeneous carbonates which formed wormholes at high flow rates. At low flow rates the homogeneous rock developed wormholes, while the heterogeneous samples showed evidence of compact dissolution. This study serves as a unique benchmark for pore-scale reactive transport modelling directly on the binarized Micro-CT images. Dynamic pore-scale imaging methods offer advantages in helping explain the dominant processes at the pore scale so that they may be up-scaled for accurate model prediction.

The Reactive Stabilisation of Aluminum-Zinc-X Foams via the Formation of a Transient Liquid Phase Using the Powder Metallurgy Approach

NASA Astrophysics Data System (ADS)

Lafrance, Maxime

During the past few decades, aluminum foam research has focused on the improvement of properties. These properties include pore structure and process reproducibility. High energy absorption capacity, lightweight and high stiffness to weight ratio are some of the properties that make these foams desirable for a number of diverse applications. The use of a transient liquid phase and melting point depressant was studied in order to improve aluminum foam manufactured through the powder metallurgy process and to create reactive Stabilisation. The transient liquid phase reacts with aluminum and helps encapsulate higher levels of hydrogen, simultaneously reducing the difference between the melting point of the alloy and the gas release temperature of the blowing agent (TiH2). A large difference is known to adversely affect foam properties. The study of pure aluminum foam formation was undertaken to understand the basic foaming mechanisms related to crack formations under in-situ conditions. Elemental zinc powder at various concentrations (Al-10wt%Zn, Al-33wt%Zn and Al-50wt%Zn) was added to produce a transient liquid phase. Subsequently, an Al-12wt%Si pre-alloyed powder was added to the Al-Zn mixture in order to further reduce the melting point of the alloy and to increase the amount of transient liquid phase available (Al-3.59wtSi-9.6%Zn and Al-2.4wt%Si-9.7wt%Zn). The mechanical properties of each system at optimal foaming conditions were assessed and compared. It was determined that pure aluminum foam crack formation could be suppressed at higher heating rates, improving the structure through the nucleation of uniform pores. The Al-10wt%Zn foams generated superior pore properties, post maximum expansion stability and mechanical properties at lower temperatures, compared to pure aluminum. The Al-Si-Zn foams revealed remarkable stability and pore structure at very low temperatures (640 to 660°C). Overall, the Al-10wt%Zn and Al-3.59wt%Si-9.6wt%Zn foams offer superior properties compared to pure aluminum.

Calculating Transition Energy Barriers and Characterizing Activation States for Steps of Fusion.

PubMed

Ryham, Rolf J; Klotz, Thomas S; Yao, Lihan; Cohen, Fredric S

2016-03-08

We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Assessment of CO2 Mineralization and Dynamic Rock Properties at the Kemper Pilot CO2 Injection Site

NASA Astrophysics Data System (ADS)

Qin, F.; Kirkland, B. L.; Beckingham, L. E.

2017-12-01

CO2-brine-mineral reactions following CO2 injection may impact rock properties including porosity, permeability, and pore connectivity. The rate and extent of alteration largely depends on the nature and evolution of reactive mineral interfaces. In this work, the potential for geochemical reactions and the nature of the reactive mineral interface and corresponding hydrologic properties are evaluated for samples from the Lower Tuscaloosa, Washita-Fredericksburg, and Paluxy formations. These formations have been identified as future regionally extensive and attractive CO2 storage reservoirs at the CO2 Storage Complex in Kemper County, Mississippi, USA (Project ECO2S). Samples from these formations were obtained from the Geological Survey of Alabama and evaluated using a suite of complementary analyses. The mineral composition of these samples will be determined using petrography and powder X-ray Diffraction (XRD). Using these compositions, continuum-scale reactive transport simulations will be developed and the potential CO2-brine-mineral interactions will be examined. Simulations will focus on identifying potential reactive minerals as well as the corresponding rate and extent of reactions. The spatial distribution and accessibility of minerals to reactive fluids is critical to understanding mineral reaction rates and corresponding changes in the pore structure, including pore connectivity, porosity and permeability. The nature of the pore-mineral interface, and distribution of reactive minerals, will be determined through imaging analysis. Multiple 2D scanning electron microscopy (SEM) backscattered electron (BSE) images and energy dispersive x-ray spectroscopy (EDS) images will be used to create spatial maps of mineral distributions. These maps will be processed to evaluate the accessibility of reactive minerals and the potential for flow-path modifications following CO2 injection. The "Establishing an Early CO2 Storage Complex in Kemper, MS" project is funded by the U.S. Department of Energy's National Energy Technology Laboratory and cost-sharing partners.

The processing of aluminum gasarites via thermal decomposition of interstitial hydrides

NASA Astrophysics Data System (ADS)

Licavoli, Joseph J.

Gasarite structures are a unique type of metallic foam containing tubular pores. The original methods for their production limited them to laboratory study despite appealing foam properties. Thermal decomposition processing of gasarites holds the potential to increase the application of gasarite foams in engineering design by removing several barriers to their industrial scale production. The following study characterized thermal decomposition gasarite processing both experimentally and theoretically. It was found that significant variation was inherent to this process therefore several modifications were necessary to produce gasarites using this method. Conventional means to increase porosity and enhance pore morphology were studied. Pore morphology was determined to be more easily replicated if pores were stabilized by alumina additions and powders were dispersed evenly. In order to better characterize processing, high temperature and high ramp rate thermal decomposition data were gathered. It was found that the high ramp rate thermal decomposition behavior of several hydrides was more rapid than hydride kinetics at low ramp rates. This data was then used to estimate the contribution of several pore formation mechanisms to the development of pore structure. It was found that gas-metal eutectic growth can only be a viable pore formation mode if non-equilibrium conditions persist. Bubble capture cannot be a dominant pore growth mode due to high bubble terminal velocities. Direct gas evolution appears to be the most likely pore formation mode due to high gas evolution rate from the decomposing particulate and microstructural pore growth trends. The overall process was evaluated for its economic viability. It was found that thermal decomposition has potential for industrialization, but further refinements are necessary in order for the process to be viable.

The role of beaded activated carbon's pore size distribution on heel formation during cyclic adsorption/desorption of organic vapors.

PubMed

Jahandar Lashaki, Masoud; Atkinson, John D; Hashisho, Zaher; Phillips, John H; Anderson, James E; Nichols, Mark

2016-09-05

The effect of activated carbon's pore size distribution (PSD) on heel formation during adsorption of organic vapors was investigated. Five commercially available beaded activated carbons (BAC) with varying PSDs (30-88% microporous) were investigated. Virgin samples had similar elemental compositions but different PSDs, which allowed for isolating the contribution of carbon's microporosity to heel formation. Heel formation was linearly correlated (R(2)=0.91) with BAC micropore volume; heel for the BAC with the lowest micropore volume was 20% lower than the BAC with the highest micropore volume. Meanwhile, first cycle adsorption capacities and breakthrough times correlated linearly (R(2)=0.87 and 0.93, respectively) with BAC total pore volume. Micropore volume reduction for all BACs confirmed that heel accumulation takes place in the highest energy pores. Overall, these results show that a greater portion of adsorbed species are converted into heel on highly microporous adsorbents due to higher share of high energy adsorption sites in their structure. This differs from mesoporous adsorbents (low microporosity) in which large pores contribute to adsorption but not to heel formation, resulting in longer adsorbent lifetime. Thus, activated carbon with high adsorption capacity and high mesopore fraction is particularly desirable for organic vapor application involving extended adsorption/regeneration cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Effect of Processing Pressure on Isolated Pore Formation during Controlled Directional Solidification in Small Channels

NASA Technical Reports Server (NTRS)

Cox, Matthew C.; Anilkumar, Amrutur V.; Grugel, RIchard N.; Lee, Chun P.

2008-01-01

Directional solidification experiments were performed, using succinonitrile saturated with nitrogen gas, to examine the effects of in-situ processing pressure changes on the formation growth, and evolution of an isolated, cylindrical gaseous pore. A novel solidification facility, capable of processing thin cylindrical samples (I.D. < 1.0 mm), under controlled pressure conditions, was used for the experiments. A new experimental method for growing the isolated pore from a seed bubble is introduced. The experimental results indicate that an in-situ processing pressure change will result in either a transient change in pore diameter or a complete termination of pore growth, indicating that pressure changes can be used as a control parameter to terminate bubble growth. A simple analytical model has been introduced to explain the experimental observations.

Laser-assisted formation of micropores and nanobubbles in sclera promote stable normalization of intraocular pressure

NASA Astrophysics Data System (ADS)

Baum, Olga; Wachsmann-Hogiu, Sebastian; Milner, Thomas; Sobol, Emil

2017-06-01

Pores in sclera enhance uveoscleral water outflow and can normalize intraocular pressure in glaucomatous eyes. The aims of this study are to demonstrate laser-induced formation of pores with a dendritic structure and to answer the questions: How is a pore system stable and can laser treatment provide a long-lasting pressure stabilization effect? Effect of 1.56 µm laser radiation on porcine eye sclera was studied using atomic force microscopy and super resolution structured irradiation microscopy with fluorescent markers. Results suggest that the pores with a complex spatial configuration can arise as a result of laser irradiation and that laser-generated stable gas nanobubbles coated with calcium ions allow pore stabilization in the sclera. Our results support a laser based approach for treatment of glaucoma.

Analytical modeling of mercury injection in high-rank coalbed methane reservoirs based on pores and microfractures: a case study of the upper carboniferous Taiyuan Formation in the Heshun block of the Qinshui Basin, central China

NASA Astrophysics Data System (ADS)

Gu, Yang; Ding, Wenlong; Yin, Shuai; Wang, Ruyue; Mei, Yonggui; Liu, Jianjun

2017-03-01

The coalbed gas reservoirs in the Qinshui Basin in central China are highly heterogeneous; thus, the reservoir characteristics are difficult to assess. Research on the pore structure of a reservoir can provide a basis for understanding the occurrence and seepage mechanisms of coal reservoirs, rock physics modeling and the formulation of rational development plans. Therefore, the pore structure characteristics of the coalbed gas reservoirs in the high rank bituminous coal in the No. 15 coal seam of the Carboniferous Taiyuan Group in the Heshun coalbed methane (CBM) blocks in the northeastern Qinshui Basin were analyzed based on pressure mercury and scanning electron microscopy data. The results showed that the effective porosity system of the coal reservoir was mainly composed of pores and microfractures and that the pore throat configuration of the coal reservoir was composed of pores and microthroats. A model was developed based on the porosity and microfractures of the high rank coal rock and the mercury injection and drainage curves. The mercury injection curve model and the coal permeability are well correlated and were more reliable for the analysis of coal and rock pore system connectivity than the mercury drainage curve model. Coal rocks with developed microfractures are highly permeable; the production levels are often high during the initial drainage stages, but they decrease rapidly. A significant portion of the natural gas remains in the strata and cannot be exploited; therefore, the ultimate recovery is rather low. Coal samples with underdeveloped microfractures have lower permeabilities. While the initial production levels are lower, the production cycle is longer, and the ultimate recovery is higher. Therefore, the initial production levels of coal reservoirs with poorly developed microfractures in some regions of China may be low. However, over the long term, due to their higher ultimate recoveries and longer production cycles, the total gas production levels will increase. This understanding can provide an important reference for developing appropriate CBM development plans.

Technique development for conducting mechanical tests to study the pore formation process in case of material fracture

NASA Astrophysics Data System (ADS)

Magomedova, D. K.; Efimov, M. A.; Murashkin, M. Yu.

2018-05-01

The main purpose of this work was the development of an experimental technique for search and analysis of pore formation in the presented material. Geometry of the samples, the procedure of experiment and processing the samples for investigation were developed.

Template-Free Synthesis of Highly Porous Boron Nitride: Insights into Pore Network Design and Impact on Gas Sorption.

PubMed

Marchesini, Sofia; McGilvery, Catriona M; Bailey, Josh; Petit, Camille

2017-10-24

Production of biocompatible and stable porous materials, e.g., boron nitride, exhibiting tunable and enhanced porosity is a prerequisite if they are to be employed to address challenges such as drug delivery, molecular separations, or catalysis. However, there is currently very limited understanding of the formation mechanisms of porous boron nitride and the parameters controlling its porosity, which ultimately prevents exploiting the material's full potential. Herein, we produce boron nitride with high and tunable surface area and micro/mesoporosity via a facile template-free method using multiple readily available N-containing precursors with different thermal decomposition patterns. The gases are gradually released, creating hierarchical pores, high surface areas (>1900 m 2 /g), and micropore volumes. We use 3D tomography techniques to reconstruct the pore structure, allowing direct visualization of the mesopore network. Additional imaging and analytical tools are employed to characterize the materials from the micro- down to the nanoscale. The CO 2 uptake of the materials rivals or surpasses those of commercial benchmarks or other boron nitride materials reported to date (up to 4 times higher), even after pelletizing. Overall, the approach provides a scalable route to porous boron nitride production as well as fundamental insights into the material's formation, which can be used to design a variety of boron nitride structures.

Storage and recovery of methane-ethane mixtures in single shale pores

NASA Astrophysics Data System (ADS)

Wu, Haiyi; Qiao, Rui

2017-11-01

Natural gas production from shale formations has received extensive attention recently. While great progress has been made in understanding the adsorption and transport of single-component gas inside shales' nanopores, the adsorption and transport of multicomponent shale gas under reservoir conditions (CH4 and C2H6 mixture) has only begun to be studied. In this work, we use molecular simulations to compute the storage of CH4 and C2H6 mixtures in single nanopores and their subsequent recovery. We show that surface adsorption contributes greatly to the storage of CH4 and C2H6 inside the pores and C2H6 is enriched over CH4. The enrichment of C2H6 is enhanced as the pore is narrowed, but is weakened as the pressure increases. We show that the recovery of gas mixtures from the nanopores approximately follows the diffusive scaling law. The ratio of the production rates of C2H6 and CH4 is close to their initial mole ratio inside the pore despite that the mobility of pure C2H6 is much smaller than that of pure CH4 inside the pores. By using scale analysis, we show that the strong coupling between the transport of CH4 and C2H6 is responsible for the effective recovery of C2H6 from the nanopores.

Amyloid pore-channel hypothesis: effect of ethanol on aggregation state using frog oocytes for an Alzheimer’s disease study

PubMed Central

Parodi, Jorge; Ormeño, David; la Paz, Lenin D. Ochoa-de

2015-01-01

Alzheimer's disease severely compromises cognitive function. One of the mechanisms to explain the pathology of Alzheimer’s disease has been the hypotheses of amyloid-pore/channel formation by complex Aβ-aggregates. Clinical studies suggested the moderate alcohol consumption can reduces probability developing neurodegenerative pathologies. A recent report explored the ability of ethanol to disrupt the generation of complex Aβ in vitro and reduce the toxicity in two cell lines. Molecular dynamics simulations were applied to understand how ethanol blocks the aggregation of amyloid. On the other hand, the in silico modeling showed ethanol effect over the dynamics assembling for complex Aβ-aggregates mediated by break the hydrosaline bridges between Asp 23 and Lys 28, was are key element for amyloid dimerization. The amyloid pore/channel hypothesis has been explored only in neuronal models, however recently experiments suggested the frog oocytes such an excellent model to explore the mechanism of the amyloid pore/channel hypothesis. So, the used of frog oocytes to explored the mechanism of amyloid aggregates is new, mainly for amyloid/pore hypothesis. Therefore, this experimental model is a powerful tool to explore the mechanism implicates in the Alzheimer’s disease pathology and also suggests a model to prevent the Alzheimer’s disease pathology. [BMB Reports 2015; 48(1): 13-18] PMID:25047445

Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation

NASA Astrophysics Data System (ADS)

Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W.; Lin, Jialing; Li, Jianing

2016-07-01

Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model — using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation.

Phenylalanine-427 of anthrax protective antigen functions in both pore formation and protein translocation.

PubMed

Sun, Jianjun; Lang, Alexander E; Aktories, Klaus; Collier, R John

2008-03-18

The protective antigen (PA) moiety of anthrax toxin forms a heptameric pore in endosomal membranes of mammalian cells and translocates the enzymatic moieties of the toxin to the cytosol of these cells. Phenylalanine-427 (F427), a solvent-exposed residue in the lumen of the pore, was identified earlier as being crucial for the transport function of PA. The seven F427 residues were shown in electrophysiological studies to form a clamp that catalyzes protein translocation through the pore. Here, we demonstrate by a variety of tests that certain F427 mutations also profoundly inhibit the conformational transition of the heptameric PA prepore to the pore and thereby block pore formation in membranes. Lysine, arginine, aspartic acid, or glycine at position 427 strongly inhibited this acidic pH-induced conformational transition, whereas histidine, serine, and threonine had virtually no effect on this step, but inhibited translocation instead. Thus, it is possible to inhibit pore formation or translocation selectively, depending on the choice of the side chain at position 427; and the net inhibition of the PA transport function by any given F427 mutation is the product of its effects on both steps. Mutations inhibiting either or both steps elicited a strong dominant-negative phenotype. These findings demonstrate the dual functions of F427 and underline its central role in transporting the enzymatic moieties of anthrax toxin across membranes.

Void and pore formation inside the hair cortex by a denaturation and super-contraction process occurring during hair setting with hot irons.

PubMed

Gamez-Garcia, Manuel

2011-01-01

An analysis of hair fibers from donors that frequently use hot irons for hair straightening showed the presence of multiple pores and voids (φ approximately 0.1-1.5 μm) that extend from the cuticle sheath to regions inside the hair cortex. Pore formation in the cortex was found to be confined at its periphery and could be reproduced in the laboratory with virgin hair fibers after the application of various hot-iron straightening cycles. The appearance of pores and voids in the cortex was found to be associated to the production of hot water vapor while the fiber is undergoing mechanical elongation or contraction. The number of pores was seen to rapidly increase with temperature in the range from 190 to 220°C and also with the number of straightening cycles. Larger hair voids (φ approximately 2-5 μm) were also detected in the cortex. The small pores found at the cortex periphery appear to occur by the simultaneous occurrence of rearrangement of hair proteins, fiber mechanical contraction/expansion, and the flow of super-heated steam. Hot irons create, thus, the conditions for the onset of pore formation as the high temperatures produce superheated steam and soften the native state of hair proteins by a process involving denaturation and changes in the crystalline regions.

Developing an Effective Model for Shale Gas Flow in Nano-scale Pore Clusters based on FIB-SEM Images

NASA Astrophysics Data System (ADS)

Jiang, W. B.; Lin, M.; Yi, Z. X.; Li, H. S.

2016-12-01

Nano-scale pores existed in the form of clusters are the controlling void space in shale gas reservoir. Gas transport in nanopores which has a significant influence on shale gas' recoverability displays multiple transport regimes, including viscous, slippage flow and Knudsen diffusion. In addition, it is also influenced by pore space characteristics. For convenience and efficiency consideration, it is necessary to develop an upscaling model from nano pore to pore cluster scale. Existing models are more like framework functions that provide a format, because the parameters that represent pore space characteristics are underdetermined and may have multiple possibilities. Therefore, it is urgent to make them clear and obtained a model that is closer to reality. FIB-SEM imaging technology is able to acquire three dimensional images with nanometer resolution that nano pores can be visible. Based on the images of two shale samples, we used a high-precision pore network extraction algorithm to generate equivalent pore networks and simulate multiple regime (non-Darcy) flow in it. Several structural parameters can be obtained through pore network modelling. It is found that although the throat-radius distributions are very close, throat flux-radius distributions of different samples can be divided into two categories. The variation of tortuosity with pressure and the overall trend of throat-flux distribution changes with pressure are disclosed. A deeper understanding of shale gas flow in nano-scale pore clusters is obtained. After all, an upscaling model that connects absolute permeability, apparent permeability and other characteristic parameters is proposed, and the best parameter scheme considering throat number-radius distribution and flowing porosity for this model is selected out of three schemes based on pore scale results, and it can avoid multiple-solution problem and is useful in reservoir modelling and experiment result analysis, etc. This work is supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB10020302), the National Natural Science Foundation of China (41574129), the Key Instrument Developing Project of the CAS (ZDYZ2012-1-08-02), the 973 Program (2014CB239004).

Two-Step Mechanism of Membrane Disruption by Aβ through Membrane Fragmentation and Pore Formation

PubMed Central

Sciacca, Michele F.M.; Kotler, Samuel A.; Brender, Jeffrey R.; Chen, Jennifer; Lee, Dong-kuk; Ramamoorthy, Ayyalusamy

2012-01-01

Disruption of cell membranes by Aβ is believed to be one of the key components of Aβ toxicity. However, the mechanism by which this occurs is not fully understood. Here, we demonstrate that membrane disruption by Aβ occurs by a two-step process, with the initial formation of ion-selective pores followed by nonspecific fragmentation of the lipid membrane during amyloid fiber formation. Immediately after the addition of freshly dissolved Aβ1–40, defects form on the membrane that share many of the properties of Aβ channels originally reported from single-channel electrical recording, such as cation selectivity and the ability to be blockaded by zinc. By contrast, subsequent amyloid fiber formation on the surface of the membrane fragments the membrane in a way that is not cation selective and cannot be stopped by zinc ions. Moreover, we observed that the presence of ganglioside enhances both the initial pore formation and the fiber-dependent membrane fragmentation process. Whereas pore formation by freshly dissolved Aβ1–40 is weakly observed in the absence of gangliosides, fiber-dependent membrane fragmentation can only be observed in their presence. These results provide insights into the toxicity of Aβ and may aid in the design of specific compounds to alleviate the neurodegeneration of Alzheimer’s disease. PMID:22947931

Studying physical properties of deformed intact and fractured rocks by micro-scale hydro-mechanical-seismicity model

NASA Astrophysics Data System (ADS)

Raziperchikolaee, Samin

The pore pressure variation in an underground formation during hydraulic stimulation of low permeability formations or CO2 sequestration into saline aquifers can induce microseismicity due to fracture generation or pre-existing fracture activation. While the analysis of microseismic data mainly focuses on mapping the location of fractures, the seismic waves generated by the microseismic events also contain information for understanding of fracture mechanisms based on microseismic source analysis. We developed a micro-scale geomechanics, fluid-flow and seismic model that can predict transport and seismic source behavior during rock failure. This model features the incorporation of microseismic source analysis in fractured and intact rock transport properties during possible rock damage and failure. The modeling method considers comprehensive grains and cements interaction through a bonded-particle-model. As a result of grain deformation and microcrack development in the rock sample, forces and displacements in the grains involved in the bond breakage are measured to determine seismic moment tensor. In addition, geometric description of the complex pore structure is regenerated to predict fluid flow behavior of fractured samples. Numerical experiments are conducted for different intact and fractured digital rock samples, representing various mechanical behaviors of rocks and fracture surface properties, to consider their roles on seismic and transport properties of rocks during deformation. Studying rock deformation in detail provides an opportunity to understand the relationship between source mechanism of microseismic events and transport properties of damaged rocks to have a better characterizing of fluid flow behavior in subsurface formations.

Expansion of Bone Marrow Mesenchymal Stromal Cells in Perfused 3D Ceramic Scaffolds Enhances In Vivo Bone Formation.

PubMed

Hoch, Allison I; Duhr, Ralph; Di Maggio, Nunzia; Mehrkens, Arne; Jakob, Marcel; Wendt, David

2017-12-01

Bone marrow-derived mesenchymal stromal cells (BMSC), when expanded directly within 3D ceramic scaffolds in perfusion bioreactors, more reproducibly form bone when implanted in vivo as compared to conventional expansion on 2D polystyrene dishes/flasks. Since the bioreactor-based expansion on 3D ceramic scaffolds encompasses multiple aspects that are inherently different from expansion on 2D polystyrene, we aimed to decouple the effects of specific parameters among these two model systems. We assessed the effects of the: 1) 3D scaffold vs. 2D surface; 2) ceramic vs. polystyrene materials; and 3) BMSC niche established within the ceramic pores during in vitro culture, on subsequent in vivo bone formation. While BMSC expanded on 3D polystyrene scaffolds in the bioreactor could maintain their in vivo osteogenic potential, results were similar as BMSC expanded in monolayer on 2D polystyrene, suggesting little influence of the scaffold 3D environment. Bone formation was most reproducible when BMSC are expanded on 3D ceramic, highlighting the influence of the ceramic substrate. The presence of a pre-formed niche within the scaffold pores had negligible effects on the in vivo bone formation. The results of this study allow a greater understanding of the parameters required for perfusion bioreactor-based manufacturing of osteogenic grafts for clinical applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding Hydraulic Fracturing: A Multi-Scale Problem

DOE PAGES

Hyman, Jeffrey De'Haven; Gimenez Martinez, Joaquin; Viswanathan, Hari S.; ...

2016-09-05

Despite the impact that hydraulic fracturing has had on the energy sector, the physical mechanisms that control its efficiency and environmental impacts remain poorly understood in part because the length scales involved range from nano-meters to kilo-meters. We characterize flow and transport in shale formations across and between these scales using integrated computational, theoretical, and experimental efforts. At the field scale, we use discrete fracture network modeling to simulate production at a well site whose fracture network is based on a site characterization of a shale formation. At the core scale, we use triaxial fracture experiments and a finite-element discrete-elementmore » fracture propagation model with a coupled fluid solver to study dynamic crack propagation in low permeability shale. We use lattice Boltzmann pore-scale simulations and microfluidic experiments in both synthetic and real micromodels to study pore-scale flow phenomenon such as multiphase flow and mixing. A mechanistic description and integration of these multiple scales is required for accurate predictions of production and the eventual optimization of hydrocarbon extraction from unconventional reservoirs.« less

U.S. DOE NETL methodology for estimating the prospective CO 2 storage resource of shales at the national and regional scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Levine, Jonathan S.; Fukai, Isis; Soeder, Daniel J.

While the majority of shale formations will serve as reservoir seals for stored anthropogenic carbon dioxide (CO2), hydrocarbon-bearing shale formations may be potential geologic sinks after depletion through primary production. Here in this paper we present the United States-Department of Energy-National Energy Technology Laboratory (US-DOE-NETL) methodology for screening-level assessment of prospective CO 2 storage resources in shale using a volumetric equation. Volumetric resource estimates are produced from the bulk volume, porosity, and sorptivity of the shale and storage efficiency factors based on formation-scale properties and petrophysical limitations on fluid transport. Prospective shale formations require: (1) prior hydrocarbon production using horizontalmore » drilling and stimulation via staged, high-volume hydraulic fracturing, (2) depths sufficient to maintain CO 2 in a supercritical state, generally >800 m, and (3) an overlying seal. The US-DOE-NETL methodology accounts for storage of CO 2 in shale as a free fluid phase within fractures and matrix pores and as an sorbed phase on organic matter and clays. Uncertainties include but are not limited to poorly-constrained geologic variability in formation thickness, porosity, existing fluid content, organic richness, and mineralogy. Knowledge of how these parameters may be linked to depositional environments, facies, and diagenetic history of the shale will improve the understanding of pore-to-reservoir scale behavior, and provide improved estimates of prospective CO 2 storage.« less

U.S. DOE NETL methodology for estimating the prospective CO 2 storage resource of shales at the national and regional scale

DOE PAGES

Levine, Jonathan S.; Fukai, Isis; Soeder, Daniel J.; ...

2016-05-31

While the majority of shale formations will serve as reservoir seals for stored anthropogenic carbon dioxide (CO2), hydrocarbon-bearing shale formations may be potential geologic sinks after depletion through primary production. Here in this paper we present the United States-Department of Energy-National Energy Technology Laboratory (US-DOE-NETL) methodology for screening-level assessment of prospective CO 2 storage resources in shale using a volumetric equation. Volumetric resource estimates are produced from the bulk volume, porosity, and sorptivity of the shale and storage efficiency factors based on formation-scale properties and petrophysical limitations on fluid transport. Prospective shale formations require: (1) prior hydrocarbon production using horizontalmore » drilling and stimulation via staged, high-volume hydraulic fracturing, (2) depths sufficient to maintain CO 2 in a supercritical state, generally >800 m, and (3) an overlying seal. The US-DOE-NETL methodology accounts for storage of CO 2 in shale as a free fluid phase within fractures and matrix pores and as an sorbed phase on organic matter and clays. Uncertainties include but are not limited to poorly-constrained geologic variability in formation thickness, porosity, existing fluid content, organic richness, and mineralogy. Knowledge of how these parameters may be linked to depositional environments, facies, and diagenetic history of the shale will improve the understanding of pore-to-reservoir scale behavior, and provide improved estimates of prospective CO 2 storage.« less

Examination of Anisotropy Using Amplitude Variation with Angle and Azimuth (AVAZ) in the Woodford Shale, Anadarko Basin, Oklahoma

NASA Astrophysics Data System (ADS)

Bailey, Austin

Amplitude Variation with Angle and Azimuth (AVAZ) is a method that examines the azimuthal change in seismic amplitude to calculate the anisotropy of a horizontally transverse isotropic (HTI) formation. Anisotropy is generally indicative of heterogeneity in the rock fabric, be it fractures, crack-like pores, or local stress changes. The aim of this study as a whole is to examine the relationship between AVAZ anisotropy magnitude from seismic data and pore pressure gradient from wells. Pore pressure is an important reservoir metric that is often used to understand the production variations within a hydrocarbon reservoir. Predicting pore pressure from seismic data can be extremely useful in not only estimating production, but also in predicting the completion and development strategies that may be most effective. However, seismic-based pore pressure prediction methods have not evolved much in the past decade, with the industry standard to rely on the Bowers (1995) or Eaton (1987) method of converting seismic velocities to pore pressure volumes. These methods may fall short as a predictive tool in many cases, due to their lack of spatial resolution and dependency on a stable velocity model, which may not always be available. Therefore, this study was begun in order to examine if an alternative method of detecting pore pressure variations could be found using AVAZ. The AVAZ methodology was applied to a merged 3D seismic dataset in the Anadarko Basin, Oklahoma provided by Cimarex Energy, in order to examine the Woodford Shale. The Woodford has been a key player in hydrocarbon production from the Anadarko Basin for decades, mainly serving as a source rock until the mid-2000's during the "unconventional revolution''. Throughout its extent, the Woodford Formation shows significant heterogeneity due to both the structure and faults of the basin, as well as changes in the rock fabric. This study aims to use the AVAZ methodology to examine heterogeneity in the Woodford and to relate its anisotropy to pore pressure. Before examining the AVAZ effect in the seismic data, forward modeling from well logs was completed to conceptualize a relationship between pore pressure and anisotropy. Theoretically, at higher pore pressures the reservoir fluid may be effectively propping the fractures open, thus having a greater effect on any pressure wave traveling through the fluid. At lower pore pressure, the overburden pressure dominates the fluid-filled fractures and closes them down. Therefore, at higher pore pressure the AVAZ anisotropy would be greater than at lower pore pressure. The forward modeling from dipole sonic well logs confirms this conceptual model by showing a positive relationship between pore pressure and AVAZ anisotropy. Before the results of the AVAZ workflow were obtained, a variety of pre-processing steps and quality controls were done on the merged 3D seismic dataset. Although the pore pressure - anisotropy relationship appears robust in modeling, the AVAZ results from the seismic data do not appear to correlate with pore pressure. It is likely that acquisition-related artifacts in the seismic data, as well as small magnitude of change in pore pressure, contribute to this lack of correlation. However, further interpretation of the AVAZ volumes shows local stress variations near faults as well as a potential secondary stress trend striking to the north-east. Such information has implications for completion and overall development of the Woodford as an unconventional resource play.

Morphology of the pore space in claystones - evidence from BIB/FIB ion beam sectioning and cryo-SEM observations

NASA Astrophysics Data System (ADS)

Desbois, G.; Urai, J. L.; Kukla, P. A.

2009-12-01

Mudrocks and clay-rich fault gouges are important mechanical elements in the Earth’s crust and form seals for crustal fluids such as groundwater and hydrocarbons. Other fields of interest are the storage of anthropogenic carbon dioxide and radioactive waste in geologic formations. In addition, coupled flows, capillary processes, and associated deformation are of importance in many applied fields. A key factor to understanding these processes is a detailed understanding of the morphology of the pore space. Classic studies of porosity in fine grained materials are performed on dried or freeze dried samples and include metal injection methods, magnetic susceptibility measurement, SEM and TEM imaging, neutron scattering, NMR spectroscopy, and ESEM. Confocal microscopy and X-ray tomography are used to image porosity in coarse grained sediments but the resolution of these techniques is not sufficient at present for applications to mudrocks or clay-rich fault gouges. Therefore, observations and interpretations remain difficult because none of these approaches is able to directly describe the in-situ porosity at the pore scale. In addition, some methods require dried samples in which the natural structure of pores may have been damaged to some extent due to desiccation and dehydration of the clay minerals. A recently developed alternative is to study wet samples using a cryo-SEM, which allows stabilization of wet media at cryo-temperature, in-situ sample preparation by ion beam cross-sectioning (BIB, FIB) and observations of the stabilized microstructure at high resolution. We report on a study of Boom clay from a proposed disposal site of radioactive waste (Mol site, Belgium) using cryo-SEM at cryogenic temperature, with ion beam cross-sectioning to prepare smooth, damage free surfaces. Pores commonly have crack-like tips, preferred orientation parallel to bedding and power law size distribution. We define a number of pore types depending on shape and location in the microstructure. 3-D reconstruction by serial cross-sectioning shows 3-D connectivity of the pore space. These findings offer a new insight into the morphology of pores down to nano-scale and provide the basis for microstructure-based models of transport in clays. SEM image (SE) of a Broad Ion Beam polished cross-section performed on dry Boom clay (Mol site, Belgium) showing the 2D apparent porosity (26.3%). The cross-section is perpendicular to the bedding.

Experimental Study of Porosity Changes in Shale Caprocks Exposed to CO 2-Saturated Brines I: Evolution of Mineralogy, Pore Connectivity, Pore Size Distribution, and Surface Area

DOE PAGES

Mouzakis, Katherine M.; Navarre-Sitchler, Alexis K.; Rother, Gernot; ...

2016-07-18

Carbon capture, utilization, and storage, one proposed method of reducing anthropogenic emissions of CO 2, relies on low permeability formations, such as shales, above injection formations to prevent upward migration of the injected CO 2. Porosity in caprocks evaluated for sealing capacity before injection can be altered by geochemical reactions induced by dissolution of injected CO 2 into pore fluids, impacting long-term sealing capacity. Therefore, long-term performance of CO 2 sequestration sites may be dependent on both initial distribution and connectivity of pores in caprocks, and on changes induced by geochemical reaction after injection of CO 2, which are currentlymore » poorly understood. This paper presents results from an experimental study of changes to caprock porosity and pore network geometry in two caprock formations under conditions relevant to CO 2 sequestration. Pore connectivity and total porosity increased in the Gothic Shale; while total porosity increased but pore connectivity decreased in the Marine Tuscaloosa. Gothic Shale is a carbonate mudstone that contains volumetrically more carbonate minerals than Marine Tuscaloosa. Carbonate minerals dissolved to a greater extent than silicate minerals in Gothic Shale under high CO 2 conditions, leading to increased porosity at length scales <~200 nm that contributed to increased pore connectivity. In contrast, silicate minerals dissolved to a greater extent than carbonate minerals in Marine Tuscaloosa leading to increased porosity at all length scales, and specifically an increase in the number of pores >~1 μm. Mineral reactions also contributed to a decrease in pore connectivity, possibly as a result of precipitation in pore throats or hydration of the high percentage of clays. Finally, this study highlights the role that mineralogy of the caprock can play in geochemical response to CO 2 injection and resulting changes in sealing capacity in long-term CO 2 storage projects.« less

Origin and heterogeneity of pore sizes in the Mount Simon Sandstone and Eau Claire Formation: Implications for multiphase fluid flow

DOE PAGES

Mozley, Peter S.; Heath, Jason E.; Dewers, Thomas A.; ...

2016-01-01

The Mount Simon Sandstone and Eau Claire Formation represent a principal reservoir - caprock system for wastewater disposal, geologic CO 2 storage, and compressed air energy storage (CAES) in the Midwestern United States. Of primary concern to site performance is heterogeneity in flow properties that could lead to non-ideal injectivity and distribution of injected fluids (e.g., poor sweep efficiency). Using core samples from the Dallas Center Structure, Iowa, we investigate pore structure that governs flow properties of major lithofacies of these formations. Methods include gas porosimetry and permeametry, mercury intrusion porosimetry, thin section petrography, and X-ray diffraction. The lithofacies exhibitmore » highly variable intra- and inter-informational distributions of pore throat and body sizes. Based on pore-throat size, samples fall into four distinct groups. Micropore-throat dominated samples are from the Eau Claire Formation, whereas the macropore-, mesopore-, and uniform-dominated samples are from the Mount Simon Sandstone. Complex paragenesis governs the high degree of pore and pore-throat size heterogeneity, due to an interplay of precipitation, non-uniform compaction, and later dissolution of cements. Furthermore, the cement dissolution event probably accounts for much of the current porosity in the unit. The unusually heterogeneous nature of the pore networks in the Mount Simon Sandstone indicates that there is a greater-than-normal opportunity for reservoir capillary trapping of non-wetting fluids — as quantified by CO 2 and air column heights — which should be taken into account when assessing the potential of the reservoir-caprock system for CO 2 storage and CAES.« less

Interaction between Proppant Packing, Reservoir Depletion, and Fluid Flow in Pore Space

NASA Astrophysics Data System (ADS)

Fan, M.; McClure, J. E.; Han, Y.; Chen, C.

2016-12-01

In the oil and gas industry, the performance of proppant pack in hydraulically created fractures has a significant influence on fracture conductivity. A better understanding of proppant transport and deposition pattern in a hydraulic fracture is vital for effective and economical production within oil and gas reservoirs. In this research, a numerical modeling approach, combining Particle Flow Code (PFC) and GPU-enhanced lattice Boltzmann simulator (GELBS), is adopted to advance the understanding of the interaction between proppant particle packing, depletion of reservoir formation, and transport of reservoir flow through the pore space. In this numerical work flow, PFC is used to simulate effective stress increase and proppant particle movement and rearrangement under increasing mechanical loading. The pore structure of the proppant pack evolves subsequently and the geometrical data are output for lattice Boltzmann (LB) simulation of proppant pack permeability. Three different proppant packs with fixed particle concentration and 12/18, 16/30, and 20/40 mesh sizes are generated. These proppant packs are compressed with specified loading stress and their subsequent geometries are used for fluid flow simulations. The simulation results are in good agreement with experimental observations, e.g., the conductivity of proppant packs decreases with increasing effective stress. Three proppant packs with the same average diameter were generated using different coefficients of variation (COVs) for the proppant diameter (namely cov5%, cov20%, and cov30%). By using the coupled PFC-LBM work flow, the proppant pack permeability as functions of effective stress and porosity is investigated. The results show that the proppant pack with a higher proppant diameter COV has lower permeability and porosity under the same effective stress, because smaller particles fill in the pore space between bigger particles. The relationship between porosity and permeability is also consistent with the Kozeny-Carman equation. In addition, relative permeability curves are obtained using multiphase LB simulation to study non-wetting phase trapping, which will benefit production forecasting and interpretation of formation damage. This research provides an advantageous alternative to expensive laboratory experiments.

Permeability-porosity relationships in sedimentary rocks

USGS Publications Warehouse

Nelson, Philip H.

1994-01-01

In many consolidated sandstone and carbonate formations, plots of core data show that the logarithm of permeability (k) is often linearly proportional to porosity (??). The slope, intercept, and degree of scatter of these log(k)-?? trends vary from formation to formation, and these variations are attributed to differences in initial grain size and sorting, diagenetic history, and compaction history. In unconsolidated sands, better sorting systematically increases both permeability and porosity. In sands and sandstones, an increase in gravel and coarse grain size content causes k to increase even while decreasing ??. Diagenetic minerals in the pore space of sandstones, such as cement and some clay types, tend to decrease log(k) proportionately as ?? decreases. Models to predict permeability from porosity and other measurable rock parameters fall into three classes based on either grain, surface area, or pore dimension considerations. (Models that directly incorporate well log measurements but have no particular theoretical underpinnings from a fourth class.) Grain-based models show permeability proportional to the square of grain size times porosity raised to (roughly) the fifth power, with grain sorting as an additional parameter. Surface-area models show permeability proportional to the inverse square of pore surface area times porosity raised to (roughly) the fourth power; measures of surface area include irreducible water saturation and nuclear magnetic resonance. Pore-dimension models show permeability proportional to the square of a pore dimension times porosity raised to a power of (roughly) two and produce curves of constant pore size that transgress the linear data trends on a log(k)-?? plot. The pore dimension is obtained from mercury injection measurements and is interpreted as the pore opening size of some interconnected fraction of the pore system. The linear log(k)-?? data trends cut the curves of constant pore size from the pore-dimension models, which shows that porosity reduction is always accompanied by a reduction in characteristic pore size. The high powers of porosity of the grain-based and surface-area models are required to compensate for the inclusion of the small end of the pore size spectrum.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mouzakis, Katherine M.; Navarre-Sitchler, Alexis K.; Rother, Gernot

Carbon capture, utilization, and storage, one proposed method of reducing anthropogenic emissions of CO 2, relies on low permeability formations, such as shales, above injection formations to prevent upward migration of the injected CO 2. Porosity in caprocks evaluated for sealing capacity before injection can be altered by geochemical reactions induced by dissolution of injected CO 2 into pore fluids, impacting long-term sealing capacity. Therefore, long-term performance of CO 2 sequestration sites may be dependent on both initial distribution and connectivity of pores in caprocks, and on changes induced by geochemical reaction after injection of CO 2, which are currentlymore » poorly understood. This paper presents results from an experimental study of changes to caprock porosity and pore network geometry in two caprock formations under conditions relevant to CO 2 sequestration. Pore connectivity and total porosity increased in the Gothic Shale; while total porosity increased but pore connectivity decreased in the Marine Tuscaloosa. Gothic Shale is a carbonate mudstone that contains volumetrically more carbonate minerals than Marine Tuscaloosa. Carbonate minerals dissolved to a greater extent than silicate minerals in Gothic Shale under high CO 2 conditions, leading to increased porosity at length scales <~200 nm that contributed to increased pore connectivity. In contrast, silicate minerals dissolved to a greater extent than carbonate minerals in Marine Tuscaloosa leading to increased porosity at all length scales, and specifically an increase in the number of pores >~1 μm. Mineral reactions also contributed to a decrease in pore connectivity, possibly as a result of precipitation in pore throats or hydration of the high percentage of clays. Finally, this study highlights the role that mineralogy of the caprock can play in geochemical response to CO 2 injection and resulting changes in sealing capacity in long-term CO 2 storage projects.« less

Disrupting a key hydrophobic pair in the oligomerization interface of the actinoporins impairs their pore‐forming activity

PubMed Central

Mesa‐Galloso, Haydeé; Delgado‐Magnero, Karelia H.; Cabezas, Sheila; López‐Castilla, Aracelys; Hernández‐González, Jorge E.; Pedrera, Lohans; Alvarez, Carlos; Peter Tieleman, D.; García‐Sáez, Ana J.; Lanio, Maria E.; Valiente, Pedro A.

2017-01-01

Abstract Crystallographic data of the dimeric and octameric forms of fragaceatoxin C (FraC) suggested the key role of a small hydrophobic protein–protein interaction surface for actinoporins oligomerization and pore formation in membranes. However, site‐directed mutagenesis studies supporting this hypothesis for others actinoporins are still lacking. Here, we demonstrate that disrupting the key hydrophobic interaction between V60 and F163 (FraC numbering scheme) in the oligomerization interface of FraC, equinatoxin II (EqtII), and sticholysin II (StII) impairs the pore formation activity of these proteins. Our results allow for the extension of the importance of FraC protein–protein interactions in the stabilization of the oligomeric intermediates of StII and EqtII pointing out that all of these proteins follow a similar pathway of membrane disruption. These findings support the hybrid pore proposal as the universal model of actinoporins pore formation. Moreover, we reinforce the relevance of dimer formation, which appears to be a functional intermediate in the assembly pathway of some different pore‐forming proteins. PMID:28000294

Multiple pore conformations driven by asynchronous movements of voltage sensors in a eukaryotic sodium channel

PubMed Central

Goldschen-Ohm, Marcel P.; Capes, Deborah L.; Oelstrom, Kevin M.; Chanda, Baron

2013-01-01

Voltage-dependent Na+ channels are crucial for electrical signalling in excitable cells. Membrane depolarization initiates asynchronous movements in four non-identical voltage-sensing domains of the Na+ channel. It remains unclear to what extent this structural asymmetry influences pore gating as compared with outwardly rectifying K+ channels, where channel opening results from a final concerted transition of symmetric pore gates. Here we combine single channel recordings, cysteine accessibility and voltage clamp fluorimetry to probe the relationships between voltage sensors and pore conformations in an inactivation deficient Nav1.4 channel. We observe three distinct conductance levels such that DI-III voltage sensor activation is kinetically correlated with formation of a fully open pore, whereas DIV voltage sensor movement underlies formation of a distinct subconducting pore conformation preceding inactivation in wild-type channels. Our experiments reveal that pore gating in sodium channels involves multiple transitions driven by asynchronous movements of voltage sensors. These findings shed new light on the mechanism of coupling between activation and fast inactivation in voltage-gated sodium channels. PMID:23322038

Pore Formation Process of Porous Ti3SiC2 Fabricated by Reactive Sintering

PubMed Central

Zhang, Huibin; Liu, Xinli; Jiang, Yao

2017-01-01

Porous Ti3SiC2 was fabricated with high purity, 99.4 vol %, through reactive sintering of titanium hydride (TiH2), silicon (Si) and graphite (C) elemental powders. The reaction procedures and the pore structure evolution during the sintering process were systematically studied by X-ray diffraction (XRD) and scanning electron microscope (SEM). Our results show that the formation of Ti3SiC2 from TiH2/Si/C powders experienced the following steps: firstly, TiH2 decomposed into Ti; secondly, TiC and Ti5Si3 intermediate phases were generated; finally, Ti3SiC2 was produced through the reaction of TiC, Ti5Si3 and Si. The pores formed in the synthesis procedure of porous Ti3SiC2 ceramics are derived from the following aspects: interstitial pores left during the pressing procedure; pores formed because of the TiH2 decomposition; pores formed through the reactions between Ti and Si and Ti and C powders; and the pores produced accompanying the final phase synthesized during the high temperature sintering process. PMID:28772515

Multi-scale Multi-dimensional Imaging and Characterization of Oil Shale Pyrolysis

NASA Astrophysics Data System (ADS)

Gao, Y.; Saif, T.; Lin, Q.; Al-Khulaifi, Y.; Blunt, M. J.; Bijeljic, B.

2017-12-01

The microstructural evaluation of fine grained rocks is challenging which demands the use of several complementary methods. Oil shale, a fine-grained organic-rich sedimentary rock, represents a large and mostly untapped unconventional hydrocarbon resource with global reserves estimated at 4.8 trillion barrels. The largest known deposit is the Eocene Green River Formation in Western Colorado, Eastern Utah, and Southern Wyoming. An improved insight into the mineralogy, organic matter distribution and pore network structure before, during and after oil shale pyrolysis is critical to understanding hydrocarbon flow behaviour and improving recovery. In this study, we image Mahogany zone oil shale samples in two dimensions (2-D) using scanning electron microscopy (SEM), and in three dimensions (3-D) using focused ion beam scanning electron microscopy (FIB-SEM), laboratory-based X-ray micro-tomography (µCT) and synchrotron X-ray µCT to reveal a complex and variable fine grained microstructure dominated by organic-rich parallel laminations which are tightly bound in a highly calcareous and heterogeneous mineral matrix. We report the results of a detailed µCT study of the Mahogany oil shale with increasing pyrolysis temperature. The physical transformation of the internal microstructure and evolution of pore space during the thermal conversion of kerogen in oil shale to produce hydrocarbon products was characterized. The 3-D volumes of pyrolyzed oil shale were reconstructed and image processed to visualize and quantify the volume and connectivity of the pore space. The results show a significant increase in anisotropic porosity associated with pyrolysis between 300-500°C with the formation of micron-scale connected pore channels developing principally along the kerogen-rich lamellar structures.

Petrophysical Properties of the Yeso, Abo and Cisco Formations in the Permian Basin in New Mexico, U.S.A

NASA Astrophysics Data System (ADS)

Mann, Griffin

The area that comprises the Northwest Shelf in Lea Co., New Mexico has been heavily drilled over the past half century. The main target being shallow reservoirs within the Permian section (San Andres and Grayburg Formations). With a focus shifting towards deeper horizons, there is a need for more petrophysical data pertaining to these formations, which is the focus of this study through a variety of techniques. This study involves the use of contact angle measurements, fluid imbibition tests, Mercury Injection Capillary Pressure (MICP) and log analysis to evaluate the nano-petrophysical properties of the Yeso, Abo and Cisco Formation within the Northwest Shelf area of southeast New Mexico. From contact angle measurements, all of the samples studied were found to be oil-wetting as n-decane spreads on to the rock surface much quicker than the other fluids (deionized water and API brine) tested. Imbibition tests resulted in a well-connected pore network being observed for all of the samples with the highest values of imbibition slopes being recorded for the Abo samples. MICP provided a variety of pore structure data which include porosity, pore-throat size distributions, permeability and tortuosity. The Abo samples saw the highest porosity percentages, which were above 15%, with all the other samples ranging from 4 - 7%. The majority of the pore-throat sizes for most of the samples fell within the 1 - 10 mum range. The only exceptions to this being the Paddock Member within the Yeso Formation, which saw a higher percentage of larger pores (10 - 1000mum) and one of the Cisco Formation samples, which had the majority of its pore sizes fall in the 0.1 - 1 mum range. The log analysis created log calculations and curves for cross-plot porosity and water saturation that were then used to derive a value for permeability. The porosity and permeability values were comparable with those measured from our MICP and literature values.

Quantitative analysis of vascular colonisation and angio-conduction in porous silicon-substituted hydroxyapatite with various pore shapes in a chick chorioallantoic membrane (CAM) model.

PubMed

Magnaudeix, Amandine; Usseglio, Julie; Lasgorceix, Marie; Lalloue, Fabrice; Damia, Chantal; Brie, Joël; Pascaud-Mathieu, Patricia; Champion, Eric

2016-07-01

The development of scaffolds for bone filling of large defects requires an understanding of angiogenesis and vascular guidance, which are crucial processes for bone formation and healing. There are few investigations on the ability of a scaffold to support blood vessel guidance and it this is of great importance because it relates to the quality and dispersion of the blood vessel network. This work reports an analysis of vascularisation of porous silicon-substituted hydroxyapatite (SiHA) bioceramics and the effects of pore shape on vascular guidance using an expedient ex ovo model, the chick embryo chorioallantoic membrane (CAM) assay. Image analysis of vascularised implants assessed the vascular density, fractal dimension and diameter of blood vessels at two different scales (the whole ceramic and pores alone) and was performed on model SiHA ceramics harbouring pores of various cross-sectional geometries (circles, square, rhombus, triangles and stars). SiHA is a biocompatible material which allows the conduction of blood vessels on its surface. The presence of pores did not influence angiogenesis related-parameters (arborisation, fractal dimension) but pore geometry affected the blood vessel guidance and angio-conductive potential (diameter and number of the blood vessels converging toward the pores). The measured angles of pore cross-section modulated the number and diameter of blood vessels converging to pores, with triangular pores appearing of particular interest. This result will be used for shaping ceramic scaffolds with specific porous architecture to promote vascular colonisation and osteointegration. An expedient and efficient method, using chick embryo chorioallantoic membrane (CAM) assays, has been set up to characterise quantitatively the angiogenesis and the vascular conduction in scaffolds. This approach complements the usual cell culture assays and could replace to a certain extent in vivo experiments. It was applied to silicon-substituted hydroxyapatite porous bioceramics with various pore shapes. The material was found to be biocompatible, allowing the conduction of blood vessels on its surface. The presence of pores does not influence the angiogenesis but the pore shape affects the blood vessel guidance and angio-conductive potential. Pores with triangular cross-section appear particularly attractive for the further design of scaffolds in order to promote their vascular colonisation and osteointegration and improve their performances. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Manipulating the membrane penetration mechanism of helical polypeptides via aromatic modification for efficient gene delivery.

PubMed

Zheng, Nan; Song, Ziyuan; Yang, Jiandong; Liu, Yang; Li, Fangfang; Cheng, Jianjun; Yin, Lichen

2017-08-01

The delivery performance of non-viral gene vectors is greatly related to their intracellular kinetics. Cationic helical polypeptides with potent membrane penetration properties and gene transfection efficiencies have been recently developed by us. However, they suffer from severe drawbacks in terms of their membrane penetration mechanisms that mainly include endocytosis and pore formation. The endocytosis mechanism leads to endosomal entrapment of gene cargos, while the charge- and helicity-induced pore formation causes appreciable cytotoxicity at high concentrations. With the attempt to overcome such critical challenges, we incorporated aromatic motifs into the design of helical polypeptides to enhance their membrane activities and more importantly, to manipulate their membrane penetration mechanisms. The aromatically modified polypeptides exhibited higher cellular internalization level than the unmodified analogue by up to 2.5 folds. Such improvement is possibly because aromatic domains promoted the polypeptides to penetrate cell membranes via direct transduction, a non-endocytosis and non-pore formation mechanism. As such, gene cargos were more efficiently delivered into cells by bypassing endocytosis and subsequently avoiding endosomal entrapment, and the material toxicity associated with excessive pore formation was also reduced. The top-performing aromatic polypeptide containing naphthyl side chains at the incorporated content of 20mol% revealed notably higher transfection efficiencies than commercial reagents in melanoma cells in vitro (by 11.7 folds) and in vivo (by 9.1 folds), and thus found potential utilities toward topical gene delivery for cancer therapy. Cationic helical polypeptides, as efficient gene delivery materials, suffer from severe drawbacks in terms of their membrane penetration mechanisms. The main cell penetration mechanisms involved are endocytosis and pore formation. However, the endocytosis mechanism has the limitation of endosomal entrapment of gene cargos, while the charge- and helicity-induced pore formation causes cytotoxicity at high concentrations. To address such critical issues toward the maximization of gene delivery efficiency, we incorporated aromatic domains into helical polypeptides to promote the cell membrane penetrations via direct transduction, which is a non-endocytosis and non-pore formation mechanism. The manipulation of their membrane penetration mechanisms allows gene cargos to be more efficiently delivered by bypassing endocytosis and subsequently avoiding endosomal entrapment. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Investigation of thermal conduction in symmetric and asymmetric nanoporous structures

NASA Astrophysics Data System (ADS)

Yu, Ziqi; Ferrer-Argemi, Laia; Lee, Jaeho

2017-12-01

Nanoporous structures with a critical dimension comparable to or smaller than the phonon mean free path have demonstrated significant thermal conductivity reductions that are attractive for thermoelectric applications, but the presence of various geometric parameters complicates the understanding of governing mechanisms. Here, we use a ray tracing technique to investigate phonon boundary scattering phenomena in Si nanoporous structures of varying pore shapes, pore alignments, and pore size distributions, and identify mechanisms that are primarily responsible for thermal conductivity reductions. Our simulation results show that the neck size, or the smallest distance between nearest pores, is the key parameter in understanding nanoporous structures of varying pore shapes and the same porosities. When the neck size and the porosity are both identical, asymmetric pore shapes provide a lower thermal conductivity compared with symmetric pore shapes, due to localized heat fluxes. Asymmetric nanoporous structures show possibilities of realizing thermal rectification even with fully diffuse surface boundaries, in which optimal arrangements of triangular pores show a rectification ratio up to 13 when the injection angles are optimally controlled. For symmetric nanoporous structures, hexagonal-lattice pores achieve larger thermal conductivity reductions than square-lattice pores due to the limited line of sight for phonons. We also show that nanoporous structures of alternating pore size distributions from large to small pores yield a lower thermal conductivity compared with those of uniform pore size distributions in the given porosity. These findings advance the understanding of phonon boundary scattering phenomena in complex geometries and enable optimal designs of artificial nanostructures for thermoelectric energy harvesting and solid-state cooling systems.

Multi-scale characterization of pore evolution in a combustion metamorphic complex, Hatrurim basin, Israel: Combining (ultra) small-angle neutron scattering and image analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hsiu-Wen; Anovitz, Lawrence; Burg, Avihu

Backscattered scanning electron micrograph and ultra small- and small-angle neutron scattering data have been combined to provide statistically meaningful data on the pore/grain structure and pore evolution of combustion metamorphic complexes from the Hatrurim basin, Israel. Three processes, anti-sintering roughening, alteration of protolith (dehydration, decarbonation, and oxidation) and crystallization of high-temperature minerals, occurred simultaneously, leading to significant changes in observed pore/grain structures. Pore structures in the protoliths, and in lowand high-grade metamorphic rocks show surface (Ds) and mass (Dm) pore fractal geometries with gradual increases in both Ds and Dm values as a function of metamorphic grade. This suggests thatmore » increases in pore volume and formation of less branching pore networks are accompanied by a roughening of pore/grain interfaces. Additionally, pore evolution during combustion metamorphism is also characterized by reduced contributions from small-scale pores to the cumulative porosity in the high-grade rocks. At high temperatures, small-scale pores may be preferentially closed by the formation of high-temperature minerals, producing a rougher morphology with increasing temperature. Alternatively, large-scale pores may develop at the expense of small-scale pores. These observations (pore fractal geometry and cumulative porosity) indicate that the evolution of pore/grain structures is correlated with the growth of high-temperature phases and is a consequence of the energy balance between pore/grain surface energy and energy arising from heterogeneous phase contacts. The apparent pore volume density further suggests that the localized time/temperature development of the high-grade Hatrurim rocks is not simply an extension of that of the low-grade rocks. The former likely represents the "hot spots (burning foci)" in the overall metamorphic terrain while the latter may represent contact aureoles.« less

Synthesis and characterization of nanocrystalline mesoporous zirconia using supercritical drying.

PubMed

Tyagi, Beena; Sidhpuria, Kalpesh; Shaik, Basha; Jasra, Raksh Vir

2006-06-01

Synthesis of nano-crystalline zirconia aerogel was done by sol-gel technique and supercritical drying using n-propanol solvent at and above supercritical temperature (235-280 degrees C) and pressure (48-52 bar) of n-propanol. Zirconia xerogel samples have also been prepared by conventional thermal drying method to compare with the super critically dried samples. Crystalline phase, crystallite size, surface area, pore volume, and pore size distribution were determined for all the samples in detail to understand the effect of gel drying methods on these properties. Supercritical drying of zirconia gel was observed to give thermally stable, nano-crystalline, tetragonal zirconia aerogels having high specific surface area and porosity with narrow and uniform pore size distribution as compared to thermally dried zirconia. With supercritical drying, zirconia samples show the formation of only mesopores whereas in thermally dried samples, substantial amount of micropores are observed along with mesopores. The samples prepared using supercritical drying yield nano-crystalline zirconia with smaller crystallite size (4-6 nm) as compared to higher crystallite size (13-20 nm) observed with thermally dried zirconia.

The distribution and mechanism of pore formation in copper foams fabricated by Lost Carbonate Sintering method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shahzeydi, Mohammad Hosein; Parvanian, Amir Masoud; Panjepour, Masoud, E-mail: panjepour@cc.iut.ac.ir

2016-01-15

In this research, utilizing X-ray computed tomography (XCT), geometrical characterization, and pore formation mechanisms of highly porous copper foams manufactured by powder metallurgical (PM) process are investigated. Open-cell copper foams with porosity percentages of 60% and 80% and with a pore size within the range of 300–600 μm were manufactured by using potassium carbonate as a space holder agent via the Lost Carbonate Sintering (LCS) technique. XCT and SEM were also employed to investigate the three-dimensional structure of foams and to find the effect of the parameters of the space holders on the structural properties of copper foams. The resultmore » showed an excellent correlation between the structural properties of the foams including the size and shape of the pores, porosity percentage, volume percentage, particle size, and the shape of the sacrificial agent used. Also, the advanced image analysis of XCT images indicated fluctuations up to ± 10% in porosity distribution across different cross-sections of the foams. Simultaneous thermal analysis (STA: DTA–TG) was also used to study the thermal history of the powders used during the manufacturing process of the foams. The results indicated that the melting and thermal decomposition of the potassium carbonate occurred simultaneously at 920 °C and created the porous structure of the foams. By combining the STA result with the result of the tension analysis of cell walls, the mechanisms of open-pore formation were suggested. In fact, most open pores in the samples were formed due to the direct contact of potassium carbonate particles with each other in green compact. Also, it was found that the thermal decomposition of potassium carbonate particles into gaseous CO{sub 2} led to the production of gas pressure inside the closed pores, which eventually caused the creation of cracks on the cell walls and the opening of the pores in foam's structure. - Highlights: • Structural characterization of copper foam produced by LCS method is investigated by tomography images. • The ability of LCS technique to control structural features of produced foams was proved. • The mechanisms of open pores formation were presented.« less

Rock physics model-based prediction of shear wave velocity in the Barnett Shale formation

NASA Astrophysics Data System (ADS)

Guo, Zhiqi; Li, Xiang-Yang

2015-06-01

Predicting S-wave velocity is important for reservoir characterization and fluid identification in unconventional resources. A rock physics model-based method is developed for estimating pore aspect ratio and predicting shear wave velocity Vs from the information of P-wave velocity, porosity and mineralogy in a borehole. Statistical distribution of pore geometry is considered in the rock physics models. In the application to the Barnett formation, we compare the high frequency self-consistent approximation (SCA) method that corresponds to isolated pore spaces, and the low frequency SCA-Gassmann method that describes well-connected pore spaces. Inversion results indicate that compared to the surroundings, the Barnett Shale shows less fluctuation in the pore aspect ratio in spite of complex constituents in the shale. The high frequency method provides a more robust and accurate prediction of Vs for all the three intervals in the Barnett formation, while the low frequency method collapses for the Barnett Shale interval. Possible causes for this discrepancy can be explained by the fact that poor in situ pore connectivity and low permeability make well-log sonic frequencies act as high frequencies and thus invalidate the low frequency assumption of the Gassmann theory. In comparison, for the overlying Marble Falls and underlying Ellenburger carbonates, both the high and low frequency methods predict Vs with reasonable accuracy, which may reveal that sonic frequencies are within the transition frequencies zone due to higher pore connectivity in the surroundings.

X-Ray Computed Tomography of Tranquility Base Moon Rock

NASA Technical Reports Server (NTRS)

Jones, Justin S.; Garvin, Jim; Viens, Mike; Kent, Ryan; Munoz, Bruno

2016-01-01

X-ray Computed Tomography (CT) was used for the first time on the Apollo 11 Lunar Sample number 10057.30, which had been previously maintained by the White House, then transferred back to NASA under the care of Goddard Space Flight Center. Results from this analysis show detailed images of the internal structure of the moon rock, including vesicles (pores), crystal needles, and crystal bundles. These crystals, possibly the common mineral ilmenite, are found in abundance and with random orientation. Future work, in particular a greater understanding of these crystals and their formation, may lead to a more in-depth understanding of the lunar surface evolution and mineral content.

Effect of Stepwise Pressure Change on Porosity Evolution during Directional Solidification in Small Cylindrical Channels

NASA Technical Reports Server (NTRS)

Grugel, R.N.; Lee, C.P.; Cox, M.C.; Blandford, B.T.; Anilkumar, A.V.

2008-01-01

Controlled directional solidification experiments were performed in capillary channels, using nitrogen-saturated succinonitrile, to examine the effect of an in-situ stepwise processing pressure increase on an isolated pore evolution. Two experiments were performed using different processing pressure input profiles. The results indicate that a processing pressure increase has a transient effect on pore growth geometry characterized by an initial phase of decreasing pore diameter, followed by a recovery phase of increasing pore diameter. The experimental results also show that processing pressure can be used as a control parameter to either increase or terminate porosity formation. A theoretical model is introduced which indicates that the pore formation process is limited by the diffusion of solute-gas through the melt, and that the observed response toa pressure increase is attributed to the re-equilibration of solute concentration in the melt associated with the increased melt pressure.

Bilayer Deformation, Pores, and Micellation Induced by Oxidized Lipids.

PubMed

Boonnoy, Phansiri; Jarerattanachat, Viwan; Karttunen, Mikko; Wong-Ekkabut, Jirasak

2015-12-17

The influence of different oxidized lipids on lipid bilayers was investigated with 16 individual 1 μs atomistic molecular dynamics (MD) simulations. Binary mixtures of lipid bilayers of 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) and its peroxide and aldehyde products were performed at different concentrations. In addition, an asymmetrical short chain lipid, 1-palmitoyl-2-decanoyl-sn-glycero-3-phosphatidylcholine (PDPC), was used to compare the effects of polar/apolar groups in the lipid tail on lipid bilayer. Although water defects occurred with both aldehyde and peroxide lipids, full pore formation was observed only for aldehyde lipids. At medium concentrations the pores were stable. At higher concentrations, however, the pores became unstable and micellation occurred. Data analysis shows that aldehyde lipids' propensity for pore formation is due to their shorter and highly mobile tail. The highly polar peroxide lipids are stabilized by strong hydrogen bonds with interfacial water.

Abnormal formation velocities and applications to pore pressure prediction

NASA Astrophysics Data System (ADS)

Liu, Libin; Shen, Guoqiang; Wang, Zhentao; Yang, Hongwei; Han, Hongwei; Cheng, Yuanfeng

2018-06-01

The pore pressure is a vital concept to the petroleum industry and cannot be ignored by either reservoir engineers or geoscientists. Based on theoretical analyses of effective stresses and the grain packing model, a new equation is proposed for predicting pore pressures from formation velocity data. The predictions agree well with both measured pressures and estimations using Eaton's empirical equation, but the application of the new equation to seismic data is simple and convenient. One application example shows that the identification of sweet spots is much easier using pore pressure data than with inverted seismic velocity data. In another application example using field seismic data, a distribution of overpressured strata is revealed, which is a crucial clue for petroleum generation and accumulation. Still, the accuracy of pore pressure prediction is hardly always guaranteed, mainly owing to the complexity of the real geology and the suitability of specific assumptions about the underlying rock physics.

On the effect of nonequilibrium vacancies on the melting and pore formation in ultrafine-grained aluminum alloys subjected to pulsed laser irradiation

NASA Astrophysics Data System (ADS)

Kikin, P. Yu.; Perevezentsev, V. N.; Rusin, E. E.

2015-08-01

An analysis has been carried out of the experimental data concerning the interaction of pulsed laser radiation with the ultrafine-grained (UFG) Al-Mg alloys obtained by the methods of severe plastic deformation. It has been shown that the melting and pore formation in the UFG alloys under the effect of laser radiation start earlier than in their coarse-grained analogs. The observed behavior of the alloys can be explained from the united positions based on the concepts of the influence of the high concentration of nonequilibrium vacancies on the ability of the alloys to absorb the laser radiation and on the process of pore formation.

Effect of Mineral Dissolution/Precipitation and CO2 Exsolution on CO2 transport in Geological Carbon Storage.

PubMed

Xu, Ruina; Li, Rong; Ma, Jin; He, Di; Jiang, Peixue

2017-09-19

Geological carbon sequestration (GCS) in deep saline aquifers is an effective means for storing carbon dioxide to address global climate change. As the time after injection increases, the safety of storage increases as the CO 2 transforms from a separate phase to CO 2 (aq) and HCO 3 - by dissolution and then to carbonates by mineral dissolution. However, subsequent depressurization could lead to dissolved CO 2 (aq) escaping from the formation water and creating a new separate phase which may reduce the GCS system safety. The mineral dissolution and the CO 2 exsolution and mineral precipitation during depressurization change the morphology, porosity, and permeability of the porous rock medium, which then affects the two-phase flow of the CO 2 and formation water. A better understanding of these effects on the CO 2 -water two-phase flow will improve predictions of the long-term CO 2 storage reliability, especially the impact of depressurization on the long-term stability. In this Account, we summarize our recent work on the effect of CO 2 exsolution and mineral dissolution/precipitation on CO 2 transport in GCS reservoirs. We place emphasis on understanding the behavior and transformation of the carbon components in the reservoir, including CO 2 (sc/g), CO 2 (aq), HCO 3 - , and carbonate minerals (calcite and dolomite), highlight their transport and mobility by coupled geochemical and two-phase flow processes, and consider the implications of these transport mechanisms on estimates of the long-term safety of GCS. We describe experimental and numerical pore- and core-scale methods used in our lab in conjunction with industrial and international partners to investigate these effects. Experimental results show how mineral dissolution affects permeability, capillary pressure, and relative permeability, which are important phenomena affecting the input parameters for reservoir flow modeling. The porosity and the absolute permeability increase when CO 2 dissolved water is continuously injected through the core. The MRI results indicate dissolution of the carbonates during the experiments since the porosity has been increased after the core-flooding experiments. The mineral dissolution changes the pore structure by enlarging the throat diameters and decreasing the pore specific surface areas, resulting in lower CO 2 /water capillary pressures and changes in the relative permeability. When the reservoir pressure decreases, the CO 2 exsolution occurs due to the reduction of solubility. The CO 2 bubbles preferentially grow toward the larger pores instead of toward the throats or the finer pores during the depressurization. After exsolution, the exsolved CO 2 phase shows low mobility due to the highly dispersed pore-scale morphology, and the well dispersed small bubbles tend to merge without interface contact driven by the Ostwald ripening mechanism. During depressurization, the dissolved carbonate could also precipitate as a result of increasing pH. There is increasing formation water flow resistance and low mobility of the CO 2 in the presence of CO 2 exsolution and carbonate precipitation. These effects produce a self-sealing mechanism that may reduce unfavorable CO 2 migration even in the presence of sudden reservoir depressurization.

An ESEM investigation of latex film formation in cement pore solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gretz, M.; Plank, J., E-mail: sekretariat@bauchemie.ch.tum.d

2011-02-15

Environmental scanning electron microscopy (ESEM) and complementary methods were employed to study the time dependent film formation of a latex dispersion in water and cement pore solution. First, a model carboxylated styrene/n-butyl acrylate latex dispersion possessing a minimum film forming temperature (MFFT) of 18 {sup o}C was synthesized in aqueous media via emulsion polymerization. Its film forming property was at a temperature of 40 {sup o}C, studied under an ESEM. The analysis revealed that upon removal of water, film formation occurs as a result of particle packing, particle deformation and finally particle coalescence. Film formation is significantly retarded when themore » latex dispersion is present in cement pore solution. This effect can be ascribed to adsorption of Ca{sup 2+} ions onto the surface of the anionic latex particles and to interfacial secondary phases. This layer of adsorbed Ca{sup 2+} ions hinders interdiffusion of the macromolecules and subsequent film formation of the latex polymer.« less

Pore size regulates cell and tissue interactions with PLGA-CaP scaffolds used for bone engineering.

PubMed

Sicchieri, Luciana Gonçalves; Crippa, Grasiele Edilaine; de Oliveira, Paulo Tambasco; Beloti, Marcio Mateus; Rosa, Adalberto Luiz

2012-02-01

A common subject in bone tissue engineering is the need for porous scaffolds to support cell and tissue interactions aiming at repairing bone tissue. As poly(lactide-co-glycolide)-calcium phosphate (PLGA-CaP) scaffolds can be manufactured with different pore sizes, the aim of this study was to evaluate the effect of pore diameter on osteoblastic cell responses and bone tissue formation. Scaffolds were prepared with 85% porosity, with pore diameters in the ranges 470-590, 590-850 and 850-1200 µm. Rat bone marrow stem cells differentiated into osteoblasts were cultured on the scaffolds for up to 10 days to evaluate cell growth, alkaline phosphatase (ALP) activity and the gene expression of the osteoblast markers RUNX2, OSX, COL, MSX2, ALP, OC and BSP by real-time PCR. Scaffolds were implanted in critical size rat calvarial defects for 2, 4, and 8 weeks for histomorphometric analysis. Cell growth and ALP activity were not affected by the pore size; however, there was an increase in the gene expression of osteoblastic markers with the increase in the pore sizes. At 2 weeks all scaffolds displayed a similar amount of bone and blood vessels formation. At 4 and 8 weeks much more bone formation and an increased number of blood vessels were observed in scaffolds with pores of 470-590 µm. These results show that PLGA-CaP is a promising biomaterial for bone engineering. However, ideally, combinations of larger (-1000 µm) and smaller (-500 µm) pores in a single scaffold would optimize cellular and tissue responses during bone healing. Copyright © 2011 John Wiley & Sons, Ltd.

Inner/Outer nuclear membrane fusion in nuclear pore assembly: biochemical demonstration and molecular analysis.

PubMed

Fichtman, Boris; Ramos, Corinne; Rasala, Beth; Harel, Amnon; Forbes, Douglass J

2010-12-01

Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in double nuclear membranes, which carry out nucleocytoplasmic exchange. The mechanism of nuclear pore assembly involves a unique challenge, as it requires creation of a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel has little evolutionary precedent. Here we mapped inner/outer nuclear membrane fusion in NPC assembly biochemically by using novel assembly intermediates and membrane fusion inhibitors. Incubation of a Xenopus in vitro nuclear assembly system at 14°C revealed an early pore intermediate where nucleoporin subunits POM121 and the Nup107-160 complex were organized in a punctate pattern on the inner nuclear membrane. With time, this intermediate progressed to diffusion channel formation and finally to complete nuclear pore assembly. Correct channel formation was blocked by the hemifusion inhibitor lysophosphatidylcholine (LPC), but not if a complementary-shaped lipid, oleic acid (OA), was simultaneously added, as determined with a novel fluorescent dextran-quenching assay. Importantly, recruitment of the bulk of FG nucleoporins, characteristic of mature nuclear pores, was not observed before diffusion channel formation and was prevented by LPC or OA, but not by LPC+OA. These results map the crucial inner/outer nuclear membrane fusion event of NPC assembly downstream of POM121/Nup107-160 complex interaction and upstream or at the time of FG nucleoporin recruitment.

Adsorption of binary gas mixtures in heterogeneous carbon predicted by density functional theory: on the formation of adsorption azeotropes.

PubMed

Ritter, James A; Pan, Huanhua; Balbuena, Perla B

2010-09-07

Classical density functional theory (DFT) was used to predict the adsorption of nine different binary gas mixtures in a heterogeneous BPL activated carbon with a known pore size distribution (PSD) and in single, homogeneous, slit-shaped carbon pores of different sizes. By comparing the heterogeneous results with those obtained from the ideal adsorbed solution theory and with those obtained in the homogeneous carbon, it was determined that adsorption nonideality and adsorption azeotropes are caused by the coupled effects of differences in the molecular size of the components in a gas mixture and only slight differences in the pore sizes of a heterogeneous adsorbent. For many binary gas mixtures, selectivity was found to be a strong function of pore size. As the width of a homogeneous pore increases slightly, the selectivity for two different sized adsorbates may change from being greater than unity to less than unity. This change in selectivity can be accompanied by the formation of an adsorption azeotrope when this same binary mixture is adsorbed in a heterogeneous adsorbent with a PSD, like in BPL activated carbon. These results also showed that the selectivity exhibited by a heterogeneous adsorbent can be dominated by a small number of pores that are very selective toward one of the components in the gas mixture, leading to adsorption azeotrope formation in extreme cases.

Human endothelial cell growth and phenotypic expression on three dimensional poly(lactide-co-glycolide) sintered microsphere scaffolds for bone tissue engineering.

PubMed

Jabbarzadeh, Ehsan; Jiang, Tao; Deng, Meng; Nair, Lakshmi S; Khan, Yusuf M; Laurencin, Cato T

2007-12-01

Bone tissue engineering offers promising alternatives to repair and restore tissues. Our laboratory has employed poly(lactide-co-glycolide) PLAGA microspheres to develop a three dimensional (3-D) porous bioresorbable scaffold with a biomimetic pore structure. Osseous healing and integration with the surrounding tissue depends in part on new blood vessel formation within the porous structure. Since endothelial cells play a key role in angiogenesis (formation of new blood vessels from pre-existing vasculature), the purpose of this study was to better understand human endothelial cell attachment, viability, growth, and phenotypic expression on sintered PLAGA microsphere scaffold. Scanning electron microscopy (SEM) examination showed cells attaching to the surface of microspheres and bridging the pores between the microspheres. Cell proliferation studies indicated that cell number increased during early stages and reached a plateau between days 10 and 14. Immunofluorescent staining for actin showed that cells were proliferating three dimensionally through the scaffolds while staining for PECAM-1 (platelet endothelial cell adhesion molecule) displayed typical localization at cell-cell contacts. Gene expression analysis showed that endothelial cells grown on PLAGA scaffolds maintained their normal characteristic phenotype. The cell proliferation and phenotypic expression were independent of scaffold pore architecture. These results demonstrate that PLAGA sintered microsphere scaffolds can support the growth and biological functions of human endothelial cells. The insights from this study should aid future studies aimed at enhancing angiogenesis in three dimensional tissue engineered scaffolds.

Ca²⁺-dependent repair of pneumolysin pores: A new paradigm for host cellular defense against bacterial pore-forming toxins.

PubMed

Wolfmeier, Heidi; Schoenauer, Roman; Atanassoff, Alexander P; Neill, Daniel R; Kadioglu, Aras; Draeger, Annette; Babiychuk, Eduard B

2015-09-01

Pneumolysin (PLY), a key virulence factor of Streptococcus pneumoniae, permeabilizes eukaryotic cells by forming large trans-membrane pores. PLY imposes a puzzling multitude of diverse, often mutually excluding actions on eukaryotic cells. Whereas cytotoxicity of PLY can be directly attributed to the pore-mediated effects, mechanisms that are responsible for the PLY-induced activation of host cells are poorly understood. We show that PLY pores can be repaired and thereby PLY-induced cell death can be prevented. Pore-induced Ca²⁺ entry from the extracellular milieu is of paramount importance for the initiation of plasmalemmal repair. Nevertheless, active Ca²⁺ sequestration that prevents excessive Ca²⁺ elevation during the execution phase of plasmalemmal repair is of no less importance. The efficacy of plasmalemmal repair does not only define the fate of targeted cells but also intensity, duration and repetitiveness of PLY-induced Ca²⁺ signals in cells that were able to survive after PLY attack. Intracellular Ca²⁺ dynamics evoked by the combined action of pore formation and their elimination mimic the pattern of receptor-mediated Ca²⁺ signaling, which is responsible for the activation of host immune responses. Therefore, we postulate that plasmalemmal repair of PLY pores might provoke cellular responses that are similar to those currently ascribed to the receptor-mediated PLY effects. Our data provide new insights into the understanding of the complexity of cellular non-immune defense responses to a major pneumococcal toxin that plays a critical role in the establishment and the progression of life-threatening diseases. Therapies boosting plasmalemmal repair of host cells and their metabolic fitness might prove beneficial for the treatment of pneumococcal infections. This article is part of a Special Issue entitled: 13th European Symposium on Calcium. Copyright © 2014 Elsevier B.V. All rights reserved.

Diagenesis and porosity evolution of tight sand reservoirs in Carboniferous Benxi Formation, Southeast Ordos Basin

NASA Astrophysics Data System (ADS)

Hu, Peng; Yu, Xinghe; Shan, Xin; Su, Dongxu; Wang, Jiao; Li, Yalong; Shi, Xin; Xu, Liqiang

2016-04-01

The Ordos Basin, situated in west-central China, is one of the oldest and most important fossil-fuel energy base, which contains large reserves of coal, oil and natural gas. The Upper Palaeozoic strata are widely distributed with rich gas-bearing and large natural gas resources, whose potential is tremendous. Recent years have witnessed a great tight gas exploration improvement of the Upper Paleozoic in Southeastern Ordos basin. The Carboniferous Benxi Formation, mainly buried more than 2,500m, is the key target strata for hydrocarbon exploration, which was deposited in a barrier island and tidal flat environment. The sandy bars and flats are the favorable sedimentary microfacies. With an integrated approach of thin-section petrophysics, constant velocity mercury injection test, scanning electron microscopy and X-ray diffractometry, diagenesis and porosity evolution of tight sand reservoirs of Benxi Formation were analyzed in detail. The result shows that the main lithology of sandstone in this area is dominated by moderately to well sorted quartz sandstone. The average porosity and permeability is 4.72% and 1.22mD. The reservoirs of Benxi Formation holds a variety of pore types and the pore throats, with obvious heterogeneity and poor connection. Based on the capillary pressure curve morphological characteristics and parameters, combined with thin section and phycical property data, the reservoir pore structure of Benxi Formation can be divided into 4 types, including mid pore mid throat type(I), mid pore fine throat type(II), small pore fine throat type(III) and micro pro micro throat type(Ⅳ). The reservoirs primarily fall in B-subsate of middle diagenesis and late diagenesis, which mainly undergo compaction, cmentation, dissolution and fracturing process. Employing the empirical formula of different sorting for unconsolideated sandstone porosity, the initial sandstone porosity is 38.32% on average. Quantitative evaluation of the increase and decrease of porosity caused by different diagenesis reveals that mechanical compaction and chemical cementation are the main mechanisms for destroying primary pores, which contribute 19.61% and 8.75% to the loss of primary posoity, respectively. Dissolution of volcanic fragments and feldspar increased reservoir porosity by 4.14%. The pores were occluded by late minerals and carbonate cements, resulting in a reduction of 9.38%. Overall, the dual influence of compaction and cementation is the key of the key, controlling formation of tight gas sandstone reservoirs. Keywords: diagenesis, porosity evolution, tight sandstone, Benxi Formation, Southeast Ordos Basin Acknowledgements: We greatfully acknowledge Yanchang Petroleum for providing the samples and data access and for permission to publish this work. The first author, Peng Hu, would like to thank the support from Prof. Xinghe Yu.

Step-wise potential development across the lipid bilayer under external electric fields

NASA Astrophysics Data System (ADS)

Majhi, Amit Kumar

2018-04-01

Pore formation across the bilayers under external electric field is an important phenomenon, which has numerous applications in biology and bio-engineering fields. However, it is not a ubiquitous event under all field applications. To initiate a pore in the bilayer a particular threshold electric field is required. The electric field alters the intrinsic potential distribution across the bilayer as we as it enhances total potential drop across the bilayer, which causes the pore formation. The intrinsic potential profile has a maximum peak value, which is 0.8 V and it gets enhanced under application of external field, 0.43 V/nm. The peak value becomes 1.4 V when a pore appears in the bilayer and it continues to evolve as along as the external electric field remains switched on.

Study of shale reservoir nanometer-sized pores in Member 1 of Shahejie Formation in JX area, Liaozhong sag

NASA Astrophysics Data System (ADS)

Cheng, Yong; Zhang, Yu; Wen, Yiming

2018-02-01

The microscopic pore structure is the key of the shale reservoir study; however, traditional Scanning Electron Microscopy (SEM) methods cannot identify the irregular morphology caused by mechanical polishing. In this work, Scanning Electron Microscopy combined argon ion polishing technology was taken to study the characteristics of shale reservoir pores of Member 1 of Shahejie Formation (E3s1) located in JX1-1 area of Liaozhong Sag. The results show that pores between clay platelets, intraplatelet pores within clay aggregates and organic-matter pores are very rich in the area and with good pore connectivity, so these types of pores are of great significance for oil-gas exporation. Pores between clay platelets are formed by directional or semi-directional contact between edge and surface, edge and edge or surface and surface of laminated clay minerals, whose shapes are linear, mesh, and irregular with the size of 500 nm to 5 μm. The intraplatelet pores within clay aggregates are formed in the process of the transformation and compaction of clay minerals, whose shapes are usually linear with the width of 30 to 500 nm and the length of 2 to 50 μm. The organic-matter pores are from the process of the conversion from organic matters to the hydrocarbon under thermal evolution, whose shapes are gneissic, irregular, pitted and elliptical with the size of 100 nm to 2 μm. This study is of certain guiding significance to selecting target zones, evaluating resource potential and exploring & developing of shale gas in this region.

Coverage Dependent Assembly of Anthraquinone on Au(111)

NASA Astrophysics Data System (ADS)

Conrad, Brad; Deloach, Andrew; Einstein, Theodore; Dougherty, Daniel

A study of adsorbate-adsorbate and surface state mediated interactions of anthraquinone (AnQ) on Au(111) is presented. We utilize scanning tunneling microscopy (STM) to characterize the coverage dependence of AnQ structure formation. Ordered structures are observed up to a single monolayer (ML) and are found to be strongly dependent on molecular surface density. While the complete ML forms a well-ordered close-packed layer, for a narrow range of sub-ML coverages irregular close-packed islands are observed to coexist with a disordered pore network linking neighboring islands. This network displays a characteristic pore size and at lower coverages, the soliton walls of the herringbone reconstruction are shown to promote formation of distinct pore nanostructures. We will discuss these nanostructure formations in the context of surface mediated and more direct adsorbate interactions.

Methane Recovery from Hydrate-bearing Sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. Carlos Santamarina; Costas Tsouris

2011-04-30

Gas hydrates are crystalline compounds made of gas and water molecules. Methane hydrates are found in marine sediments and permafrost regions; extensive amounts of methane are trapped in the form of hydrates. Methane hydrate can be an energy resource, contribute to global warming, or cause seafloor instability. This study placed emphasis on gas recovery from hydrate bearing sediments and related phenomena. The unique behavior of hydrate-bearing sediments required the development of special research tools, including new numerical algorithms (tube- and pore-network models) and experimental devices (high pressure chambers and micromodels). Therefore, the research methodology combined experimental studies, particle-scale numerical simulations,more » and macro-scale analyses of coupled processes. Research conducted as part of this project started with hydrate formation in sediment pores and extended to production methods and emergent phenomena. In particular, the scope of the work addressed: (1) hydrate formation and growth in pores, the assessment of formation rate, tensile/adhesive strength and their impact on sediment-scale properties, including volume change during hydrate formation and dissociation; (2) the effect of physical properties such as gas solubility, salinity, pore size, and mixed gas conditions on hydrate formation and dissociation, and it implications such as oscillatory transient hydrate formation, dissolution within the hydrate stability field, initial hydrate lens formation, and phase boundary changes in real field situations; (3) fluid conductivity in relation to pore size distribution and spatial correlation and the emergence of phenomena such as flow focusing; (4) mixed fluid flow, with special emphasis on differences between invading gas and nucleating gas, implications on relative gas conductivity for reservoir simulations, and gas recovery efficiency; (5) identification of advantages and limitations in different gas production strategies with emphasis; (6) detailed study of CH4-CO2 exchange as a unique alternative to recover CH4 gas while sequestering CO2; (7) the relevance of fines in otherwise clean sand sediments on gas recovery and related phenomena such as fines migration and clogging, vuggy structure formation, and gas-driven fracture formation during gas production by depressurization.« less

Monitoring the kinetics of the pH driven transition of the anthrax toxin prepore to the pore by biolayer interferometry and surface plasmon resonance

PubMed Central

Naik, Subhashchandra; Brock, Susan; Akkaladevi, Narahari; Tally, Jon; Mcginn-Straub, Wesley; Zhang, Na; Gao, Phillip; Gogol, E. P.; Pentelute, B. L.; Collier, R. John; Fisher, Mark T.

2013-01-01

Domain 2 of the anthrax protective antigen (PA) prepore heptamer unfolds and refolds during endosome acidification to generate an extended 100 Å beta barrel pore that inserts into the endosomal membrane. The PA pore facilitates the pH dependent unfolding and translocation of bound toxin enzymic components, lethal factor (LF) and/or edema factor (EF), from the endosome into the cytoplasm. We constructed immobilized complexes of the prepore with the PA-binding domain of LF (LFN) to monitor the real-time prepore to pore kinetic transition using surface plasmon resonance (SPR) and bio-layer interferometry (BLI). The kinetics of this transition increased as the solution pH was decreased from pH 7.5 to pH 5.0, mirroring acidification of the endosome. Once transitioned, the LFN-PA pore complex was removed from the BLI biosensor tip and deposited onto EM grids, where the PA pore formation was confirmed by negative stain electron microscopy. When the soluble receptor domain (ANTRX2/CMG2) binds the immobilized PA prepore, the transition to the pore state was observed only after the pH was lowered to early or late endosomal pH conditions (5.5 to 5.0 respectively). Once the pore formed, the soluble receptor readily dissociated from the PA pore. Separate binding experiments with immobilized PA pores and soluble receptor indicate that the receptor has a weakened propensity to bind to the transitioned pore. This immobilized anthrax toxin platform can be used to identify or validate potential antimicrobial lead compounds capable of regulating and/or inhibiting anthrax toxin complex formation or pore transitions. PMID:23964683

Monitoring the kinetics of the pH-driven transition of the anthrax toxin prepore to the pore by biolayer interferometry and surface plasmon resonance.

PubMed

Naik, Subhashchandra; Brock, Susan; Akkaladevi, Narahari; Tally, Jon; McGinn-Straub, Wesley; Zhang, Na; Gao, Phillip; Gogol, E P; Pentelute, B L; Collier, R John; Fisher, Mark T

2013-09-17

Domain 2 of the anthrax protective antigen (PA) prepore heptamer unfolds and refolds during endosome acidification to generate an extended 100 Å β barrel pore that inserts into the endosomal membrane. The PA pore facilitates the pH-dependent unfolding and translocation of bound toxin enzymic components, lethal factor (LF) and/or edema factor, from the endosome to the cytoplasm. We constructed immobilized complexes of the prepore with the PA-binding domain of LF (LFN) to monitor the real-time prepore to pore kinetic transition using surface plasmon resonance and biolayer interferometry (BLI). The kinetics of this transition increased as the solution pH was decreased from 7.5 to 5.0, mirroring acidification of the endosome. Once it had undergone the transition, the LFN-PA pore complex was removed from the BLI biosensor tip and deposited onto electron microscopy grids, where PA pore formation was confirmed by negative stain electron microscopy. When the soluble receptor domain (ANTRX2/CMG2) binds the immobilized PA prepore, the transition to the pore state was observed only after the pH was lowered to early (pH 5.5) or late (pH 5.0) endosomal pH conditions. Once the pore formed, the soluble receptor readily dissociated from the PA pore. Separate binding experiments with immobilized PA pores and the soluble receptor indicate that the receptor has a weakened propensity to bind to the transitioned pore. This immobilized anthrax toxin platform can be used to identify or validate potential antimicrobial lead compounds capable of regulating and/or inhibiting anthrax toxin complex formation or pore transitions.

Feedbacks Between Soil Structure and Microbial Activities in Soil

NASA Astrophysics Data System (ADS)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate formation could alter how we currently treat our predictions of soil biogeochemistry. Current predictions are largely site- or biome-specific; quantitative mechanisms could underpin "rules" that operate at the pore-scale leading to more robust, mechanistic models.

Pore Scale Dynamics of Microemulsion Formation.

PubMed

Unsal, Evren; Broens, Marc; Armstrong, Ryan T

2016-07-19

Experiments in various porous media have shown that multiple parameters come into play when an oleic phase is displaced by an aqueous solution of surfactant. In general, the displacement efficiency is improved when the fluids become quasi-miscible. Understanding the phase behavior oil/water/surfactant systems is important because microemulsion has the ability to generate ultralow interfacial tension (<10(-2) mN m(-1)) that is required for miscibility to occur. Many studies focus on microemulsion formation and the resulting properties under equilibrium conditions. However, the majority of applications where microemulsion is present also involve flow, which has received relatively less attention. It is commonly assumed that the characteristics of an oil/water/surfactant system under flowing conditions are identical to the one under equilibrium conditions. Here, we show that this is not necessarily the case. We studied the equilibrium phase behavior of a model system consisting of n-decane and an aqueous solution of olefin sulfonate surfactant, which has practical applications for enhanced oil recovery. The salt content of the aqueous solution was varied to provide a range of different microemulsion compositions and oil-water interfacial tensions. We then performed microfluidic flow experiments to study the dynamic in situ formation of microemulsion by coinjecting bulk fluids of n-decane and surfactant solution into a T-junction capillary geometry. A solvatochromatic fluorescent dye was used to obtain spatially resolved compositional information. In this way, we visualized the microemulsion formation and the flow of it along with the excess phases. A complex interaction between the flow patterns and the microemulsion properties was observed. The formation of microemulsion influenced the flow regimes, and the flow regimes affected the characteristics of the microemulsion formation. In particular, at low flow rates, slug flow was observed, which had profound consequences on the pore scale mixing behavior and resulting microemulsion properties.

Methane and CO2 Adsorption and Transport in Carbon-based Systems from Experiments and Molecular Simulation

NASA Astrophysics Data System (ADS)

Wilcox, Jennifer; Firouzi, Mahnaz; Rupp, Erik; Haghapanah, Reza; Wang, Beibei

2013-04-01

Carbon capture and sequestration is one strategy that could potentially mitigate gigatons of CO2 emissions per year; however, technical obstacles have thus far hindered wide-scale deployment of this strategy. To design efficient and reliable strategies for either carbon capture or sequestration at the full-scale, one needs to understand the chemical and physical properties of CO2 and its interaction with its local surroundings at the molecular-scale. To investigate the chemical and physical properties of CO2 and its local surroundings at the molecular-scale, surface characterization studies are carried out alongside theoretical model efforts. Experimental investigation of CO2 interactions with organic-based porous materials ranging in complexity from functionalized graphene and activated carbon to various-rank coal and gas shale samples to create a set of realistic models that take into account both surface and pore heterogeneity. Integration of theory and experiments takes place to allow for the relevant physics at the molecular-level to be revealed. Determining adsorption and transport phenomena of CO2 (and mixtures, including H2O, and CH4) within the model pore systems can be used to understand the complex pore matrices of carbon-based sorbents, coal, and the organic components of gas shale that are crucial to determining their carbon capture or sequestration potential. Non-equilibrium molecular dynamics (NEMD) simulations of pure carbon dioxide, methane, helium and their mixtures have been carried out in carbon slit pores to investigate gas slippage and Klinkenberg effects in the organic matrices of coal and gas shale rocks. NEMD techniques are ideally suited for the experimental situation in which an external driving force, such as a chemical potential or pressure gradient, are applied on the system. Simulations have been conducted to determine the effect of pore size and exposure to an external potential on the velocity profile and slip-stick boundary conditions. The simulations indicate that molecule-wall collisions influence the velocity profile, which deviates significantly from the Navier-Stokes hydrodynamic prediction for micro and mesopores. Also, the shape of the velocity profile is found to be independent of the applied pressure gradient in micropores. The results indicate that the velocity profile is uniform for pore sizes less than 2 nm (micropores). As pore sizes increase to 10 nm, parabolic profiles are observed due to the reduced interaction of gas molecules with the pore walls. Interestingly, in small pores unlike in large pores, the gas velocity at the walls is non-zero and predicted gas transport is somewhat enhanced as the gas flow transitions from a parabolic velocity profile to plug-flow. In addition, a 3-D pore network, representative of porous carbon-based materials, has been generated atomistically using the Voronoi tessellation method. Simulations have been carried out to determine the effect of the pore structure and modeled viscosity on permeability and Klinkenberg parameters. The use of the bulk-phase viscosity for estimating the permeability of CO2 in units of Darcy in a 3-D micropore network is not an appropriate assumption as it significantly underestimates the CO2 permeability given that CO2 is an adsorbing gas with strong pore wall interactions. On the other hand, since the transport properties of CH4 are less influenced by the pore walls compared with CO2, the use of the bulk-phase CH4 viscosity estimates are a reasonable assumption. The application of this work is to advance our understanding of gas transport and to provide insight into mechanisms of gas-surface interactions in the complex natural systems such as gas shale so that we can make accurate capacity estimates in addition to assisting in enhancing natural gas recovery from these systems. These results will potentially have important implications on CO2 adsorption and transport in carbon-based materials and geologic formations and may provide an understanding of the limitations of the use of bulk-phase fluid viscosities to model transport properties for nanoconfined fluids.

An Analytical Solution and Numerical Modeling Study of Gas Hydrate Saturation Effects on Porosity and Permeability of Porous Media

NASA Astrophysics Data System (ADS)

Zerpa, L.; Gao, F.; Wang, S.

2017-12-01

There are two major types of natural gas hydrate distributions in porous media: pore filling and contact cementing. The difference between these two distribution types is related to hydrate nucleation and growth processes. In the pore filling distribution, hydrate nucleates from a gas-dissolved aqueous phase at the grain boundary and grows away from grain contacts and surfaces into the pore space. In the contact cementing distribution, hydrate nucleates and grows at the gas-water interface and at intergranular contacts. Previous attempts to correlate changes on porosity and permeability during hydrate formation/dissociation were based on the length difference between the pore body and pore throat, and only considered contact cementing hydrate distribution. This work consists of a study of mathematical models of permeability and porosity as a function of gas hydrate saturation during formation and dissociation of gas hydrates in porous media. In this work, first we derive the permeability equation for the pore filling hydrate deposition as a function of hydrate saturation. Then, a more comprehensive model considering both types of gas hydrate deposition is developed to represent changes in permeability and porosity during hydrate formation and dissociation. This resulted in a model that combines pore filling and contact cementing deposition types in the same reservoir. Finally, the TOUGH+Hydrate numerical reservoir simulator was modified to include these models to analyze the response of production and saturation during a depressurization process, considering different combinations of pore filling and contact cementing hydrate distributions. The empirical exponent used in the permeability adjustment factor model influences both production profile and saturation results. This empirical factor describes the permeability dependence to changes in porosity caused by solid phase formation in the porous medium. The use of the permeability exponent decreases the permeability of the system for a given hydrate saturation, which affects the hydraulic performance of the system. However, from published experimental work, there is only a rough estimation of this permeability exponent. This factor could be represented with an empirical equation if more laboratory and field data becomes available.

Structure formation control of foam concrete

NASA Astrophysics Data System (ADS)

Steshenko, Aleksei; Kudyakov, Aleksander; Konusheva, Viktoriya; Syrkin, Oleg

2017-01-01

The process of predetermined foam concrete structure formation is considered to be a crucial issue from the point of process control and it is currently understudied thus defining the need for additional research. One of the effective ways of structure formation control in naturally hardening foam concrete is reinforcement with dispersed fibers or introduction of plasticizers. The paper aims at studying the patterns of influence of microreinforcing and plasticizing additives on the structure and performance properties of foam concrete. Preparation of foam concrete mix has been conducted using one-step technology. The structure of modified foam concrete has been studied by means of electron microscopy. The cellular structure of foam concrete samples with the additives is homogeneous; the pores are uniformly distributed over the total volume. It has been revealed that introduction of the Neolas 5.2 plasticizer and microreinforcing fibers in the foam concrete mixture in the amount of 0.4 - 0.1 % by weight of cement leads to reduction of the average pore diameter in the range of 45.3 to 30.2 microns and the standard deviation of the pore average diameter from 23.6 to 9.2 in comparison with the sample without additive. Introduction of modifying additives has stimulated formation of a large number of closed pores. Thus porosity of conditionally closed pores has increased from 16.06 % to 34.48 %, which has lead to increase of frost resistance brand of foam concrete from F15 to F50 and to reduction of its water absorption by weight by 20 %.

Effects of pore-scale dispersion, degree of heterogeneity, sampling size, and source volume on the concentration moments of conservative solutes in heterogeneous formations

Treesearch

Daniele Tonina; Alberto Bellin

2008-01-01

Pore-scale dispersion (PSD), aquifer heterogeneity, sampling volume, and source size influence solute concentrations of conservative tracers transported in heterogeneous porous formations. In this work, we developed a new set of analytical solutions for the concentration ensemble mean, variance, and coefficient of variation (CV), which consider the effects of all these...

Characterization of Bc1-2, Bc1-xL, and Bax Pore Formation and Their Role in Apoptosis Regulation

DTIC Science & Technology

2002-01-01

Bcl-2, Bcl-xL, and Bax Pore Formation and Their Role in Apoptosis Regulation PRINCIPAL INVESTIGATOR: Frank Stenner -Liewen, Ph.D. Sharon Schendel, Ph.D...AUTHOR(S) Frank Stenner -Liewen, Ph.D. Sharon Schendel, Ph.D. John C. Reed, M.D., Ph.D. 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING

The Effect of Dynamic Evaporation Rates on the Mobility of Pharmaceuticals in Unsaturated Environments

NASA Astrophysics Data System (ADS)

Normile, H.; Papelis, C.; Kibbey, T. C. G.

2015-12-01

The focus of this work was on investigating how dynamic rates of evaporation affect the fate and transport of pharmaceutical compounds in unsaturated porous media. The environmental processes of saturation and evaporation control local concentrations of contaminants in pore water of porous media. Specifically, the rate of evaporation can affect the identity and extent of solid formation of a pharmaceutical compound. A range of experiments with different evaporation rates were conducted on sand columns saturated with a solution of ciprofloxacin, a fluoroquinolone antibiotic. Experiments were designed to simulate increased and decreased pore-water concentrations of a compound due to evaporation and resaturation, respectively. Results suggest that varied rates of evaporation cause differences in compound adsorption behavior. This result has significant implications for understanding fate and transport within the unsaturated zone. Preliminary models exploring the impact on contaminant mobility are discussed.

Variation and correlation of hydrologic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, J.S.Y.

1991-06-01

Hydrological properties vary within a given geological formation and even more so among different soil and rock media. The variance of the saturated permeability is shown to be related to the variance of the pore-size distribution index of a given medium by a simple equation. This relationship is deduced by comparison of the data from Yucca Mountain, Nevada (Peters et al., 1984), Las Cruces, New Mexico (Wierenga et al., 1989), and Apache Leap, Arizona (Rasmussen et al., 1990). These and other studies in different soils and rocks also support the Poiseuille-Carmen relationship between the mean value of saturated permeability andmore » the mean value of capillary radius. Correlations of the mean values and variances between permeability and pore-geometry parameters can lead us to better quantification of heterogeneous flow fields and better understanding of the scaling laws of hydrological properties.« less

Fabrication of anodic aluminium oxide templates on curved surfaces.

PubMed

Yin, Aijun; Guico, Rodney S; Xu, Jimmy

2007-01-24

Aluminium anodization provides a simple and inexpensive way to obtain nanoporous templates with uniform and controllable pore diameters and periods over a wide range. Moreover, one of the interesting possibilities afforded by the anodization process is that the anodization can take place on arbitrary surfaces, such as curved surfaces, which has not yet been well studied or applied in nanofabrication. In this paper, we characterize the anodization of Al films on silicon substrates with a curved top surface. The structures of the resultant anodic aluminium oxide (AAO) films are examined by scanning electron microscopy. Unique features including cessation, bending, and branching of pore channels are observed in the curved area. Possible growth mechanisms are proposed, which can also contribute to the understanding of the self-organization mechanism in the formation of porous AAO membranes. The new structures may open new opportunities in optical, electronic and electrochemical applications.

Omega-3 docosahexaenoic acid induces pyroptosis cell death in triple-negative breast cancer cells.

PubMed

Pizato, Nathalia; Luzete, Beatriz Christina; Kiffer, Larissa Fernanda Melo Vasconcelos; Corrêa, Luís Henrique; de Oliveira Santos, Igor; Assumpção, José Antônio Fagundes; Ito, Marina Kiyomi; Magalhães, Kelly Grace

2018-01-31

The implication of inflammation in pathophysiology of several type of cancers has been under intense investigation. Omega-3 fatty acids can modulate inflammation and present anticancer effects, promoting cancer cell death. Pyroptosis is an inflammation related cell death and so far, the function of docosahexaenoic acid (DHA) in pyroptosis cell death has not been described. This study investigated the role of DHA in triggering pyroptosis activation in breast cancer cells. MDA-MB-231 breast cancer cells were supplemented with DHA and inflammation cell death was analyzed. DHA-treated breast cancer cells triggered increased caspase-1and gasdermin D activation, enhanced IL-1β secretion, translocated HMGB1 towards the cytoplasm, and membrane pore formation when compared to untreated cells, suggesting DHA induces pyroptosis programmed cell death in breast cancer cells. Moreover, caspase-1 inhibitor (YVAD) could protect breast cancer cells from DHA-induced pyroptotic cell death. In addition, membrane pore formation showed to be a lysosomal damage and ROS formation-depended event in breast cancer cells. DHA triggered pyroptosis cell death in MDA-MB-231by activating several pyroptosis markers in these cells. This is the first study that shows the effect of DHA triggering pyroptosis programmed cell death in breast cancer cells and it could improve the understanding of the omega-3 supplementation during breast cancer treatment.

Development of a New Analog Test System Capable of Modeling Tectonic Deformation Incorporating the Effects of Pore Fluid Pressure

NASA Astrophysics Data System (ADS)

Zhang, M.; Nakajima, H.; Takeda, M.; Aung, T. T.

2005-12-01

Understanding and predicting the tectonic deformation within geologic strata has been a very important research subject in many fields such as structural geology and petroleum geology. In recent years, such research has also become a fundamental necessity for the assessment of active fault migration, site selection for geological disposal of radioactive nuclear waste and exploration for methane hydrate. Although analog modeling techniques have played an important role in the elucidation of the tectonic deformation mechanisms, traditional approaches have typically used dry materials and ignored the effects of pore fluid pressure. In order for analog models to properly depict the tectonic deformation of the targeted, large-prototype system within a small laboratory-scale configuration, physical properties of the models, including geometry, force, and time, must be correctly scaled. Model materials representing brittle rock behavior require an internal friction identical to the prototype rock and virtually zero cohesion. Granular materials such as sand, glass beads, or steel beads of dry condition have been preferably used for this reason in addition to their availability and ease of handling. Modeling protocols for dry granular materials have been well established but such model tests cannot account for the pore fluid effects. Although the concept of effective stress has long been recognized and the role of pore-fluid pressure in tectonic deformation processes is evident, there have been few analog model studies that consider the effects of pore fluid movement. Some new applications require a thorough understanding of the coupled deformation and fluid flow processes within the strata. Taking the field of waste management as an example, deep geological disposal of radioactive waste has been thought to be an appropriate methodology for the safe isolation of the wastes from the human environment until the toxicity of the wastes decays to non-hazardous levels. For the deep geological disposal concept, besides containing the wastes with engineering methods such as the glassification of the radioactive wastes, the geological formation itself is expected to serve as a natural barrier that retards migration of radionuclides. To evaluate the long-term safety of deep geological disposal, a better understanding of the fate and transport of radionuclides in a geologically heterogeneous environment is necessary. To meet such requirements, a new analog test sandbox model system was developed. This model system allows the pore fluid flows to be controlled during the model tests and permits the study of flow and transport phenomena in the deformed heterogeneous model. One- or two-dimensional fluid flow is controlled using a side-wall piston. Deformation processes can be observed through a transparent front panel, and pore fluid movement can be also visualized using a color tracer. In this study, the scaling requirements for analog modeling, including pore water pressure, are discussed based on the theory of dimensional analysis, supplemented by data from a series of laboratory shear tests, and a detailed description of the model system. Preliminary experimental results are presented.

The mechanism of a nuclear pore assembly: a molecular biophysics view.

PubMed

Kuvichkin, Vasily V

2011-06-01

The basic problem of nuclear pore assembly is the big perinuclear space that must be overcome for nuclear membrane fusion and pore creation. Our investigations of ternary complexes: DNA-PC liposomes-Mg²⁺, and modern conceptions of nuclear pore structure allowed us to introduce a new mechanism of nuclear pore assembly. DNA-induced fusion of liposomes (membrane vesicles) with a single-lipid bilayer or two closely located nuclear membranes is considered. After such fusion on the lipid bilayer surface, traces of a complex of ssDNA with lipids were revealed. At fusion of two identical small liposomes (membrane vesicles) < 100 nm in diameter, a "big" liposome (vesicle) with ssDNA on the vesicle equator is formed. ssDNA occurrence on liposome surface gives a biphasic character to the fusion kinetics. The "big" membrane vesicle surrounded by ssDNA is the base of nuclear pore assembly. Its contact with the nuclear envelope leads to fast fusion of half of the vesicles with one nuclear membrane; then ensues a fusion delay when ssDNA reaches the membrane. The next step is to turn inside out the second vesicle half and its fusion to other nuclear membrane. A hole is formed between the two membranes, and nucleoporins begin pore complex assembly around the ssDNA. The surface tension of vesicles and nuclear membranes along with the kinetic energy of a liquid inside a vesicle play the main roles in this process. Special cases of nuclear pore formation are considered: pore formation on both nuclear envelope sides, the difference of pores formed in various cell-cycle phases and linear nuclear pore clusters.

Fractal Characteristics of Pores in Taiyuan Formation Shale from Hedong Coal Field, China

NASA Astrophysics Data System (ADS)

Li, Kunjie; Zeng, Fangui; Cai, Jianchao; Sheng, Guanglong; Xia, Peng; Zhang, Kun

For the purpose of investigating the fractal characteristics of pores in Taiyuan formation shale, a series of qualitative and quantitative experiments were conducted on 17 shale samples from well HD-1 in Hedong coal field of North China. The results of geochemical experiments show that Total organic carbon (TOC) varies from 0.67% to 5.32% and the organic matters are in the high mature or over mature stage. The shale samples consist mainly of clay minerals and quartz with minor pyrite and carbonates. The FE-SEM images indicate that three types of pores, organic-related pores, inorganic-related pores and micro-fractures related pores, are developed well, and a certain number of intragranular pores are found inside quartz and carbonates formed by acid liquid corrosion. The pore size distributions (PSDs) broadly range from several to hundreds nanometers, but most pores are smaller than 10nm. As the result of different adsorption features at relative pressure (0-0.5) and (0.5-1) on the N2 adsorption isotherm, two fractal dimensions D1 and D2 were obtained with the Frenkel-Halsey-Hill (FHH) model. D1 and D2 vary from 2.4227 to 2.6219 and from 2.6049 to 2.7877, respectively. Both TOC and brittle minerals have positive effect on D1 and D2, whereas clay minerals, have a negative influence on them. The fractal dimensions are also influenced by the pore structure parameters, such as the specific surface area, BJH pore volume, etc. Shale samples with higher D1 could provide more adsorption sites leading to a greater methane adsorption capacity, whereas shale samples with higher D2 have little influence on methane adsorption capacity.

The influence of pore textures on the permeability of volcanic rocks

NASA Astrophysics Data System (ADS)

Mueller, S.; Spieler, O.; Scheu, B.; Dingwell, D.

2006-12-01

The permeability of a porous medium is strongly dependent on its porosity, as a higher proportion of pore volume is generally expected to lead to a greater probability of pore interconnectedness and the formation of a fluid-flow providing pathway. However, the relationship between permeability and porosity is not a unique one, as many other textural parameters may play an important role and substantially affect gas flow properties. Among these parameters are (a) the connection geometry (i.e. intergranular pore spaces in clastic sediments vs. bubble interconnections), (b) the pore sizes, (c) pore shape and (d) pore size distribution. The gas permeability of volcanic rocks may influence various eruptive processes. The transition from a quiescent degassing dome to rock failure (fragmentation) may, for example, be controlled by the rock's permeability, in as much as it affects the speed by which a gas overpressure in vesicles is reduced in response to decompression. It is therefore essential to understand and quantify influences of different pore textures on the degassing properties of volcanic rocks, as well as investigate the effects of permeability on eruptive processes. Using a modified shock-tube-based fragmentation apparatus, we have measured unsteady-state permeability at a high initial pressure differential. Following sudden decompression above the rock cylinder, pressurized gas flows through the sample in a steel autoclave. A transient 1D filtration code has been developed to calculate permeability using the experimental pressure decay curve within a defined volume below the sample. An external furnace around the autoclave and the use of compressed salt as sealant allows also measurements at high temperatures up to 800 °C. Over 130 permeability measurements have been performed on samples of different volcanic settings, covering a wide range of porosity. The results show a general positive relationship between porosity and permeability with a high data scatter. Analysis of the samples eruptive origin as well as the pore sizes, shapes and size distribution allow an estimation of the contribution of various textural effects to the overall permeability.

Annealing effect on thermodynamic and physical properties of mesoporous silicon: A simulation and nitrogen sorption study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Pushpendra, E-mail: pkumar-iitd@yahoo.com; Huber, Patrick, E-mail: patrick.huber@tuhh.de

Discovery of porous silicon formation in silicon substrate in 1956 while electro-polishing crystalline Si in hydrofluoric acid (HF), has triggered large scale investigations of porous silicon formation and their changes in physical and chemical properties with thermal and chemical treatment. A nitrogen sorption study is used to investigate the effect of thermal annealing on electrochemically etched mesoporous silicon (PS). The PS was thermally annealed from 200°C to 800°C for 1 hr in the presence of air. It was shown that the pore diameter and porosity of PS vary with annealing temperature. The experimentally obtained adsorption / desorption isotherms show hysteresis typicalmore » for capillary condensation in porous materials. A simulation study based on Saam and Cole model was performed and compared with experimentally observed sorption isotherms to study the physics behind of hysteresis formation. We discuss the shape of the hysteresis loops in the framework of the morphology of the layers. The different behavior of adsorption and desorption of nitrogen in PS with pore diameter was discussed in terms of concave menisci formation inside the pore space, which was shown to related with the induced pressure in varying the pore diameter from 7.2 nm to 3.4 nm.« less

Hierarchical Pore Morphology of Cretaceous Shale: A Small-Angle Neutron Scattering and Ultrasmall-Angle Neutron Scattering Study

DOE PAGES

Bahadur, J.; Melnichenko, Y. B.; Mastalerz, Maria; ...

2014-09-25

Shale reservoirs are becoming an increasingly important source of oil and natural gas supply and a potential candidate for CO 2 sequestration. Understanding the pore morphology in shale may provide clues to making gas extraction more efficient and cost-effective. The porosity of Cretaceous shale samples from Alberta, Canada, collected from different depths with varying mineralogical compositions, has been investigated by small- and ultrasmall-angle neutron scattering. Moreover these samples come from the Second White Specks and Belle Fourche formations, and their organic matter content ranges between 2 and 3%. The scattering length density of the shale specimens has been estimated usingmore » the chemical composition of the different mineral components. Scattering experiments reveal the presence of fractal and non-fractal pores. It has been shown that the porosity and specific surface area are dominated by the contribution from meso- and micropores. The fraction of closed porosity has been calculated by comparing the porosities estimated by He pycnometry and scattering techniques. There is no correlation between total porosity and mineral components, a strong correlation has been observed between closed porosity and major mineral components in the studied specimens.« less

Role of Pore-Forming Toxins in Bacterial Infectious Diseases

PubMed Central

Los, Ferdinand C. O.; Randis, Tara M.

2013-01-01

SUMMARY Pore-forming toxins (PFTs) are the most common bacterial cytotoxic proteins and are required for virulence in a large number of important pathogens, including Streptococcus pneumoniae, group A and B streptococci, Staphylococcus aureus, Escherichia coli, and Mycobacterium tuberculosis. PFTs generally disrupt host cell membranes, but they can have additional effects independent of pore formation. Substantial effort has been devoted to understanding the molecular mechanisms underlying the functions of certain model PFTs. Likewise, specific host pathways mediating survival and immune responses in the face of toxin-mediated cellular damage have been delineated. However, less is known about the overall functions of PFTs during infection in vivo. This review focuses on common themes in the area of PFT biology, with an emphasis on studies addressing the roles of PFTs in in vivo and ex vivo models of colonization or infection. Common functions of PFTs include disruption of epithelial barrier function and evasion of host immune responses, which contribute to bacterial growth and spreading. The widespread nature of PFTs make this group of toxins an attractive target for the development of new virulence-targeted therapies that may have broad activity against human pathogens. PMID:23699254

An effective medium approach to modelling the pressure-dependent electrical properties of porous rocks

NASA Astrophysics Data System (ADS)

Han, Tongcheng

2018-07-01

Understanding the electrical properties of rocks under varying pressure is important for a variety of geophysical applications. This study proposes an approach to modelling the pressure-dependent electrical properties of porous rocks based on an effective medium model. The so-named Textural model uses the aspect ratios and pressure-dependent volume fractions of the pores and the aspect ratio and electrical conductivity of the matrix grains. The pores were represented by randomly oriented stiff and compliant spheroidal shapes with constant aspect ratios, and their pressure-dependent volume fractions were inverted from the measured variation of total porosity with differential pressure using a dual porosity model. The unknown constant stiff and compliant pore aspect ratios and the aspect ratio and electrical conductivity of the matrix grains were inverted by best fitting the modelled electrical formation factor to the measured data. Application of the approach to three sandstone samples covering a broad porosity range showed that the pressure-dependent electrical properties can be satisfactorily modelled by the proposed approach. The results demonstrate that the dual porosity concept is sufficient to explain the electrical properties of porous rocks under pressure through the effective medium model scheme.

Lattice Boltzmann simulation of immiscible fluid displacement in porous media: Homogeneous versus heterogeneous pore network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Haihu, E-mail: haihu.liu@mail.xjtu.edu.cn; James Weir Fluids Laboratory, Department of Mechanical and Aerospace Engineering, University of Strathclyde, Glasgow G1 1XJ; Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801

Injection of anthropogenic carbon dioxide (CO{sub 2}) into geological formations is a promising approach to reduce greenhouse gas emissions into the atmosphere. Predicting the amount of CO{sub 2} that can be captured and its long-term storage stability in subsurface requires a fundamental understanding of multiphase displacement phenomena at the pore scale. In this paper, the lattice Boltzmann method is employed to simulate the immiscible displacement of a wetting fluid by a non-wetting one in two microfluidic flow cells, one with a homogeneous pore network and the other with a randomly heterogeneous pore network. We have identified three different displacement patterns,more » namely, stable displacement, capillary fingering, and viscous fingering, all of which are strongly dependent upon the capillary number (Ca), viscosity ratio (M), and the media heterogeneity. The non-wetting fluid saturation (S{sub nw}) is found to increase nearly linearly with logCa for each constant M. Increasing M (viscosity ratio of non-wetting fluid to wetting fluid) or decreasing the media heterogeneity can enhance the stability of the displacement process, resulting in an increase in S{sub nw}. In either pore networks, the specific interfacial length is linearly proportional to S{sub nw} during drainage with equal proportionality constant for all cases excluding those revealing considerable viscous fingering. Our numerical results confirm the previous experimental finding that the steady state specific interfacial length exhibits a linear dependence on S{sub nw} for either favorable (M ≥ 1) or unfavorable (M < 1) displacement, and the slope is slightly higher for the unfavorable displacement.« less

Nucleation and growth of chimney pores during electron-beam additive manufacturing

DOE PAGES

Cordero, Zachary C.; Dinwiddie, Ralph B.; Immel, David; ...

2016-12-05

The nucleation and growth of chimney pores during powder-bed, electron-beam additive manufacturing is investigated using in-situ infrared thermography as well as microcomputed tomography of as-printed parts. The pores are found to nucleate at dimples on the part s surface, clearly demonstrating how process parameters can affect surface roughness, which can in turn affect the internal defect structure in an additive manufactured part. Based on the results of this study, several strategies for suppressing the formation of chimney pores are discussed.

Bubble Formation Modeling in IE-911

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fondeur, F.F.

2000-09-27

The author used diffusion modeling to determine the hydrogen and oxygen concentration inside IE-911. The study revealed gas bubble nucleation will not occur in the bulk solution inside the pore or on the pore wall. This finding results from the fast oxygen and hydrogen gas molecular diffusion and a very confined pore space. The net steady state concentration of these species inside the pore proves too low to drive bubble nucleation. This study did not investigate other gas bubble nucleating mechanism such as suspended particles in solution.

Direct numerical simulation of supercritical gas flow in complex nanoporous media: Elucidating the relationship between permeability and pore space geometry

NASA Astrophysics Data System (ADS)

Landry, C. J.; Prodanovic, M.; Eichhubl, P.

2015-12-01

Mudrocks and shales are currently a significant source of natural gas and understanding the basic transport properties of these formations is critical to predicting long-term production, however, the nanoporous nature of mudrocks presents a unique challenge. Mudrock pores are predominantly in the range of 1-100 nm, and within this size range the flow of gas at reservoir conditions will fall within the slip-flow and early transition-flow regime (0.001 < Kn < 1.0). Therefore, flow-rates will significantly deviate from Navier-Stokes predictions. Currently, the study of slip-flows is mostly limited to simple tube and channel geometries, but the geometry of mudrock pores is often sponge-like (organic matter) and/or platy (clays). Here we present a local effective viscosity lattice Boltzmann model (LEV-LBM) constructed for flow simulation in the slip- and early-transition flow regimes, adapted here for complex geometries. At the macroscopic scale the LEV-LBM is parameterized with local effective viscosities at each node to capture the variance of the mean free path of gas molecules in a bounded system. The LEV-LBM is first validated in simple tube geometries, where excellent agreement with linearized Boltzmann solutions is found for Knudsen numbers up to 1.0. The LEV-LBM is then employed to quantify the length effect on the apparent permeability of tubes, which suggests pore network modeling of flow in the slip and early-transition regime will result in overestimation unless the length effect is considered. Furthermore, the LEV-LBM is used to evaluate the predictive value of commonly measured pore geometry characteristics such as porosity, pore size distribution, and specific solid surface area for the calculation of permeability. We show that bundle of tubes models grossly overestimate apparent permeability, as well as underestimate the increase in apparent permeability with decreasing pressure as a result of excluding topology and pore shape from calculations.

Macroporous Semiconductors

PubMed Central

Föll, Helmut; Leisner, Malte; Cojocaru, Ala; Carstensen, Jürgen

2010-01-01

Pores in single crystalline semiconductors come in many forms (e.g., pore sizes from 2 nm to > 10 µm; morphologies from perfect pore crystal to fractal) and exhibit many unique properties directly or as nanocompounds if the pores are filled. The various kinds of pores obtained in semiconductors like Ge, Si, III-V, and II-VI compound semiconductors are systematically reviewed, emphasizing macropores. Essentials of pore formation mechanisms will be discussed, focusing on differences and some open questions but in particular on common properties. Possible applications of porous semiconductors, including for example high explosives, high efficiency electrodes for Li ion batteries, drug delivery systems, solar cells, thermoelectric elements and many novel electronic, optical or sensor devices, will be introduced and discussed.

Deposition Nucleation or Pore Condensation and Freezing?

NASA Astrophysics Data System (ADS)

David, Robert O.; Mahrt, Fabian; Marcolli, Claudia; Fahrni, Jonas; Brühwiler, Dominik; Lohmann, Ulrike; Kanji, Zamin A.

2017-04-01

Ice nucleation plays an important role in moderating Earth's climate and precipitation formation. Over the last century of research, several mechanisms for the nucleation of ice have been identified. Of the known mechanisms for ice nucleation, only deposition nucleation occurs below water saturation. Deposition nucleation is defined as the formation of ice from supersaturated water vapor on an insoluble particle without the prior formation of liquid. However, recent work has found that the efficiency of so-called deposition nucleation shows a dependence on the homogeneous freezing temperature of water even though no liquid phase is presumed to be present. Additionally, the ability of certain particles to nucleate ice more efficiently after being pre-cooled (pre-activation) raises questions on the true mechanism when ice nucleation occurs below water saturation. In an attempt to explain the dependence of the efficiency of so-called deposition nucleation on the onset of homogeneous freezing of liquid water, pore condensation and freezing has been proposed. Pore condensation and freezing suggests that the liquid phase can exist under sub-saturated conditions with respect to liquid in narrow confinements or pores due to the inverse Kelvin effect. Once the liquid-phase condenses, it is capable of nucleating ice either homogeneously or heterogeneously. The role of pore condensation and freezing is assessed in the Zurich Ice Nucleation Chamber, a continuous flow diffusion chamber, using spherical nonporous and mesoporous silica particles. The mesoporous silica particles have a well-defined particle size range of 400 to 600nm with discreet pore sizes of 2.5, 2.8, 3.5 and 3.8nm. Experiments conducted between 218K and 238K show that so-called deposition nucleation only occurs below the homogenous freezing temperature of water and is highly dependent on the presence of pores and their size. The results strongly support pore condensation and freezing, questioning the role of deposition nucleation as an ice nucleation pathway.

Recent Progress and Required Developments in Atmospheric Corrosion of Galvanised Steel and Zinc

PubMed Central

Cole, Ivan S.

2017-01-01

This paper reviews the progress in atmospheric corrosion of zinc since 2009. It firstly summarises the state of the art in 2009, then outlines progress since 2009, and then looks at the significance of this progress and the areas the need more research. Within this framework, it looks at climate effects, oxide formation, oxide properties, pitting, laboratory duplication of atmospheric corrosion, and modelling. The major findings are that there have been major advances in the fields understanding of the structure of corrosion patina, in particular their layered structure and the presence of compact layers, local corrosion attacks have been found to be a significant process in atmospheric corrosion and experiments under droplets are leading to new understanding of the criticality of drop size in regulating atmospheric corrosion processes. Further research is indicating that zinc oxide within corrosion products may promote the oxygen reduction reaction (ORR) and that, in porous oxides, the ORR would control pore chemistry and may promote oxide densification. There is a strong need for more research to understand more deeply the formation and properties of these layered oxides as well as additional research to refine and quantify our emerging understanding of corrosion under droplets. PMID:29120373

Small-angle neutron scattering study of micropore collapse in amorphous solid water.

PubMed

Mitterdorfer, Christian; Bauer, Marion; Youngs, Tristan G A; Bowron, Daniel T; Hill, Catherine R; Fraser, Helen J; Finney, John L; Loerting, Thomas

2014-08-14

Vapor-deposited amorphous solid water (ASW) is the most abundant solid molecular material in space, where it plays a direct role in both the formation of more complex chemical species and the aggregation of icy materials in the earliest stages of planet formation. Nevertheless, some of its low temperature physics such as the collapse of the micropore network upon heating are still far from being understood. Here we characterize the nature of the micropores and their collapse using neutron scattering of gram-quantities of D2O-ASW of internal surface areas up to 230 ± 10 m(2) g(-1) prepared at 77 K. The model-free interpretation of the small-angle scattering data suggests micropores, which remain stable up to 120-140 K and then experience a sudden collapse. The exact onset temperature to pore collapse depends on the type of flow conditions employed in the preparation of ASW and, thus, the specific surface area of the initial deposit, whereas the onset of crystallization to cubic ice is unaffected by the flow conditions. Analysis of the small-angle neutron scattering signal using the Guinier-Porod model suggests that a sudden transition from three-dimensional cylindrical pores with 15 Å radius of gyration to two-dimensional lamellae is the mechanism underlying the pore collapse. The rather high temperature of about 120-140 K of micropore collapse and the 3D-to-2D type of the transition unraveled in this study have implications for our understanding of the processing and evolution of ices in various astrophysical environments.

Thermal conductivity of hydrate-bearing sediments

USGS Publications Warehouse

Cortes, Douglas D.; Martin, Ana I.; Yun, Tae Sup; Francisca, Franco M.; Santamarina, J. Carlos; Ruppel, Carolyn D.

2009-01-01

A thorough understanding of the thermal conductivity of hydrate-bearing sediments is necessary for evaluating phase transformation processes that would accompany energy production from gas hydrate deposits and for estimating regional heat flow based on the observed depth to the base of the gas hydrate stability zone. The coexistence of multiple phases (gas hydrate, liquid and gas pore fill, and solid sediment grains) and their complex spatial arrangement hinder the a priori prediction of the thermal conductivity of hydrate-bearing sediments. Previous studies have been unable to capture the full parameter space covered by variations in grain size, specific surface, degree of saturation, nature of pore filling material, and effective stress for hydrate-bearing samples. Here we report on systematic measurements of the thermal conductivity of air dry, water- and tetrohydrofuran (THF)-saturated, and THF hydrate–saturated sand and clay samples at vertical effective stress of 0.05 to 1 MPa (corresponding to depths as great as 100 m below seafloor). Results reveal that the bulk thermal conductivity of the samples in every case reflects a complex interplay among particle size, effective stress, porosity, and fluid-versus-hydrate filled pore spaces. The thermal conductivity of THF hydrate–bearing soils increases upon hydrate formation although the thermal conductivities of THF solution and THF hydrate are almost the same. Several mechanisms can contribute to this effect including cryogenic suction during hydrate crystal growth and the ensuing porosity reduction in the surrounding sediment, increased mean effective stress due to hydrate formation under zero lateral strain conditions, and decreased interface thermal impedance as grain-liquid interfaces are transformed into grain-hydrate interfaces.

A detailed study of CO 2-brine capillary trapping mechanisms as applied to geologic carbon storage. Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wildenschild, Dorthe

2017-04-06

The proposed research focuses on improved fundamental understanding of the efficiency of physical trapping mechanisms, and as such will provide the basis for subsequent upscaling efforts. The overarching hypothesis of the proposed research is that capillary pressure plays a significant role in capillary trapping of CO 2, especially during the water imbibition stage of the sequestration process. We posit that the relevant physics of the sequestration process is more complex than is currently captured in relative permeability models, which are often based on so-called trapping models to represent relative permeability hysteresis. Our 4 main questions, guiding the 4 main tasksmore » of the proposed research, are as follows: (1) What is the morphology of capillary trapped CO 2 at the pore scale as a function of temperature, pressure, brine concentration, interfacial tension, and pore-space morphology under injection and subsequent imbibition? (2) Is it possible to describe the capillary trapping process using formation-dependent, but otherwise unique continuum-scale functions in permeability-capillary pressure, interfacial area and saturation space, rather than hysteretic functions in permeability-saturation or capillary pressure-saturation space? (3) How do continuum-scale relationships between kr-Pc-S-Anw developed based on pore-scale observations compare with traditional models incorporating relative permeability hysteresis (such as Land’s and other models,) and with observations at the core (5-10cm) scale? (4) How can trapped CO 2 volume be optimized via engineered injection and sweep strategies, and as a function of formation type (incl. heterogeneity)?« less

Freeze-thaw durability of concrete: Ice formation process in pores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, H.; Liu, X.

1998-09-01

Freeze-thaw durability of concrete is of great importance to hydraulic structures in cold areas. Study of ice formation process in concrete pores is necessary to evaluate the damages in concrete caused by freezing. In this paper, freezing of pore solution in concrete exposed to a freeze-thaw cycle is studied by following the change of concrete electrical conductivity with freezing temperatures. Concretes were subjected to freeze-thaw cycles with temperature varying between {minus}0 C and {minus}20 C. In the freezing process, the changing rate of concrete electrical conductivity obviously decreases at about {minus}10 C, indicating that more pore solution in concrete freezesmore » above {minus}10 C than below {minus}10C. According to Powers` static hydraulic pressure hypothesis, it is thought that frost damage mainly occurs between 0 C and {minus}100 C. To ordinary concrete, frost damages below {minus}10 C are negligible.« less

Multiscale Pores in TBCs for Lower Thermal Conductivity

NASA Astrophysics Data System (ADS)

Zhang, Wei-Wei; Li, Guang-Rong; Zhang, Qiang; Yang, Guan-Jun

2017-08-01

The morphology and pattern (including orientation and aspect ratio) of pores in thermal barrier coatings (TBCs) significantly affect their thermal insulation performance. In this work, finite element analysis was used to comprehensively understand the thermal insulation effect of pores and correlate the effective thermal conductivity with the structure. The results indicated that intersplat pores, and in particular their aspect ratio, dominantly affect the heat transfer in the top coat. The effective thermal conductivity decreased as a function of aspect ratio, since a larger aspect ratio often corresponds to a greater proportion of effective length of the pores. However, in conventional plasma-sprayed TBCs, intersplat pores often fail to maximize thermal insulation due to their distinct lower aspect ratios. Therefore, considering this effect of aspect ratio, a new structure design with multiscale pores is proposed and a corresponding structural model developed to correlate the thermal properties with this pore-rich structure. The predictions of the model are well consistent with experimental data. This study provides comprehensive understanding of the effect of pores on the thermal insulation performance, shedding light on the possibility of structural tailoring to obtain advanced TBCs with lower thermal conductivity.

Amyloid-β annular protofibrils evade fibrillar fate in Alzheimer disease brain.

PubMed

Lasagna-Reeves, Cristian A; Glabe, Charles G; Kayed, Rakez

2011-06-24

Annular protofibrils (APFs) represent a new and distinct class of amyloid structures formed by disease-associated proteins. In vitro, these pore-like structures have been implicated in membrane permeabilization and ion homeostasis via pore formation. Still, evidence for their formation and relevance in vivo is lacking. Herein, we report that APFs are in a distinct pathway from fibril formation in vitro and in vivo. In human Alzheimer disease brain samples, amyloid-β APFs were associated with diffuse plaques, but not compact plaques; moreover, we show the formation of intracellular APFs. Our results together with previous studies suggest that the prevention of amyloid-β annular protofibril formation could be a relevant target for the prevention of amyloid-β toxicity in Alzheimer disease.

Numerical Modeling of Anaerobic Microzones Development in Bulk Oxic Porous Media: An Assessment of Different Microzone Formation Processes

NASA Astrophysics Data System (ADS)

Roy Chowdhury, S.; Zarnetske, J. P.; Briggs, M. A.; Day-Lewis, F. D.; Singha, K.

2017-12-01

Soil and groundwater research indicates that unique biogeochemical "microzones" commonly form within bulk soil masses. The formation of these microzones at the pore-scale has been attributed to a number of causes, including variability of in situ carbon or nutrient sources, intrinsic physical conditions that lead to dual-porosity and mass transfer conditions, or microbial bioclogging of the porous media. Each of these causes, while documented in different porous media systems, potentially can lead to the presence of anaerobic pores residing in a bulk oxic domain. The relative role of these causes operating independently or in conjunction with each other to form microzones is not known. Here, we use a single numerical modeling framework to assess the relative roles of each process in creating anaerobic microzones. Using a two-dimensional pore-network model, coupled with a microbial growth model based on Monod kinetics, simulations were performed to explore the development of these anoxic microzones and their fate under a range of hydrologic, nutrient, and microbial conditions. Initial results parameterized for a stream-groundwater exchange environment (i.e., a hyporheic zone) indicate that external forcing of fluid flux in the domain is a key soil characteristic to anaerobic microzone development as fluid flux governs the nutrient flux. The initial amount of biomass present in the system also plays a major role in the development of the microzones. In terms of dominant in situ causes, the intrinsic physical structure of the local pore space is found to play the key role in development of anaerobic sites by regulating fluxes to reaction sites. Acknowledging and understanding the drivers of these microzones will improve the ability of multiple disciplines to measure and model reactive mass transport in soils and assess if they play a significant role for particular biogeochemical processes and ecosystem functions, such as denitrification and greenhouse gas production.

Size effects of pore density and solute size on water osmosis through nanoporous membrane.

PubMed

Zhao, Kuiwen; Wu, Huiying

2012-11-15

Understanding the behavior of osmotic transport across nanoporous membranes at molecular level is critical to their design and applications, and it is also beneficial to the comprehension of the mechanism of biological transmembrane transport processes. Pore density is an important parameter for nanoporous membranes. To better understand the influence of pore density on osmotic transport, we have performed systematic molecular dynamics simulations on water osmosis across nanoporous membranes with different pore densities (i.e., number of pores per unit area of membrane). The simulation results reveal that significant size effects occur when the pore density is so high that the center-to-center distance between neighboring nanopores is comparable to the solute size. The size effects are independent of the pore diameter and solute concentration. A simple quantitative correlation between pore density, solute size, and osmotic flux has been established. The results are excellently consistent with the theoretical predictions. It is also shown that solute hydration plays an important role in real osmotic processes. Solute hydration strengthens the size effects of pore density on osmotic processes due to the enlarged effective solute size induced by hydration. The influence of pore density, solute size, and solute hydration on water osmosis through nanoporous membranes can be introduced to eliminate the deviations of real osmotic processes from ideal behavior.

Molecular mechanism for lipid flip-flops.

PubMed

Gurtovenko, Andrey A; Vattulainen, Ilpo

2007-12-06

Transmembrane lipid translocation (flip-flop) processes are involved in a variety of properties and functions of cell membranes, such as membrane asymmetry and programmed cell death. Yet, flip-flops are one of the least understood dynamical processes in membranes. In this work, we elucidate the molecular mechanism of pore-mediated transmembrane lipid translocation (flip-flop) acquired from extensive atomistic molecular dynamics simulations. On the basis of 50 successful flip-flop events resolved in atomic detail, we demonstrate that lipid flip-flops may spontaneously occur in protein-free phospholipid membranes under physiological conditions through transient water pores on a time scale of tens of nanoseconds. While the formation of a water pore is induced here by a transmembrane ion density gradient, the particular way by which the pore is formed is irrelevant for the reported flip-flop mechanism: the appearance of a transient pore (defect) in the membrane inevitably leads to diffusive translocation of lipids through the pore, which is driven by thermal fluctuations. Our findings strongly support the idea that the formation of membrane defects in terms of water pores is the rate-limiting step in the process of transmembrane lipid flip-flop, which, on average, requires several hours. The findings are consistent with available experimental and computational data and provide a view to interpret experimental observations. For example, the simulation results provide a molecular-level explanation in terms of pores for the experimentally observed fact that the exposure of lipid membranes to electric field pulses considerably reduces the time required for lipid flip-flops.

Authigenic molybdenum formation in marine sediments: A link to pore water sulfide in the Santa Barbara Basin

USGS Publications Warehouse

Zheng, Yen; Anderson, Robert F.; VanGeen, A.; Kuwabara, J.

2000-01-01

Pore water and sediment Mo concentrations were measured in a suite of multicores collected at four sites along the northeastern flank of the Santa Barbara Basin to examine the connection between authigenic Mo formation and pore water sulfide concentration. Only at the deepest site (580 m), where pore water sulfide concentrations rise to >0.1 ??M right below the sediment water interface, was there active authigenic Mo formation. At shallower sites (550,430, and 340 m), where pore water sulfide concentrations were consistently <0.05 ??M, Mo precipitation was not occuring at the time of sampling. A sulfide concentration of ???0.1 ??M appears to be a threshold for the onset of Mo-Fe-S co-precipitation. A second threshold sulfide concentration of ???100 ??M is required for Mo precipitation without Fe, possibly as Mo-S or as particle-bound Mo. Mass budgets for Mo were constructed by combining pore water and sediment results for Mo with analyses of sediment trap material from Santa Barbara Basin as well as sediment accumulation rates derived from 210Pb. The calculations show that most of the authigenic Mo in the sediment at the deepest site is supplied by diffusion from overlying bottom waters. There is, however, a non-lithogenic particulate Mo associated with sinking particles that contributes ???15% to the total authigenic Mo accumulation. Analysis of sediment trap samples and supernant brine solutions indicates the presence of non-lithogenic particulate Mo, a large fraction of which is easily remobilized and, perhaps, associated with Mn-oxides. Our observations show that even with the very high flux of organic carbon reaching the sediment of Santa Barbara Basin, active formation of sedimentary authigenic Mo requires a bottom water oxygen concentration below 3 ??M. However, small but measurable rates of authigenic Mo accumulation were observed at sites where bottom water oxygen ranged between 5 and 23 ??M, indicating that the formation of authigenic Mo occured in the recent past, but not at the time of sampling. Copyright ?? 2000 Elsevier Science Ltd.

Laser powder-bed fusion additive manufacturing: Physics of complex melt flow and formation mechanisms of pores, spatter, and denudation zones

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khairallah, Saad A.; Anderson, Andrew T.; Rubenchik, Alexander

Our study demonstrates the significant effect of the recoil pressure and Marangoni convection in laser powder bed fusion (L-PBF) of 316L stainless steel. A three-dimensional high fidelity powder-scale model reveals how the strong dynamical melt flow generates pore defects, material spattering (sparking), and denudation zones. The melt track is divided into three sections: a topological depression, a transition and a tail region, each being the location of specific physical effects. The inclusion of laser ray-tracing energy deposition in the powder-scale model improves over traditional volumetric energy deposition. It enables partial particle melting, which impacts pore defects in the denudation zone.more » Different pore formation mechanisms are observed at the edge of a scan track, at the melt pool bottom (during collapse of the pool depression), and at the end of the melt track (during laser power ramp down). Finally, we discuss remedies to these undesirable pores are discussed. The results are validated against the experiments and the sensitivity to laser absorptivity.« less

Laser powder-bed fusion additive manufacturing: Physics of complex melt flow and formation mechanisms of pores, spatter, and denudation zones

DOE PAGES

Khairallah, Saad A.; Anderson, Andrew T.; Rubenchik, Alexander; ...

2016-02-23

Our study demonstrates the significant effect of the recoil pressure and Marangoni convection in laser powder bed fusion (L-PBF) of 316L stainless steel. A three-dimensional high fidelity powder-scale model reveals how the strong dynamical melt flow generates pore defects, material spattering (sparking), and denudation zones. The melt track is divided into three sections: a topological depression, a transition and a tail region, each being the location of specific physical effects. The inclusion of laser ray-tracing energy deposition in the powder-scale model improves over traditional volumetric energy deposition. It enables partial particle melting, which impacts pore defects in the denudation zone.more » Different pore formation mechanisms are observed at the edge of a scan track, at the melt pool bottom (during collapse of the pool depression), and at the end of the melt track (during laser power ramp down). Finally, we discuss remedies to these undesirable pores are discussed. The results are validated against the experiments and the sensitivity to laser absorptivity.« less

Unraveling supported lipid bilayer formation kinetics: osmotic effects.

PubMed

Hain, Nicole; Gallego, Marta; Reviakine, Ilya

2013-02-19

Solid-supported lipid bilayers are used as cell membrane models and form the basis of biomimetic and biosensor platforms. The mechanism of their formation from adsorbed liposomes is not well-understood. Using membrane-permeable solute glycerol, impermeable solutes sucrose and dextran, and a pore forming peptide melittin, we studied experimentally how osmotic effects affect the kinetics of the adsorbed liposome-to-bilayer transition. We find that its rate is enhanced if adsorbed liposomes are made permeable but is not significantly retarded by impermeable solutes. The results are explained in terms of adsorbed liposome deformation and formation of transmembrane pores.

Fabrication of ultra thin anodic aluminium oxide membranes by low anodization voltages

NASA Astrophysics Data System (ADS)

Pastore, I.; Poplausks, R.; Apsite, I.; Pastare, I.; Lombardi, F.; Erts, D.

2011-06-01

Formation of ultrathin anodised aluminium oxide (AAO) membranes with high aspect ratio by Al anodization in sulphuric and oxalic acids at low potentials was investigated. Low anodization potentials ensure slow electrochemical reaction speeds and formation of AAO membranes with pore diameter and thickness below 20 nm and 70 nm respectively. Minimum time necessary for formation of continuous AAO membranes was determined. AAO membrane pore surface was covered with polymer Paraloid B72TM to transport it to the selected substrate. The fabricated ultra thin AAO membranes could be used to fabricate nanodot arrays on different surfaces.

Membrane pore formation in atomistic and coarse-grained simulations.

PubMed

Kirsch, Sonja A; Böckmann, Rainer A

2016-10-01

Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. Copyright © 2015 Elsevier B.V. All rights reserved.

Pore growth in U-Mo/Al dispersion fuel

NASA Astrophysics Data System (ADS)

Kim, Yeon Soo; Jeong, G. Y.; Sohn, D.-S.; Jamison, L. M.

2016-09-01

U-Mo/Al dispersion fuel is currently under development in the DOE's Material Management and Minimization program to convert HEU-fueled research reactors to LEU-fueled reactors. In some demanding conditions in high-power and high-performance reactors, large pores form in the interaction layers between the U-Mo fuel particles and the Al matrix, which pose a potential to cause fuel failure. In this study, comprehension of the formation and growth of these pores was explored. As a product, a model to predict pore growth and porosity increase was developed. The model includes three major topics: fission gas release from the U-Mo and the IL to the pores, stress evolution in the fuel meat, and the effect of amorphous IL growth. Well-characterized in-pile data from reduced-size plates were used to fit the model parameters. A data set from full-sized plates, independent and distinctively different from those used to fit the model parameters, was used to examine the accuracy of the model. The model showed fair agreement with the measured data. The model suggested that the growth of the IL has a critical effect on pore growth, as both its material properties and energetics are favorable to pore formation. Therefore, one area of the current effort, focused on suppressing IL growth, appears to be on the right track to improve the performance of this fuel.

Measuring temporal variability in pore-fluid chemistry to assess gas hydrate stability: development of a continuous pore-fluid array.

PubMed

Lapham, Laura L; Chanton, Jeffrey P; Martens, Christopher S; Higley, Paul D; Jannasch, Hans W; Woolsey, J Robert

2008-10-01

A specialized pore-fluid array (PFA) sampler was designed to collect and store pore fluids to monitor temporal changes of ions and gases in gas hydrate bearing sediments. We tested the hypothesis that pore-fluid chemistry records hydrate formation or decomposition events and reflects local seismic activity. The PFA is a seafloor probe that consists of an interchangeable instrument package that houses OsmoSamplers, long-term pore-fluid samplers, a specialized low-dead volume fluid coupler, and eight sample ports along a 10 m sediment probe shaft. The PFA was deployed at Mississippi Canyon 118, a Gulf of Mexico hydrate site. A 170 day record was acquired from the overlying water and 1.3 m below seafloor (mbsf). Fluids were measured for dissolved chloride, sulfate, and methane concentrations and dissolved inorganic carbon and methane stable carbon and deuterium isotope ratios. Chloride and sulfate did not change significantly over time, suggesting the absence of gas hydrate formation or decomposition events. Over the temporal record, methane concentrations averaged 4 mM at 1.3 mbsf, and methane was thermogenic in origin (delta13C-CH4 = -32.4 +/- 3.4 per thousand). The timing of an anomalous 14 mM methane spike coincided with a nearby earthquake (Mw = 5.8), consistent with the hypothesis that pore-fluid chemistry reflects seismic events.

Thermo-mechanical mechanism of laser-assisted alteration and stabilization of micro pore structure in eye-sclera

NASA Astrophysics Data System (ADS)

Baum, Olga; Wachsmann-Hogiu, Sebastian; Sobol, Emil

2018-02-01

Thermo-mechanical effect of laser radiation is a basis of new method of normalization of intraocular pressure in glaucomatous eyes due to laser-assisted pore formation in eye sclera. Laser-induced creation of pores in sclera increases hydraulic permeability. Stability of laser-induced pore system is achieved via gas nano-bubbles arisen in the sclera under laser radiation as a result of temperature dependency of gas solubility. The stabilization of laser-induced gas and pore systems in the tissue is an important mechanism for a long lasting healing of glaucoma observed in clinical trials with one year follow-up.

An investigation of pore cracking in titanium welds

NASA Astrophysics Data System (ADS)

Khaled, Z.

1994-06-01

Two welded Ti-6A1- 4V pressure vessels leaked prematurely in service. The leaks were caused by cracks emanating from weld porosity. The cracks originated during fabrication, with subsequent growth in serv-ice leading to the formation of the leak paths. Pore cracking is thought to be caused by a mechanism that involves both sustained- load and cyclic contributions, with the former being the more prominent. It is shown that the tendency for cracking is influenced by pore position and that pore size is not a deciding factor in that regard. The factors that govern pore cracking are discussed, and the possible role of inter-stitial embrittlement is assessed.

An investigation of pore cracking in titanium welds

NASA Astrophysics Data System (ADS)

Khaled, T.

1994-02-01

Two welded Ti-6A1-4V pressure vessels leaked prematurely in service. The leaks were caused by cracks emanating from weld porosity. The cracks originated during fabrication, with subsequent growth in service leading to the formation of the leak paths. Pore cracking is thought to be caused by a mechanism that involves both sustained-load and cyclic contributions, with the former being the more prominent. It is shown that the tendency for cracking is influenced by pore position and that pore size is not a deciding factor in that regard. The factors that govern pore cracking are discussed, and the possible role of interstitial embrittlement is assessed.

Numerical Modeling of Wastewater Injection in the Denver Basin combined disposal zone in northeast Colorado

NASA Astrophysics Data System (ADS)

Brown, M. R. M.; Ge, S.; Sheehan, A. F.

2016-12-01

Previous studies have correlated seismicity with high rate injection at Underground Injection Control Class II wastewater disposal wells. In this study, we examine the impact of injection in the Denver Basin combined disposal zone that is used by numerous Class II wells. The disposal zone includes the Lyons Formation, a sandstone unit, and the Fountain Formation, an arkose unit just above the basement. Within a 30-km radius of the deep Class II injection well (NGL C4A) closest to the June 1, 2014 M3.2 Greeley earthquake, there are fifteen deep wastewater disposal wells injecting into the disposal zone and two shallow wastewater disposal wells injecting into the Lyons Formation only. One of the shallow wells is located at the same disposal facility as NGL-C4A and started injection in October 2004; the earliest deep injection in this region, at well NGL-C6, began in November 2007. The major episode of seismicity in the area started in November 2013. The timing of injection operation and seismicity occurrence raises several questions. Why did seismicity not begin in the area until nearly 10 years after the start of injection? Nine of the deep wastewater disposal wells began injection after the M3.2 earthquake on June 1, 2014; how does the large increase in the number of injection wells in the area change the pore-pressure in the disposal zone? How does the injection from the various wells interact? Does this increase the chances of induced seismicity? We conduct numerical modeling of 18 injection wells from 2004 to 2016 to explore these questions by better understanding the pore-pressure changes through time, pore-pressure changes in areas of induced earthquakes, and the interactions between injection wells. We include the asymmetry of the basin geometry in the model. We also use this case study to refine how well spacing and injection rate influences the occurrence of induced earthquakes.

Evidence for earthquake triggering of large landslides in coastal Oregon, USA

USGS Publications Warehouse

Schulz, W.H.; Galloway, S.L.; Higgins, J.D.

2012-01-01

Landslides are ubiquitous along the Oregon coast. Many are large, deep slides in sedimentary rock and are dormant or active only during the rainy season. Morphology, observed movement rates, and total movement suggest that many are at least several hundreds of years old. The offshore Cascadia subduction zone produces great earthquakes every 300–500 years that generate tsunami that inundate the coast within minutes. Many slides and slide-prone areas underlie tsunami evacuation and emergency response routes. We evaluated the likelihood of existing and future large rockslides being triggered by pore-water pressure increase or earthquake-induced ground motion using field observations and modeling of three typical slides. Monitoring for 2–9 years indicated that the rockslides reactivate when pore pressures exceed readily identifiable levels. Measurements of total movement and observed movement rates suggest that two of the rockslides are 296–336 years old (the third could not be dated). The most recent great Cascadia earthquake was M 9.0 and occurred during January 1700, while regional climatological conditions have been stable for at least the past 600 years. Hence, the estimated ages of the slides support earthquake ground motion as their triggering mechanism. Limit-equilibrium slope-stability modeling suggests that increased pore-water pressures could not trigger formation of the observed slides, even when accompanied by progressive strength loss. Modeling suggests that ground accelerations comparable to those recorded at geologically similar sites during the M 9.0, 11 March 2011 Japan Trench subduction-zone earthquake would trigger formation of the rockslides. Displacement modeling following the Newmark approach suggests that the rockslides would move only centimeters upon coseismic formation; however, coseismic reactivation of existing rockslides would involve meters of displacement. Our findings provide better understanding of the dynamic coastal bluff environment and hazards from future subduction-zone earthquakes.

Paired measurements of K and Mg isotopes and clay authigenesis in marine sediments

NASA Astrophysics Data System (ADS)

Santiago Ramos, D. P.; Dunlea, A. G.; Higgins, J. A.

2016-12-01

Despite its importance as a major sink for seawater K and Mg, estimates of clay authigenesis in marine sediments remain poorly constrained. Previous work on Mg isotope fractionation during clay formation has revealed a preferential uptake of 26Mg, yielding authigenic clay products with potentially distinct δ26Mg compared to the detrital component. In a similar manner, we aim to quantify the K isotope fractionation during authigenic clay formation and to use paired δ26Mg and δ41K measurements as proxies for the identification and quantification of authigenic clays in shallow and deep marine sedimentary systems. To better understand the behavior of paired Mg and K isotopes during authigenic clay formation in marine sediments, we measured δ26Mg and δ41K values of pore-fluids and sediments from ODP/IODP sites 1052, U1395, U1403 and U1366. We find that while pore-fluid K concentrations at sites 1052, U1395 and U1403 all decline with depth, δ41K profiles differ significantly. These differences might be a result of a complex interplay between clay authigenesis, sedimentation rate, and fractionation of K isotopes during diffusion. Results from 1-D diffusion-advection-reaction models suggest that, in contrast to Mg, diffusion may play an important role in determining the overall K isotope fractionation during clay authigenesis in sites with low-sedimentation rates. Sites with high sedimentation rates may act as close systems where diffusion is negligible. In such cases, K uptake can be modeled as a Rayleigh distillation process and K isotope fractionation can be estimated. Measurements of δ26Mg and δ41K of pore-fluids from site U1395 and bulk sediments from U1366 suggest that paired measurements of these isotopic systems in siliciclastic marine sediments can provide new insights into rates of marine clay authigenesis, a globally important but understudied component of many geochemical cycles.

Biochar from Coffee Residues: A New Promising Sorbent

NASA Astrophysics Data System (ADS)

Fotopoulou, Kalliopi; Karapanagioti, Hrissi; Manariotis, Ioannis

2014-05-01

Biochar is a carbon-rich material produced by heating biomass in an oxygen-limited environment. Biochar is mainly used as an additive to soils to sequester carbon and improve soil fertility as well as a sorbent for environmental remediation processes. Surface properties such as point of zero charge, surface area and pore volume, surface topography, surface functional groups and acid-base behavior are important factors, which affect sorption efficiency. Understanding the surface alteration of biochars increases our understanding of the pollutant-sorbent interaction. The objective of the present study was to characterize the surface properties of biochar produced, and to investigate the effect of thermal treatment conditions on key characteristics that affect sorptive properties. The espresso coffee residue was obtained after the coffee was brewed through espresso machines in coffee shops. The coffee residue was dried and kept in an oven at 50oC until its pyrolysis at 850oC. Pyrolysis with different coffee mass and containers were tested in order to find optimum biochar characteristics. Detailed characterization techniques were carried out to determine the properties of the produced biochar. The surface area, the pore volume, and the average pore size of the biochars were determined using gas (N2) adsorption-desorption cycles using the Brunauer, Emmett, and Teller (BET) equation. Open surface area and micropore volume were determined using the t-plot method and the Harkins & Jura equation. Total organic carbon was also determined because it is an important factor that affects sorption. The results were compared with the corresponding properties of activated carbons. The biochar produced exhibited a wide range of surface area from 21 to 770 m2/g and open surface area from 21 to 65 m2/g. It is obvious that the surface area results from the formation of pores. Actually it was calculated that up to 90% of the porosity is due to the micropores. More specifically the average size of the pores for the high surface area biochars was 32 A. Finally, the organic carbon content of the produced biochar ranged from 45 to 75%.

Gelatin Scaffolds with Controlled Pore Structure and Mechanical Property for Cartilage Tissue Engineering.

PubMed

Chen, Shangwu; Zhang, Qin; Nakamoto, Tomoko; Kawazoe, Naoki; Chen, Guoping

2016-03-01

Engineering of cartilage tissue in vitro using porous scaffolds and chondrocytes provides a promising approach for cartilage repair. However, nonuniform cell distribution and heterogeneous tissue formation together with weak mechanical property of in vitro engineered cartilage limit their clinical application. In this study, gelatin porous scaffolds with homogeneous and open pores were prepared using ice particulates and freeze-drying. The scaffolds were used to culture bovine articular chondrocytes to engineer cartilage tissue in vitro. The pore structure and mechanical property of gelatin scaffolds could be well controlled by using different ratios of ice particulates to gelatin solution and different concentrations of gelatin. Gelatin scaffolds prepared from ≥70% ice particulates enabled homogeneous seeding of bovine articular chondrocytes throughout the scaffolds and formation of homogeneous cartilage extracellular matrix. While soft scaffolds underwent cellular contraction, stiff scaffolds resisted cellular contraction and had significantly higher cell proliferation and synthesis of sulfated glycosaminoglycan. Compared with the gelatin scaffolds prepared without ice particulates, the gelatin scaffolds prepared with ice particulates facilitated formation of homogeneous cartilage tissue with significantly higher compressive modulus. The gelatin scaffolds with highly open pore structure and good mechanical property can be used to improve in vitro tissue-engineered cartilage.

Methods to control ectomycorrhizal colonization: effectiveness of chemical and physical barriers.

PubMed

Teste, François P; Karst, Justine; Jones, Melanie D; Simard, Suzanne W; Durall, Daniel M

2006-12-01

We conducted greenhouse experiments using Douglas-fir (Pseudotsuga menziesii var. glauca) seedlings where chemical methods (fungicides) were used to prevent ectomycorrhizal colonization of single seedlings or physical methods (mesh barriers) were used to prevent formation of mycorrhizal connections between neighboring seedlings. These methods were chosen for their ease of application in the field. We applied the fungicides, Topas (nonspecific) and Senator (ascomycete specific), separately and in combination at different concentrations and application frequencies to seedlings grown in unsterilized forest soils. Additionally, we assessed the ability of hyphae to penetrate mesh barriers of various pore sizes (0.2, 1, 20, and 500 microm) to form mycorrhizas on roots of neighboring seedlings. Ectomycorrhizal colonization was reduced by approximately 55% with the application of Topas at 0.5 g l(-1). Meshes with pore sizes of 0.2 and 1 microm were effective in preventing the formation of mycorrhizas via hyphal growth across the mesh barriers. Hence, meshes in this range of pore sizes could also be used to prevent the formation of common mycorrhizal networks in the field. Depending on the ecological question of interest, Topas or the employment of mesh with pore sizes <1 microm are suitable for restricting mycorrhization in the field.

Integrating SANS and fluid-invasion methods to characterize pore structure of typical American shale oil reservoirs.

PubMed

Zhao, Jianhua; Jin, Zhijun; Hu, Qinhong; Jin, Zhenkui; Barber, Troy J; Zhang, Yuxiang; Bleuel, Markus

2017-11-13

An integration of small-angle neutron scattering (SANS), low-pressure N 2 physisorption (LPNP), and mercury injection capillary pressure (MICP) methods was employed to study the pore structure of four oil shale samples from leading Niobrara, Wolfcamp, Bakken, and Utica Formations in USA. Porosity values obtained from SANS are higher than those from two fluid-invasion methods, due to the ability of neutrons to probe pore spaces inaccessible to N 2 and mercury. However, SANS and LPNP methods exhibit a similar pore-size distribution, and both methods (in measuring total pore volume) show different results of porosity and pore-size distribution obtained from the MICP method (quantifying pore throats). Multi-scale (five pore-diameter intervals) inaccessible porosity to N 2 was determined using SANS and LPNP data. Overall, a large value of inaccessible porosity occurs at pore diameters <10 nm, which we attribute to low connectivity of organic matter-hosted and clay-associated pores in these shales. While each method probes a unique aspect of complex pore structure of shale, the discrepancy between pore structure results from different methods is explained with respect to their difference in measurable ranges of pore diameter, pore space, pore type, sample size and associated pore connectivity, as well as theoretical base and interpretation.

A Framework for Fracture Network Formation in Overpressurised Impermeable Shale: Deformability Versus Diagenesis

NASA Astrophysics Data System (ADS)

Alevizos, Sotiris; Poulet, Thomas; Sari, Mustafa; Lesueur, Martin; Regenauer-Lieb, Klaus; Veveakis, Manolis

2017-03-01

Understanding the formation, geometry and fluid connectivity of nominally impermeable unconventional shale gas and oil reservoirs is crucial for safe unlocking of these vast energy resources. We present a recent discovery of volumetric instabilities of ductile materials that may explain why impermeable formations become permeable. Here, we present the fundamental mechanisms, the critical parameters and the applicability of the novel theory to unconventional reservoirs. We show that for a reservoir under compaction, there exist certain ambient and permeability conditions at which diagenetic (fluid-release) reactions may provoke channelling localisation instabilities. These channels are periodically interspersed in the matrix and represent areas where the excess fluid from the reaction is segregated at high velocity. We find that channelling instabilities are favoured from pore collapse features for extremely low-permeability formations and fluid-release diagenetic reactions, therefore providing a natural, periodic network of efficient fluid pathways in an otherwise impermeable matrix (i.e. fractures). Such an outcome is of extreme importance the for exploration and extraction phases of unconventional reservoirs.

Expression of DNAJB12 or DNAJB14 Causes Coordinate Invasion of the Nucleus by Membranes Associated with a Novel Nuclear Pore Structure

PubMed Central

Goodwin, Edward C.; Motamedi, Nasim; Lipovsky, Alex; Fernández-Busnadiego, Rubén; DiMaio, Daniel

2014-01-01

DNAJB12 and DNAJB14 are transmembrane proteins in the endoplasmic reticulum (ER) that serve as co-chaperones for Hsc70/Hsp70 heat shock proteins. We demonstrate that over-expression of DNAJB12 or DNAJB14 causes the formation of elaborate membranous structures within cell nuclei, which we designate DJANGOS for DNAJ-associated nuclear globular structures. DJANGOS contain DNAJB12, DNAJB14, Hsc70 and markers of the ER lumen and ER and nuclear membranes. Strikingly, they are evenly distributed underneath the nuclear envelope and are of uniform size in any one nucleus. DJANGOS are composed primarily of single-walled membrane tubes and sheets that connect to the nuclear envelope via a unique configuration of membranes, in which the nuclear pore complex appears anchored exclusively to the outer nuclear membrane, allowing both the inner and outer nuclear membranes to flow past the circumference of the nuclear pore complex into the nucleus. DJANGOS break down rapidly during cell division and reform synchronously in the daughter cell nuclei, demonstrating that they are dynamic structures that undergo coordinate formation and dissolution. Genetic studies showed that the chaperone activity of DNAJ/Hsc70 is required for the formation of DJANGOS. Further analysis of these structures will provide insight into nuclear pore formation and function, activities of molecular chaperones, and mechanisms that maintain membrane identity. PMID:24732912

Molecular-level understanding of the carbonisation of polysaccharides.

PubMed

Shuttleworth, Peter S; Budarin, Vitaliy; White, Robin J; Gun'ko, Vladimir M; Luque, Rafael; Clark, James H

2013-07-08

Understanding of both the textural and functionality changes occurring during (mesoporous) polysaccharide carbonisation at the molecular level provides a deeper insight into the whole spectrum of material properties, from chemical activity to pore shape and surface energy, which is crucial for the successful application of carbonaceous materials in adsorption, catalysis and chromatography. Obtained information will help to identify the most appropriate applications of the carbonaceous material generated during torrefaction and different types of pyrolysis processes and therefore will be important for the development of cost- and energy-efficient zero-waste biorefineries. The presented approach is informative and semi-quantitative with the potential to be extended to the formation of other biomass-derived carbonaceous materials. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adsorption of organic ligands on low surface charge clay minerals: the composition in the aqueous interface region.

PubMed

Jelavić, S; Stipp, S L S; Bovet, N

2018-06-27

An understanding of the mechanisms that control the adsorption of organic molecules on clay minerals is of interest in several branches of science and industry. Oil production using low salinity injection fluids can increase yields by as much as 40% over standard injection with seawater or formation water. The mechanism responsible for the low salinity response is still debated, but one hypothesis is a change in pore surface wettability. Organic contamination in soil and drinking water aquifers is a challenge for municipal water suppliers and for agriculture. A better understanding is needed for how mineral species, solution composition and pH affect the desorption of low molecular weight organic ligands from clay minerals and consequently their wettability. We used X-ray photoelectron spectroscopy under cryogenic conditions to investigate the in situ composition in the mineral-solution interface region in a series of experiments with a range of pH and ion concentrations. We demonstrate that both chlorite and kaolinite release organic molecules under conditions relevant for low salinity water flooding. This release increases with a higher solution pH but is only slightly affected by the character of the organic ligand. This is consistent with the observation that low salinity enhanced oil recovery correlates with the presence of chlorite and kaolinite. Our results indicate that the pore surface charge and salinity of formation water and injection fluids are key parameters in determining the low salinity response. In general, our results imply that clay mineral surface charge influences the composition in the interface through an affinity for organic molecules.

Metal oxide porous ceramic membranes with small pore sizes

DOEpatents

Anderson, Marc A.; Xu, Qunyin

1992-01-01

A method is disclosed for the production of metal oxide ceramic membranes of very small pore size. The process is particularly useful in the creation of titanium and other transition metal oxide membranes. The method utilizes a sol-gel process in which the rate of particle formation is controlled by substituting a relatively large alcohol in the metal alkoxide and by limiting the available water. Stable, transparent metal oxide ceramic membranes are created having a narrow distribution of pore size, with the pore diameter being manipulable in the range of 5 to 40 Angstroms.

Metal oxide porous ceramic membranes with small pore sizes

DOEpatents

Anderson, Marc A.; Xu, Qunyin

1991-01-01

A method is disclosed for the production of metal oxide ceramic membranes of very small pore size. The process is particularly useful in the creation of titanium and other transition metal oxide membranes. The method utilizes a sol-gel process in which the rate of particle formation is controlled by substituting a relatively large alcohol in the metal alkoxide and by limiting the available water. Stable, transparent metal oxide ceramic membranes are created having a narrow distribution of pore size, with the pore diameter being manipulable in the range of 5 to 40 Angstroms.

Homologous versus heterologous interactions in the bicomponent staphylococcal γ-haemolysin pore1

PubMed Central

Viero, Gabriella; Cunaccia, Romina; Prévost, Gilles; Werner, Sandra; Monteil, Henri; Keller, Daniel; Joubert, Olivier; Menestrina, Gianfranco; Dalla Serra, Mauro

2005-01-01

Staphylococcal γ-haemolysin HlgA–HlgB forms a β-barrel transmembrane pore in cells and in model membranes. The pore is formed by the oligomerization of two different proteins and a still debated number of monomers. To clarify the topology of the pore, we have mutated single residues – placed near the right and left interfaces of each monomer into cysteine. The mutants were labelled with fluorescent probes, forming a donor–acceptor pair for FRET (fluorescence resonance energy transfer). Heterologous couples (labelled on complementary left and right interfaces) displayed a marked FRET, suggesting extensive HlgA–HlgB or HlgB–HlgA contacts. Heterologous control couples (with both components labelled on the same side) showed absent or low FRET. We found the same result for the homologous couple formed by HlgA [i.e. HlgA–HlgA in the presence of wt (wild-type) HlgB]. The homologous HlgB couple (HlgB–HlgB labelled on left and right interfaces and in the presence of wt HlgA) displayed a transient, declining FRET, which may indicate fast formation of an intermediate that is consumed during pore formation. We conclude that bicomponent pores are assembled by alternating heterologous monomers. PMID:16241903

Laboratory characterization of shale pores

NASA Astrophysics Data System (ADS)

Nur Listiyowati, Lina

2018-02-01

To estimate the potential of shale gas reservoir, one needs to understand the characteristics of pore structures. Characterization of shale gas reservoir microstructure is still a challenge due to ultra-fine grained micro-fabric and micro level heterogeneity of these sedimentary rocks. The sample used in the analysis is a small portion of any reservoir. Thus, each measurement technique has a different result. It raises the question which methods are suitable for characterizing pore shale. The goal of this paper is to summarize some of the microstructure analysis tools of shale rock to get near-real results. The two analyzing pore structure methods are indirect measurement (MIP, He, NMR, LTNA) and direct observation (SEM, TEM, Xray CT). Shale rocks have a high heterogeneity; thus, it needs multiscale quantification techniques to understand their pore structures. To describe the complex pore system of shale, several measurement techniques are needed to characterize the surface area and pore size distribution (LTNA, MIP), shapes, size and distribution of pore (FIB-SEM, TEM, Xray CT), and total porosity (He pycnometer, NMR). The choice of techniques and methods should take into account the purpose of the analysis and also the time and budget.

Influence of acylation sites of influenza B virus hemagglutinin on fusion pore formation and dilation.

PubMed

Ujike, Makoto; Nakajima, Katsuhisa; Nobusawa, Eri

2004-11-01

The cytoplasmic tail (CT) of hemagglutinin (HA) of influenza B virus (BHA) contains at positions 578 and 581 two highly conserved cysteine residues (Cys578 and Cys581) that are modified with palmitic acid (PA) through a thioester linkage. To investigate the role of PA in the fusion activity of BHA, site-specific mutagenesis was performed with influenza B virus B/Kanagawa/73 HA cDNA. All of the HA mutants were expressed on Cos cells by an expression vector. The membrane fusion ability of the HA mutants at a low pH was quantitatively examined with lipid (octadecyl rhodamine B chloride) and aqueous (calcein) dye transfer assays and with the syncytium formation assay. Two deacylation mutants lacking a CT or carrying serine residues substituting for Cys578 and Cys581 promoted full fusion. However, one of the single-acylation-site mutants, C6, in which Cys581 is replaced with serine, promoted hemifusion but not pore formation. In contrast, four other single-acylation-site mutants that have a sole cysteine residue in the CT at position 575, 577, 579, or 581 promoted full fusion. The impaired pore-forming ability of C6 was improved by amino acid substitution between residues 578 and 582 or by deletion of the carboxy-terminal leucine at position 582. Syncytium-forming ability, however, was not adequately restored by these mutations. These facts indicated that the acylation was not significant in membrane fusion by BHA but that pore formation and pore dilation were appreciably affected by the particular amino acid sequence of the CT and the existence of a single acylation site in CT residue 578.

Pharmacological characterization of P2X7 receptors in rat peritoneal cells.

PubMed

Chen, Y-W; Donnelly-Roberts, D L; Namovic, M T; Gintant, G A; Cox, B F; Jarvis, M F; Harris, R R

2005-03-01

P2X(7) receptor activation by ATP results in the release of IL-1beta and IL-18. Prolonged stimulation can lead to pore formation and cell death. In this study we pharmacologically characterized P2X(7) receptors on rat peritoneal cells (RPC) and on 1321N1 cells transfected with rat P2X(7) receptor (1321rP2X(7)-11). RPC were isolated from rats by lavage. P2X(7) agonist induced pore formation in RPC was measured by EtBr uptake. P2X(7)-stimulated pore formation and Ca(++) influx in 1321rP2X(7)-11 cells were measured by a fluorometric imaging plate reader. The effects of pyridoxal phosphate-6-azo phenyl -2'-4'-disulfonic acid (PPADS) on pore formation and Ca(++) influx were examined in both RPC and 1321rP2X(7)-11. P2X(7)-mediated IL-1beta release in RPC and the effect of PPADS were determined. RPC express functional P2X(7) receptors that were activated by ATP analogs with a rank order of potency of 2'- 3'-O-(4-Benzoylbenzoyl) adenosine 5'-triphosphate (BzATP) > ATP > alpha,beta-methylene ATP. Activation of P2X(7) receptors by BzATP was inhibited by PPADS. Similar results were also obtained in 1321rP2X(7)-11 cells. Activation of P2X(7) receptors on RPC resulted in IL-1 beta secretion, which was inhibited by PPADS. RPC express functional P2X(7) receptors that form pores and mediate the release of IL-1beta.

Energetics and Self-Assembly of Amphipathic Peptide Pores in Lipid Membranes

PubMed Central

Zemel, Assaf; Fattal, Deborah R.; Ben-Shaul, Avinoam

2003-01-01

We present a theoretical study of the energetics, equilibrium size, and size distribution of membrane pores composed of electrically charged amphipathic peptides. The peptides are modeled as cylinders (mimicking α-helices) carrying different amounts of charge, with the charge being uniformly distributed over a hydrophilic face, defined by the angle subtended by polar amino acid residues. The free energy of a pore of a given radius, R, and a given number of peptides, s, is expressed as a sum of the peptides' electrostatic charging energy (calculated using Poisson-Boltzmann theory), and the lipid-perturbation energy associated with the formation of a membrane rim (which we model as being semitoroidal) in the gap between neighboring peptides. A simple phenomenological model is used to calculate the membrane perturbation energy. The balance between the opposing forces (namely, the radial free energy derivatives) associated with the electrostatic free energy that favors large R, and the membrane perturbation term that favors small R, dictates the equilibrium properties of the pore. Systematic calculations are reported for circular pores composed of various numbers of peptides, carrying different amounts of charge (1–6 elementary, positive charges) and characterized by different polar angles. We find that the optimal R's, for all (except, possibly, very weakly) charged peptides conform to the “toroidal” pore model, whereby a membrane rim larger than ∼1 nm intervenes between neighboring peptides. Only weakly charged peptides are likely to form “barrel-stave” pores where the peptides essentially touch one another. Treating pore formation as a two-dimensional self-assembly phenomenon, a simple statistical thermodynamic model is formulated and used to calculate pore size distributions. We find that the average pore size and size polydispersity increase with peptide charge and with the amphipathic polar angle. We also argue that the transition of peptides from the adsorbed to the inserted (membrane pore) state is cooperative and thus occurs rather abruptly upon a change in ambient conditions. PMID:12668433

Formation of NO + and its possible roles during the selective catalytic reduction of NOx with NH 3 on Cu-CHA catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Hai-Ying; Kollar, Marton; Wei, Zhehao

The catalytic activities of small-pore Cu-CHA and large-pore Cu-BEA catalysts for the selective catalytic reduction of NO with NH 3 were measured at a very high flow rate. Cu-CHA clearly exhibited much higher intrinsic SCR activity and lower N 2O selectivity. In situ DRIFT spectra were recorded during the adsorption and desorption following NO and (NO+O 2) exposure to fully oxidized samples in a flow cell. The results are in agreement with what we have reported previously based on in situ transmission IR studies of partially reduced samples. Both suggest that different SCR reaction pathways might exist on these twomore » catalysts and that NO + could be an important reaction intermediate for Cu-CHA. Detailed IR studies with various isotopically labeled gas mixtures of (NO+O 2), ( 15NO+O 2), (NO+ 18O 2) and ( 15N 18O+O 2) were conducted to understand the origin of the surface adsorption complexes on Cu-CHA. Formation of NO + was not the consequence of a simple charge transfer reaction, NO+Cu 2+=NO+ + Cu +. Instead, O 2 was found to be essential in changing the oxidation state of N from +2 to +3 although it did not participate in new N$-$O bond formation. In conclusion, the majority of the adsorbed NO + maintained its isotopic origin of the feed gas.« less

Formation of NO + and its possible roles during the selective catalytic reduction of NOx with NH 3 on Cu-CHA catalysts

DOE PAGES

Chen, Hai-Ying; Kollar, Marton; Wei, Zhehao; ...

2017-12-21

The catalytic activities of small-pore Cu-CHA and large-pore Cu-BEA catalysts for the selective catalytic reduction of NO with NH 3 were measured at a very high flow rate. Cu-CHA clearly exhibited much higher intrinsic SCR activity and lower N 2O selectivity. In situ DRIFT spectra were recorded during the adsorption and desorption following NO and (NO+O 2) exposure to fully oxidized samples in a flow cell. The results are in agreement with what we have reported previously based on in situ transmission IR studies of partially reduced samples. Both suggest that different SCR reaction pathways might exist on these twomore » catalysts and that NO + could be an important reaction intermediate for Cu-CHA. Detailed IR studies with various isotopically labeled gas mixtures of (NO+O 2), ( 15NO+O 2), (NO+ 18O 2) and ( 15N 18O+O 2) were conducted to understand the origin of the surface adsorption complexes on Cu-CHA. Formation of NO + was not the consequence of a simple charge transfer reaction, NO+Cu 2+=NO+ + Cu +. Instead, O 2 was found to be essential in changing the oxidation state of N from +2 to +3 although it did not participate in new N$-$O bond formation. In conclusion, the majority of the adsorbed NO + maintained its isotopic origin of the feed gas.« less

Dynamic Pore-Scale Imaging of Reactive Transport in Heterogeneous Carbonates at Reservior Conditions

NASA Astrophysics Data System (ADS)

Menke, Hannah; Bijeljic, Branko; Andrew, Matthew; Blunt, Martin

2014-05-01

Sequestering carbon in deep geologic formations is one way of reducing anthropogenic CO2 emissions. Carbon capture, Utilization, and Storage (CCUS) in carbonate reservoirs has the added benefit of mobilizing more oil for extraction, increasing oil reservoir yield, and generating revenue while also mitigating climate change. The magnitude, speed, and type of dissolution are dependent the intrinsic properties of the rock. Understanding how small changes in the pore structure affect dissolution is paramount for successful predictive modelling both on the pore-scale and for up-scaled reservoir simulations. We propose an experimental method whereby both 'Pink Beam' synchrotron radiation and a Micro-CT lab source are used in dynamic X-ray microtomography to investigate the pore structure changes in carbonate rocks of varying heterogeneity at high temperatures and pressures. Four carbonate rock types were studied, two relatively homogeneous carbonates, Ketton and Mt. Gambier, and two very heterogeneous carbonates, Estalliades and Portland Basebed. Each rock type was imaged under the same reservoir and flow conditions to gain insight into the impact of heterogeneity. A 4-mm carbonate core was injected with CO2-saturated brine at 10 MPa and 50oC for 2 hours. Depending on sample heterogeneity and X-ray source, tomographic images were taken at between 30-second and 20-minute time-resolutions and a 4-micron spatial resolution during injection. Changes in porosity, permeability, and structure were obtained by first binning and filtering the images, then binarizing them with watershed segmentation, and finally extracting a pore/throat network. Furthermore, pore-scale flow modelling was performed directly on the binarized image and used to track velocity distributions as the pore network evolved. Significant differences in dissolution type and magnitude were found for each rock type. The most homogeneous carbonate, Ketton, was seen to have predominately uniform dissolution with minor dissolution rate differences between the pores and pore throats. This was not true for the heterogeneous carbonates, Estalliades and Portland Basebed, which formed wormholes. Pore-scale modelling of flow directly on the voxels showed the differences in the evolution of complex flow fields with changes in dissolution regime. The PDFs of normalized velocity for uniform dissolution showed that the maximum pore velocity within the system decreased as dissolution occurred. This is due to dissolution enlarging pores and pore throats. However, in the wormholing regime, there was a large increase in maximum velocity once the wormhole broke through the length of the core and a preferential flow path was created. Additionally, this study serves as a unique benchmark for pore-scale reactive transport modelling directly on the binarized Micro-CT images. This dynamic pore-scale imaging method offers advantages in helping fully explain the dominant physical and chemical processes at the pore scale so that they may be up-scaled to the reservoir scale for increased accuracy in model prediction.

Damage of Escherichia coli membrane by bactericidal agent polyhexamethylene guanidine hydrochloride: micrographic evidences.

PubMed

Zhou, Z X; Wei, D F; Guan, Y; Zheng, A N; Zhong, J J

2010-03-01

The purpose of this study was to provide micrographic evidences for the damaged membrane structure and intracellular structure change of Escherichia coli strain 8099, induced by polyhexamethylene guanidine hydrochloride (PHMG). The bactericidal effect of PHMG on E. coli was investigated based on beta-galactosidase activity assay, fluorescein-5-isothiocyanate confocal laser scanning microscopy, field emission scanning electron microscopy and transmission electron microscopy. The results revealed that a low dose (13 microg ml(-1)) of PHMG slightly damaged the outer membrane structure of the treated bacteria and increased the permeability of the cytoplasmic membrane, while no significant damage was observed to the morphological structure of the cells. A high dose (23 microg ml(-1)) of PHMG collapsed the outer membrane structure, led to the formation of a local membrane pore across the membrane and badly damaged the internal structure of the cells. Subsequently, intracellular components were leaked followed by cell inactivation. Dose-dependent membrane disruption was the main bactericidal mechanism of PHMG. The formation of the local membrane pores was probable after exposure to a high dose (23 microg ml(-1)) of PHMG. Micrographic evidences were provided about the damaged membrane structure and intracellular structure change of E. coli. The presented information helps understand the bactericidal mechanism of PHMG by membrane damage.

Spatial Persistence of Macropores and Authigenic Clays in a Reservoir Sandstone: Implications for Enhanced Oil Recovery and CO2 Storage

NASA Astrophysics Data System (ADS)

Dewers, T. A.

2015-12-01

Multiphase flow in clay-rich sandstone reservoirs is important to enhanced oil recovery (EOR) and the geologic storage of CO2. Understanding geologic controls on pore structure allows for better identification of lithofacies that can contain, storage, and/or transmit hydrocarbons and CO2, and may result in better designs for EOR-CO2 storage. We examine three-dimensional pore structure and connectivity of sandstone samples from the Farnsworth Unit, Texas, the site of a combined EOR-CO2 storage project by the Southwest Regional Partnership on Carbon Sequestration (SWP). We employ a unique set of methods, including: robotic serial polishing and reflected-light imaging for digital pore-structure reconstruction; electron microscopy; laser scanning confocal microscopy; mercury intrusion-extrusion porosimetry; and relative permeability and capillary pressure measurements using CO2 and synthetic formation fluid. Our results link pore size distributions, topology of porosity and clay-rich phases, and spatial persistence of connected flow paths to multiphase flow behavior. The authors gratefully acknowledge the U.S. Department of Energy's National Energy Technology Laboratory for sponsoring this project through the SWP under Award No. DE-FC26-05NT42591. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Probing structural features of Alzheimer's amyloid-β pores in bilayers using site-specific amino acid substitutions.

PubMed

Capone, Ricardo; Jang, Hyunbum; Kotler, Samuel A; Kagan, Bruce L; Nussinov, Ruth; Lal, Ratnesh

2012-01-24

A current hypothesis for the pathology of Alzheimer's disease (AD) proposes that amyloid-β (Aβ) peptides induce uncontrolled, neurotoxic ion flux across cellular membranes. The mechanism of ion flux is not fully understood because no experiment-based Aβ channel structures at atomic resolution are currently available (only a few polymorphic states have been predicted by computational models). Structural models and experimental evidence lend support to the view that the Aβ channel is an assembly of loosely associated mobile β-sheet subunits. Here, using planar lipid bilayers and molecular dynamics (MD) simulations, we show that amino acid substitutions can be used to infer which residues are essential for channel structure. We created two Aβ(1-42) peptides with point mutations: F19P and F20C. The substitution of Phe19 with Pro inhibited channel conductance. MD simulation suggests a collapsed pore of F19P channels at the lower bilayer leaflet. The kinks at the Pro residues in the pore-lining β-strands induce blockage of the solvated pore by the N-termini of the chains. The cysteine mutant is capable of forming channels, and the conductance behavior of F20C channels is similar to that of the wild type. Overall, the mutational analysis of the channel activity performed in this work tests the proposition that the channels consist of a β-sheet rich organization, with the charged/polar central strand containing the mutation sites lining the pore, and the C-terminal strands facing the hydrophobic lipid tails. A detailed understanding of channel formation and its structure should aid studies of drug design aiming to control unregulated Aβ-dependent ion fluxes.

Probing Structural Features of Alzheimer’s Amyloid-β Pores in Bilayers Using Site-Specific Amino Acid Substitutions

PubMed Central

2012-01-01

A current hypothesis for the pathology of Alzheimer’s disease (AD) proposes that amyloid-β (Aβ) peptides induce uncontrolled, neurotoxic ion flux across cellular membranes. The mechanism of ion flux is not fully understood because no experiment-based Aβ channel structures at atomic resolution are currently available (only a few polymorphic states have been predicted by computational models). Structural models and experimental evidence lend support to the view that the Aβ channel is an assembly of loosely associated mobile β-sheet subunits. Here, using planar lipid bilayers and molecular dynamics (MD) simulations, we show that amino acid substitutions can be used to infer which residues are essential for channel structure. We created two Aβ1–42 peptides with point mutations: F19P and F20C. The substitution of Phe19 with Pro inhibited channel conductance. MD simulation suggests a collapsed pore of F19P channels at the lower bilayer leaflet. The kinks at the Pro residues in the pore-lining β-strands induce blockage of the solvated pore by the N-termini of the chains. The cysteine mutant is capable of forming channels, and the conductance behavior of F20C channels is similar to that of the wild type. Overall, the mutational analysis of the channel activity performed in this work tests the proposition that the channels consist of a β-sheet rich organization, with the charged/polar central strand containing the mutation sites lining the pore, and the C-terminal strands facing the hydrophobic lipid tails. A detailed understanding of channel formation and its structure should aid studies of drug design aiming to control unregulated Aβ-dependent ion fluxes. PMID:22242635

DOE Office of Scientific and Technical Information (OSTI.GOV)

DiStefano, Victoria H.; McFarlane, Joanna; Anovitz, Lawrence M.

This study is an attempt to understand how native organics are distributed with respect to pore size to determine the relationship between hydrocarbon chemistry and pore structure in shales, as the location and accessibility of hydrocarbons is key to understanding and improving the extractability of hydrocarbons in hydraulic fracturing. Selected shale cores from the Eagle Ford and Marcellus formations were subjected to pyrolysis gas chromatography (GC), thermogravimetric analysis, and organic solvent extraction with the resulting effluent analyzed by GC-mass spectrometry (MS). Organics representing the oil and gas fraction (0.1 to 1 wt. %) were observed by GC-MS. For most ofmore » the samples, the amount of native organic extracted directly related to the percentage of clay in the shale. The porosity and pore size distribution (0.95 nm to 1.35 m) in the Eagle Ford and Marcellus shales was measured before and after solvent extraction using small angle neutron scattering (SANS). An unconventional method was used to quantify the background from incoherent scattering as the Porod transformation obscures the Bragg peak from the clay minerals. Furthermore, the change in porosity from SANS is indicative of the extraction or breakdown of higher molecular weight bitumen with high C/H ratios (asphaltenes and resins). This is mostly likely attributed to complete dissolution or migration of asphaltenes and resins. These longer carbon chain lengths, C30-C40, were observed by pyrolysis GC, but either were too heavy to be analyzed in the extracts by GC-MS or were not effectively leached into the organic solvents. Thus, experimental limitations meant that the amount of extractable material could not be directly correlated to the changes in porosity measured by SANS. But, the observable porosity generally increased with solvent extraction. A decrease in porosity after extraction as observed in a shale with high clay content and low maturity was attributed to swelling of pores with solvent uptake or migration of resins and asphaltenes.« less

Extraction of organic compounds from representative shales and the effect on porosity

DOE PAGES

DiStefano, Victoria H.; McFarlane, Joanna; Anovitz, Lawrence M.; ...

2016-09-01

This study is an attempt to understand how native organics are distributed with respect to pore size to determine the relationship between hydrocarbon chemistry and pore structure in shales, as the location and accessibility of hydrocarbons is key to understanding and improving the extractability of hydrocarbons in hydraulic fracturing. Selected shale cores from the Eagle Ford and Marcellus formations were subjected to pyrolysis gas chromatography (GC), thermogravimetric analysis, and organic solvent extraction with the resulting effluent analyzed by GC-mass spectrometry (MS). Organics representing the oil and gas fraction (0.1 to 1 wt. %) were observed by GC-MS. For most ofmore » the samples, the amount of native organic extracted directly related to the percentage of clay in the shale. The porosity and pore size distribution (0.95 nm to 1.35 m) in the Eagle Ford and Marcellus shales was measured before and after solvent extraction using small angle neutron scattering (SANS). An unconventional method was used to quantify the background from incoherent scattering as the Porod transformation obscures the Bragg peak from the clay minerals. Furthermore, the change in porosity from SANS is indicative of the extraction or breakdown of higher molecular weight bitumen with high C/H ratios (asphaltenes and resins). This is mostly likely attributed to complete dissolution or migration of asphaltenes and resins. These longer carbon chain lengths, C30-C40, were observed by pyrolysis GC, but either were too heavy to be analyzed in the extracts by GC-MS or were not effectively leached into the organic solvents. Thus, experimental limitations meant that the amount of extractable material could not be directly correlated to the changes in porosity measured by SANS. But, the observable porosity generally increased with solvent extraction. A decrease in porosity after extraction as observed in a shale with high clay content and low maturity was attributed to swelling of pores with solvent uptake or migration of resins and asphaltenes.« less

Pore Space Partition in Metal-Organic Frameworks.

PubMed

Zhai, Quan-Guo; Bu, Xianhui; Zhao, Xiang; Li, Dong-Sheng; Feng, Pingyun

2017-02-21

Metal-organic framework (MOF) materials have emerged as one of the favorite crystalline porous materials (CPM) because of their compositional and geometric tunability and many possible applications. In efforts to develop better MOFs for gas storage and separation, a number of strategies including creation of open metal sites and implantation of Lewis base sites have been used to tune host-guest interactions. In addition to these chemical factors, the geometric features such as pore size and shape, surface area, and pore volume also play important roles in sorption energetics and uptake capacity. For efficient capture of small gas molecules such as carbon dioxide under ambient conditions, large surface area or high pore volume are often not needed. Instead, maximizing host-guest interactions or the density of binding sites by encaging gas molecules in snug pockets of pore space can be a fruitful approach. To put this concept into practice, the pore space partition (PSP) concept has been proposed and has achieved a great experimental success. In this account, we will highlight many efforts to implement PSP in MOFs and impact of PSP on gas uptake performance. In the synthetic design of PSP, it is helpful to distinguish between factors that contribute to the framework formation and factors that serve the purpose of PSP. Because of the need for complementary structural roles, the synthesis of MOFs with PSP often involves multicomponent systems including mixed ligands, mixed inorganic nodes, or both. It is possible to accomplish both framework formation and PSP with a single type of polyfunctional ligands that use some functional groups (called framework-forming group) for framework formation and the remaining functional groups (called pore-partition group) for PSP. Alternatively, framework formation and PSP can be shouldered by different chemical species. For example, in a mixed-ligand system, one ligand (called framework-forming agent) can play the role of the framework formation while the other type of ligand (called pore-partition agent) can assume the role of PSP. PSP is sensitive to the types of inorganic secondary building units (SBUs). The coexistence of SBUs complementary in charge, connectivity, and so on can promote PSP. The use of heterometallic systems can promote the diversity of SBUs coexistent under a given condition. Heterometallic system with metal ions of different oxidation states also provides the charge tunability of SBUs and the overall framework, providing an additional level of control in self-assembly and ultimately in the materials' properties. Of particular interest is the PSP in MIL-88 type (acs-type topology) structure, which has led to a huge family of CPMs (called pacs CPMs, pacs = partitioned acs) exhibiting low isosteric heat of adsorption and yet superior CO 2 uptake capacity.

Lipid intermediates in membrane fusion: formation, structure, and decay of hemifusion diaphragm.

PubMed

Kozlovsky, Yonathan; Chernomordik, Leonid V; Kozlov, Michael M

2002-11-01

Lipid bilayer fusion is thought to involve formation of a local hemifusion connection, referred to as a fusion stalk. The subsequent fusion stages leading to the opening of a fusion pore remain unknown. The earliest fusion pore could represent a bilayer connection between the membranes and could be formed directly from the stalk. Alternatively, fusion pore can form in a single bilayer, referred to as hemifusion diaphragm (HD), generated by stalk expansion. To analyze the plausibility of stalk expansion, we studied the pathway of hemifusion theoretically, using a recently developed elastic model. We show that the stalk has a tendency to expand into an HD for lipids with sufficiently negative spontaneous splay, (~)J(s)< 0. For different experimentally relevant membrane configurations we find two characteristic values of the spontaneous splay. (~)J*(s) and (~)J**(s), determining HD dimension. The HD is predicted to have a finite equilibrium radius provided that the spontaneous splay is in the range (~)J**(s)< (~)J(s)<(~)J*(s), and to expand infinitely for (~)J(s)<(~)J**(s). In the case of common lipids, which do not fuse spontaneously, an HD forms only under action of an external force pulling the diaphragm rim apart. We calculate the dependence of the HD radius on this force. To address the mechanism of fusion pore formation, we analyze the distribution of the lateral tension emerging in the HD due to the establishment of lateral equilibrium between the deformed and relaxed portions of lipid monolayers. We show that this tension concentrates along the HD rim and reaches high values sufficient to rupture the bilayer and form the fusion pore. Our analysis supports the hypothesis that transition from a hemifusion to a fusion pore involves radial expansion of the stalk.

The scavenger activity of the human P2X7 receptor differs from P2X7 pore function by insensitivity to antagonists, genetic variation and sodium concentration: Relevance to inflammatory brain diseases.

PubMed

Ou, Amber; Gu, Ben J; Wiley, James S

2018-04-01

Activation of P2X7 receptors is widely recognised to initiate proinflammatory responses. However P2X7 also has a dual function as a scavenger receptor which is active in the absence of ATP and plasma proteins and may be important in central nervous system (CNS) diseases. Here, we investigated both P2X7 pore formation and its phagocytic function in fresh human monocytes (as a model of microglia) by measuring ATP-induced ethidium dye uptake and fluorescent bead uptake respectively. This was studied in monocytes expressing various polymorphic variants as well as in the presence of different P2X7 antagonists and ionic media. P2X7-mediated phagocytosis was found to account for about half of Latrunculin (or Cytochalasin D)-sensitive bead engulfment by fresh human monocytes. Monocytes harbouring P2X7 Ala348Thr or Glu496Ala polymorphic variants showed increase or loss of ethidium uptake respectively, but these changes in pore formation did not always correspond to the changes in phagocytosis of YG beads. Unlike pore function, P2X7-mediated phagocytosis was not affected by three potent selective P2X7 antagonists and remained identical in Na + and K + media. Taken together, our results show that P2X7 is a scavenger receptor with important function in the CNS but its phagocytic function has features distinct from its pore function. Both P2X7 pore formation and P2X7-mediated phagocytosis should be considered in the design of new P2X7 antagonists for the treatment of CNS diseases. Copyright © 2018 Elsevier B.V. All rights reserved.

Phonon bottleneck identification in disordered nanoporous materials

NASA Astrophysics Data System (ADS)

Romano, Giuseppe; Grossman, Jeffrey C.

2017-09-01

Nanoporous materials are a promising platform for thermoelectrics in that they offer high thermal conductivity tunability while preserving good electrical properties, a crucial requirement for high-efficiency thermal energy conversion. Understanding the impact of the pore arrangement on thermal transport is pivotal to engineering realistic materials, where pore disorder is unavoidable. Although there has been considerable progress in modeling thermal size effects in nanostructures, it has remained a challenge to screen such materials over a large phase space due to the slow simulation time required for accurate results. We use density functional theory in connection with the Boltzmann transport equation to perform calculations of thermal conductivity in disordered porous materials. By leveraging graph theory and regressive analysis, we identify the set of pores representing the phonon bottleneck and obtain a descriptor for thermal transport, based on the sum of the pore-pore distances between such pores. This approach provide a simple tool to estimate phonon suppression in realistic porous materials for thermoelectric applications and enhance our understanding of heat transport in disordered materials.

Micro-computed tomography pore-scale study of flow in porous media: Effect of voxel resolution

NASA Astrophysics Data System (ADS)

Shah, S. M.; Gray, F.; Crawshaw, J. P.; Boek, E. S.

2016-09-01

A fundamental understanding of flow in porous media at the pore-scale is necessary to be able to upscale average displacement processes from core to reservoir scale. The study of fluid flow in porous media at the pore-scale consists of two key procedures: Imaging - reconstruction of three-dimensional (3D) pore space images; and modelling such as with single and two-phase flow simulations with Lattice-Boltzmann (LB) or Pore-Network (PN) Modelling. Here we analyse pore-scale results to predict petrophysical properties such as porosity, single-phase permeability and multi-phase properties at different length scales. The fundamental issue is to understand the image resolution dependency of transport properties, in order to up-scale the flow physics from pore to core scale. In this work, we use a high resolution micro-computed tomography (micro-CT) scanner to image and reconstruct three dimensional pore-scale images of five sandstones (Bentheimer, Berea, Clashach, Doddington and Stainton) and five complex carbonates (Ketton, Estaillades, Middle Eastern sample 3, Middle Eastern sample 5 and Indiana Limestone 1) at four different voxel resolutions (4.4 μm, 6.2 μm, 8.3 μm and 10.2 μm), scanning the same physical field of view. Implementing three phase segmentation (macro-pore phase, intermediate phase and grain phase) on pore-scale images helps to understand the importance of connected macro-porosity in the fluid flow for the samples studied. We then compute the petrophysical properties for all the samples using PN and LB simulations in order to study the influence of voxel resolution on petrophysical properties. We then introduce a numerical coarsening scheme which is used to coarsen a high voxel resolution image (4.4 μm) to lower resolutions (6.2 μm, 8.3 μm and 10.2 μm) and study the impact of coarsening data on macroscopic and multi-phase properties. Numerical coarsening of high resolution data is found to be superior to using a lower resolution scan because it avoids the problem of partial volume effects and reduces the scaling effect by preserving the pore-space properties influencing the transport properties. This is evidently compared in this study by predicting several pore network properties such as number of pores and throats, average pore and throat radius and coordination number for both scan based analysis and numerical coarsened data.

Pore Diameter Dependence and Segmental Dynamics of Poly-Z-L-lysine and Poly-L-alanine Confined in 1D Nanocylindrical Geometry

NASA Astrophysics Data System (ADS)

Tuncel, Eylul; Suzuki, Yasuhito; Iossifidis, Agathaggelos; Steinhart, Martin; Butt, Hans-Jurgen; Floudas, George; Duran, Hatice

Structure formation, thermodynamic stability, phase and dynamic behaviors of polypeptides are strongly affected by confinement. Since understanding the changes in these behaviors will allow their rational design as functional devices with tunable properties, herein we investigated Poly-Z-L-lysine (PZLL) and Poly-L-alanine (PAla) homopolypeptides confined in nanoporous alumina containing aligned cylindrical nanopores as a function of pore size by differential scanning calorimetry (DSC), Fourier Transform Infrared Spectroscopy, Solid-state NMR, X-ray diffraction, Dielectric spectroscopy(DS). Bulk PZLL exhibits a glass transition temperature (Tg) at about 301K while PZLL nanorods showed slightly lower Tg (294K). The dynamic investigation by DS also revealed a decrease (4K) in Tg between bulk and PZLL nanorods. DS is a very sensitive probe of the local and global secondary structure relaxation through the large dipole to study effect of confinement. The results revealed that the local segmental dynamics, associated with broken hydrogen bonds, and segmental dynamics speed-up on confinement.

Drug release through liposome pores.

PubMed

Dan, Nily

2015-02-01

Electrical, ultrasound and other types of external fields are known to induce the formation of pores in cellular and model membranes. This paper examines drug release through field induced liposome pores using Monte Carlo simulations. We find that drug release rates vary as a function of pore size and spacing, as well as the overall fraction of surface area covered by pores: The rate of release from liposomes is found to increase rapidly with pore surface coverage, approaching that of the fully ruptured liposome at fractional pore areas. For a given pore surface coverage, the pore size affects the release rate in the limit of low coverage, but not when the pores cover a relatively high fraction of the liposome surface area. On the other hand, for a given pore size and surface coverage, the distribution of pores significantly affects the release in the limit of high surface coverage: The rate of release from a liposome covered with a regularly spaced array of pores is, in this limit, higher than the release rate from (most) systems where the pores are distributed randomly on the liposome surface. In contrast, there is little effect of the pore distribution on release when the pore surface coverage is low. The simulation results are in good agreement with the predictions of detailed diffusion models. Copyright © 2014 Elsevier B.V. All rights reserved.

Nup155 regulates nuclear envelope and nuclear pore complex formation in nematodes and vertebrates

PubMed Central

Franz, Cerstin; Askjaer, Peter; Antonin, Wolfram; Iglesias, Carmen López; Haselmann, Uta; Schelder, Malgorzata; de Marco, Ario; Wilm, Matthias; Antony, Claude; Mattaj, Iain W

2005-01-01

Nuclear envelope (NE) formation during cell division in multicellular organisms is a central yet poorly understood biological process. We report that the conserved nucleoporin Nup155 has an essential function in NE formation in Caenorhabditis elegans embryos and in Xenopus laevis egg extracts. In vivo depletion of Nup155 led to failure of nuclear lamina formation and defects in chromosome segregation at anaphase. Nup155 depletion inhibited accumulation of nucleoporins at the nuclear periphery, including those recruited to chromatin early in NE formation. Electron microscopy analysis revealed that Nup155 is also required for the formation of a continuous nuclear membrane in vivo and in vitro. Time-course experiments indicated that Nup155 is recruited to chromatin at the time of NE sealing, suggesting that nuclear pore complex assembly has to progress to a relatively late stage before NE membrane assembly occurs. PMID:16193066

Collagen and collagen-chondroitin sulfate scaffolds with uniaxially aligned pores for the biomimetic, three dimensional culture of trabecular meshwork cells.

PubMed

Osmond, Matthew; Bernier, Sarah M; Pantcheva, Mina B; Krebs, Melissa D

2017-04-01

Glaucoma is a disease in which damage to the optic nerve leads to progressive, irreversible vision loss. The intraocular pressure (IOP) is the only modifiable risk factor for glaucoma and its lowering is considered a useful strategy for preventing or slowing down the progression of glaucomatous neuropathy. Elevated intraocular pressure associated with glaucoma is due to increased aqueous humor outflow resistance, primarily through the trabecular meshwork (TM) of the eye. Current in vitro models of the trabecular meshwork are oversimplified and do not capture the organized and complex three-dimensional nature of this tissue that consists primarily of collagen and glycoasaminoglycans. In this work, collagen and collagen-chondroitin sulfate (CS) scaffolds were fabricated via unidirectional freezing and lyophilization to induce the formation of aligned pores. Scaffolds were characterized by scanning electron microscopy, dynamic mechanical analysis, and a chondroitin sulfate quantification assay. Scaffold characterization confirmed the formation of aligned pores, and also that the CS was leaching out of the scaffolds over time. Primary porcine trabecular meshwork (TM) cells were seeded onto the surface of scaffolds and their gene expression, proliferation, viability, migration into the scaffolds, and morphology were examined. The TM cells were viable and proliferated 2 weeks after seeding. The cells migrated down into the internal scaffold structure and their morphology reflected the topography and alignment of the scaffold structure. This work is a promising step toward the development of a three dimensional in vitro model of the TM that can be used for testing of glaucoma pharmacological agents in future experimentation and to better our understanding of the trabecular meshwork and its complex physiology. Biotechnol. Bioeng. 2017;114: 915-923. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Maximization of permanent trapping of CO{sub 2} and co-contaminants in the highest-porosity formations of the Rock Springs Uplift (Southwest Wyoming): experimentation and multi-scale modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Piri, Mohammad

2014-03-31

Under this project, a multidisciplinary team of researchers at the University of Wyoming combined state-of-the-art experimental studies, numerical pore- and reservoir-scale modeling, and high performance computing to investigate trapping mechanisms relevant to geologic storage of mixed scCO{sub 2} in deep saline aquifers. The research included investigations in three fundamental areas: (i) the experimental determination of two-phase flow relative permeability functions, relative permeability hysteresis, and residual trapping under reservoir conditions for mixed scCO{sub 2}-­brine systems; (ii) improved understanding of permanent trapping mechanisms; (iii) scientifically correct, fine grid numerical simulations of CO{sub 2} storage in deep saline aquifers taking into account themore » underlying rock heterogeneity. The specific activities included: (1) Measurement of reservoir-­conditions drainage and imbibition relative permeabilities, irreducible brine and residual mixed scCO{sub 2} saturations, and relative permeability scanning curves (hysteresis) in rock samples from RSU; (2) Characterization of wettability through measurements of contact angles and interfacial tensions under reservoir conditions; (3) Development of physically-­based dynamic core-­scale pore network model; (4) Development of new, improved high-­performance modules for the UW-­team simulator to provide new capabilities to the existing model to include hysteresis in the relative permeability functions, geomechanical deformation and an equilibrium calculation (Both pore-­ and core-­scale models were rigorously validated against well-­characterized core-­ flooding experiments); and (5) An analysis of long term permanent trapping of mixed scCO{sub 2} through high-­resolution numerical experiments and analytical solutions. The analysis takes into account formation heterogeneity, capillary trapping, and relative permeability hysteresis.« less

Dynamical and phase behavior of a phospholipid membrane altered by an antimicrobial peptide at low concentration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mamontov, Eugene; Tyagi, M.; Qian, Shuo

Here we discuss that the mechanism of action of antimicrobial peptides is traditionally attributed to the formation of pores in the lipid cell membranes of pathogens, which requires a substantial peptide to lipid ratio. However, using incoherent neutron scattering, we show that even at a concentration too low for pore formation, an archetypal antimicrobial peptide, melittin, disrupts the regular phase behavior of the microscopic dynamics in a phospholipid membrane, dimyristoylphosphatidylcholine (DMPC). At the same time, another antimicrobial peptide, alamethicin, does not exert a similar effect on the DMPC microscopic dynamics. The melittin-altered lateral motion of DMPC at physiological temperature nomore » longer resembles the fluid-phase behavior characteristic of functional membranes of the living cells. The disruptive effect demonstrated by melittin even at low concentrations reveals a new mechanism of antimicrobial action relevant in more realistic scenarios, when peptide concentration is not as high as would be required for pore formation, which may facilitate treatment with antimicrobial peptides.« less

Dynamical and phase behavior of a phospholipid membrane altered by an antimicrobial peptide at low concentration

DOE PAGES

Mamontov, Eugene; Tyagi, M.; Qian, Shuo; ...

2016-05-27

Here we discuss that the mechanism of action of antimicrobial peptides is traditionally attributed to the formation of pores in the lipid cell membranes of pathogens, which requires a substantial peptide to lipid ratio. However, using incoherent neutron scattering, we show that even at a concentration too low for pore formation, an archetypal antimicrobial peptide, melittin, disrupts the regular phase behavior of the microscopic dynamics in a phospholipid membrane, dimyristoylphosphatidylcholine (DMPC). At the same time, another antimicrobial peptide, alamethicin, does not exert a similar effect on the DMPC microscopic dynamics. The melittin-altered lateral motion of DMPC at physiological temperature nomore » longer resembles the fluid-phase behavior characteristic of functional membranes of the living cells. The disruptive effect demonstrated by melittin even at low concentrations reveals a new mechanism of antimicrobial action relevant in more realistic scenarios, when peptide concentration is not as high as would be required for pore formation, which may facilitate treatment with antimicrobial peptides.« less

Gasdermin: A new player to the inflammasome game.

PubMed

Ramos-Junior, Erivan S; Morandini, Ana Carolina

2017-12-01

Pyroptosis is a lytic type of programmed cell death that was traditionally associated with the involvement of inflammatory caspases, such as caspase-1. These inflammatory caspases are activated within multi-protein complexes called inflammasomes that are assembled in response to invading pathogens and/or danger signals. Pyroptotic cell death was suggested to evolve via the formation of pores in the plasma membrane, but the exact mechanism underlying the formation of these pores remained unclear. Recently, gasdermin D, a member of the gasdermin protein family was identified as a caspase substrate and essential effector of pyroptosis, being identified as the protagonist of membrane pore formation. Gasdermins have emerged as a family of new class of cell death inducers, but many questions remain unanswered. Here, we present an overview of recent work being done in the area of programmed cell death and the latest evidence regarding the role and participation of gasdermin D as an effector of pyroptosis. Copyright © 2017 Chang Gung University. Published by Elsevier B.V. All rights reserved.

Provenance study through analysis of microstructural characteristics using an optical microscope and scanning electron microscopy for Goryeo celadon excavated from the seabed.

PubMed

Min-su, Han

2013-08-01

This paper aims at identifying the provenance of Goryeo celadons by understanding its microstructural characteristics, such as particles, blisters, forms and amount of pores, and the presence of crystal formation, bodies, and glazes and its boundary, using an optical microscope and scanning electron microscopy (SEM). The analysis of the reproduced samples shows that the glazed layer of the sherd fired at higher temperatures has lower viscosity and therefore it encourages the blisters to be combined together and the layer to become more transparent. In addition, the result showed that the vitrification and melting process of clay minerals such as feldspars and quartzs on the bodies was accelerated for those samples. To factor such characteristics of the microstructure and apply it to the sherds, the samples could be divided into six categories based on status, such as small particles with many small pores or mainly large and small circular pores in the bodies, only a limited number of varied sized blisters in the glazes, and a few blisters and needle-shaped crystals on the boundary surface. In conclusion, the analysis of the microstructural characteristics using an optical microscope and SEM have proven to be useful as a categorizing reference factor in a provenance study on Goryeo celadons.

Structure modification of natural zeolite for waste removal application

NASA Astrophysics Data System (ADS)

Widayatno, W. B.

2018-03-01

Tremendous industrialization in the last century has led to the generation of huge amount of waste. One of the recent hot research topics is utilizing any advance materials and methods for waste removal. Natural zeolite as an inexpensive porous material with a high abundance holds a key for efficient waste removal owing to its high surface area. However, the microporous structure of natural zeolite hinders the adsorption of waste with a bigger molecular size. In addition, the recovery of natural zeolite after waste adsorption into its pores should also be considered for continuous utilization of this material. In this study, the porosity of natural zeolite from Tasikmalaya, Indonesia, was hydrothermally-modified in a Teflon-lined autoclave filled with certain pore directing agent such as distilled water, KOH, and NH4OH to obtain hierarchical pore structure. After proper drying process, the as-treated natural zeolite is impregnated with iron cation and heat-treated at specified temperature to get Fe-embedded zeolite structure. XRD observation is carried out to ensure the formation of magnetic phase within the zeolite pores. The analysis results show the formation of maghemite phase (γ-Fe2O3) within the zeolite pore structure.

Synchrotron-Based X-ray Microtomography Characterization of the Effect of Processing Variables on Porosity Formation in Laser Power-Bed Additive Manufacturing of Ti-6Al-4V

NASA Astrophysics Data System (ADS)

Cunningham, Ross; Narra, Sneha P.; Montgomery, Colt; Beuth, Jack; Rollett, A. D.

2017-03-01

The porosity observed in additively manufactured (AM) parts is a potential concern for components intended to undergo high-cycle fatigue without post-processing to remove such defects. The morphology of pores can help identify their cause: irregularly shaped lack of fusion or key-holing pores can usually be linked to incorrect processing parameters, while spherical pores suggest trapped gas. Synchrotron-based x-ray microtomography was performed on laser powder-bed AM Ti-6Al-4V samples over a range of processing conditions to investigate the effects of processing parameters on porosity. The process mapping technique was used to control melt pool size. Tomography was also performed on the powder to measure porosity within the powder that may transfer to the parts. As observed previously in experiments with electron beam powder-bed fabrication, significant variations in porosity were found as a function of the processing parameters. A clear connection between processing parameters and resulting porosity formation mechanism was observed in that inadequate melt pool overlap resulted in lack-of-fusion pores whereas excess power density produced keyhole pores.

Method of making metal oxide ceramic membranes with small pore sizes

DOEpatents

Anderson, Marc A.; Xu, Qunyin

1992-01-01

A method for the production of metal oxide ceramic membranes is composed of very small pore size. The process is particularly useful in the creation of titanium and other transition metal oxide membranes. The method utilizes a sol-gel process in which the rate of particle formation is controlled by substituting a relatively large alcohol in the metal alkoxide and by limiting the available water. Stable, transparent metal oxide ceramic membranes are created having a narrow distribution of pore size, with the pore diameter being manipulable in the range of 5 to 40 Angstroms.

Effect of hydrocarbon to nuclear magnetic resonance (NMR) logging in tight sandstone reservoirs and method for hydrocarbon correction

NASA Astrophysics Data System (ADS)

Xiao, Liang; Mao, Zhi-qiang; Xie, Xiu-hong

2017-04-01

It is crucial to understand the behavior of the T2 distribution in the presence of hydrocarbon to properly interpret pore size distribution from NMR logging. The NMR T2 spectrum is associated with pore throat radius distribution under fully brine saturated. However, when the pore space occupied by hydrocarbon, the shape of NMR spectrum is changed due to the bulk relaxation of hydrocarbon. In this study, to understand the effect of hydrocarbon to NMR logging, the kerosene and transformer oil are used to simulate borehole crude oils with different viscosity. 20 core samples, which were separately drilled from conventional, medium porosity and permeability and tight sands are saturated with four conditions of irreducible water saturation, fully saturated with brine, hydrocarbon-bearing condition and residual oil saturation, and the corresponding NMR experiments are applied to acquire NMR measurements. The residual oil saturation is used to simulate field NMR logging due to the shallow investigation depth of NMR logging. The NMR spectra with these conditions are compared, the results illustrate that for core samples drilled from tight sandstone reservoirs, the shape of NMR spectra have much change once they pore space occupied by hydrocarbon. The T2 distributions are wide, and they are bimodal due to the effect of bulk relaxation of hydrocarbon, even though the NMR spectra are unimodal under fully brine saturated. The location of the first peaks are similar with those of the irreducible water, and the second peaks are close to the bulk relaxation of viscosity oils. While for core samples drilled from conventional formations, the shape of T2 spectra have little changes. The T2 distributions overlap with each other under these three conditions of fully brine saturated, hydrocarbon-bearing and residual oil. Hence, in tight sandstone reservoirs, the shape of NMR logging should be corrected. In this study, based on the lab experiments, seven T2 times of 1ms, 3ms, 10ms, 33ms, 100ms, 300ms and 1000ms are first used to separate the T2 distributions of the residual oil saturation as 8 parts, and 8 pore components percentage compositions are calculated, second, an optimal T2 cutoff is determined to cut the T2 spectra of fully brine saturated conditions into two parts, the left parts (with short T2 time) represent to the irreducible water, and they do not need to be corrected, only the shape for the right parts of the T2 spectra needed to be corrected. Third the relationships among the amplitudes corresponding to the T2 times large than the optimal T2 cut off and 8 pore components percentage compositions are established, and they are used to predict corrected T2 amplitudes from NMR logging under residual oil saturation. Finally, the amplitudes corresponding to the left parts and the estimated amplitudes are spliced as the corrected NMR amplitudes, and a corrected T2 spectrum can be obtained. The reliability of this method is verified by comparing the corrected results and the experimental measurements. This method is extended to field application, fully water saturated T2 distributions are extracted from field NMR logging, and they are used to precisely evaluate hydrocarbon-bearing formations pore structure.

Liposome Disruption Assay to Examine Lytic Properties of Biomolecules.

PubMed

Jimah, John R; Schlesinger, Paul H; Tolia, Niraj H

2017-08-05

Proteins may have three dimensional structural or amino acid features that suggest a role in targeting and disrupting lipids within cell membranes. It is often necessary to experimentally investigate if these proteins and biomolecules are able to disrupt membranes in order to conclusively characterize the function of these biomolecules. Here, we describe an in vitro assay to evaluate the membrane lytic properties of proteins and biomolecules. Large unilamellar vesicles (liposomes) containing carboxyfluorescein at fluorescence-quenching concentrations are treated with the biomolecule of interest. A resulting increase in fluorescence due to leakage of the dye from liposomes and subsequent dilution in the buffer demonstrates that the biomolecule is sufficient for disrupting liposomes and membranes. Additionally, since liposome disruption may occur via pore-formation or via general solubilization of lipids similar to detergents, we provide a method to distinguish between these two mechanisms. Pore-formation can be identified and evaluated by examining the blockade of carboxyfluorescein release with dextran molecules that fit the pore. The methods described here were used to determine that the malaria vaccine candidate CelTOS and proapoptotic Bax disrupt liposomes by pore formation (Saito et al. , 2000; Jimah et al. , 2016). Since membrane lipid binding by a biomolecule precedes membrane disruption, we recommend the companion protocol: Jimah et al. , 2017.

Membrane-on-a-chip: microstructured silicon/silicon-dioxide chips for high-throughput screening of membrane transport and viral membrane fusion.

PubMed

Kusters, Ilja; van Oijen, Antoine M; Driessen, Arnold J M

2014-04-22

Screening of transport processes across biological membranes is hindered by the challenge to establish fragile supported lipid bilayers and the difficulty to determine at which side of the membrane reactants reside. Here, we present a method for the generation of suspended lipid bilayers with physiological relevant lipid compositions on microstructured Si/SiO2 chips that allow for high-throughput screening of both membrane transport and viral membrane fusion. Simultaneous observation of hundreds of single-membrane channels yields statistical information revealing population heterogeneities of the pore assembly and conductance of the bacterial toxin α-hemolysin (αHL). The influence of lipid composition and ionic strength on αHL pore formation was investigated at the single-channel level, resolving features of the pore-assembly pathway. Pore formation is inhibited by a specific antibody, demonstrating the applicability of the platform for drug screening of bacterial toxins and cell-penetrating agents. Furthermore, fusion of H3N2 influenza viruses with suspended lipid bilayers can be observed directly using a specialized chip architecture. The presented micropore arrays are compatible with fluorescence readout from below using an air objective, thus allowing high-throughput screening of membrane transport in multiwell formats in analogy to plate readers.

An investigation into the effects of pore connectivity on T2 NMR relaxation

NASA Astrophysics Data System (ADS)

Ghomeshi, Shahin; Kryuchkov, Sergey; Kantzas, Apostolos

2018-04-01

Nuclear Magnetic Resonance (NMR) is a powerful technique used to characterize fluids and flow in porous media. The NMR relaxation curves are closely related to pore geometry, and the inversion of the NMR relaxometry data is known to give useful information with regards to pore size distribution (PSD) through the relative amplitudes of the fluids stored in the small and large pores. While this information is crucial, the main challenge for the successful use of the NMR measurements is the proper interpretation of the measured signals. Natural porous media patterns consist of complex pore structures with many interconnected or "coupled" regions, as well as isolated pores. This connectivity along the throats changes the relaxation distribution and in order to properly interpret this data, a thorough understanding of the effects of pore connectivity on the NMR relaxation distribution is warranted. In this paper we address two main points. The first pertains to the fact that there is a discrepancy between the relaxation distribution obtained from experiments, and the ones obtained from solving the mathematical models of diffusion process in the digitized images of the pore space. There are several reasons that may attribute to this such as the lack of a proper incorporation of surface roughness into the model. However, here we are more interested in the effects of pore connectivity and to understand why the typical NMR relaxation distribution obtained from experiments are wider, while the numerical simulations predict that a wider NMR relaxation distribution may indicate poor connectivity. Secondly, by not taking into account the pore coupling effects, from our experience in interpreting the data, we tend to underestimate the pore volume of small pores and overestimate the amplitudes in the large pores. The role of pore coupling becomes even more prominent in rocks with small pore sizes such as for example in shales, clay in sandstones, and in the microstructures of carbonates.

Towards a rigorous mesoscale modeling of reactive flow and transport in an evolving porous medium and its applications to soil science

NASA Astrophysics Data System (ADS)

Ray, Nadja; Rupp, Andreas; Knabner, Peter

2016-04-01

Soil is arguably the most prominent example of a natural porous medium that is composed of a porous matrix and a pore space. Within this framework and in terms of soil's heterogeneity, we first consider transport and fluid flow at the pore scale. From there, we develop a mechanistic model and upscale it mathematically to transfer our model from the small scale to that of the mesoscale (laboratory scale). The mathematical framework of (periodic) homogenization (in principal) rigorously facilitates such processes by exactly computing the effective coefficients/parameters by means of the pore geometry and processes. In our model, various small-scale soil processes may be taken into account: molecular diffusion, convection, drift emerging from electric forces, and homogeneous reactions of chemical species in a solvent. Additionally, our model may consider heterogeneous reactions at the porous matrix, thus altering both the porosity and the matrix. Moreover, our model may additionally address biophysical processes, such as the growth of biofilms and how this affects the shape of the pore space. Both of the latter processes result in an intrinsically variable soil structure in space and time. Upscaling such models under the assumption of a locally periodic setting must be performed meticulously to preserve information regarding the complex coupling of processes in the evolving heterogeneous medium. Generally, a micro-macro model emerges that is then comprised of several levels of couplings: Macroscopic equations that describe the transport and fluid flow at the scale of the porous medium (mesoscale) include averaged time- and space-dependent coefficient functions. These functions may be explicitly computed by means of auxiliary cell problems (microscale). Finally, the pore space in which the cell problems are defined is time- and space dependent and its geometry inherits information from the transport equation's solutions. Numerical computations using mixed finite elements and potentially random initial data, e.g. that of porosity, complement our theoretical results. Our investigations contribute to the theoretical understanding of the link between soil formation and soil functions. This general framework may be applied to various problems in soil science for a range of scales, such as the formation and turnover of microaggregates or soil remediation.

Pore space analysis of NAPL distribution in sand-clay media

USGS Publications Warehouse

Matmon, D.; Hayden, N.J.

2003-01-01

This paper introduces a conceptual model of clays and non-aqueous phase liquids (NAPLs) at the pore scale that has been developed from a mathematical unit cell model, and direct micromodel observation and measurement of clay-containing porous media. The mathematical model uses a unit cell concept with uniform spherical grains for simulating the sand in the sand-clay matrix (???10% clay). Micromodels made with glass slides and including different clay-containing porous media were used to investigate the two clays (kaolinite and montmorillonite) and NAPL distribution within the pore space. The results were used to understand the distribution of NAPL advancing into initially saturated sand and sand-clay media, and provided a detailed analysis of the pore-scale geometry, pore size distribution, NAPL entry pressures, and the effect of clay on this geometry. Interesting NAPL saturation profiles were observed as a result of the complexity of the pore space geometry with the different packing angles and the presence of clays. The unit cell approach has applications for enhancing the mechanistic understanding and conceptualization, both visually and mathematically, of pore-scale processes such as NAPL and clay distribution. ?? 2003 Elsevier Science Ltd. All rights reserved.

Pore Scale Investigation of Wettability Alteration Through Chemically-Tuned Waterflooding in Oil-Wet Carbonate Rocks Using X-Ray Micro-Ct Imaging

NASA Astrophysics Data System (ADS)

Tawfik, M. S.; Karpyn, Z.

2017-12-01

Carbonate reservoirs host more than half of the remaining oil reserves worldwide. Due to their complex pore structure and intermediate to oil-wet nature, it is challenging to produce the remaining oil from these formations. For two decades, chemically tuned waterflooding (CTWF) has gained the attention of many researchers. Experimental, numerical, and field studies suggest that changes in ion composition of injected brine can increase oil recovery in carbonate reservoirs via wettability alteration. However, previous studies explaining the improvement in oil recovery by wettability alteration deduce wettability based on indirect measurements, including sessile drop contact angle measurements on polished rocks, relative permeability, chromatographic separation of SCN- and potential determining ions (PDIs), etc. CTWF literature offers no direct measurement of wettability alteration at the pore scale. This study proposes a direct pore-scale measurement of changes in interfacial curvatures before and after CTWF. Micro-coreflood experiments are performed to investigate the effect of injection brine salinity, ion composition and temperature on rock wettability at the pore scale. X-ray micro-CT scanning is used to obtain 3D image sets to calculate in-situ contact angle distributions. The study also aims to find a correlation between the magnitude of improvement in oil recovery at the macro-scale and the corresponding contact angle distribution at the pore-scale at different experimental conditions. Hence, macro-scale coreflood experiments are performed using the same conditions as the micro-corefloods. Macro-scale coreflood experiments have shown that brines with higher concentration of Ca2+, Mg2+ and SO42- ions have higher recoveries compared to standard seawater. This translates to wettability alteration into a more intermediate-wet state. This study enhances the understanding of the pore-scale physico-chemical mechanisms controlling wettability alteration via CTWF, which helps tune existing CTWF models, and therefore results in more well-informed candidate reservoir selection and the development of a workflow to determine the optimum injection brine properties for a given crude oil-brine-rock system.

The dynamic nature of crystal growth in pores

DOE PAGES

Godinho, Jose R. A.; Gerke, Kirill M.; Stack, Andrew G.; ...

2016-09-12

We report that the kinetics of crystal growth in porous media controls a variety of natural processes such as ore genesis and crystallization induced fracturing that can trigger earthquakes and weathering, as well as, sequestration of CO 2 and toxic metals into geological formations. Progress on understanding those processes has been limited by experimental difficulties of dynamically studying the reactive surface area and permeability during pore occlusion. Here, we show that these variables cause a time-dependency of barite growth rates in microporous silica. The rate is approximately constant and similar to that observed on free surfaces if fast flow velocitiesmore » predominate and if the time-dependent reactive surface area is accounted for. As the narrower flow paths clog, local flow velocities decrease, which causes the progressive slowing of growth rates. We conclude that mineral growth in a microporous media can be estimated based on free surface studies when a) the growth rate is normalized to the time-dependent surface area of the growing crystals, and b) the local flow velocities are above the limit at which growth is transport-limited. Lastly, accounting for the dynamic relation between microstructure, flow velocity and growth rate is shown to be crucial towards understanding and predicting precipitation in porous rocks.« less

Hydroxyapatite coatings containing Zn and Si on Ti-6Al-4Valloy by plasma electrolytic oxidation

NASA Astrophysics Data System (ADS)

Hwang, In-Jo; Choe, Han-Cheol

2018-02-01

In this study, hydroxyapatite coatings containing Zn and Si on Ti-6Al-4Valloy by plasma electrolytic oxidation were researched using various experimental instruments. The pore size is depended on the electrolyte concentration and the particle size and number of pore increase on surface part and pore part. In the case of Zn/Si sample, pore size was larger than that of Zn samples. The maximum size of pores decreased and minimum size of pores increased up to 10Zn/Si and Zn and Si affect the formation of pore shapes. As Zn ion concentration increases, the size of the particle tends to increase, the number of particles on the surface part is reduced, whereas the size of the particles and the number of particles on pore part increased. Zn is mainly detected at pore part, and Si is mainly detected at surface part. The crystallite size of anatase increased as the Zn ion concentration, whereas, in the case of Si ion added, crystallite size of anatase decreased.

Colon targeted delivery systems of metronidazole based on osmotic technology: development and evaluation.

PubMed

Kumar, Pramod; Singh, Sanjay; Mishra, Brahmeshwar

2008-09-01

Colon targeted delivery systems of metronidazole (MTZ) based on osmotic technology were developed. The developed systems consisted of osmotic core (drug, osmotic agent and wicking agent), coated with semipermeable membrane (SPM) containing guar gum as pore former, coated core were then further coated with enteric coating to protect the system from acidic environment of stomach. The effect of various formulation variables namely the level of wicking agent (sodium lauryl sulphate), osmotic agent in the osmotic core, the level of pore former (guar gum) in SPM, and the thickness of SPM, were studied on physical parameters and drug release characteristics of developed formulations. MTZ release was inversely proportional to SPM thickness, but directly related to the level of pore former, wicking agent and osmotic agent. On the other hand burst strength of the exhausted shells was decreased with the increase in level of pore former in the membrane but increased with the increase in the thickness of SPM. The drug release from the developed formulations was independent of pH, and agitation intensity, but dependent on the osmotic pressure of the release media. The thickness of enteric coating could prevent formation of delivery pores before contact with simulated colonic fluid, but had no effect on drug release. Result of SEM studies showed the formation of in-situ delivery pores in the membrane from where the drug release occurred, and the number of pores formed were directly related to the initial level of pore former (guar gum) in SPM. The manufacturing procedure was found to be reproducible and formulations were found to be stable during 3 months of accelerated stability studies.

Understanding Nanoemulsion Formation and Developing a Procedure for Porous Material Growth using Assembled Nanoemulsions

NASA Astrophysics Data System (ADS)

Yeranossian, Vahagn Frounzig

Nanoemulsions as an emerging technology have found many applications in consumer products, drug delivery, and even particle formation. However, knowledge gaps exist in how some of these emulsions are formed, specifically what pathways are traversed to reach the final state. Moreover, how these pathways affect the final properties of the nanoemulsions would affect the applications that these droplets possess. Some nanoemulsions possess unique properties, including the assembly of droplets. While the assembly of droplets is being studied in the Helgeson lab, work must be done to understand how the assembly itself could be used to control the growth of porous materials, such a hydrogels. Thus, this thesis aims to address two factors of nanoemulsions: the formation of water-in-oil nanoemulsions and the use of assemblying droplets in oil-in-water nanoemulsions to form macroporous hydrogels. To elucidate the formation mechanism of water-in-oil nanoemulsions, a combination of dynamic light scattering and small angle neutron scattering were used to study the intermediate and final states of the nanoemulsion during its formation. These nanoemulsions were prepared by slowly adding water to an oil and surfactant mixture and were diluted to effectively measure using scattering techniques without multiple scattering events. To develop a procedure to use assembled nanoemulsions for the growth of porous materials, a combination of optical microscopy and diffusional studies were employed. Optical microscopy images taken at various stages of the procedure help elucidate how the pore sizes of the final porous material is related to the droplet-rich domains of the assembled nanoemulsion. Meanwhile, diffusional measurements help confirm the size and interconnectedness of the macropores. From the work done in the completion of my thesis, the formation mechanism of the water-in-oil nanoemulsion studied has been elucidated. The neutron scattering measurements show that during the formation of the nanoemulsion, a combination of droplets and vesicles form. The presence of vesicles provides insight into how chemical additives in the water would affect the final droplet properties. This insight can be used to design water-in-oil nanoemulsions to be used for the controlled synthesis of solid nanoparticles. Additionally, this work demonstrates a potential procedure for developing macroporous hydrogels using nanoemulsions that are assembled into droplet-rich and droplet-poor domains. Through mild UV cross-linking conditions and mild solvent extraction techniques, the pore sizes could be equivalent to the droplet-rich domain sizes. The final hydrogels can control diffusivity of molecules, giving them potential applications in drug delivery.

Mechanism of Diphtheria Toxin Catalytic Domain Delivery to the Eukaryotic Cell Cytosol and the Cellular Factors that Directly Participate in the Process

PubMed Central

Murphy, John R.

2011-01-01

Research on diphtheria and anthrax toxins over the past three decades has culminated in a detailed understanding of their structure function relationships (e.g., catalytic (C), transmembrane (T), and receptor binding (R) domains), as well as the identification of their eukaryotic cell surface receptor, an understanding of the molecular events leading to the receptor-mediated internalization of the toxin into an endosomal compartment, and the pH triggered conformational changes required for pore formation in the vesicle membrane. Recently, a major research effort has been focused on the development of a detailed understanding of the molecular interactions between each of these toxins and eukaryotic cell factors that play an essential role in the efficient translocation of their respective catalytic domains through the trans-endosomal vesicle membrane pore and delivery into the cell cytosol. In this review, I shall focus on recent findings that have led to a more detailed understanding of the mechanism by which the diphtheria toxin catalytic domain is delivered to the eukaryotic cell cytosol. While much work remains, it is becoming increasingly clear that the entry process is facilitated by specific interactions with a number of cellular factors in an ordered sequential fashion. In addition, since diphtheria, anthrax lethal factor and anthrax edema factor all carry multiple coatomer I complex binding motifs and COPI complex has been shown to play an essential role in entry process, it is likely that the initial steps in catalytic domain entry of these divergent toxins follow a common mechanism. PMID:22069710

Spatial and temporal dependencies of structure II to structure I methane hydrate transformation in porous media under moderate pressure and temperature conditions

NASA Astrophysics Data System (ADS)

Dong, T.; Lin, J. F.; Gu, J. T.; Polito, P. J.; O'Connell, J.; Flemings, P. B.

2017-12-01

We used Raman spectroscopy to monitor methane hydrates transforming from structure II to structure I at the pore scale as a function of space and time. It is well documented that structure I hydrate is the thermodynamically stable phase for pure methane hydrate (<100 MPa, < 20 °C), but due to kinetic limitation, initial methane hydrate formation produces a mixture of structure I and structure II hydrates. We observed that the structure transformation originated around the porous medium grains and over time slowly migrated into the pore space. We synthesized methane hydrates in spherical glass beads (210-297 µm in diameter) in a pressure cell with a sapphire window to integrate optical observations with Raman measurements. We injected CH4 vapor into the cell and supplied only deionized water thereafter to maintain a constant pressure of 14.6 MPa at 3.5 °C, with 14.5 °C subcooling. We used Raman spectroscopy to map the methane hydrates in pore spaces at 5-25 µm resolution, in order to monitor the occupancy ratio of CH4 in large cages to CH4 in small cages, by their Raman peak intensity ratio, i.e., I( 2905 cm-1)/I( 2915 cm-1). We identified 3 stages of hydrate formation at the pore scale: (1) after the initial hydrate formation, Raman mapping revealed that the occupancy ratio ranged from 0.5 to 3, indicating a mixture of structure I and II hydrates; (2) within 1 week, we observed that all structure I hydrates occurred on the glass bead surfaces and structure II hydrates occupied the pore spaces; (3) over the following 2 weeks, structure II hydrates gradually recrystallized into structure I hydrates from glass bead surfaces towards the pore space. These results imply that (1) due to kinetics, the formation of methane hydrate in porous media is more complex than previously thought, and (2) the bulk physical and chemical properties of laboratory-synthesized methane hydrates in porous media may drift over time, as methane hydrates recrystallize from a metastable phase (structure II) to the thermodynamically stable phase (structure I).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Jian; Vemuri, Rama S.; Estevez, Luis

Metal–organic frameworks (MOFs) are found to be promising sorbents for adsorption cooling applications. Using organic ligands with 1, 2, and 3 phenylene rings, we construct moisture-stable Ni-MOF-74 members with adjustable pore apertures. These pore-engineered materials exhibit excellent sorption capabilities towards water and fluorocarbons. The adsorption patterns for these materials differ significantly and are attributed to variances in the hydrophobic/hydrophilic pore character, associated with differences in pore size. Complementary ex situ characterizations and in situ FTIR spectra are deployed to understand the correlations between the mechanisms of gas loadings and the pore environment of the MOFs.

Pore Formation and Mobility Furnace within the MSG

NASA Technical Reports Server (NTRS)

2003-01-01

Dr. Richard Grugel, a materials scientist at NASA's Marshall Space Flight in Huntsville, Ala., examines the furnace used to conduct his Pore Formation and Mobility Investigation -- one of the first two materials science experiments to be conducted on the International Space Station. This experiment studies materials processes similar to those used to make components used in jet engines. Grugel's furnace was installed in the Microgravity Science Glovebox through the circular port on the side. In space, crewmembers are able to change out samples using the gloves on the front of the facility's work area.

30 CFR 250.1617 - Application for permit to drill.

Code of Federal Regulations, 2011 CFR

2011-07-01

... well and for well control, including the following: (i) Pore pressure; (ii) Formation fracture..., fracture gradients of the exposed formations, casing setting depths, and cementing intervals, total well...

Synthesis of mesoporous carbon nanoparticles with large and tunable pore sizes

NASA Astrophysics Data System (ADS)

Liu, Chao; Yu, Meihua; Li, Yang; Li, Jiansheng; Wang, Jing; Yu, Chengzhong; Wang, Lianjun

2015-07-01

Mesoporous carbon nanoparticles (MCNs) with large and adjustable pores have been synthesized by using poly(ethylene oxide)-b-polystyrene (PEO-b-PS) as a template and resorcinol-formaldehyde (RF) as a carbon precursor. The resulting MCNs possess small diameters (100-126 nm) and high BET surface areas (up to 646 m2 g-1). By using home-designed block copolymers, the pore size of MCNs can be tuned in the range of 13-32 nm. Importantly, the pore size of 32 nm is the largest among the MCNs prepared by the soft-templating route. The formation mechanism and structure evolution of MCNs were studied by TEM and DLS measurements, based on which a soft-templating/sphere packing mechanism was proposed. Because of the large pores and small particle sizes, the resulting MCNs were excellent nano-carriers to deliver biomolecules into cancer cells. MCNs were further demonstrated with negligible toxicity. It is anticipated that this carbon material with large pores and small particle sizes may have excellent potential in drug/gene delivery.Mesoporous carbon nanoparticles (MCNs) with large and adjustable pores have been synthesized by using poly(ethylene oxide)-b-polystyrene (PEO-b-PS) as a template and resorcinol-formaldehyde (RF) as a carbon precursor. The resulting MCNs possess small diameters (100-126 nm) and high BET surface areas (up to 646 m2 g-1). By using home-designed block copolymers, the pore size of MCNs can be tuned in the range of 13-32 nm. Importantly, the pore size of 32 nm is the largest among the MCNs prepared by the soft-templating route. The formation mechanism and structure evolution of MCNs were studied by TEM and DLS measurements, based on which a soft-templating/sphere packing mechanism was proposed. Because of the large pores and small particle sizes, the resulting MCNs were excellent nano-carriers to deliver biomolecules into cancer cells. MCNs were further demonstrated with negligible toxicity. It is anticipated that this carbon material with large pores and small particle sizes may have excellent potential in drug/gene delivery. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr02389k

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronchi, C.; Sari, C.

Lenticular pore migration rates in oxide nuclear fuels were measured in out-of-pile heating experiments. It is deduced that those pores which are in part responsible for the formation of columnar grains, are only produced in the absence of relevant amourts of filling gas. Specimens containing important concentrations of He, produced by Pu alpha decay, show columnar grain restructuring by grain boundary migration. Some consequences are drawn concerning the possible role played by lenticular pores in the mechanisms of fission gas release from nuclear fuels. (5 figures) (auth)

CO2 breakthrough pressure and permeability for unsaturated low-permeability sandstone of the Ordos Basin

NASA Astrophysics Data System (ADS)

Zhao, Yan; Yu, Qingchun

2017-07-01

With rising threats from greenhouse gases, capture and injection of CO2 into suitable underground formations is being considered as a method to reduce anthropogenic emissions of CO2 to the atmosphere. As the injected CO2 will remain in storage for hundreds of years, the safety of CO2 geologic sequestration is a major concern. The low-permeability sandstone of the Ordos Basin in China is regarded as both caprock and reservoir rock, so understanding the breakthrough pressure and permeability of the rock is necessary. Because part of the pore volume experiences a non-wetting phase during the CO2 injection and migration process, the rock may be in an unsaturated condition. And if accidental leakage occurs, CO2 will migrate up into the unsaturated zone. In this study, breakthrough experiments were performed at various degrees of water saturation with five core samples of low-permeability sandstone obtained from the Ordos Basin. The experiments were conducted at 40 °C and pressures of >8 MPa to simulate the geological conditions for CO2 sequestration. The results indicate that the degree of water saturation and the pore structure are the main factors affecting the rock breakthrough pressure and permeability, since the influence of calcite dissolution and clay mineral swelling during the saturation process is excluded. Increasing the average pore radius or most probable pore radius leads to a reduction in the breakthrough pressure and an increase by several orders of magnitude in scCO2 effective permeability. In addition, the breakthrough pressure rises and the scCO2 effective permeability decreases when the water saturation increases. However, when the average pore radius is greater than 0.151 μm, the degree of water saturation will has a little effect on the breakthrough pressure. On this foundation, if the most probable pore radius of the core sample reaches 1.760 μm, the breakthrough pressure will not be impacted by the increasing water saturation. We establish correlations between (1) the breakthrough pressure and average pore radius or most probable pore radius, (2) the breakthrough pressure and scCO2 effective permeability, (3) the breakthrough pressure and water saturation, and (4) the scCO2 effective permeability and water saturation. This study provides practical information for further studies of CO2 sequestration as well as the caprock evaluation.

Pore-scale Simulation and Imaging of Multi-phase Flow and Transport in Porous Media (Invited)

NASA Astrophysics Data System (ADS)

Crawshaw, J.; Welch, N.; Daher, I.; Yang, J.; Shah, S.; Grey, F.; Boek, E.

2013-12-01

We combine multi-scale imaging and computer simulation of multi-phase flow and reactive transport in rock samples to enhance our fundamental understanding of long term CO2 storage in rock formations. The imaging techniques include Confocal Laser Scanning Microscopy (CLSM), micro-CT and medical CT scanning, with spatial resolutions ranging from sub-micron to mm respectively. First, we report a new sample preparation technique to study micro-porosity in carbonates using CLSM in 3 dimensions. Second, we use micro-CT scanning to generate high resolution 3D pore space images of carbonate and cap rock samples. In addition, we employ micro-CT to image the processes of evaporation in fractures and cap rock degradation due to exposure to CO2 flow. Third, we use medical CT scanning to image spontaneous imbibition in carbonate rock samples. Our imaging studies are complemented by computer simulations of multi-phase flow and transport, using the 3D pore space images obtained from the scanning experiments. We have developed a massively parallel lattice-Boltzmann (LB) code to calculate the single phase flow field in these pore space images. The resulting flow fields are then used to calculate hydrodynamic dispersion using a novel scheme to predict probability distributions for molecular displacements using the LB method and a streamline algorithm, modified for optimal solid boundary conditions. We calculate solute transport on pore-space images of rock cores with increasing degree of heterogeneity: a bead pack, Bentheimer sandstone and Portland carbonate. We observe that for homogeneous rock samples, such as bead packs, the displacement distribution remains Gaussian with time increasing. In the more heterogeneous rocks, on the other hand, the displacement distribution develops a stagnant part. We observe that the fraction of trapped solute increases from the beadpack (0 %) to Bentheimer sandstone (1.5 %) to Portland carbonate (8.1 %), in excellent agreement with PFG-NMR experiments. We then use our preferred multi-phase model to directly calculate flow in pore space images of two different sandstones and observe excellent agreement with experimental relative permeabilities. Also we calculate cluster size distributions in good agreement with experimental studies. Our analysis shows that the simulations are able to predict both multi-phase flow and transport properties directly on large 3D pore space images of real rocks. Pore space images, left and velocity distributions, right (Yang and Boek, 2013)

The distribution of saturated clusters in wetted granular materials

NASA Astrophysics Data System (ADS)

Li, Shuoqi; Hanaor, Dorian; Gan, Yixiang

2017-06-01

The hydro-mechanical behaviour of partially saturated granular materials is greatly influenced by the spatial and temporal distribution of liquid within the media. The aim of this paper is to characterise the distribution of saturated clusters in granular materials using an optical imaging method under different water drainage conditions. A saturated cluster is formed when a liquid phase fully occupies the pore space between solid grains in a localized region. The samples considered here were prepared by vibrating mono-sized glass beads to form closely packed assemblies in a rectangular container. A range of drainage conditions were applied to the specimen by tilting the container and employing different flow rates, and the liquid pressure was recorded at different positions in the experimental cell. The formation of saturated clusters during the liquid withdrawal processes is governed by three competing mechanisms arising from viscous, capillary, and gravitational forces. When the flow rate is sufficiently large and the gravity component is sufficiently small, the viscous force tends to destabilize the liquid front leading to the formation of narrow fingers of saturated material. As the water channels along these liquid fingers break, saturated clusters are formed inside the specimen. Subsequently, a spatial and temporal distribution of saturated clusters can be observed. We investigated the resulting saturated cluster distribution as a function of flow rate and gravity to achieve a fundamental understanding of the formation and evolution of such clusters in partially saturated granular materials. This study serves as a bridge between pore-scale behavior and the overall hydro-mechanical characteristics in partially saturated soils.

Microfluidic study for investigating migration and residual phenomena of supercritical CO2 in porous media

NASA Astrophysics Data System (ADS)

Park, Gyuryeong; Wang, Sookyun; Lee, Minhee; Um, Jeong-Gi; Kim, Seon-Ok

2017-04-01

The storage of CO2 in underground geological formation such as deep saline aquifers or depleted oil and gas reservoirs is one of the most promising technologies for reducing the atmospheric CO2 release. The processes in geological CO2 storage involves injection of supercritical CO2 (scCO2) into porous formations saturated with brine and initiates CO2 flooding with immiscible displacement. The CO2 migration and porewater displacement within geological formations, and , consequentially, the storage efficiency are governed by the interaction of fluid and rock properties and are affected by the interfacial tension, capillarity, and wettability in supercritical CO2-brine-mineral systems. This study aims to observe the displacement pattern and estimate storage efficiency by using micromodels. This study aims to conduct scCO2 injection experiments for visualization of distribution of injected scCO2 and residual porewater in transparent pore networks on microfluidic chips under high pressure and high temperature conditions. In order to quantitatively analyze the porewater displacement by scCO2 injection under geological CO2 storage conditions, the images of invasion patterns and distribution of CO2 in the pore network are acquired through a imaging system with a microscope. The results from image analysis were applied in quantitatively investigating the effects of major environmental factors and scCO2 injection methods on porewater displacement process by scCO2 and storage efficiency. The experimental observation results could provide important fundamental information on capillary characteristics of reservoirs and improve our understanding of CO2 sequestration progress.

Thermally-driven Coupled THM Processes in Shales

NASA Astrophysics Data System (ADS)

Rutqvist, J.

2017-12-01

Temperature changes can trigger strongly coupled thermal-hydrological-mechanical (THM) processes in shales that are important to a number of subsurface energy applications, including geologic nuclear waste disposal and hydrocarbon extraction. These coupled processes include (1) direct pore-volume couplings, by thermal expansion of trapped pore-fluid that triggers instantaneous two-way couplings between pore fluid pressure and mechanical deformation, and (2) indirect couplings in terms of property changes, such as changes in mechanical stiffness, strength, and permeability. Direct pore-volume couplings have been studied in situ during borehole heating experiments in shale (or clay stone) formations at Mont Terri and Bure underground research laboratories in Switzerland and France. Typically, the temperature changes are accompanied with a rapid increase in pore pressure followed by a slower decrease towards initial (pre-heating) pore pressure. Coupled THM modeling of these heater tests shows that the pore pressure increases because the thermal expansion coefficient of the fluid is much higher than that of the porous clay stone. Such thermal pressurization induces fluid flow away from the pressurized area towards areas of lower pressure. The rate of pressure increase and magnitude of peak pressure depends on the rate of heating, pore-compressibility, and permeability of the shale. Modeling as well as laboratory experiments have shown that if the pore pressure increase is sufficiently large it could lead to fracturing of the shale or shear slip along pre-existing bedding planes. Another set of data and observations have been collected associated with studies related to concentrated heating and cooling of oil-shales and shale-gas formations. Heating may be used to enhance production from tight oil-shale, whereas thermal stimulation has been attempted for enhanced shale-gas extraction. Laboratory experiments on shale have shown that strength and elastic deformation modulus decreases with temperature while the rate creep deformations increase with temperature. Such temperature dependency also affects the well stability and zonal sealing across shale layers.

Restore the change process of Longmaxi shale pore structure during the diagenesis by the potassium and the magnesium

NASA Astrophysics Data System (ADS)

Zhou, W.

2016-12-01

The pore structure of Longmaxi shale was changing during the diagenetic process, mainly caused by the illitization and serpentinzation. The evolution of shale pore structure mainly relates to the element migration. Based on the result of electron microprobe analyser (EMPA), it is possible to find the distribution of element in shale directly and to distinguish the destroyed primary pore structure as element will remain in the migration way. The migration of potassium in Longmaxi shale mainly happened during early diagenesis phase to middle diagenesis phase (Geothermal temperature: 60°-140°). During the illitization, potassium mainly came from potassium feldspar, migrated though the connected pore structure and reacted with smectite. Illite and illite/smectite in Longmaxi shale distribute continuously in 10micron-level flocculent formation, which means that primary connective pore structure in Longmaxi shale has a same scale. The concentration of potassium has an obvious gradient that potassium content in middle of flocculation of Illite/smectite is about 6.8% and 4.8% in the boundary parts (Fig.). In addition, as SiO2 was generated during the illitization, which makes Longmaxi shale very compacted. The migration of magnesium in Longmaxi shale happened during low temperature serpentinization (Geothermal temperature: 140°-350°). Magnesium mainly came from dolomite and migrated in primary pores. According to the result of EMPA, it can be recognized that the migration path of magnesium is much simpler than potassium, which is caused as serpentinization do not have much reaction with clay minerals around (Fig.). Serpentine jams the primary pores of Longmaxi shale too. As reaction temperature of serpentinization is higher than illitization and serpentine is inserts in illite/smectite, the formation process of Longmaxi shale pore structure can be mainly divided into two phases: geothermal temperature˜140° and˜140°.

Quantitative Assessment of Potentially Active Faults in Oklahoma Utilizing Detailed Information on In Situ Stress Orientation and Relative Magnitude

NASA Astrophysics Data System (ADS)

Walsh, R.; Zoback, M. D.

2015-12-01

Over the past six years, the earthquake rate in the central and eastern U.S. has increased markedly, and is related to fluid injection. Nowhere has seismicity increased more than in Oklahoma, where large volumes of saline pore water are co-produced with oil and gas, then injected into deeper sedimentary formations. These deeper formations appear to be in hydraulic communication with potentially active faults in crystalline basement, where nearly all the earthquakes are occurring. Although the majority of the recent earthquakes have posed little danger to the public, the possibility of triggering damaging earthquakes on potentially active basement faults cannot be discounted. To understand probability of slip on a given fault, we invert for stresses from the hundreds of M4+ events in Oklahoma for which moment tensors have been made. We then resolve these stresses, while incorporating uncertainties, on the faults from the preliminary Oklahoma fault map. The result is a probabilistic understanding of which faults are most likely active and best avoided.

Ectopic bone formation by marrow stromal osteoblast transplantation using poly(DL-lactic-co-glycolic acid) foams implanted into the rat mesentery

NASA Technical Reports Server (NTRS)

Ishaug-Riley, S. L.; Crane, G. M.; Gurlek, A.; Miller, M. J.; Yasko, A. W.; Yaszemski, M. J.; Mikos, A. G.; McIntire, L. V. (Principal Investigator)

1997-01-01

Porous biodegradable poly(DL-lactic-co-glycolic acid) foams were seeded with rat marrow stromal cells and implanted into the rat mesentery to investigate in vivo bone formation at an ectopic site. Cells were seeded at a density of 6.83 x 10(5) cells/cm2 onto polymer foams having pore sizes ranging from either 150 to 300 to 710 microns and cultured for 7 days in vitro prior to implantation. The polymer/cell constructs were harvested after 1, 7, 28, or 49 days in vivo and processed for histology and gel permeation chromatography. Visual observation of hematoxylin and eosin-stained sections and von Kossa-stained sections revealed the formation of mineralized bonelike tissue in the constructs within 7 days postimplantation. Ingrowth of vascular tissue was also found adjacent to the islands of bone, supplying the necessary metabolic requirements to the newly formed tissue. Mineralization and bone tissue formation were investigated by histomorphometry. The average penetration depth of mineralized tissue in the construct ranged from 190 +/- 50 microns for foams with 500-710-microns pores to 370 +/- 160 microns for foams with 150-300-microns pores after 49 days in vivo. The mineralized bone volume per surface area and total bone volume per surface area had maximal values of 0.28 +/- 0.21 mm (500-710-microns pore size, day 28) and 0.038 +/- 0.024 mm (150-300-microns, day 28), respectively. As much as 11% of the foam volume penetrated by bone tissue was filled with mineralized tissue. No significant trends over time were observed for any of the measured values (penetration depth, bone volume/surface area, or percent mineralized bone volume). These results suggest the feasibility of bone formation by osteoblast transplantation in an orthotopic site where not only bone formation from transplanted cells but also ingrowth from adjacent bone may occur.

Dolomite Formation within Microbial Mats in the Sabkha of Abu Dhabi (UAE) and Associated Microsedimentary Structures

NASA Astrophysics Data System (ADS)

Bontognali, T. R.; Vasconcelos, C.; McKenzie, J. A.

2008-12-01

The link between microbial activity and dolomite formation has been evaluated in the coastal sabkha of Abu Dhabi (UAE). This modern dolomite-forming environment is frequently cited as the type analogue for the interpretation of many ancient evaporitic sequences. The investigation of sabkha sediments along a transect from intertidal to supratidal zones revealed a close association between microbial mats and dolomite. Authigenic dolomite occurs within surface and buried microbial mats, which are comprised of exopolymeric substances (EPS). Dolomite forms as a direct consequence of mineral nucleation and growth within microbially produced EPS. The cation-binding effect of the EPS molecules influences the composition of the precipitate. The early stage of this process is characterized by the complexation of an amorphous Mg-Si precipitate, which promotes dolomite development. Mineral formation within EPS appears to be enhanced by evaporation with consequent supersaturation of the pore waters with respect to dolomite. Partial EPS degradation during diagenesis may also provide an additional source of cations. However, the specific mineral-template property of EPS, rather than an increase in cation concentrations, is the key factor for dolomite formation in the studied area of the sabkha. Indeed, within the modern microbial mat located at the surface, dolomite precipitates from pore waters whose composition is very close to seawater. In the supratidal zone, pore water analysis and stable isotope values did not reveal any linkage between dolomite formation and microbial excretion and/or consumption of metabolites along the sediment profiles. This is in contrast with current models, in which dolomite formation is mainly linked to microbial increase of pH and alkalinity or consumption of dissolved SO4 in pore-waters. The EPS of the microbial mats is characterized by an alveolar microfabric, which can be mineralized during early diagenesis, preserving fossil imprints of the original biofilm. Recognition of this biostructure, combined with the atypical Mg-Si phase, may be used to interpret ancient microbial dolomite throughout the geological record.

Fines migration during CO 2 injection: Experimental results interpreted using surface forces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Quan; Saeedi, Ali; Delle Piane, Claudio

The South West Hub project is one of the Australian Flagship Carbon Capture and Storage projects located in the south-west of Western Australia. To evaluate the injectivity potential during the forthcoming full-scale CO 2 injection, we conducted three core-flooding experiments using reservoir core plugs from the well Harvey-1. We aimed to investigate in this paper whether the injection of CO 2 leads to fines migration and permeability reduction due to the relatively high kaolinite content (up to 13%) in the injection interval of the target formation (i.e. the Wonnerup Member of the Lesueur Formation). We imaged the core samples beforemore » flooding to verify the presence of kaolinite at the pore-scale using scanning electron microscopy (SEM). We also examined the pore network of the core plugs before and after the core-flooding experiments using Nuclear Magnetic Resonance (NMR). Moreover, to gain a better understanding of any kaolinite fines migration, we delineated surface force using two models based on Derjaguin-Landau-Verwey-Overbeek (denoted by DLVO) theory coupled hydrodynamic force: (1) sphere/flat model representing interaction between kaolinite/quartz, and (2) flat/flat model representing interaction between kaolinite/kaolinite. Our core-flooding experimental results showed that CO 2/brine injection triggered moderate to significant reduction in the permeability of the core samples with a negligible porosity change. NMR measurements supported the core-flooding results, suggesting that the relatively large pores disappeared in favour of a higher proportion of the medium to small pores after flooding. The DLVO calculations showed that some kaolinite particles probably lifted off and detached from neighbouring kaolinite particles rather than quartz grains. Moreover, the modelling results showed that the kaolinite fines migration would not occur under normal reservoir multiphase flow conditions. This is not because of the low hydrodynamic force. It is rather because the geometries of the particles dominate their interplay. Finally and overall, both of the experimental and analytical modelling results point to the fines migration to be the most likely cause of the permeability impairment observed during core-flooding experiments.« less

Fines migration during CO 2 injection: Experimental results interpreted using surface forces

DOE PAGES

Xie, Quan; Saeedi, Ali; Delle Piane, Claudio; ...

2017-09-04

The South West Hub project is one of the Australian Flagship Carbon Capture and Storage projects located in the south-west of Western Australia. To evaluate the injectivity potential during the forthcoming full-scale CO 2 injection, we conducted three core-flooding experiments using reservoir core plugs from the well Harvey-1. We aimed to investigate in this paper whether the injection of CO 2 leads to fines migration and permeability reduction due to the relatively high kaolinite content (up to 13%) in the injection interval of the target formation (i.e. the Wonnerup Member of the Lesueur Formation). We imaged the core samples beforemore » flooding to verify the presence of kaolinite at the pore-scale using scanning electron microscopy (SEM). We also examined the pore network of the core plugs before and after the core-flooding experiments using Nuclear Magnetic Resonance (NMR). Moreover, to gain a better understanding of any kaolinite fines migration, we delineated surface force using two models based on Derjaguin-Landau-Verwey-Overbeek (denoted by DLVO) theory coupled hydrodynamic force: (1) sphere/flat model representing interaction between kaolinite/quartz, and (2) flat/flat model representing interaction between kaolinite/kaolinite. Our core-flooding experimental results showed that CO 2/brine injection triggered moderate to significant reduction in the permeability of the core samples with a negligible porosity change. NMR measurements supported the core-flooding results, suggesting that the relatively large pores disappeared in favour of a higher proportion of the medium to small pores after flooding. The DLVO calculations showed that some kaolinite particles probably lifted off and detached from neighbouring kaolinite particles rather than quartz grains. Moreover, the modelling results showed that the kaolinite fines migration would not occur under normal reservoir multiphase flow conditions. This is not because of the low hydrodynamic force. It is rather because the geometries of the particles dominate their interplay. Finally and overall, both of the experimental and analytical modelling results point to the fines migration to be the most likely cause of the permeability impairment observed during core-flooding experiments.« less

Mechanical and electromagnetic properties of northern Gulf of Mexico sediments with and without THF hydrates

USGS Publications Warehouse

Lee, J.Y.; Santamarina, J.C.; Ruppel, C.

2008-01-01

Using an oedometer cell instrumented to measure the evolution of electromagnetic properties, small strain stiffness, and temperature, we conducted consolidation tests on sediments recovered during drilling in the northern Gulf of Mexico at the Atwater Valley and Keathley Canyon sites as part of the 2005 Chevron Joint Industry Project on Methane Hydrates. The tested specimens include both unremolded specimens (as recovered from the original core liner) and remolded sediments both without gas hydrate and with pore fluid exchanged to attain 100% synthetic (tetrahydrofuran) hydrate saturation at any stage of loading. Test results demonstrate the extent to which the electromagnetic and mechanical properties of hydrate-bearing marine sediments are governed by the vertical effective stress, stress history, porosity, hydrate saturation, fabric, ionic concentration of the pore fluid, and temperature. We also show how permittivity and electrical conductivity data can be used to estimate the evolution of hydrate volume fraction during formation. The gradual evolution of geophysical properties during hydrate formation probably reflects the slow increase in ionic concentration in the pore fluid due to ion exclusion in closed systems and the gradual decrease in average pore size in which the hydrate forms. During hydrate formation, the increase in S-wave velocity is delayed with respect to the decrease in permittivity, consistent with hydrate formation on mineral surfaces and subsequent crystal growth toward the pore space. No significant decementation/debonding occurred in 100% THF hydrate-saturated sediments during unloading, hence the probability of sampling hydrate-bearing sediments without disturbing the original sediment fabric is greatest for samples in which the gas hydrate is primarily responsible for maintaining the sediment fabric and for which the time between core retrieval and restoration of in situ effective stress in the laboratory is minimized. In evaluating the impact of core retrieval on specimen properties, it is also important to consider how far removed hydrate-bearing samples are from hydrate stability conditions. ?? 2008 Elsevier Ltd.

Effect of Electric Field on Gas Hydrate Nucleation Kinetics: Evidence for the Enhanced Kinetics of Hydrate Nucleation by Negatively Charged Clay Surfaces.

PubMed

Park, Taehyung; Kwon, Tae-Hyuk

2018-03-06

Natural gas hydrates are found widely in oceanic clay-rich sediments, where clay-water interactions have a profound effect on the formation behavior of gas hydrates. However, it remains unclear why and how natural gas hydrates are formed in clay-rich sediments in spite of factors that limit gas hydrate formation, such as small pore size and high salinity. Herein, we show that polarized water molecules on clay surfaces clearly promote gas hydrate nucleation kinetics. When water molecules were polarized with an electric field of 10 4 V/m, gas hydrate nucleation occurred significantly faster with an induction time reduced by 5.8 times. Further, the presence of strongly polarized water layers at the water-gas interface hindered gas uptake and thus hydrate formation, when the electric field was applied prior to gas dissolution. Our findings expand our understanding of the formation habits of naturally occurring gas hydrates in clay-rich sedimentary deposits and provide insights into gas production from natural hydrate deposits.

Formation of bone-like mineralized matrix by periodontal ligament cells in vivo: a morphological study in rats.

PubMed

Hiraga, Toru; Ninomiya, Tadashi; Hosoya, Akihiro; Takahashi, Masafumi; Nakamura, Hiroaki

2009-01-01

Periodontal ligament (PDL) is a unique connective tissue that not only connects cementum and alveolar bone to support teeth, but also plays an important role in reconstructing periodontal tissues. Previous studies have suggested that PDL cells have osteogenic potential; however, they lack precise histological examinations. Here, we studied bone-like matrix formation by PDL cells in rats using morphological techniques. Rat and human PDL cells exhibited substantial alkaline phosphatase activity and induced mineralization in vitro. RT-PCR analyses showed that PDL cells expressed the osteoblast markers, Runx2, osterix, and osteocalcin. These results suggest that PDL cells share similar phenotypes with osteoblasts. To examine the bone-like matrix formation in vivo, PDL cells isolated from green fluorescent protein (GFP)-transgenic rats were inoculated with hydroxyapatite (HA) disks into wild-type rats. Five weeks after the implantation, the pores in HA disks were occupied by GFP-positive cells. Mineralized matrix formation was also found on the surface of HA pores. At 12 weeks, some of the pores were filled with bone-like mineralized matrices (BLMM), which were positive for the bone matrix proteins, osteopontin, bone sialoprotein, and osteocalcin. Immunohistochemical examination revealed that most of the osteoblast- and osteocyte-like cells on or in the BLMM were GFP-positive, suggesting that the BLMM were directly formed by the inoculated PDL cells. On the pore surfaces, Sharpey's fiber-like structures embedded in cementum-like mineralized layers were also observed. These results collectively suggest that PDL cells have the ability to form periodontal tissues and could be a useful source for regenerative therapies of periodontal diseases.

Visual and functional demonstration of growing Bax-induced pores in mitochondrial outer membranes

PubMed Central

Gillies, Laura A; Du, Han; Peters, Bjoern; Knudson, C. Michael; Newmeyer, Donald D.; Kuwana, Tomomi

2015-01-01

Bax induces mitochondrial outer membrane permeabilization (MOMP), a critical step in apoptosis in which proteins are released into the cytoplasm. To resolve aspects of the mechanism, we used cryo-electron microscopy (cryo-EM) to visualize Bax-induced pores in purified mitochondrial outer membranes (MOMs). We observed solitary pores that exhibited negative curvature at their edges. Over time, the pores grew to ∼100–160 nm in diameter after 60–90 min, with some pores measuring more than 300 nm. We confirmed these results using flow cytometry, which we used to monitor the release of fluorescent dextrans from isolated MOM vesicles. The dextran molecules were released gradually, in a manner constrained by pore size. However, the release rates were consistent over a range of dextran sizes (10–500 kDa). We concluded that the pores were not static but widened dramatically to release molecules of different sizes. Taken together, the data from cryo-EM and flow cytometry argue that Bax promotes MOMP by inducing the formation of large, growing pores through a mechanism involving membrane-curvature stress. PMID:25411335

Effects of Post-Pyrolysis Air Oxidation of Biomass Chars on Adsorption of Neutral and Ionizable Compounds.

PubMed

Xiao, Feng; Pignatello, Joseph J

2016-06-21

This study was conducted to understand the effects of thermal air oxidation of biomass chars experienced during formation or production on their adsorptive properties toward various compounds, including five neutral nonpolar and polar compounds and seven weak acids and bases (pKa = 3-5.2) selected from among industrial chemicals and the triazine and phenoxyacetic acid herbicide classes. Post-pyrolysis air oxidation (PPAO) at 400 °C of anoxically prepared wood and pecan shell chars for up to 40 min enhanced the mass-normalized adsorption at pH ∼ 7.4 of all test compounds, especially the weak acids and bases, by up to 100-fold. Both general and specific effects were identified. The general effect results from "reaming" of pores by the oxidative removal of pore wall matter and/or tarry deposits generated during the pyrolysis step. Reaming creates new surface area and enlarges nanopores, which helps relieve steric hindrance to adsorption. The specific effect results from creation of new acidic functionality that provides sites for the formation of very strong, charge-assisted hydrogen bonds (CAHB) with solutes having comparable pKa. The CAHB hypothesis was supported by competition experiments and the finding that weak acid anion adsorption increased with surface carboxyl content, despite electrostatic repulsion from the growing negative charge. The results provide insight into the effects of air oxidation on pollutant retention.

Formation patterns of water clusters in CMK-3 and CMK-5 mesoporous carbons: a computational recognition study.

PubMed

Peng, Xuan; Jain, Surendra Kumar; Singh, Jayant Kumar; Liu, Anqi; Jin, Qibing

2018-06-13

Grand canonical Monte Carlo simulations are performed to study the adsorption of water in realistic CMK-3 and CMK-5 models at 300 K. The adsorption isotherms are characterized by negligible uptake at lower chemical potentials and complete pore filling once the threshold chemical potential is increased. Results for the isosteric heat of adsorption, radial distribution function (O-O and O-H), hydrogen bond statistics and the cluster size distribution of water molecules are presented. The snapshots of GCMC simulations in CMK-3 and CMK-5 models show that the adsorption happens via the formation of water clusters. For the CMK-3 model, it was found that the pore filling occurred via the formation of a single water cluster and a few very small clusters. The water cluster size increased with an increase in pore size of the CMK-3 model. For the CMK-5 model, it was found that the adsorption first occurred in the inner porosity (via cluster formation). There was no adsorption of water in the outer porosity during the filling of the inner porosity. After the inner porosity was completely filled, the water begins to fill the outer porosity. Snapshots from GCMC simulations of the CMK-5 model clearly show that the water adsorption in the outer porosity occurs via the formation and growth of clusters and there was no formation of layers of water in the porosity as seen for nonpolar fluids like nitrogen.

Simulations of transient membrane behavior in cells subjected to a high-intensity ultrashort electric pulse.

PubMed

Hu, Q; Viswanadham, S; Joshi, R P; Schoenbach, K H; Beebe, S J; Blackmore, P F

2005-03-01

A molecular dynamics (MD) scheme is combined with a distributed circuit model for a self-consistent analysis of the transient membrane response for cells subjected to an ultrashort (nanosecond) high-intensity (approximately 0.01-V/nm spatially averaged field) voltage pulse. The dynamical, stochastic, many-body aspects are treated at the molecular level by resorting to a course-grained representation of the membrane lipid molecules. Coupling the Smoluchowski equation to the distributed electrical model for current flow provides the time-dependent transmembrane fields for the MD simulations. A good match between the simulation results and available experimental data is obtained. Predictions include pore formation times of about 5-6 ns. It is also shown that the pore formation process would tend to begin from the anodic side of an electrically stressed membrane. Furthermore, the present simulations demonstrate that ions could facilitate pore formation. This could be of practical importance and have direct relevance to the recent observations of calcium release from the endoplasmic reticulum in cells subjected to such ultrashort, high-intensity pulses.

Killing machines: three pore-forming proteins of the immune system

PubMed Central

McCormack, Ryan; de Armas, Lesley; Shiratsuchi, Motoaki

2014-01-01

The evolution of early multicellular eukaryotes 400–500 million years ago required a defensive strategy against microbial invasion. Pore-forming proteins containing the membrane-attack-complex-perforin (MACPF) domain were selected as the most efficient means to destroy bacteria or virally infected cells. The mechanism of pore formation by the MACPF domain is distinctive in that pore formation is purely physical and unspecific. The MACPF domain polymerizes, refolds, and inserts itself into bilayer membranes or bacterial outer cell walls. The displacement of surface lipid/carbohydrate molecules by the polymerizing MACPF domain creates clusters of large, water-filled holes that destabilize the barrier function and provide access for additional anti-bacterial or anti-viral effectors to sensitive sites that complete the destruction of the invader via enzymatic or chemical attack. The highly efficient mechanism of anti-microbial defense by a combined physical and chemical strategy using pore-forming MACPF-proteins has been retargeted during evolution of vertebrates and mammals for three purposes: (1) to kill extracellular bacteria C9/polyC9 evolved in conjunction with complement, (2) to kill virus infected and cancer cells perforin-1/polyperforin-1 CTL evolved targeted by NK and CTL, and (3) to kill intracellular bacteria transmembrane perforin-2/putative polyperforin-2 evolved targeted by phagocytic and nonphagocytic cells. Our laboratory has been involved in the discovery and description of each of the three pore-formers that will be reviewed here. PMID:24293008

The nature of porosity in organic-rich mudstones of the Upper Jurassic Kimmeridge Clay Formation, North Sea, offshore United Kingdom

USGS Publications Warehouse

Fishman, Neil S.; Hackley, Paul C.; Lowers, Heather; Hill, Ronald J.; Egenhoff, Sven O.; Eberl, Dennis D.; Blum, Alex E.

2012-01-01

Analyses of organic-rich mudstones from wells that penetrated the Upper Jurassic Kimmeridge Clay Formation, offshore United Kingdom, were performed to evaluate the nature of both organic and inorganic rock constituents and their relation to porosity in this world-class source rock. The formation is at varying levels of thermal maturity, ranging from immature in the shallowest core samples to mature in the deepest core samples. The intent of this study was to evaluate porosity as a function of both organic macerals and thermal maturity. At least four distinct types of organic macerals were observed in petrographic and SEM analyses and they all were present across the study area. The macerals include, in decreasing abundance: 1) bituminite admixed with clays; 2) elongate lamellar masses (alginite or bituminite) with small quartz, feldspar, and clay entrained within it; 3) terrestrial (vitrinite, fusinite, semifusinite) grains; and 4) Tasmanites microfossils. Although pores in all maceral types were observed on ion-milled surfaces of all samples, the pores (largely nanopores with some micropores) vary as a function of maceral type. Importantly, pores in the macerals do not vary systematically as a function of thermal maturity, insofar as organic pores are of similar size and shape in both the immature and mature Kimmeridge rocks. If any organic pores developed during the generation of hydrocarbons, they were apparently not preserved, possibly because of the highly ductile nature of much of the rock constituents of Kimmeridge mudstones (clays and organic material). Inorganic pores (largely micropores with some nanopores) have been observed in all Kimmeridge mudstones. These pores, particularly interparticle (i.e., between clay platelets), and intraparticle (i.e., in framboidal pyrite, in partially dissolved detrital K-feldspar, and in both detrital and authigenic dolomite) are noteworthy because they compose much of the observable porosity in the shales in both immature and mature samples. The absence of a systematic increase in organic porosity as a function of either maceral type or thermal maturity indicates that such porosity was probably unrelated to hydrocarbon generation. Instead, much of the porosity within mudstones of the Kimmeridge appears to be largely intraparticle and interparticle (adjacent to inorganic constituents), so the petroleum storage potential in these organic-rich mudstones largely resides in inorganic pores.

Pore network extraction from pore space images of various porous media systems

NASA Astrophysics Data System (ADS)

Yi, Zhixing; Lin, Mian; Jiang, Wenbin; Zhang, Zhaobin; Li, Haishan; Gao, Jian

2017-04-01

Pore network extraction, which is defined as the transformation from irregular pore space to a simplified network in the form of pores connected by throats, is significant to microstructure analysis and network modeling. A physically realistic pore network is not only a representation of the pore space in the sense of topology and morphology, but also a good tool for predicting transport properties accurately. We present a method to extract pore network by employing the centrally located medial axis to guide the construction of maximal-balls-like skeleton where the pores and throats are defined and parameterized. To validate our method, various rock samples including sand pack, sandstones, and carbonates were used to extract pore networks. The pore structures were compared quantitatively with the structures extracted by medial axis method or maximal ball method. The predicted absolute permeability and formation factor were verified against the theoretical solutions obtained by lattice Boltzmann method and finite volume method, respectively. The two-phase flow was simulated through the networks extracted from homogeneous sandstones, and the generated relative permeability curves were compared with the data obtained from experimental method and other numerical models. The results show that the accuracy of our network is higher than that of other networks for predicting transport properties, so the presented method is more reliable for extracting physically realistic pore network.

Materials Research Conducted Aboard the International Space Station: Facilities Overview, Operational Procedures, and Experimental Outcomes

NASA Technical Reports Server (NTRS)

Grugel, Richard N.; Luz, Paul; Smith, Guy; Spivey, Reggie; Jeter, Linda; Gillies, Donald; Hua, Fay; Anikumar, A. V.

2007-01-01

The Microgravity Science Glovebox (MSG) and Maintenance Work Area (MWA) are facilities aboard the International Space Station (ISS) that were used to successfully conduct experiments in support of, respectively, the Pore Formation and Mobility Investigation (PFMI) and the In-Space Soldering Investigation (ISSI). The capabilities of these facilities are briefly discussed and then demonstrated by presenting "real-time" and subsequently down-linked video-taped examples from the abovementioned experiments. Data interpretation, ISS telescience, some lessons learned, and the need of such facilities for conducting work in support of understanding materials behavior, particularly fluid processing and transport scenarios, in low-gravity environments is discussed.

Materials Research Conducted Aboard the International Space Station: Facilities Overview, Operational Procedures, and Experimental Outcomes

NASA Technical Reports Server (NTRS)

Grugel, R. N.; Luz, P.; Smith, G. A.; Spivey, R.; Jeter, L.; Gillies, D. C.; Hua, F.; Anilkumar, A. V.

2006-01-01

The Microgravity Science Glovebox (MSG) and Maintenance Work Area (MWA) are facilities aboard the International Space Station (ISS) that were used to successfully conduct experiments in support of, respectively, the Pore Formation and Mobility Investigation (PFMI) and the In-Space Soldering Investigation (ISSI). The capabilities of these facilities are briefly discussed and then demonstrated by presenting real-time and subsequently down-linked video-taped examples from the abovementioned experiments. Data interpretation, ISS telescience, some lessons learned, and the need of such facilities for conducting work in support of understanding materials behavior, particularly fluid processing and transport scenarios, in low-gravity environments is discussed.

Multi-Scale Transport Properties of Fine-Grained Rocks: A Case Study of the Kirtland Formation, San Juan Basin, USA

NASA Astrophysics Data System (ADS)

Heath, J. E.; Dewers, T. A.; McPherson, B. J.; Wilson, T. H.; Flach, T.

2009-12-01

Understanding and characterizing transport properties of fine-grained rocks is critical in development of shale gas plays or assessing retention of CO2 at geologic storage sites. Difficulties arise in that both small scale (i.e., ~ nm) properties of the rock matrix and much larger scale fractures, faults, and sedimentological architecture govern migration of multiphase fluids. We present a multi-scale investigation of sealing and transport properties of the Kirtland Formation, which is a regional aquitard and reservoir seal in the San Juan Basin, USA. Sub-micron dual FIB/SEM imaging and reconstruction of 3D pore networks in core samples reveal a variety of pore types, including slit-shaped pores that are co-located with sedimentary structures and variations in mineralogy. Micron-scale chemical analysis and XRD reveal a mixture of mixed-layer smectite/illite, chlorite, quartz, and feldspar with little organic matter. Analysis of sub-micron digital reconstructions, mercury capillary injection pressure, and gas breakthrough measurements indicate a high quality sealing matrix. Natural full and partially mineralized fractures observed in core and in FMI logs include those formed from early soil-forming processes, differential compaction, and tectonic events. The potential impact of both fracture and matrix properties on large-scale transport is investigated through an analysis of natural helium from core samples, 3D seismic data and poro-elastic modeling. While seismic interpretations suggest considerable fracturing of the Kirtland, large continuous fracture zones and faults extending through the seal to the surface cannot be inferred from the data. Observed Kirtland Formation multi-scale transport properties are included as part of a risk assessment methodology for CO2 storage. Acknowledgements: The authors gratefully acknowledge the U.S. Department of Energy’s (DOE) National Energy Technology Laboratory for sponsoring this project. The DOE’s Basic Energy Science Office funded the dual FIB/SEM analysis. The Kirtland Formation overlies the coal seams of the Fruitland into which CO2 has been injected as a Phase II demonstration of the Southwest Regional Partnership on Carbon Sequestration. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the U.S. Department of Energy under contract DE-ACOC4-94AL85000.

The role of stress in self-ordered porous anodic oxide formation and corrosion of aluminum

NASA Astrophysics Data System (ADS)

Capraz, Omer Ozgur

The phenomenon of plastic flow induced by electrochemical reactions near room temperature is significant in porous anodic oxide (PAO) films, charging of lithium batteries and stress-corrosion cracking (SCC). As this phenomenon is poorly understood, fundamental insight into flow from our work may provide useful information for these problems. In-situ monitoring of the stress state allows direct correlation between stress and the current or potential, thus providing fundamental insight into technologically important deformation and failure mechanisms induced by electrochemical reactions. A phase-shifting curvature interferometry was designed to investigate the stress generation mechanisms on different systems. Resolution of our curvature interferometry was found to be ten times more powerful than that obtained by state-of-art multiple deflectometry technique and the curvature interferometry helps to resolve the conflicting reports in the literature. During this work, formation of surface patterns during both aqueous corrosion of aluminum and formation of PAO films were investigated. Interestingly, for both cases, stress induced plastic flow controls the formation of surface patterns. Pore formation mechanisms during anodizing of the porous aluminum oxide films was investigated . PAO films are formed by the electrochemical oxidation of metals such as aluminum and titanium in a solution where oxide is moderately soluble. They have been used extensively to design numerous devices for optical, catalytic, and biological and energy related applications, due to their vertically aligned-geometry, high-specific surface area and tunable geometry by adjusting process variables. These structures have developed empirically, in the absence of understanding the process mechanism. Previous experimental studies of anodizing-induced stress have extensively focused on the measurement of average stress, however the measurement of stress evolution during anodizing does not provide sufficient information to understand the potential stress mechanisms. We developed a new method, which enables us to discriminate the potential stress mechanisms during anodizing and characterize the evolution of the stress profile during film growth. Using stress measurement and characterization techniques, we demonstrated the evolution of the stress profile during the film formation and discussed the role of stress on the PAO film formation. Compressive stress builds up linearly during the anodizing, while barrier oxide film gets thicker until the onset of the pore initiation. Both barrier layer thickness and the integrated oxide stress decreased rapidly to the steady-state period when pore initiation began. The morphology change and stress transients points out the transition from elastic to plastic oxide behavior, similar to those observed in other situations such as lithium intercalation into silicon. The stress profile is consistent with the stress gradient needed to drive plastic flow observed experimentally. We also addressed the dependence of overall stress generation on applied current density. Apparently, stress caused by expansion or contraction of oxide and metal interface depends on the volume change due to overall reactions. In the last chapter, the stress generation during alkaline Al corrosion will be discussed. The enhancement of mechanical degradation by corrosion is the basis for the damage process such as stress-corrosion cracking. Understanding the synergistic effect of stress on stress-corrosion cracking mechanism is necessary to design new materials to improve the safety and viability of existing energy conversion systems. the high-resolution in-situ stress measurements during Al corrosion in alkaline solution was presented, supported by characterization techniques and Fast Fourier Transform analysis. Unprecedented curvature resolution of curvature interferometry permits the monitoring of stress during extended periods of corrosion of thick metal samples. Evolution of concaved-shaped surface patterns is in a great harmony with recorded tensile stress. Furthermore, absolute value of tensile stress onset of the plasticity depends on the dissolution rate of metal and yield stress of metal. The measurements reveal corrosion-induced tensile stress generation, leading to surface plasticity. This finding is evidence that corrosion can directly bring about plasticity, and may be relevant to mechanism of corrosion-induced degradation.

Geomechanical Characterization and Modeling of the Newark Basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collins, Daniel; Goldberg, Dave; Zakharova, Natalia

Many effective techniques for evaluation if in-situ stress and geomechanical formation properties have been developed over the years but detailed understanding of these parameters in-situ, and standard characterization and monitoring protocols for carbon dioxide storage sites are lacking. A case study is performed in the northern Newark Basin, a candidate carbon dioxide-storage site located near the New York Metropolitan area. Possible impacts of seismic hazard and carbon dioxide leakage are particularly important due to a high population density across the basin. As one of the best-studied Mesozoic rift basins, the Newark Basin represents a great type locality for similar basinsmore » along the east coast and the results established in this project provide a robust tool for comparison to other Mesozoic basin data sets and locations (e.g., Georgia Rift Basin), where similar comprehensive core data sets and well testing results are not available. The project leveraged existing core samples to characterize and measure the strength of a series of differing lithologies and formations in the basin, with 28 samples fully tested. The orientation and magnitude of in-situ stresses were measured in an existing test well using a novel wireline tool set-up. This new methodology employed a “pre-stress” packer module to attempt to create an initial formation break using the force of the packer itself against the borehole wall. This enhancement in the testing methodology can be used in places where traditional methods are insufficient to break down a formation. Following the pre-stress packer sets, the improved Schlumberger Modular Formation Dynamics Tester tool-string was then used to perform traditional straddled formation breakdown testing of selected intervals. Testing indicated that formation breakdown was successfully achieved at two of the six test intervals, with an additional two tests sets indicating re-opening and propagation of pre-existing breaks out into the formation. New laboratory strength data acquired by this project, coupled with an updated basin-specific compressional acoustic velocity to unconfined compressional strength (Vp-UCS) relationship, was used for evaluation of the state of stress in the northern Newark Basin. Formation breakdown testing in the Lamont-Doherty Earth Observatory Test Well No. 3 allows for the determination of the full stress field at this location. The evaluation indicates that the natural fractures in the depth range of 244 to 457 meters (800 to 1,500 feet) are not critically stressed, however, they are close to their failure limit. Therefore, they likely could not withstand significant pore pressure increases anticipated with industrial scale geologic carbon sequestration. Failure modeling with the updated formation strength data shows that in-situ stresses must be at the frictional failure limit in the reverse-faulting stress regime at all depths in the northern portion of the basin, where borehole breakouts are observed. The disappearance of breakouts below a depth of 1,372 meters (4,500 feet) in the northern portion of the basin coincides with a significant increase in formation strength. In this deeper section, the apparent higher stress gradient would place existing fractures further away from their failure limit, making them more suitable for injection. Forward modeling of the effective stresses under increased pore pressure conditions suggest that a mere 2,758 kPa (400 psi) change in pore pressure could bring select fractures to failure. This is a fairly small-change in expected pore pressure increases at industrial scale injection operations. Therefore, given the presence of nearly critically stressed fractures located just a few hundred meters above these depths, large-volume fluid injections appear to increase geological risk in the northern portion of the Newark Basin.« less

Comparison of Pore Fractal Characteristics Between Marine and Continental Shales

NASA Astrophysics Data System (ADS)

Liu, Jun; Yao, Yanbin; Liu, Dameng; Cai, Yidong; Cai, Jianchao

Fractal characterization offers a quantitative evaluation on the heterogeneity of pore structure which greatly affects gas adsorption and transportation in shales. To compare the fractal characteristics between marine and continental shales, nine samples from the Lower Silurian Longmaxi formation in the Sichuan basin and nine from the Middle Jurassic Dameigou formation in the Qaidam basin were collected. Reservoir properties and fractal dimensions were characterized for all the collected samples. In this study, fractal dimensions were originated from the Frenkel-Halsey-Hill (FHH) model with N2 adsorption data. Compared to continental shale, marine shale has greater values of quartz content, porosity, specific surface area and total pore volume but lower level of clay minerals content, permeability, average pore diameter and methane adsorption capacity. The quartz in marine shale is mostly associated with biogenic origin, while that in continental shale is mainly due to terrigenous debris. The N2 adsorption-desorption isotherms exhibit that marine shale has fewer inkbottle-shaped pores but more plate-like and slit-shaped pores than continental shale. Two fractal dimensions (D1 and D2) were obtained at P/Po of 0-0.5 and 0.5-1. The dimension D2 is commonly greater than D1, suggesting that larger pores (diameter >˜ 4nm) have more complex structures than small pores (diameter <˜ 4nm). The fractal dimensions (both D1 and D2) positively correlate to clay minerals content, specific surface area and methane adsorption capacity, but have negative relationships with porosity, permeability and average pore diameter. The fractal dimensions increase proportionally with the increasing quartz content in marine shale but have no obvious correlation with that in continental shale. The dimension D1 is correlative to the TOC content and permeability of marine shale at a similar degree with dimension D2, while the dimension D1 is more sensitive to those of continental shale than dimension D2. Compared with dimension D2, for two shales, dimension D1 is better associated with the content of clay minerals but has worse correlations with the specific surface area and average pore diameter.

Multi-Scale Investigation of the Formation and Breakdown of Passive Films on Carbon Steel Rebar in Concrete

NASA Astrophysics Data System (ADS)

Ghods, Pouria

The multi-scale investigation presented in this thesis was carried out to understand better the mechanisms of passivation and chloride-induced depassivation of carbon steel reinforcement in concrete. The study consisted of electrochemical experiments (electrochemical impedance spectroscopy, linear polarization resistance, free corrosion potential, anodic polarization), microscopic examinations (scanning electron microscopy, transmission electron microscopy, selected area diffraction, convergent beam electron diffraction), numerical modeling (finite element method), and spectroscopic studies (x-ray photoelectron, energy dispersed x-ray, electron energy loss). Electrochemical and microscopic studies showed that the composition of the pore solution and the surface conditions of the rebar affect the passivity and depassivation of carbon steel in concrete. It was demonstrated that crevices between mill scale and steel may become potential sites for depassivation and pit nucleation. The numerical investigation that was carried out to test this hypothesis confirmed that the ratio of chloride to hydroxide concentrations, Cl-/OH-, in crevices increased to levels higher than that of the bulk pore solution, making crevices more vulnerable to depassivation. Therefore, it was concluded that the variability associated with reported chloride thresholds might be attributed, at least in part, to the variability in mill scale properties resulting from the variability in manufacturing. The nano-scale microscopic and spectroscopic studies indicated the formation of 4-10 nm-thick passive oxide films on carbon steel in simulated concrete pore solutions, and these films consisted of two layers separated with an indistinct border. The inner layer was mainly composed of protective Fe2+-rich oxides that are in epitaxial relationship with the underlying steel surface; while the outer layer mostly consisted of (possibly porous) Fe3+-rich oxides, through which chlorides can penetrate. It was proposed that, in the presence of chlorides, Fe+2-rich oxides in the inner layer transform into Fe+3-rich oxides and potentially become un-protective. Although how this transformation occurs is still subject of future research, there are evidences showing that the process most likely leads to the formation of local anodic and cathodic sites on the steel surface.

Fibril growth kinetics link buffer conditions and topology of 3D collagen I networks.

PubMed

Kalbitzer, Liv; Pompe, Tilo

2018-02-01

Three-dimensional fibrillar networks reconstituted from collagen I are widely used as biomimetic scaffolds for in vitro and in vivo cell studies. Various physicochemical parameters of buffer conditions for in vitro fibril formation are well known, including pH-value, ion concentrations and temperature. However, there is a lack of a detailed understanding of reconstituting well-defined 3D network topologies, which is required to mimic specific properties of the native extracellular matrix. We screened a wide range of relevant physicochemical buffer conditions and characterized the topology of the reconstituted 3D networks in terms of mean pore size and fibril diameter. A congruent analysis of fibril formation kinetics by turbidimetry revealed the adjustment of the lateral growth phase of fibrils by buffer conditions to be key in the determination of pore size and fibril diameter of the networks. Although the kinetics of nucleation and linear growth phase were affected by buffer conditions as well, network topology was independent of those two growth phases. Overall, the results of our study provide necessary insights into how to engineer 3D collagen matrices with an independent control over topology parameters, in order to mimic in vivo tissues in in vitro experiments and tissue engineering applications. The study reports a comprehensive analysis of physicochemical conditions of buffer solutions to reconstitute defined 3D collagen I matrices. By a combined analysis of network topology, i.e., pore size and fibril diameter, and the kinetics of fibril formation we can reveal the dependence of 3D network topology on buffer conditions, such as pH-value, phosphate concentration and sodium chloride content. With those results we are now able to provide engineering strategies to independently tune the topology parameters of widely used 3D collagen scaffolds based on the buffer conditions. By that, we enable the straightforward mimicking of extracellular matrices of in vivo tissues for in vitro cell culture experiments and tissue engineering applications. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Shale Gas Petrophysical Models: an evaluation of contrasting approaches and assumptions

NASA Astrophysics Data System (ADS)

Inwood, Jennifer; Lovell, Mike; Davies, Sarah; Fishwick, Stewart; Taylor, Kevin

2015-04-01

Shale gas refers to fine-grained formations, or mudstones, where organic matter has matured sufficiently to produce predominantly gas, but that gas has not migrated any significant distance and hence the source rock is effectively the reservoir. Due to the success of shale gas extraction in the USA, many European countries are assessing their potential resources. A key uncertainty in evaluating the resource is the estimation of gas in place and most models are based on North American plays. However, it would seem that no single model to date can confidently predict the gas in place for a 'new' shale formation. Shale gas is frequently characterized by two distinct gas components: free gas is able to move and occupies the pores, while adsorbed gas is fixed onto organic surfaces and held in place by pressure. There are a number of different published methodologies that attempt to take account for this complicated distribution of gas within the rock ranging from models where the importance of the adsorbed gas is assumed to be negligible to those where all gas is assumed to exist within the organic pores and none within the mineral pore spaces. Models that assume both components are important and occupy adjacent volumes need to consider how to separate out the two to avoid double counting. Due to the heterogeneity of mudstones the most appropriate model may vary downhole as well as across adjacent wells. In this pilot study we consider the underlying assumptions and categorize models dependent on the deterministic or probabilistic approach used. We use an initial dataset from North America to test and compare a number of different approaches before expanding the analysis to further formations that span a range of geological and petrophysical characteristics. We then review and evaluate the models, identifying key variables and, where possible, determining their importance through sensitivity analysis. This work aims to establish guidelines for selecting the most appropriate petrophysical model for evaluating the gas in place in a shale gas play, and as such provides a more informed understanding of this petrophysical maze for both specialists and non-specialists.

Pore Formation and Mobility Investigation video images

NASA Technical Reports Server (NTRS)

2003-01-01

Video images sent to the ground allow scientists to watch the behavior of the bubbles as they control the melting and freezing of the material during the Pore Formation and Mobility Investigation (PFMI) in the Microgravity Science Glovebox aboard the International Space Station. While the investigation studies the way that metals behave at the microscopic scale on Earth -- and how voids form -- the experiment uses a transparent material called succinonitrile that behaves like a metal to study this problem. The bubbles do not float to the top of the material in microgravity, so they can study their interactions.

The exocytotic fusion pore modeled as a lipidic pore.

PubMed Central

Nanavati, C; Markin, V S; Oberhauser, A F; Fernandez, J M

1992-01-01

Freeze-fracture electron micrographs from degranulating cells show that the lumen of the secretory granule is connected to the extracellular compartment via large (20 to 150 nm diameter) aqueous pores. These exocytotic fusion pores appear to be made up of a highly curved bilayer that spans the plasma and granule membranes. Conductance measurements, using the patch-clamp technique, have been used to study the fusion pore from the instant it conducts ions. These measurements reveal the presence of early fusion pores that are much smaller than those observed in electron micrographs. Early fusion pores open abruptly, fluctuate, and then either expand irreversibly or close. The molecular structure of these early fusion pores is unknown. In the simplest extremes, these early fusion pores could be either ion channel like protein pores or lipidic pores. Here, we explored the latter possibility, namely that of the early exocytotic fusion pore modeled as a lipid-lined pore whose free energy was composed of curvature elastic energy and work done by tension. Like early exocytotic fusion pores, we found that these lipidic pores could open abruptly, fluctuate, and expand irreversibly. Closure of these lipidic pores could be caused by slight changes in lipid composition. Conductance distributions for stable lipidic pores matched those of exocytotic fusion pores. These findings demonstrate that lipidic pores can exhibit the properties of exocytotic fusion pores, thus providing an alternate framework with which to understand and interpret exocytotic fusion pore data. PMID:1420930

Impact of S fertilizers on pore-water Cu dynamics and transformation in a contaminated paddy soil with various flooding periods.

PubMed

Yang, Jianjun; Zhu, Shenhai; Zheng, Cuiqing; Sun, Lijuan; Liu, Jin; Shi, Jiyan

2015-04-09

Impact of S fertilization on Cu mobility and transformation in contaminated paddy soils has been little reported. In this study, we investigated the dynamics and transformation of dissolved and colloidal Cu in the pore water of a contaminated paddy soil after applying ammonium sulphate (AS) and sulfur coated urea (SCU) with various flooding periods (1, 7 and 60 days). Compared to the control soil, the AS-treated soil released more colloidal and dissolved Cu over the entire flooding period, while the SCU-treated soil had lower colloidal Cu after 7-day flooding but higher colloidal and dissolved Cu after 60-day flooding. Microscopic X-ray fluorescence (μ-XRF) analysis found a close relationship between Fe and Cu distribution on soil colloids after 60-day flooding, implying the formation of colloidal Fe/Cu sulphide coprecipitates. Cu K-edge X-ray absorption near-edge structure (XANES) spectroscopy directly revealed the transformation of outer-sphere complexed Cu(II) species to Cu(II) sulphide and reduced Cu2O in the colloids of S-treated soils after 60-day flooding. These results demonstrated the great influence of S fertilization on pore-water Cu mobility by forming Cu sulphide under flooding conditions, which facilitated our understanding and control of Cu loss in contaminated paddy soils under S fertilization. Copyright © 2015 Elsevier B.V. All rights reserved.

Spectro-microscopic study of the formation of supramolecular networks

NASA Astrophysics Data System (ADS)

Sadowski, Jerzy T.

2015-03-01

Metal-organic frameworks (MOFs) are emerging as a new class of materials for CO2 capture. There are many fundamental questions, including the optimum pore size and arrangement of the molecules in the structure to achieve highest CO2 uptake. As only the surface is of interest for potential applications such as heterogeneous catalysis, nano-templating, and sensing, 2D analogs of MOFs can serve as good model systems. Utilizing capabilities of LEEM/PEEM for non-destructive interrogation of the real-time molecular self-assembly, we investigated supramolecular systems based on carboxylic acid-metal complexes, such as trimesic and mellitic acid, doped with transition metals. Such 2D networks act as host systems for transition-metal phthalocyanines (MPc; M = Fe, Ti, Sc) and the electrostatic interactions of CO2 molecules with transition metal ions, can be tuned by controlling the type of TM ion and the size of the pore in the host network. The understanding of directed self-assembly by controlling the molecule-substrate interaction can enable us to engineer the pore size and density, and thus tune the host's chemical activity. Research carried out at the Center for Functional Nanomaterials and National Synchrotron Light Source, Brookhaven National Laboratory, which are supported by the U.S. Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10.

Impacts of hydrogeological characteristics on groundwater-level changes induced by earthquakes

NASA Astrophysics Data System (ADS)

Liu, Ching-Yi; Chia, Yeeping; Chuang, Po-Yu; Chiu, Yung-Chia; Tseng, Tai-Lin

2018-03-01

Changes in groundwater level during earthquakes have been reported worldwide. In this study, field observations of co-seismic groundwater-level changes in wells under different aquifer conditions and sampling intervals due to near-field earthquake events in Taiwan are presented. Sustained changes, usually observed immediately after earthquakes, are found in the confined aquifer. Oscillatory changes due to the dynamic strain triggered by passing earthquake waves can only be recorded by a high-frequency data logger. While co-seismic changes recover rapidly in an unconfined aquifer, they can sustain for months or longer in a confined aquifer. Three monitoring wells with long-term groundwater-level data were examined to understand the association of co-seismic changes with local hydrogeological conditions. The finite element software ABAQUS is used to simulate the pore-pressure changes induced by the displacements due to fault rupture. The calculated co-seismic change in pore pressure is related to the compressibility of the formation. The recovery rate of the change is rapid in the unconfined aquifer due to the hydrostatic condition at the water table, but slow in the confined aquifer due to the less permeable confining layer. Fracturing of the confining layer during earthquakes may enhance the dissipation of pore pressure and induce the discharge of the confined aquifer. The study results indicated that aquifer characteristics play an important role in determining groundwater-level changes during and after earthquakes.

Transmembrane Pores Formed by Human Antimicrobial Peptide LL-37

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qian, Shuo

Human LL-37 is a multifunctional cathelicidin peptide that has shown a wide spectrum of antimicrobial activity by permeabilizing microbial membranes similar to other antimicrobial peptides; however, its molecular mechanism has not been clarified. Two independent experiments revealed LL-37 bound to membranes in the {alpha}-helical form with the axis lying in the plane of membrane. This led to the conclusion that membrane permeabilization by LL-37 is a nonpore carpet-like mechanism of action. Here we report the detection of transmembrane pores induced by LL-37. The pore formation coincided with LL-37 helices aligning approximately normal to the plane of the membrane. We observedmore » an unusual phenomenon of LL-37 embedded in stacked membranes, which are commonly used in peptide orientation studies. The membrane-bound LL-37 was found in the normal orientation only when the membrane spacing in the multilayers exceeded its fully hydrated value. This was achieved by swelling the stacked membranes with excessive water to a swollen state. The transmembrane pores were detected and investigated in swollen states by means of oriented circular dichroism, neutron in-plane scattering, and x-ray lamellar diffraction. The results are consistent with the effect of LL-37 on giant unilamellar vesicles. The detected pores had a water channel of radius 2333 {angstrom}. The molecular mechanism of pore formation by LL-37 is consistent with the two-state model exhibited by magainin and other small pore-forming peptides. The discovery that peptide-membrane interactions in swollen states are different from those in less hydrated states may have implications for other large membrane-active peptides and proteins studied in stacked membranes.« less

Pore Pressure and Field stress variation from Salt Water Injection; A case Study from Beaver Lodge Field in Williston Basin

NASA Astrophysics Data System (ADS)

Mohammed, R. A.; Khatibi, S.

2017-12-01

One of the major concerns in producing from oil and gas reservoirs in North American Basins is the disposal of high salinity salt water. It is a misconception that Hydro frack triggers Earthquakes, but due to the high salinity and density of water being pumped to the formation that has pore space of the rock already filled, which is not the case in Hydro-frack or Enhanced Oil Recovery in which fracturing fluid is pumped into empty pore space of rocks in depleted reservoirs. A review on the Bakken history showed that the concerns related to induce seismicity has increased over time due to variations in Pore pressure and In-situ stress that have shown steep changes in the region over the time. In this study, we focused on Pore pressure and field Stress variations in lower Cretaceous Inyan Kara and Mississippian Devonian Bakken, Inyan Kara is the major source for class-II salt-water disposal in the basin. Salt-water disposal is the major cause for induced seismicity. A full field study was done on Beaver Lodge Field, which has many salt-water disposal wells Adjacent to Oil and Gas Wells. We analyzed formation properties, stresses, pore-pressure, and fracture gradient profile in the field and. The constructed Mechanical Earth Model (MEM) revealed changes in pore pressure and stresses over time due to saltwater injection. Well drilled in the past were compared to recently drilled wells, which showed much stress variations. Safe mud weight Window of wells near proximity of injection wells was examined which showed many cases of wellbore instabilities. Results of this study will have tremendous impact in studying environmental issues and the future drilling and Fracking operations.

Synthesis of flower-like Boehmite (γ-AlOOH) via a one-step ionic liquid-assisted hydrothermal route

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Zhe, E-mail: tangzhe1983@163.com; Liang, Jilei, E-mail: liangjilei_httplan@126.com; Li, Xuehui, E-mail: lxhhmx@163.com

A simple and novel synthesis process, one-step ionic liquid-assisted hydrothermal synthesis route, has been developed in the work to synthesize Bohemithe (γ-AlOOH) with flower-like structure. The samples were characterized by X-ray Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FT-IR) and Scanning Electron Microscope (SEM). Ionic liquid [Omim]{sup +}Cl{sup −}, as a template, plays an important role in the morphology and pore structure of the products due to its strong interactions with reaction particles. With the increase in the dosage of ionic liquid [Omim]{sup +}Cl{sup −}, the morphology of the γ-AlOOH was changed from initial bundles of nanosheets (without ionic liquid) intomore » final well-developed monodispersed 3D flower-like architectures ([Omim]{sup +}Cl{sup −}=72 mmol). The pore structure was also altered gradually from initial disordered slit-like pore into final relatively ordered ink-bottle pore. Furthermore, the proposed formation mechanism and other influencing factors such as reaction temperature and urea on formation and morphology of the γ-AlOOH have also been investigated. - Graphical abstract: The flower-like γ-AlOOH architectures composed by nanosheets with narrow size distribution (1.6–2.2 μm) and uniform pore size (6.92 nm) have been synthesized via a one-step ionic liquid-assisted hydrothermal route. - Highlights: • The γ-AlOOH microflowers were synthesized via an ionic liquid-assisted hydrothermal route. • Ionic liquid plays an important role on the morphology and porous structure of the products. • Ionic liquid can be easily removed from the products and reused in recycling experiments. • A “aggregation–recrystallization–Ostwald Ripening“formation mechanism may occur.« less

Effects of fluid-rock interactions on faulting within active fault zones - evidence from fault rock samples retrieved from international drilling projects

NASA Astrophysics Data System (ADS)

Janssen, C.; Wirth, R.; Kienast, M.; Yabe, Y.; Sulem, J.; Dresen, G. H.

2015-12-01

Chemical and mechanical effects of fluids influence the fault mechanical behavior. We analyzed fresh fault rocks from several scientific drilling projects to study the effects of fluids on fault strength. For example, in drill core samples on a rupture plane of an Mw 2.2 earthquake in a deep gold mine in South Africa the main shock occurred on a preexisting plane of weakness that was formed by fluid-rock interaction (magnesiohornblende was intensively altered to chlinochlore). The plane acted as conduit for hydrothermal fluids at some time in the past. The chemical influence of fluids on mineralogical alteration and geomechanical processes in fault core samples from SAFOD (San Andreas Fault Observatory at Depth) is visible in pronounced dissolution-precipitation processes (stylolites, solution seams) as well as in the formation of new phases. Detrital quartz and feldspar grains are partially dissolved and replaced by authigenic illite-smectite (I-S) mixed-layer clay minerals. Transmission Electron Microscopy (TEM) imaging of these grains reveals that the alteration processes and healing were initiated within pores and small intra-grain fissures. Newly formed phyllosilicates growing into open pore spaces likely reduced the fluid permeability. The mechanical influence of fluids is indicated by TEM observations, which document open pores that formed in-situ in the gouge material during or after deformation. Pores were possibly filled with formation water and/or hydrothermal fluids suggesting elevated fluid pressure preventing pore collapse. Fluid-driven healing of fractures in samples from SAFOD and the DGLab Gulf of Corinth project is visible in cementation. Cathodoluminescence microscopy (CL) reveals different generations of calcite veins. Differences in CL-colors suggest repeated infiltration of fluids with different chemical composition from varying sources (formation and meteoric water).

Pore-scale simulation of CO2-water-rock interactions

NASA Astrophysics Data System (ADS)

Deng, H.; Molins, S.; Steefel, C. I.; DePaolo, D. J.

2017-12-01

In Geologic Carbon Storage (GCS) systems, the migration of scCO2 versus CO2-acidifed brine ultimately determines the extent of mineral trapping and caprock integrity, i.e. the long-term storage efficiency and security. While continuum scale multiphase reactive transport models are valuable for large scale investigations, they typically (over-)simplify pore-scale dynamics and cannot capture local heterogeneities that may be important. Therefore, pore-scale models are needed in order to provide mechanistic understanding of how fine scale structural variations and heterogeneous processes influence the transport and geochemistry in the context of multiphase flow, and to inform parameterization of continuum scale modeling. In this study, we investigate the interplay of different processes at pore scale (e.g. diffusion, reactions, and multiphase flow) through the coupling of a well-developed multiphase flow simulator with a sophisticated reactive transport code. The objectives are to understand where brine displaced by scCO2 will reside in a rough pore/fracture, and how the CO2-water-rock interactions may affect the redistribution of different phases. In addition, the coupled code will provide a platform for model testing in pore-scale multiphase reactive transport problems.

Phosphatidylinositol 4,5-Bisphosphate (PI(4,5)P2)-dependent Oligomerization of Fibroblast Growth Factor 2 (FGF2) Triggers the Formation of a Lipidic Membrane Pore Implicated in Unconventional Secretion*

PubMed Central

Steringer, Julia P.; Bleicken, Stephanie; Andreas, Helena; Zacherl, Sonja; Laussmann, Mareike; Temmerman, Koen; Contreras, F. Xabier; Bharat, Tanmay A. M.; Lechner, Johannes; Müller, Hans-Michael; Briggs, John A. G.; García-Sáez, Ana J.; Nickel, Walter

2012-01-01

Fibroblast growth factor 2 (FGF2) is a critical mitogen with a central role in specific steps of tumor-induced angiogenesis. It is known to be secreted by unconventional means bypassing the endoplasmic reticulum/Golgi-dependent secretory pathway. However, the mechanism of FGF2 membrane translocation into the extracellular space has remained elusive. Here, we show that phosphatidylinositol 4,5-bisphosphate-dependent membrane recruitment causes FGF2 to oligomerize, which in turn triggers the formation of a lipidic membrane pore with a putative toroidal structure. This process is strongly up-regulated by tyrosine phosphorylation of FGF2. Our findings explain key requirements of FGF2 secretion from living cells and suggest a novel self-sustained mechanism of protein translocation across membranes with a lipidic membrane pore being a transient translocation intermediate. PMID:22730382

Genus Distichopora (Cnidaria, Hydrozoa): from primary cyclosystem to adult pore organisation

NASA Astrophysics Data System (ADS)

Puce, S.; Pica, D.; Brun, F.; Mancini, L.; Bavestrello, G.

2012-09-01

This investigation provides the first detailed description of the growth stages of two Distichopora species showing the formation of a primary cyclosystem and explaining the growth process leading from primary cyclosystem to adult pore organisation. The earliest observed stage is an oval calcareous disc from which, at a later stage, a primary cyclosystem raises up. Then, the addition of new gastropores and dactylopores leads to the pore rows typical of the genus. Using X-ray computed microtomography, we are able to visualise the dense canal network that permeates the coenosteum and envelops the gastropores and the dactylopores in all the observed growth stages. In both species, the thin canals surrounding the gastropores are responsible for the formation of the new gastropores that originate between the old ones, while the thin canals placed on the external side of the dactylopore rows produce the new dactylopores.

Cytotoxic T cells use mechanical force to potentiate target cell killing

PubMed Central

Basu, Roshni; Whitlock, Benjamin M.; Husson, Julien; Le Floc’h, Audrey; Jin, Weiyang; Oyler-Yaniv, Alon; Dotiwala, Farokh; Giannone, Gregory; Hivroz, Claire; Biais, Nicolas; Lieberman, Judy; Kam, Lance C.; Huse, Morgan

2016-01-01

SUMMARY The immunological synapse formed between a cytotoxic T lymphocyte (CTL) and an infected or transformed target cell is a physically active structure capable of exerting mechanical force. Here, we investigated whether synaptic forces promote the destruction of target cells. CTLs kill by secreting toxic proteases and the pore forming protein perforin into the synapse. Biophysical experiments revealed a striking correlation between the magnitude of force exertion across the synapse and the speed of perforin pore formation on the target cell, implying that force potentiates cytotoxicity by enhancing perforin activity. Consistent with this interpretation, we found that increasing target cell tension augmented pore formation by perforin and killing by CTLs. Our data also indicate that CTLs coordinate perforin release and force exertion in space and time. These results reveal an unappreciated physical dimension to lymphocyte function and demonstrate that cells use mechanical forces to control the activity of outgoing chemical signals. PMID:26924577

Pore configuration landscape of granular crystallization.

PubMed

Saadatfar, M; Takeuchi, H; Robins, V; Francois, N; Hiraoka, Y

2017-05-12

Uncovering grain-scale mechanisms that underlie the disorder-order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics.

Pore configuration landscape of granular crystallization

PubMed Central

Saadatfar, M.; Takeuchi, H.; Robins, V.; Francois, N.; Hiraoka, Y.

2017-01-01

Uncovering grain-scale mechanisms that underlie the disorder–order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics. PMID:28497794

Pore configuration landscape of granular crystallization

NASA Astrophysics Data System (ADS)

Saadatfar, M.; Takeuchi, H.; Robins, V.; Francois, N.; Hiraoka, Y.

2017-05-01

Uncovering grain-scale mechanisms that underlie the disorder-order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics.

Temperature and Pressure from Collapsing Pores in HMX

NASA Astrophysics Data System (ADS)

Hardin, D. Barrett

2017-06-01

The thermal and mechanical response of collapsing voids in HMX is analyzed. In this work, the focus is simulating the temperature and pressure fields arising from isolated, idealized pores as they collapse in the presence of a shock. HMX slabs are numerically generated which contain a single pore, isolated from the boundaries to remove all wave reflections. In order to understand the primary pore characteristics leading to temperature rise, a series of 2D, plane strain simulations are conducted on HMX slabs containing both cylindrical and elliptical pores of constant size equal to the area of a circular pore with a 1 micron diameter. Each of these pore types is then subjected to shock pressures ranging from a weak shock that is unable to fully collapse the pore to a strong shock which overwhelms the tendency for localization. Results indicate that as shock strength increases, pore collapse phenomenology for a cylindrical pore transitions from a mode dominated by localized melt cracking to an idealized hydrodynamic pore collapse. For the case of elliptical pores, the orientation causing maximum temperature and pressure rise is found. The relative heating in elliptical pores is then quantified as a function of pore orientation and aspect ratio for a pore of a given area. Distribution A: Distribution unlimited. (96TW 2017-0036).

Coupling root architecture and pore network modeling - an attempt towards better understanding root-soil interactions

NASA Astrophysics Data System (ADS)

Leitner, Daniel; Bodner, Gernot; Raoof, Amir

2013-04-01

Understanding root-soil interactions is of high importance for environmental and agricultural management. Root uptake is an essential component in water and solute transport modeling. The amount of groundwater recharge and solute leaching significantly depends on the demand based plant extraction via its root system. Plant uptake however not only responds to the potential demand, but in most situations is limited by supply form the soil. The ability of the plant to access water and solutes in the soil is governed mainly by root distribution. Particularly under conditions of heterogeneous distribution of water and solutes in the soil, it is essential to capture the interaction between soil and roots. Root architecture models allow studying plant uptake from soil by describing growth and branching of root axes in the soil. Currently root architecture models are able to respond dynamically to water and nutrient distribution in the soil by directed growth (tropism), modified branching and enhanced exudation. The porous soil medium as rooting environment in these models is generally described by classical macroscopic water retention and sorption models, average over the pore scale. In our opinion this simplified description of the root growth medium implies several shortcomings for better understanding root-soil interactions: (i) It is well known that roots grow preferentially in preexisting pores, particularly in more rigid/dry soil. Thus the pore network contributes to the architectural form of the root system; (ii) roots themselves can influence the pore network by creating preferential flow paths (biopores) which are an essential element of structural porosity with strong impact on transport processes; (iii) plant uptake depend on both the spatial location of water/solutes in the pore network as well as the spatial distribution of roots. We therefore consider that for advancing our understanding in root-soil interactions, we need not only to extend our root models, but also improve the description of the rooting environment. Until now there have been no attempts to couple root architecture and pore network models. In our work we present a first attempt to join both types of models using the root architecture model of Leitner et al., (2010) and a pore network model presented by Raoof et al. (2010). The two main objectives of coupling both models are: (i) Representing the effect of root induced biopores on flow and transport processes: For this purpose a fixed root architecture created by the root model is superimposed as a secondary root induced pore network to the primary soil network, thus influencing the final pore topology in the network generation. (ii) Representing the influence of pre-existing pores on root branching: Using a given network of (rigid) pores, the root architecture model allocates its root axes into these preexisting pores as preferential growth paths with thereby shape the final root architecture. The main objective of our study is to reveal the potential of using a pore scale description of the plant growth medium for an improved representation of interaction processes at the interface of root and soil. References Raoof, A., Hassanizadeh, S.M. 2010. A New Method for Generating Pore-Network Models. Transp. Porous Med. 81, 391-407. Leitner, D, Klepsch, S., Bodner, G., Schnepf, S. 2010. A dynamic root system growth model based on L-Systems. Tropisms and coupling to nutrient uptake from soil. Plant Soil 332, 177-192.

Rich in life but poor in data: the known knowns and known unknowns of modelling how soil biology drives soil structure

NASA Astrophysics Data System (ADS)

Hallett, Paul; Ogden, Mike

2015-04-01

Soil biology has a fascinating capacity to manipulate pore structure by altering or overcoming hydrological and mechanical properties of soil. Many have postulated, quite rightly, that this capacity of soil biology to 'engineer' its habitat drives its diversity, improves competitiveness and increases resilience to external stresses. A large body of observational research has quantified pore structure evolution accompanied by the growth of organisms in soil. Specific compounds that are exuded by organisms or the biological structures they create have been isolated and found to correlate well with observed changes to pore structure or soil stability. This presentation will provide an overview of basic mechanical and hydrological properties of soil that are affected by biology, and consider missing data that are essential to model how they impact soil structure evolution. Major knowledge gaps that prevent progress will be identified and suggestions will be made of how research in this area should progress. We call for more research to gain a process based understanding of structure formation by biology, to complement observational studies of soil structure before and after imposed biological activity. Significant advancement has already been made in modelling soil stabilisation by plant roots, by combining data on root biomechanics, root-soil interactions and soil mechanical properties. Approaches for this work were developed from earlier materials science and geotechnical engineering research, and the same ethos should be adopted to model the impacts of other biological compounds. Fungal hyphae likely reinforce soils in a similar way to plant roots, with successful biomechanical measurements of these micron diameter structures achieved with micromechanical test frames. Extending root reinforcement models to fungi would not be a straightforward exercise, however, as interparticle bonding and changes to pore water caused by fungal exudates could have a major impact on structure formation and stability. Biological exudates from fungi, bacteria or roots have been found to decrease surface tension and increase viscosity of pore water, with observed impacts to soil strength and water retention. Modelling approaches developed in granular mechanics and geotechnical engineering could be built upon to incorporate biological transformations of hydrological and mechanical properties of soil. With new testing approaches, adapted from materials science, pore scale hydromechanical impacts from biological exudates can be quantified. The research can be complemented with model organisms with differences in biological structures (e.g. root hair mutants), exudation or other properties. Coupled with technological advances that provide 4D imaging of soil structure at relatively rapid capture rates, the potential opportunities to disentangle and model how biology drives soil structure evolution and stability are vast. By quantifying basic soil hydrological and mechanical processes that are driven by soil biology, unknown unknowns may also emerge, providing new insight into how soils function.

Extraction of pore-morphology and capillary pressure curves of porous media from synchrotron-based tomography data

DOE PAGES

Yang, Feifei; Hingerl, Ferdinand F.; Xiao, Xianghui; ...

2015-06-03

The elevated level of atmospheric carbon dioxide (CO 2) has caused serious concern of the progression of global warming. Geological sequestration is considered as one of the most promising techniques for mitigating the damaging effect of global climate change. Investigations over wide range of length-scales are important for systematic evaluation of the underground formations from prospective CO 2 reservoir. Understanding the relationship between the micro morphology and the observed macro phenomena is even more crucial. Here we show Synchrotron based X-ray micro tomographic study of the morphological buildup of Sandstones. We present a numerical method to extract the pore sizesmore » distribution of the porous structure directly, without approximation or complex calculation. We have also demonstrated its capability in predicting the capillary pressure curve in a mercury intrusion porosimetry (MIP) measurement. The method presented in this work can be directly applied to the morphological studies of heterogeneous systems in various research fields, ranging from Carbon Capture and Storage, and Enhanced Oil Recovery to environmental remediation in the vadose zone.« less

The interaction of Clostridium perfringens enterotoxin with receptor claudins

PubMed Central

Shrestha, Archana; Uzal, Francisco A.; McClane, Bruce A.

2016-01-01

Clostridium perfringens enterotoxin (CPE) has significant medical importance due to its involvement in several common human gastrointestinal diseases. This 35 kDa single polypeptide toxin consists of two domains: a C-terminal domain involved in receptor binding and an N-terminal domain involved in oligomerization, membrane insertion and pore formation. The action of CPE starts with its binding to receptors, which include certain members of the claudin tight junction protein family; bound CPE then forms a series of complexes, one of which is a pore that causes the calcium influx responsible for host cell death. Recent studies have revealed that CPE binding to claudin receptors involves interactions between the C-terminal CPE domain and both the 1st and 2nd extracellular loops (ECL-1 and ECL-2) of claudin receptors. Of particular importance for this binding is the docking of ECL-2 into a pocket present in the C-terminal domain of the toxin. This increased understanding of CPE interactions with claudin receptors is now fostering the development of receptor decoy therapeutics for CPE-mediated gastrointestinal disease, reagents for cancer therapy/diagnoses and enhancers of drug delivery. PMID:27090847

a Fractal Analysis for Net Present Value of Multi-Stage Hydraulic Fractured Horizontal Well

NASA Astrophysics Data System (ADS)

Lu, Hong-Lin; Zhang, Ji-Jun; Tan, Xiao-Hua; Li, Xiao-Ping; Zhao, Jia-Hui

Because of the low permeability, multi-stage hydraulic fractured horizontal wells (MHFHWs) occupy a dominant position among production wells in tight gas reservoir. However, net present value (NPV) estimation method for MHFHW in tight gas reservoirs often ignores the effect of heterogeneity in microscopic pore structure. Apart from that, a new fractal model is presented for NPV of MHFHW, based on the fractal expressions of formation parameters. First, with the aid of apparent permeability model, a pseudo pressure expression considering both reservoir fractal features and slippage effect is derived, contributing to establish the productivity model. Secondly, economic assessment method is built based on the fractal productivity model, in order to obtain the NPV of MHFHW. Thirdly, the type curves are illustrated and the influences of different fractal parameters are discussed. The pore fractal dimensions Df and the capillary tortuosity fractal dimensions DT have significant effects on the NPV of an MHFHW. Finally, the proposed model in this paper provides a new methodology for analyzing and predicting the NPV of an MHFHW and may be conducive to a better understanding of the optimal design of MHFHW.

Evapotranspiration versus oxygen intrusion: which is the main force in alleviating bioclogging of vertical-flow constructed wetlands during a resting operation?

PubMed

Hua, Guofen; Chen, Qiuwen; Kong, Jun; Li, Man

2017-08-01

Clogging is the most significant challenge limiting the application of constructed wetlands. Application of a forced resting period is a practical way to relieve clogging, particularly bioclogging. To reveal the alleviation mechanisms behind such a resting operation, evapotranspiration and oxygen flux were studied during a resting period in a laboratory vertical-flow constructed wetland model through physical simulation and numerical model analysis. In addition, the optimum theoretical resting duration was determined based on the time required for oxygen to completely fill the pores, i.e., formation of a sufficiently thick and completely dry layer. The results indicated that (1) evapotranspiration was not the key factor, but was a driving force in the alleviation of bioclogging; (2) the rate of oxygen diffusion into the pores was sufficient to oxidize and disperse the flocculant biofilm, which was essential to alleviate bioclogging. This study provides important insights into understanding how clogging/bioclogging can be alleviated in vertical-flow constructed wetlands. Graphical abstract Evapotranspiration versus oxygen intrusion in alleviating bioclogging in vertical flow constructed wetlands.

Distribution of long-lived radioactive iodine isotope (I-129) in pore waters from the gas hydrate fields on the continental margins: Indication for methane source of gas hydrate deposits

NASA Astrophysics Data System (ADS)

Tomaru, H.; Lu, Z.; Fehn, U.

2011-12-01

Because iodine has a strong association with organic matters in marine environments, pore waters in high methane potential region, in particular gas hydrate occurrences on the continental margins, are enriched significantly in iodine compared with seawater. Natural iodine system is composed of stable and radioactive species, I-129 (half-life of 15.7 Myr) has been used for estimating the age of source formations both for methane and iodine, because iodine can be liberated into pore water during the degradation of organic matter to methane in deep sediments. Here we present I-129 age data in pore waters collected from variety of gas hydrate occurrences on the continental margins. The I-129 ages in pore waters from these locations are significantly older than those of host sediments, indicating long-term transport and accumulation from deep/old sediments. The I-129 ages in the Japan Sea and Okhotsk Sea along the plate boundary between the North American and Amurian Plates correspond to the ages of initial spreading of these marginal seas, pointing to the massive deposition of organic matter for methane generation in deep sediments within limited periods. On the Pacific side of these areas, organic matter-rich back stop is responsible for methane in deep-seated gas hydrate deposits along the Nankai Trough. Deep coaly sequences responsible for deep conventional natural gas deposits are also responsible for overlying gas hydrate deposits off Shimokita Peninsula, NE Japan. Those in the Gulf of Mexico are correlative to the ages of sediments where the top of salt diapirs intrude. Marine sediments on the Pacific Plate subducting beneath the Australian Plate are likely responsible for the methane and iodine in the Hikurangi Trough, New Zealand. These ages reflect well the regional geological settings responsible for generation, transport, and accumulation of methane, I-129 is a key to understand the geological history of gas hydrate deposition.

A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Jingquan; Rouse, Sarah L.; Li, Dianfan

2014-08-01

Crystal structures of the β-barrel porin AlgE reveal a mechanism whereby alginate is exported from P. aeruginosa for biofilm formation. The exopolysaccharide alginate is an important component of biofilms produced by Pseudomonas aeruginosa, a major pathogen that contributes to the demise of cystic fibrosis patients. Alginate exits the cell via the outer membrane porin AlgE. X-ray structures of several AlgE crystal forms are reported here. Whilst all share a common β-barrel constitution, they differ in the degree to which loops L2 and T8 are ordered. L2 and T8 have been identified as an extracellular gate (E-gate) and a periplasmic gatemore » (P-gate), respectively, that reside on either side of an alginate-selectivity pore located midway through AlgE. Passage of alginate across the membrane is proposed to be regulated by the sequential opening and closing of the two gates. In one crystal form, the selectivity pore contains a bound citrate. Because citrate mimics the uronate monomers of alginate, its location is taken to highlight a route through AlgE taken by alginate as it crosses the pore. Docking and molecular-dynamics simulations support and extend the proposed transport mechanism. Specifically, the P-gate and E-gate are flexible and move between open and closed states. Citrate can leave the selectivity pore bidirectionally. Alginate docks stably in a linear conformation through the open pore. To translate across the pore, a force is required that presumably is provided by the alginate-synthesis machinery. Accessing the open pore is facilitated by complex formation between AlgE and the periplasmic protein AlgK. Alginate can thread through a continuous pore in the complex, suggesting that AlgK pre-orients newly synthesized exopolysaccharide for delivery to AlgE.« less

Micro-fabric damages in Boom Clay inferred from cryo-BIB-SEM experiment: recent results

NASA Astrophysics Data System (ADS)

Desbois, Guillaume; Schmatz, Joyce; Klaver, Jop; Urai, Janos L.

2017-04-01

The Boom Clay is considered as a potential host rock in Belgium for nuclear waste disposal in a deep geological formation. One of the keys to understand the long-term performance of such a host rock is the fundamental understanding of coupling between microstructural evolution, poromechanical behaviour and the state of hydration of the system. At in situ conditions, Boom Clay is a nearly water-saturated (>94%) clay-rich geomaterial. Subsequently, for measurement of mechanical and transport properties in laboratory, cores of Boom Clay are vacuum-packed in Al-coated-poly-ethylene barrier foil to be best preserved at original hydric state. Because clay microstructures are very sensitive to dehydration, the validity of investigations done on such preserved or/and dried samples is often questionable. Desbois et al. (2009, 2013, 2014) showed the possibility to image fluid-filled porosity in Boom Clay, by using the FIB-cryo-SEM (FIB: Focussed Ion Beam) and FIB-cryo-SEM (BIB: Broad Ion Beam) techniques. However, surprisingly in Desbois et al. (2014), BIB-cryo-SEM experiments on Boom Clay, shown that the majority of the pores were fluid-free, contrasting with result in Desbois et al. (2009). In Desbois et al. (2014), several reasons were discussed to explain such discrepancies. The likely ones are the sealing efficiency of the Al-barrier foil at long term and the volume expansion due to the release of in-situ stress after core extraction, contributing both to dehydration and microfabric damage. This contribution presents the newest results based on cryo-BIB-SEM. Small pieces (30 mm3) of Boom Clay were preserved in liquid nitrogen after the core extraction at the MOL/Dessel Underground Research Laboratory in Belgium. A maximum of ten minutes time span was achieved between opening the core, the sub-sample extraction and the quenching of sub-samples in liquid nitrogen. First results show that all pores visible at cryo-SEM resolution are water saturated. However, water-filled micro-cracks are also present and they are interpreted to result from the releasing of in-situ stress after the core extraction. Moreover, the comparison of the clay micro-fabrics in the same preserved and dried sample suggests collapsing of the clay aggregates' pores in dried sample. These newest results are still preliminary and they need to be analysed in more details. However, if they are confirmed they may be important input to discuss about the validity of measurement of mechanical and transport properties done in laboratory. Desbois G., Urai J.L. and Kukla P.A. (2009). Morphology of the pore space in claystones - evidence from BIB/FIB ion beam sectioning and cryo-SEM observations. E-Earth, 4 :15-22. Desbois G., J.L. Urai, F. Pérez-Willard, Z. Radi, S. van Offern, I. Burkart, P.A. Kukla, U. Wollenberg (2013). Argon broad ion beam tomography in a cryogenic scanning electron microscope: a novel tool for the investigation of representative microstructures in sedimentary rocks containing pore fluid. Journal of Microscopy, 249(3): 215-235. Desbois G., Urai J.L., Hemes S., Brassinnes S., De Craen M., Sillen X. (2014). Nanometer-scale pore fluid distribution and drying damage in preserved clay cores from Belgian clay formations inferred by BIB-cryo-SEM. Engineering Geology, 170:117-131.

Capillary-Driven Solute Transport and Precipitation in Porous Media during Dry-Out

NASA Astrophysics Data System (ADS)

Ott, Holger; Andrew, Matthew; Blunt, Martin; Snippe, Jeroen

2014-05-01

The injection of dry or under-saturated gases or supercritical (SC) fluids into water bearing formations might lead to a formation dry-out in the vicinity of the injection well. The dry-out is caused by the evaporation/dissolution of formation water into the injected fluid and the subsequent transport of dissolved water in the injected fluid away from the injection well. Dry-out results in precipitation from solutes of the formation brine and consequently leads to a reduction of the rock's pore space (porosity) and eventually to a reduction of permeability near the injection well, or even to the loss of injectivity. Recently evidence has been found that the complexity of the pore space and the respective capillary driven solute transport plays a key role. While no effective-permeability (Keff) reduction was observed in a single-porosity sandstone, multi porosity carbonate rocks responded to precipitation with a strong reduction of Keff. The reason for the different response of Keff to salt precipitation is suspected to be in the exact location of the precipitate (solid salt) in the pore space. In this study, we investigate dry-out and salt precipitation due to supercritical CO2 injection in single and multi-porosity systems under near well-bore conditions. We image fluid saturation changes by means of μCT scanning during desaturation. We are able to observe capillary driven transport of the brine phase and the respective transport of solutes on the rock's pore scale. Finally we have access to the precipitated solid-salt phase and their distribution. The results can proof the thought models behind permeability porosity relationships K(φ) for injectivity modeling. The topic and the mechanisms we show are of general interest for drying processes in porous material such as soils and paper.

Porosity characterization for heterogeneous shales using integrated multiscale microscopy

NASA Astrophysics Data System (ADS)

Rassouli, F.; Andrew, M.; Zoback, M. D.

2016-12-01

Pore size distribution analysis plays a critical role in gas storage capacity and fluid transport characterization of shales. Study of the diverse distribution of pore size and structure in such low permeably rocks is withheld by the lack of tools to visualize the microstructural properties of shale rocks. In this paper we try to use multiple techniques to investigate the full pore size range in different sample scales. Modern imaging techniques are combined with routine analytical investigations (x-ray diffraction, thin section analysis and mercury porosimetry) to describe pore size distribution of shale samples from Haynesville formation in East Texas to generate a more holistic understanding of the porosity structure in shales, ranging from standard core plug down to nm scales. Standard 1" diameter core plug samples were first imaged using a Versa 3D x-ray microscope at lower resolutions. Then we pick several regions of interest (ROIs) with various micro-features (such as micro-cracks and high organic matters) in the rock samples to run higher resolution CT scans using a non-destructive interior tomography scans. After this step, we cut the samples and drill 5 mm diameter cores out of the selected ROIs. Then we rescan the samples to measure porosity distribution of the 5 mm cores. We repeat this step for samples with diameter of 1 mm being cut out of the 5 mm cores using a laser cutting machine. After comparing the pore structure and distribution of the samples measured form micro-CT analysis, we move to nano-scale imaging to capture the ultra-fine pores within the shale samples. At this stage, the diameter of the 1 mm samples will be milled down to 70 microns using the laser beam. We scan these samples in a nano-CT Ultra x-ray microscope and calculate the porosity of the samples by image segmentation methods. Finally, we use images collected from focused ion beam scanning electron microscopy (FIB-SEM) to be able to compare the results of porosity measurements from all different imaging techniques. These multi-scale characterization techniques are then compared with traditional analytical techniques such as Mercury Porosimetry.

Final Report for DE-SC0008059

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karnik, Rohit

Graphene, a one-atom thick material comprising hexagonally bonded carbon atoms, is one of the strongest materials known and is impermeable to even helium gas. The potential for creation of tunable nanometer-scale pores in graphene, combined with mechanical strength, chemical resistance, and atomic thickness, make it a promising material for improving selectivity, permeability, and energy efficiency in a diverse range of membrane separations. However, fundamental understanding of creation of porous graphene, its mass transport properties, and the relationship between porosity and membrane performance is lacking. This project studied methods to create pores in graphene by ion irradiation and etching, and investigatedmore » the effect of the porosity of graphene on mass transport properties at the membrane level as well as across individual pores. Detailed characterization of pore size distributions in graphene using high-resolution scanning transmission electron microscopy was performed to elucidate the relationship between different pore creation processes and the resulting porosity. New methods to create tunable nanometer-scale pores in graphene at high density over large areas were developed. Graphene membranes were fabricated comprising single-layer porous graphene on appropriate support membranes. Mass transport of ions, molecules, water, and gases across the membranes was investigated, and predictive models were developed to relate the graphene porosity and support membrane structure to the mass transport properties of the membranes. The effect of graphene porosity on permeance of the membranes to water, salts, and small molecules was experimentally quantified. Single-pore measurements were performed and a model was developed to understand ion transport across graphene pores, which led to the experimental observation of heterogeneity in transport behaviors and spontaneous fluctuations of ion transport. Functional single-layer nanoporous graphene membranes comprising a high density of pores over macro-scale areas with molecular selectivity were demonstrated for the first time. This project led to three patent applications and 9 journal articles. The fundamental developments in understanding nanoporous graphene membranes have laid the foundations to develop energy-efficient nanoporous graphene membranes for various applications in water desalination, oil and natural gas separations, biotechnology, and chemical processing.« less

Research progress in formation mechanism of anodizing aluminum oxide

NASA Astrophysics Data System (ADS)

Lv, Yudong

2017-12-01

The self-ordering porous anodizing aluminum oxide (AAO) has attracted much attention because of its potential value of application. Valve metals (Al, Ti, Zr etc.) anodic studies have been conducted for more than 80 years, but the mechanism of the formation of hexagonal prismatic cell structure has so far been different. In this paper, the research results of AAO film formation mechanism are reviewed, and the growth models of several AAO films are summarized, including the field-assisted dissolution (FAD), the viscous flow model, the critical current density effect model, the bulk expansion stress model and the steady-state pore growth model and so on. It analyzed the principle of each model and its rationality. This paper will be of great help to reveal the nature of pore formation and self-ordering, and with the hope that through the study of AAO film formation mechanism, the specific effects of various oxidation parameters on AAO film morphology can be obtained.

Mitochondrial Ca2+ and Regulation of the Permeability Transition Pore

PubMed Central

Hurst, Stephen; Hoek, Jan; Sheu, Shey-Shing

2017-01-01

The mitochondrial permeability transition pore was originally described in the 1970’s as a Ca2+ activated pore and has since been attributed to the pathogenesis of many diseases. Here we evaluate how each of the current models of the pore complex fit to what is known about how Ca2+ regulates the pore, and any insight that provides into the molecular identity of the pore complex. We also discuss the central role of Ca2+ in modulating the pore’s open probability by directly regulating processes, such as ATP/ADP balance through the tricarboxylic acid cycle, electron transport chain, and mitochondrial membrane potential. We review how Ca2+ influences second messengers such as reactive oxygen/nitrogen species production and polyphosphate formation. We discuss the evidence for how Ca2+ regulates post-translational modification of cyclophilin D including phosphorylation by glycogen synthase kinase 3 beta, deacetylation by sirtuins, and oxidation/nitrosylation of key residues. Lastly we introduce a novel view into how Ca2+ activated proteolysis through calpains in the mitochondria may be a driver of sustained pore opening during pathologies such as ischemia reperfusion injury. PMID:27497945

Formation of porous inner architecture at the interface of magnetic pulse welded Al/Cu joints

NASA Astrophysics Data System (ADS)

Sapanathan, T.; Raoelison, R. N.; Yang, K.; Buiron, N.; Rachik, M.

2016-10-01

Porous inner architecture has been revealed at the interface of magnetic pulse welded aluminum/copper (Al/Cu) joints. These materials could serve the purpose of heterogeneous architectured materials, while their makeup of inner architecture of porous interface with the pore sizes of sub-micron to a few microns, could offer potential attributes in energy storage application. Two welding cases with various impact intensities are compared. An input voltage of 6.5 kV with an initial air gap of 1.5 mm and a higher voltage of 7.5 kV with a large initial air gap of 5 mm are respectively considered as two cases with low and high velocity impacts. Overall morphology of the porous medium was revealed at the interface either in layered or pocketed structures. The allocation of the porous zone and pore sizes vary with the impact condition. The low velocity impact welding conditions also produces smaller pores compared to the high velocity impact case, where the pore sizes varies in submicron to a few microns (<10μm). By investigating the potential mechanism of the porous zone formation, it was identified that a combined phenomena of cavitation and coalescence play a major role in nucleation and growth of the pores where a rapid cooling that eventually freezes the porous structure at the interface.

Cryo-EM structure of the gasdermin A3 membrane pore.

PubMed

Ruan, Jianbin; Xia, Shiyu; Liu, Xing; Lieberman, Judy; Wu, Hao

2018-05-01

Gasdermins mediate inflammatory cell death after cleavage by caspases or other, unknown enzymes. The cleaved N-terminal fragments bind to acidic membrane lipids to form pores, but the mechanism of pore formation remains unresolved. Here we present the cryo-electron microscopy structures of the 27-fold and 28-fold single-ring pores formed by the N-terminal fragment of mouse GSDMA3 (GSDMA3-NT) at 3.8 and 4.2 Å resolutions, and of a double-ring pore at 4.6 Å resolution. In the 27-fold pore, a 108-stranded anti-parallel β-barrel is formed by two β-hairpins from each subunit capped by a globular domain. We identify a positively charged helix that interacts with the acidic lipid cardiolipin. GSDMA3-NT undergoes radical conformational changes upon membrane insertion to form long, membrane-spanning β-strands. We also observe an unexpected additional symmetric ring of GSDMA3-NT subunits that does not insert into the membrane in the double-ring pore, which may represent a pre-pore state of GSDMA3-NT. These structures provide a basis that explains the activities of several mutant gasdermins, including defective mutants that are associated with cancer.

Performance of Small Pore Microchannel Plates

NASA Technical Reports Server (NTRS)

Siegmund, O. H. W.; Gummin, M. A.; Ravinett, T.; Jelinsky, S. R.; Edgar, M.

1995-01-01

Small pore size microchannel plates (MCP's) are needed to satisfy the requirements for future high resolution small and large format detectors for astronomy. MCP's with pore sizes in the range 5 micron to 8 micron are now being manufactured, but they are of limited availability and are of small size. We have obtained sets of Galileo 8 micron and 6.5 micron MCP's, and Philips 6 micron and 7 micron pore MCP's, and compared them to our larger pore MCP Z stacks. We have tested back to back MCP stacks of four of these MCP's and achieved gains greater than 2 x 1O(exp 7) with pulse height distributions of less than 40% FWHM, and background rates of less than 0.3 events sec(exp -1) cm(exp -2). Local counting rates up to approx. 100 events/pore/sec have been attained with little drop of the MCP gain. The bare MCP quantum efficiencies are somewhat lower than those expected, however. Flat field images are characterized by an absence of MCP fixed pattern noise.

On the size of pores arising in erythrocytes under the action of detergents.

PubMed

Senkovich, O A; Chernitsky, E A

1998-01-01

The size of pores arising in human erythrocytes under the action of two detergents (Triton X-100 and sodium dodecyl sulfate) and causing the slow component of hemolysis was estimated by the method of osmotic protectors. The pore diameters were found to be about 40 A. The pores responsible for the fast component of hemolysis induced by sodium dodecyl sulfate were shown to be of greater size and even molecules of polyethylene glycol 4000 could pass through them. The unusual decrease. In the rate and percentage of this hemolytic component was caused by the side action of the protectors, i.e., by the acceleration of erythrocyte vesiculation, a process that competed with pore formation. Vesiculation protected erythrocytes against fast and slow detergent-induced hemolysis. It is shown that the method of osmotic protectors can not be used for estimation of pore size in fast hemolysis by sodium dodecyl sulfate. The application of this method for hemolysis by other amphiphilic compounds is discussed.

Anomalous or regular capacitance? The influence of pore size dispersity on double-layer formation

NASA Astrophysics Data System (ADS)

Jäckel, N.; Rodner, M.; Schreiber, A.; Jeongwook, J.; Zeiger, M.; Aslan, M.; Weingarth, D.; Presser, V.

2016-09-01

The energy storage mechanism of electric double-layer capacitors is governed by ion electrosorption at the electrode surface. This process requires high surface area electrodes, typically highly porous carbons. In common organic electrolytes, bare ion sizes are below one nanometer but they are larger when we consider their solvation shell. In contrast, ionic liquid electrolytes are free of solvent molecules, but cation-anion coordination requires special consideration. By matching pore size and ion size, two seemingly conflicting views have emerged: either an increase in specific capacitance with smaller pore size or a constant capacitance contribution of all micro- and mesopores. In our work, we revisit this issue by using a comprehensive set of electrochemical data and a pore size incremental analysis to identify the influence of certain ranges in the pore size distribution to the ion electrosorption capacity. We see a difference in solvation of ions in organic electrolytes depending on the applied voltage and a cation-anion interaction of ionic liquids in nanometer sized pores.

Size Control of Porous Silicon-Based Nanoparticles via Pore-Wall Thinning.

PubMed

Secret, Emilie; Leonard, Camille; Kelly, Stefan J; Uhl, Amanda; Cozzan, Clayton; Andrew, Jennifer S

2016-02-02

Photoluminescent silicon nanocrystals are very attractive for biomedical and electronic applications. Here a new process is presented to synthesize photoluminescent silicon nanocrystals with diameters smaller than 6 nm from a porous silicon template. These nanoparticles are formed using a pore-wall thinning approach, where the as-etched porous silicon layer is partially oxidized to silica, which is dissolved by a hydrofluoric acid solution, decreasing the pore-wall thickness. This decrease in pore-wall thickness leads to a corresponding decrease in the size of the nanocrystals that make up the pore walls, resulting in the formation of smaller nanoparticles during sonication of the porous silicon. Particle diameters were measured using dynamic light scattering, and these values were compared with the nanocrystallite size within the pore wall as determined from X-ray diffraction. Additionally, an increase in the quantum confinement effect is observed for these particles through an increase in the photoluminescence intensity of the nanoparticles compared with the as-etched nanoparticles, without the need for a further activation step by oxidation after synthesis.

Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaitheeswaran, S.; Reddy, G.; Thirumalai, D.

2009-03-07

We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled pores. Confinement strongly alters the interactions between the nonpolar solutes and completely eliminates the solvent separated minimum (SSM) that is seen in bulk water. The free energy profiles show that the methane molecules are either in contact or at separations corresponding to the diameter and the length of the cylindrical pore. Analytic calculations that estimate the entropy of the solutes, which are solvated at the pore surface, qualitatively explain the shape of the freemore » energy profiles. Adding charges of opposite sign and magnitude 0.4e or e (where e is the electronic charge) to the methane molecules decreases their tendency for surface solvation and restores the SSM. We show that confinement induced ion-pair formation occurs whenever l{sub B}/D{approx}O(1), where l{sub B} is the Bjerrum length and D is the pore diameter. The extent of stabilization of the SSM increases with ion charge density as long as l{sub B}/D<1. In pores with D{<=}1.2 nm, in which the water is strongly layered, increasing the charge magnitude from 0.4e to e reduces the stability of the SSM. As a result, ion-pair formation that occurs with negligible probability in the bulk is promoted. In larger diameter pores that can accommodate a complete hydration layer around the solutes, the stability of the SSM is enhanced.« less

Application of Dst Interpretation Results by Log - Log Method in the Pore Space Type Estimation for the Upper Jurassic Carbonate Reservoir Rocks of the Carpathian Foredeep Basement / Interpretacja Testów Wykonywanych Rurowymi Próbnikami Złoża - Rpz w Skałach Węglanowych Górnej Jury Podłoża Zapadliska Przedkarpackiego

NASA Astrophysics Data System (ADS)

Dubiel, Stanisław; Zubrzycki, Adam; Rybicki, Czesław; Maruta, Michał

2012-11-01

In the south part of the Carpathian Foredeep basement, between Bochnia and Ropczyce, the Upper Jurassic (Oxfordian, Kimmeridian and Tithonian) carbonate complex plays important role as a hydrocarbon bearing formation. It consists of shallow marine carbonates deposited in environments of the outer carbonate ramp as reef limestones (dolomites), microbial - sponge or coral biostromes and marly or micrite limestones as well. The inner pore space system of these rocks was affected by different diagenetic processes as calcite cementation, dissolution, dolomitization and most probably by tectonic fracturing as well. These phenomena have modified pore space systems within limestone / dolomite series forming more or less developed reservoir zones (horizons). According to the interpretation of DST results (analysis of pressure build up curves by log - log method) for 11 intervals (marked out previously by well logging due to porosity increase readings) within the Upper Jurassic formation 3 types of pore/fracture space systems were distinguished: - type I - fracture - vuggy porosity system in which fractures connecting voids and vugs within organogenic carbonates are of great importance for medium flow; - type II - vuggy - fracture porosity system where a pore space consists of weak connected voids and intergranular/intercrystalline pores with minor influence of fractures; - type III - cavern porosity system in which a secondary porosity is developed due to dolomitization and cement/grain dissolution processes.

Microstructural and strength improvements through the use of Na{sub 2}CO{sub 3} in a cementless Ca(OH){sub 2}-activated Class F fly ash system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeon, Dongho; Jun, Yubin; Jeong, Yeonung

2015-01-15

This study explores the beneficial effects of Na{sub 2}CO{sub 3} as an additive for microstructural and strength improvements in a Ca(OH){sub 2}-activated fly ash system. NaOH-activated fly ash samples were also tested to compare the effect of Na{sub 2}CO{sub 3}. Compressive strength testing, XRD, SEM/BSE/EDS, {sup 29}Si/{sup 27}Al MAS-NMR, MIP and TGA were performed. The testing results indicate that the use of Na{sub 2}CO{sub 3} for Ca(OH){sub 2}-activation led to a noticeable improvement in strength and microstructure, primarily due to (1) more dissolution of raw fly ash at an early age, (2) more formation of C–S–H [or C–S–H(I)], (3) porositymore » reduction, and (4) pore-size refinement. We also found that (1) an early high alkalinity from the NaOH formation was not a major cause of strength, (2) geopolymer was not formed despite the early NaOH formation, and (3) no visible pore-filling action of CaCO{sub 3} was observed. However, Na{sub 2}CO{sub 3} did not produce any improvement in strength for NaOH-activated fly ash. -- Highlights: •The use of Na{sub 2}CO{sub 3} significantly improved strength and microstructure. •The use of Na{sub 2}CO{sub 3} induced more dissolution of raw fly ash at early ages. •The use of Na{sub 2}CO{sub 3} promoted more C–S–H [or C–S–H(I)] formation. •The use of Na{sub 2}CO{sub 3} reduced total porosity and refined pore-size distribution. •The use of Na{sub 2}CO{sub 3} produced neither geopolymer formations nor pore-filling actions from CaCO{sub 3}.« less

Internal Domains of Natural Porous Media Revealed: Critical Locations for Transport, Storage, and Chemical Reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zachara, John M.; Brantley, Susan L.; Chorover, Jon D.

2016-03-16

Internal pore domains exist within rocks, lithic fragments, subsurface sediments and soil aggregates. These domains, which we term internal domains in porous media (IDPM), contain a significant fraction of their porosity as nanopores, dominate the reactive surface area of diverse porous media types, and are important locations for chemical reactivity and hydrocarbon storage. Traditionally difficult to interrogate, advances in instrumentation and imaging methods are providing new insights on the physical structures and chemical attributes of IDPM. In this review we: discuss analytical methods to characterize IDPM, evaluate what has been learned about their size distributions, connectivity, and extended structures; determinemore » whether they exhibit unique chemical reactivity; and assess potential for their inclusion in reactive transport models. Three key findings are noteworthy. 1) A combination of methods now allows complete characterization of the porosity spectrum of natural materials and its connectivity; while imaging microscopies are providing three dimensional representations of the interconnected pore network. 2) Chemical reactivity in pores <10 nm is expected to be different from micro and macropores, yet research performed to date is inconclusive on the nature, direction, and magnitude of effect. 3) Existing continuum reactive transport models treat IDPM as a sub-grid feature with average, empirical, scale-dependent parameters; and are not formulated to include detailed information on pore networks. Overall we find that IDPM are key features controlling hydrocarbon release from shales in hydrofracking systems, organic matter stabilization and recalcitrance in soil, weathering and soil formation, and long term inorganic and organic contaminant behavior in the vadose zone and groundwater. We conclude with an assessment of impactful research opportunities to advance understanding of IDPM, and to incorporate their important effects in reactive transport models for improved environmental simulation and prediction.« less

Oxygen transport and pyrite oxidation in unsaturated coal-mine spoil

USGS Publications Warehouse

Guo, Weixing; Cravotta, Charles A.

1996-01-01

An understanding of the mechanisms of oxygen (02) transport in unsaturated mine spoil is necessary to design and implement effective measures to exclude 02 from pyritic materials and to control the formation of acidic mine drainage. Partial pressure of oxygen (Po2) in pore gas, chemistry of pore water, and temperature were measured at different depths in unsaturated spoil at two reclaimed surface coal mines in Pennsylvania. At mine 1, where spoil was loose, blocky sandstone, Po2 changed little with depth, decreasing from 21 volume percent (vol%) at the ground surface to a minimum of about 18 vol% at 10 m depth. At mine 2, where spoil was compacted, friable shale, Po2 decreased to less than 2 vol% at depth of about 10 m. Although pore-water chemistry and temperature data indicate that acid-forming reactions were active at both mines, the pore-gas data indicate that mechanisms for 0 2 transport were different at each mine. A numerical model was developed to simulate 02 transport and pyrite oxidation in unsaturated mine spoil. The results of the numerical simulations indicate that differences in 02 transport at the two mines can be explained by differences in the air permeability of spoil. Po2 changes little with depth if advective transport of 02 dominates as at mine 1, but decreases greatly with depth if diffusive transport of 02 dominates, as in mine 2. Model results also indicate that advective transport becomes significant if the air permeability of spoil is greater than 10-9 m2, which is expected for blocky sandstone spoil. In the advective-dominant system, thermally-induced convective air flow, as a consequence of the exothermic oxidation of pyrite, supplies the 02 to maintain high Po2 within the deep unsaturated zone.

In vivo single human sweat gland activity monitoring using coherent anti-Stokes Raman scattering and two-photon excited autofluorescence microscopy.

PubMed

Chen, X; Gasecka, P; Formanek, F; Galey, J-B; Rigneault, H

2016-04-01

Eccrine sweat secretion is of central importance for control of body temperature. Although the incidence of sweat gland dysfunction might appear of minor importance, it can be a real concern for people with either hypohidrosis or hyperhidrosis. However, sweat gland function remains relatively poorly explored. To investigate the function of single human sweat glands. We describe a new approach for noninvasive imaging of single sweat gland activity in human palms in vivo up to a depth of 100 μm, based on nonlinear two-photon excited autofluorescence (TPEF) and coherent anti-Stokes Raman scattering (CARS). These techniques appear to be useful compared with approaches already described for imaging single sweat gland activity, as they allow better three-dimensional spatial resolution of sweat pore inner morphology and real-time monitoring of individual sweat events. By filling the sweat pore with oil and tuning the CARS contrast at 2845 cm(-1) , we imaged the ejection of sweat droplets from a single sweat gland when oil is pushed out by sweat flow. On average, sweat events lasted for about 30 s every 3 min under the conditions studied. On the other hand, about 20% of sweat glands were found inactive. TPEF and CARS were also used to study, at the single pore level, the antiperspirant action of aluminium chlorohydrate (ACH) and to reveal, for the first time in vivo, the formation of a plug at the pore entrance, in agreement with reported ACH antiperspirant mechanisms. Although data were acquired on human palms, these techniques show great promise for a better understanding of sweat secretion physiology and should be helpful to improve the efficacy of antiperspirant formulations. © 2015 British Association of Dermatologists.

δ30Si systematics in a granitic saprolite, Puerto Rico

USGS Publications Warehouse

Ziegler, Karen; Chadwick, Oliver A.; White, Arthur F.; Brzezinski, Mark A.

2005-01-01

Granite weathering and clay mineral formation impart distinct and interpretable stable Si isotope (δ30Si) signatures to their solid and aqueous products. Within a saprolite, clay minerals have δ30Si values ∼2.0‰ more negative than their parent mineral and the δ30Si signature of the bulk solid is determined by the ratio of primary to secondary minerals. Mineral-specific weathering reactions predominate at different depths, driving changes in differing δ30Sipore watervalues. At the bedrock-saprolite interface, dissolution of plagioclase and hornblende creates δ30Sipore water signatures more positive than granite by up to 1.2‰; these reactions are the main contributor of Si to stream water and determine its δ30Si value. Throughout the saprolite, biotite weathering releases Si to pore waters but kaolinite overgrowth formation modulates its contribution to pore-water Si. The influence of biotite on δ30Sipore water is greatest near the bedrock where biotite-derived Si mixes with bulk pore water prior to kaolinite formation. Higher in the saprolite, biotite grains have become more isolated by kaolinite overgrowth, which consumes biotite-derived Si that would otherwise influence δ30Sipore water. Because of this isolation, which shifts the dominant source of pore-water Si from biotite to quartz, δ30Sipore water values are more negative than granite by up to 1.3‰ near the top of the saprolite.

Laboratory experiments simulating poroelastic stress changes associated with depletion and injection in low-porosity sedimentary rocks

NASA Astrophysics Data System (ADS)

Ma, Xiaodong; Zoback, Mark D.

2017-04-01

We characterized the poroelastic deformation of six cores from three formations associated with the Bakken play in the Williston Basin (the Lodgepole, Middle Bakken, and Three Forks formations). All are low-porosity, low-permeability formations, but vary considerably in clay, kerogen, and carbonate content. The experimental program simulated reservoir stress changes associated with depletion and injection via cycling both the confining pressure (Pc) and pore pressure (Pp). We measured volumetric strain, derived the corresponding bulk modulus, and calculated the Biot coefficient (α). We found α, which generally ranges between 0.3 and 0.9, to vary systematically with Pc and Pp for each of the specimens tested. The effect of pore pressure on α is much larger at low simple effective stress (σ = Pc-Pp) during depletion than injection. The α decreases with σ for all pore pressures. For the same Pc and Pp, the Biot coefficient is consistently higher during injection than during depletion. Given the observed variations of α with Pc and Pp, the modeling of reservoir stress changes using a constant α could be problematic as poroelastic stress changes during depletion and injection are not likely to follow the same path. Scanning electron microscope examination of microstructures suggests that the variations of the bulk modulus and the Biot coefficient can be attributed to the abundance of compliant components (pores, microcracks, clays, and organic matter) and how they are distributed throughout the rock matrix.

Dual-beam laser welding of AZ31B magnesium alloy in zero-gap lap joint configuration

NASA Astrophysics Data System (ADS)

Harooni, Masoud; Carlson, Blair; Kovacevic, Radovan

2014-03-01

Porosity within laser welds of magnesium alloys is one of the main roadblocks to achieving high quality joints. One of the causes of pore formation is the presence of pre-existing coatings on the surface of magnesium alloy such as oxide or chromate layers. In this study, single-beam and dual-beam laser heat sources are investigated in relation to mitigation of pores resulting from the presence of the as-received oxide layer on the surface of AZ31B-H24 magnesium alloy during the laser welding process. A fiber laser with a power of up to 4 kW is used to weld samples in a zero-gap lap joint configuration. The effect of dual-beam laser welding with different beam energy ratios is studied on the quality of the weld bead. The purpose of this paper is to identify the beam ratio that best mitigates pore formation in the weld bead. The laser molten pool and the keyhole condition, as well as laser-induced plasma plume are monitored in real-time by use of a high speed charge-coupled device (CCD) camera assisted with a green laser as an illumination source. Tensile and microhardness tests were used to measure the mechanical properties of the laser welded samples. Results showed that a dual-beam laser configuration can effectively mitigate pore formation in the weld bead by a preheating-welding mechanism.

FORMATION OF THE PENUMBRA AND START OF THE EVERSHED FLOW

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murabito, M.; Guglielmino, S. L.; Zuccarello, F.

We studied the variations of line of sight photospheric plasma flows during the formation phase of the penumbra around a pore in active region NOAA 11490. We used a high spatial, spectral, and temporal resolution data set acquired by the Interferometric BIdimensional Spectrometer operating at the NSO/Dunn Solar Telescope as well as data taken by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory satellite ( SDO /HMI). Before the penumbra formed we observed a redshift of the spectral line in the inner part of the annular zone surrounding the pore as well as a blueshift of materialmore » associated with opposite magnetic polarity farther away from the pore. We found that the onset of the classical Evershed flow occurs on a very short timescale (1 to 3 hr) while the penumbra is forming. During the same time interval we found changes in the magnetic field inclination in the penumbra, with the vertical field actually changing sign near the penumbral edge, while the total magnetic field showed a significant increase, about 400 G. To explain these and other observations related to the formation of the penumbra and the onset of the Evershed flow we propose a scenario in which the penumbra is formed by magnetic flux dragged down from the canopy surrounding the initial pore. The Evershed flow starts when the sinking magnetic field dips below the solar surface and magnetoconvection sets in.« less

Broad neutralization of calcium-permeable amyloid pore channels with a chimeric Alzheimer/Parkinson peptide targeting brain gangliosides.

PubMed

Di Scala, Coralie; Yahi, Nouara; Flores, Alessandra; Boutemeur, Sonia; Kourdougli, Nazim; Chahinian, Henri; Fantini, Jacques

2016-02-01

Growing evidence supports a role for brain gangliosides in the pathogenesis of neurodegenerative diseases including Alzheimer's and Parkinson's. Recently we deciphered the ganglioside-recognition code controlling specific ganglioside binding to Alzheimer's β-amyloid (Aβ1-42) peptide and Parkinson's disease-associated protein α-synuclein. Cracking this code allowed us to engineer a short chimeric Aβ/α-synuclein peptide that recognizes all brain gangliosides. Here we show that ganglioside-deprived neural cells do no longer sustain the formation of zinc-sensitive amyloid pore channels induced by either Aβ1-42 or α-synuclein, as assessed by single-cell Ca(2+) fluorescence microscopy. Thus, amyloid channel formation, now considered a key step in neurodegeneration, is a ganglioside-dependent process. Nanomolar concentrations of chimeric peptide competitively inhibited amyloid pore formation induced by Aβ1-42 or α-synuclein in cultured neural cells. Moreover, this peptide abrogated the intracellular calcium increases induced by Parkinson's-associated mutant forms of α-synuclein (A30P, E46K and A53T). The chimeric peptide also prevented the deleterious effects of Aβ1-42 on synaptic vesicle trafficking and decreased the Aβ1-42-induced impairment of spontaneous activity in rat hippocampal slices. Taken together, these data show that the chimeric peptide has broad anti-amyloid pore activity, suggesting that a common therapeutic strategy based on the prevention of amyloid-ganglioside interactions is a reachable goal for both Alzheimer's and Parkinson's diseases. Copyright © 2015 Elsevier B.V. All rights reserved.

Mechanism of membrane damage by El Tor hemolysin of Vibrio cholerae O1.

PubMed

Ikigai, H; Akatsuka, A; Tsujiyama, H; Nakae, T; Shimamura, T

1996-08-01

El Tor hemolysin (ETH; molecular mass, 65 kDa) derived from Vibrio cholerae O1 spontaneously assembled oligomeric aggregates on the membranes of rabbit erythrocyte ghosts and liposomes. Membrane-associated oligomers were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting into two to nine bands with apparent molecular masses of 170 to 350 kDa. ETH assembled oligomers on a liposomal membrane consisting of phosphatidylcholine and cholesterol, but not on a membrane of phosphatidylcholine alone. Cholesterol could be replaced with diosgenin or ergosterol but not with 5alpha-cholestane-3-one, suggesting that sterol is essential for the oligomerization. The treatment of carboxyfluorescein-encapsulated liposomes with ETH caused a rapid release of carboxyfluorescein into the medium. Because dextrin 20 (molecular mass, 900 Da) osmotically protected ETH-mediated hemolysis, this hemolysis is likely to be caused by pore formation on the membrane. The pore size(s) estimated from osmotic protection assays was in the range of 1.2 to 1.6 nm. The pore formed on a rabbit erythrocyte membrane was confirmed morphologically by electron microscopy. Thus, we provide evidence that ETH damages the target by the assembly of hemolysin oligomers and pore formation on the membrane.

Mechanism of membrane damage by El Tor hemolysin of Vibrio cholerae O1.

PubMed Central

Ikigai, H; Akatsuka, A; Tsujiyama, H; Nakae, T; Shimamura, T

1996-01-01

El Tor hemolysin (ETH; molecular mass, 65 kDa) derived from Vibrio cholerae O1 spontaneously assembled oligomeric aggregates on the membranes of rabbit erythrocyte ghosts and liposomes. Membrane-associated oligomers were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting into two to nine bands with apparent molecular masses of 170 to 350 kDa. ETH assembled oligomers on a liposomal membrane consisting of phosphatidylcholine and cholesterol, but not on a membrane of phosphatidylcholine alone. Cholesterol could be replaced with diosgenin or ergosterol but not with 5alpha-cholestane-3-one, suggesting that sterol is essential for the oligomerization. The treatment of carboxyfluorescein-encapsulated liposomes with ETH caused a rapid release of carboxyfluorescein into the medium. Because dextrin 20 (molecular mass, 900 Da) osmotically protected ETH-mediated hemolysis, this hemolysis is likely to be caused by pore formation on the membrane. The pore size(s) estimated from osmotic protection assays was in the range of 1.2 to 1.6 nm. The pore formed on a rabbit erythrocyte membrane was confirmed morphologically by electron microscopy. Thus, we provide evidence that ETH damages the target by the assembly of hemolysin oligomers and pore formation on the membrane. PMID:8757822

Full paleostress tensor reconstruction using quartz veins of Panasqueira Mine, central Portugal; part I: Paleopressure determination

NASA Astrophysics Data System (ADS)

Jaques, Luís; Pascal, Christophe

2017-09-01

Paleostress tensor restoration methods are traditionally limited to reconstructing geometrical parameters and are unable to resolve stress magnitudes. Based on previous studies we further developed a methodology to restore full paleostress tensors. We concentrated on inversion of Mode I fractures and acquired data in Panasqueira Mine, Portugal, where optimal exposures of mineralized quartz veins can be found. To carry out full paleostress restoration we needed to determine (1) pore (paleo)pressure and (2) vein attitudes. The present contribution focuses specifically on the determination of pore pressure. To these aims we conducted an extensive fluid inclusion study to derive fluid isochores from the quartz of the studied veins. To constrain P-T conditions, we combined these isochores with crystallisation temperatures derived from geochemical analyses of coeval arsenopyrite. We also applied the sphalerite geobarometer and considered two other independent pressure indicators. Our results point to pore pressures of ∼300 MPa and formation depths of ∼10 km. Such formation depths are in good agreement with the regional geological evolution. The obtained pore pressure will be merged with vein inversion results, in order to achieve full paleostress tensor restoration, in a forthcoming companion paper.

Shock Loading of Granular Ni/Al Composites. Part 1. Mechanics of Loading

DOE PAGES

Cherukara, Mathew J.; Germann, Timothy C.; Kober, Edward M.; ...

2014-10-16

We present molecular dynamics simulations of the thermomechanical response under shock loading of a granular material consisting of laminated Ni/Al grains. We observe two regimes: At low piston velocities (up ≲ 1km/s), the shock wave is diffuse, and the width of the shock front decreases with increasing piston velocity. Beyond a critical shock strength, however, the width remains relatively constant at approximately the mean grain radius. This change in behavior follows from an evolution of the mechanism of compaction with increasing insult strength. Furthermore, the mechanism evolves from plastic deformation-mediated pore collapse for relatively weak shocks, to solid extrusion andmore » fluid ejecta filling pores ahead of the shock front at intermediate strengths, and finally to atomic jetting into the pore for very strong shocks (up ≳ 2 km/s). High-energy fluid ejecta into pores leads to the formation of flow vorticity and can result in a large fraction of the input energy localizing into translational kinetic energy components including the formation of hot spots. This has implications for the mechanical mixing of Ni and Al in these reactive composites.« less

Ceramic membrane by tape casting and sol-gel coating for microfiltration and ultrafiltration application

NASA Astrophysics Data System (ADS)

Das, Nandini; Maiti, H. S.

2009-11-01

Alumina membrane filters in the form of thin (0.3-0.8 mm) discs of 25-30 mm diameter suitable for microfiltration application have been fabricated by tape-casting technique. Further using this microfiltration membrane as substrate, boehmite sol coating was applied on it and ultrafiltration membrane with very small thickness was formed. The pore size of the microfiltration membrane could be varied in the range of 0.1-0.7 μm through optimisation of experimental parameter. In addition, each membrane shows a very narrow pore size distribution. The most important factor, which determines the pore size of the membrane, is the initial particle size and its distribution of the ceramic powder. The top thin ultrafiltration, boehmite layer was prepared by sol-gel method, with a thickness of 0.5 μm. Particle size of the sol was approximately 30-40 nm. The structure and formation of the layer was analysed through TEM. At 550 °C formation of the top layer was completed. The pore size of the ultrafiltration membrane measured from TEM micrograph was almost 10 nm. Results of microbial (Escherichia coli—smallest-sized water-borne bacteria) test confirm the possibility of separation through this membrane

Pre-activation of aerosol particles by ice preserved in pores

NASA Astrophysics Data System (ADS)

Marcolli, Claudia

2017-02-01

Pre-activation denotes the capability of particles or materials to nucleate ice at lower relative humidities or higher temperatures compared to their intrinsic ice nucleation efficiency after having experienced an ice nucleation event or low temperature before. This review presumes that ice preserved in pores is responsible for pre-activation and analyses pre-activation under this presumption. Idealized trajectories of air parcels are used to discuss the pore characteristics needed for ice to persist in pores and to induce macroscopic ice growth out of the pores. The pore width needed to keep pores filled with water decreases with decreasing relative humidity as described by the inverse Kelvin equation. Thus, narrow pores remain filled with ice well below ice saturation. However, the smaller the pore width, the larger the melting and freezing point depressions within the pores. Therefore, pre-activation due to pore ice is constrained by the melting of ice in narrow pores and the sublimation of ice from wide pores imposing restrictions on the temperature and relative humidity range of pre-activation for cylindrical pores. Ice is better protected in ink-bottle-shaped pores with a narrow opening leading to a large cavity. However, whether pre-activation is efficient also depends on the capability of ice to grow macroscopically, i.e. out of the pore. A strong effect of pre-activation is expected for swelling pores, because at low relative humidity (RH) their openings narrow and protect the ice within them against sublimation. At high relative humidities, they open up and the ice can grow to macroscopic size and form an ice crystal. Similarly, ice protected in pockets is perfectly sheltered against sublimation but needs the dissolution of the surrounding matrix to be effective. Pores partially filled with condensable material may also show pre-activation. In this case, complete filling occurs at lower RH than for empty pores and freezing shifts to lower temperatures.Pre-activation experiments confirm that materials susceptible to pre-activation are indeed porous. Pre-activation was observed for clay minerals like illite, kaolinite, and montmorillonite with inherent porosity. The largest effect was observed for the swelling clay mineral montmorillonite. Some materials may acquire porosity, depending on the formation and processing conditions. Particles of CaCO3, meteoritic material, and volcanic ash showed pre-activation for some samples or in some studies but not in other ones. Quartz and silver iodide were not susceptible to pre-activation.Atmospheric relevance of pre-activation by ice preserved in pores may not be generally given but depend on the atmospheric scenario. Lower-level cloud seeding by pre-activated particles released from high-level clouds crucially depends on the ability of pores to retain ice at the relative humidities and temperatures of the air masses they pass through. Porous particles that are recycled in wave clouds may show pre-activation with subsequent ice growth as soon as ice saturation is exceeded after having passed a first cloud event. Volcanic ash particles and meteoritic material likely influence ice cloud formation by pre-activation. Therefore, the possibility of pre-activation should be considered when ice crystal number densities in clouds exceed the number of ice-nucleating particles measured at the cloud forming temperature.

Sequential protein unfolding through a carbon nanotube pore

NASA Astrophysics Data System (ADS)

Xu, Zhonghe; Zhang, Shuang; Weber, Jeffrey K.; Luan, Binquan; Zhou, Ruhong; Li, Jingyuan

2016-06-01

An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable ``unfoldon'' motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability.An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable ``unfoldon'' motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr00410e

Amino acid residues involved in membrane insertion and pore formation of Clostridium botulinum C2 toxin.

PubMed

Lang, Alexander E; Neumeyer, Tobias; Sun, Jianjun; Collier, R John; Benz, Roland; Aktories, Klaus

2008-08-12

The actin-ADP-ribosylating Clostridium botulinum C2 toxin consists of the enzymatic component C2I and the binding component C2II. C2II forms heptameric channels involved in translocation of the enzymatic component into the target cell. On the basis of the heptameric toxin channel, we studied functional consequences of mutagenesis of amino acid residues probably lining the lumen of the toxin channel. Substitution of glutamate-399 of C2II with alanine blocked channel formation and cytotoxicity of the holotoxin. Although cytotoxicity and rounding up of cells by C2I were completely blocked by exchange of phenylalanine-428 with alanine, the mutation increased potassium conductance caused by C2II in artificial membranes by about 2-3-fold over that of wild-type toxin. In contrast to its effects on single-channel potassium conductance in artificial membranes, the F428A mutation delayed the kinetics of pore formation in lipid vesicles and inhibited the activity of C2II in promoting (86)Rb (+) release from preloaded intact cells after pH shift of the medium. Moreover, F428A C2II exhibited delayed and diminished formation of C2II aggregates at low pH, indicating major changes of the biophysical properties of the toxin. The data indicate that phenylalanine-428 of C2II plays a major role in conformational changes occurring during pore formation of the binding component of C2II.

Unplugging the callose plug from sieve pores.

PubMed

Xie, Bo; Hong, Zonglie

2011-04-01

The presence of callose in sieve plates has been known for a long time, but how this polysaccharide plug is synthesized has remained unsolved. Two independent laboratories have recently reported the identification of callose synthase 7 (CalS7), also known as glucan synthase-like 7 (GSL7), as the enzyme responsible for callose deposition in sieve plates. Mutant plants defective in this enzyme failed to synthesize callose in developing sieve plates during phloem formation and were unable to accumulate callose in sieve pores in response to stress treatments. The mutant plants developed less open pores per sieve plate and the pores were smaller in diameter. As a result, phloem conductivity was reduced significantly and the mutant plants were shorter and set fewer seeds.

Development of eco-friendly porous fired clay bricks using pore-forming agents: a review.

PubMed

Bories, Cecile; Borredon, Marie-Elisabeth; Vedrenne, Emeline; Vilarem, Gerard

2014-10-01

Today, clay bricks are facing technological challenges and are uncompetitive compared to materials such as concrete. Their performance must be improved if they are to stand up to the competition. Increasing environmental concerns over the accumulation of unmanaged wastes from agricultural or industrial productions have made these good candidates for incorporation into building materials to improve their performance. This process leads to the formation of pores in the bricks, producing lightweight and sustainable building materials. This paper reviews the different pore-forming agents from renewable or mineral resources as described in the literature. It also presents the impact of pore-forming agents on the physical, mechanical and thermal properties of clay bricks. Copyright © 2014 Elsevier Ltd. All rights reserved.

MORPH-I (Ver 1.0) a software package for the analysis of scanning electron micrograph (binary formatted) images for the assessment of the fractal dimension of enclosed pore surfaces

USGS Publications Warehouse

Mossotti, Victor G.; Eldeeb, A. Raouf; Oscarson, Robert

1998-01-01

MORPH-I is a set of C-language computer programs for the IBM PC and compatible minicomputers. The programs in MORPH-I are used for the fractal analysis of scanning electron microscope and electron microprobe images of pore profiles exposed in cross-section. The program isolates and traces the cross-sectional profiles of exposed pores and computes the Richardson fractal dimension for each pore. Other programs in the set provide for image calibration, display, and statistical analysis of the computed dimensions for highly complex porous materials. Requirements: IBM PC or compatible; minimum 640 K RAM; mathcoprocessor; SVGA graphics board providing mode 103 display.

Unplugging the callose plug from sieve pores

PubMed Central

Xie, Bo

2011-01-01

The presence of callose in sieve plates has been known for a long time, but how this polysaccharide plug is synthesized has remained unsolved. Two independent laboratories have recently reported the identification of callose synthase 7 (CalS7), also known as glucan synthase-like 7 (GSL7), as the enzyme responsible for callose deposition in sieve plates. Mutant plants defective in this enzyme failed to synthesize callose in developing sieve plates during phloem formation and were unable to accumulate callose in sieve pores in response to stress treatments. The mutant plants developed less open pores per sieve plate and the pores were smaller in diameter. As a result, phloem conductivity was reduced significantly and the mutant plants were shorter and set fewer seeds. PMID:21386663

Characterizing TPS Microstructure: A Review of Some techniques

NASA Technical Reports Server (NTRS)

Gasch, Matthew; Stackpole, Mairead; Agrawal, Parul; Chavez-Garcie, Jose

2011-01-01

I. When seeking to understand ablator microstructure and morphology there are several useful techniques A. SEM 1) Visual characteriza3on at various length scales. 2) Chemical mapping by backscatter or x-ray highlights areas of interest. 3) Combined with other techniques (density, weight change, chemical analysis) SEM is a powerful tool to aid in explaining thermo/structural data. B. ASAP. 1) Chemical characteriza3on at various length scales. 2) Chemical mapping of pore structure by gas adsorption. 3) Provides a map of pore size vs. pore volume. 4) Provided surface area of exposed TPS. II. Both methods help characterize and understand how ablators react with other chemical species and provides insight into how they oxidize.

Molecular Dynamics Simulation of the Crystal Nucleation and Growth Behavior of Methane Hydrate in the Presence of the Surface and Nanopores of Porous Sediment.

PubMed

Yan, Ke-Feng; Li, Xiao-Sen; Chen, Zhao-Yang; Xia, Zhi-Ming; Xu, Chun-Gang; Zhang, Zhiqiang

2016-08-09

The behavior of hydrate formation in porous sediment has been widely studied because of its importance in the investigation of reservoirs and in the drilling of natural gas hydrate. However, it is difficult to understand the hydrate nucleation and growth mechanism on the surface and in the nanopores of porous media by experimental and numerical simulation methods. In this work, molecular dynamics simulations of the nucleation and growth of CH4 hydrate in the presence of the surface and nanopores of clay are carried out. The molecular configurations and microstructure properties are analyzed for systems containing one H2O hydrate layer (System A), three H2O hydrate layers (System B), and six H2O hydrate layers (System C) in both clay and the bulk solution. It is found that hydrate formation is more complex in porous media than in the pure bulk solution and that there is cooperativity between hydrate growth and molecular diffusion in clay nanopores. The hydroxylated edge sites of the clay surface could serve as a source of CH4 molecules to facilitate hydrate nucleation. The diffusion velocity of molecules is influenced by the growth of the hydrate that forms a block in the throats of the clay nanopore. Comparing hydrate growth in different clay pore sizes reveals that the pore size plays an important role in hydrate growth and molecular diffusion in clay. This simulation study provides the microscopic mechanism of hydrate nucleation and growth in porous media, which can be favorable for the investigation of the formation of natural gas hydrate in sediments.

Secondary water pore formation for proton transport in a ClC exchanger revealed by an atomistic molecular-dynamics simulation.

PubMed

Ko, Youn Jo; Jo, Won Ho

2010-05-19

Several prokaryotic ClC proteins have been demonstrated to function as exchangers that transport both chloride ions and protons simultaneously in opposite directions. However, the path of the proton through the ClC exchanger, and how the protein brings about the coupled movement of both ions are still unknown. In this work, we use an atomistic molecular dynamics (MD) simulation to demonstrate that a previously unknown secondary water pore is formed inside an Escherichia coli ClC exchanger. The secondary water pore is bifurcated from the chloride ion pathway at E148. From the systematic simulations, we determined that the glutamate residue exposed to the intracellular solution, E203, plays an important role as a trigger for the formation of the secondary water pore, and that the highly conserved tyrosine residue Y445 functions as a barrier that separates the proton from the chloride ion pathways. Based on our simulation results, we conclude that protons in the ClC exchanger are conducted via a water network through the secondary water pore, and we propose a new mechanism for the coupled transport of chloride ions and protons. It has been reported that several members of ClC proteins are not just channels that simply transport chloride ions across lipid bilayers; rather, they are exchangers that transport both the chloride ion and proton in opposite directions. However, the ion transit pathways and the mechanism of the coupled movement of these two ions have not yet been unveiled. In this article, we report a new finding (to our knowledge) of a water pore inside a prokaryotic ClC protein as revealed by computer simulation. This water pore is bifurcated from the putative chloride ion, and water molecules inside the new pore connect two glutamate residues that are known to be key residues for proton transport. On the basis of our simulation results, we conclude that the water wire that is formed inside the newly found pore acts as a proton pathway, which enables us to resolve many problems that could not be addressed by previous experimental studies. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Direct Numerical Simulation of Low Capillary Number Pore Scale Flows

NASA Astrophysics Data System (ADS)

Esmaeilzadeh, S.; Soulaine, C.; Tchelepi, H.

2017-12-01

The arrangement of void spaces and the granular structure of a porous medium determines multiple macroscopic properties of the rock such as porosity, capillary pressure, and relative permeability. Therefore, it is important to study the microscopic structure of the reservoir pores and understand the dynamics of fluid displacements through them. One approach for doing this, is direct numerical simulation of pore-scale flow that requires a robust numerical tool for prediction of fluid dynamics and a detailed understanding of the physical processes occurring at the pore-scale. In pore scale flows with a low capillary number, Eulerian multiphase methods are well-known to produce additional vorticity close to the interface. This is mainly due to discretization errors which lead to an imbalance of capillary pressure and surface tension forces that causes unphysical spurious currents. At the pore scale, these spurious currents can become significantly stronger than the average velocity in the phases, and lead to unphysical displacement of the interface. In this work, we first investigate the capability of the algebraic Volume of Fluid (VOF) method in OpenFOAM for low capillary number pore scale flow simulations. Afterward, we compare VOF results with a Coupled Level-Set Volume of Fluid (CLSVOF) method and Iso-Advector method. It has been shown that the former one reduces the VOF's unphysical spurious currents in some cases, and both are known to capture interfaces sharper than VOF. As the conclusion, we will investigate that whether the use of CLSVOF or Iso-Advector will lead to less spurious velocities and more accurate results for capillary driven pore-scale multiphase flows or not. Keywords: Pore-scale multiphase flow, Capillary driven flows, Spurious currents, OpenFOAM

Controlled morphology and optical properties of n-type porous silicon: effect of magnetic field and electrode-assisted LEF.

PubMed

Antunez, Edgar E; Campos, Jose; Basurto, Miguel A; Agarwal, Vivechana

2014-01-01

Fabrication of photoluminescent n-type porous silicon (nPS), using electrode-assisted lateral electric field accompanied with a perpendicular magnetic field, is reported. The results have been compared with the porous structures fabricated by means of conventional anodization and electrode-assisted lateral electric field without magnetic field. The lateral electric field (LEF) applied across the silicon substrate leads to the formation of structural gradient in terms of density, dimension, and depth of the etched pores. Apart from the pore shape tunability, the simultaneous application of LEF and magnetic field (MF) contributes to a reduction of the dimension of the pores and promotes relatively more defined pore tips as well as a decreased side-branching in the pore walls of the macroporous structure. Additionally, when using magnetic field-assisted etching, within a certain range of LEF, an enhancement of the photoluminescence (PL) response was obtained.

Controlled morphology and optical properties of n-type porous silicon: effect of magnetic field and electrode-assisted LEF

PubMed Central

2014-01-01

Fabrication of photoluminescent n-type porous silicon (nPS), using electrode-assisted lateral electric field accompanied with a perpendicular magnetic field, is reported. The results have been compared with the porous structures fabricated by means of conventional anodization and electrode-assisted lateral electric field without magnetic field. The lateral electric field (LEF) applied across the silicon substrate leads to the formation of structural gradient in terms of density, dimension, and depth of the etched pores. Apart from the pore shape tunability, the simultaneous application of LEF and magnetic field (MF) contributes to a reduction of the dimension of the pores and promotes relatively more defined pore tips as well as a decreased side-branching in the pore walls of the macroporous structure. Additionally, when using magnetic field-assisted etching, within a certain range of LEF, an enhancement of the photoluminescence (PL) response was obtained. PMID:25313298

Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation

PubMed Central

Lawrence, Sara L.; Feil, Susanne C.; Morton, Craig J.; Farrand, Allison J.; Mulhern, Terrence D.; Gorman, Michael A.; Wade, Kristin R.; Tweten, Rodney K.; Parker, Michael W.

2015-01-01

Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world’s leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface. PMID:26403197

Induction of “Pore” Formation in Plant Cell Membranes by Toluene 1

PubMed Central

Lerner, Henri R.; Ben-Bassat, David; Reinhold, Leonora; Poljakoff-Mayber, Alexandra

1978-01-01

Treatment with aqueous toluene-ethanol has been shown to induce “pore” formation in plant cell membranes. The evidence is as follows: [List: see text] While the principal experimental material was roots of Atriplex nummularia Lindl., the fact that similar results were also observed with leaves of Pisum sativum L. and with the alga Chlorella pyrenoidosa Chik. suggests that the phenomenon is general. Although the phenomenon of pore induction is qualitatively similar to that in microorganisms, the pores induced appear to be smaller. It is proposed that induced leakage could be the basis for the development of simple and rapid methods for plant biochemical studies. PMID:16660262

Modeling Vascularized Bone Regeneration Within a Porous Biodegradable CaP Scaffold Loaded with Growth Factors

PubMed Central

Sun, X; Kang, Y; Bao, J; Zhang, Y; Yang, Y; Zhou, X

2013-01-01

Osteogenetic microenvironment is a complex constitution in which extracellular matrix (ECM) molecules, stem cells and growth factors each interact to direct the coordinate regulation of bone tissue development. Importantly, angiogenesis improvement and revascularization are critical for osteogenesis during bone tissue regeneration processes. In this study, we developed a three-dimensional (3D) multi-scale system model to study cell response to growth factors released from a 3D biodegradable porous calcium phosphate (CaP) scaffold. Our model reconstructed the 3D bone regeneration system and examined the effects of pore size and porosity on bone formation and angiogenesis. The results suggested that scaffold porosity played a more dominant role in affecting bone formation and angiogenesis compared with pore size, while the pore size could be controlled to tailor the growth factor release rate and release fraction. Furthermore, a combination of gradient VEGF with BMP2 and Wnt released from the multi-layer scaffold promoted angiogenesis and bone formation more readily than single growth factors. These results demonstrated that the developed model can be potentially applied to predict vascularized bone regeneration with specific scaffold and growth factors. PMID:23566802

Single-phase and two-phase flow properties of mesaverde tight sandstone formation; random-network modeling approach

NASA Astrophysics Data System (ADS)

Bashtani, Farzad; Maini, Brij; Kantzas, Apostolos

2016-08-01

3D random networks are constructed in order to represent the tight Mesaverde formation which is located in north Wyoming, USA. The porous-space is represented by pore bodies of different shapes and sizes which are connected to each other by pore throats of varying length and diameter. Pore bodies are randomly distributed in space and their connectivity varies based on the connectivity number distribution which is used in order to generate the network. Network representations are then validated using publicly available mercury porosimetry experiments. The network modeling software solves the fundamental equations of two-phase immiscible flow incorporating wettability and contact angle variability. Quasi-static displacement is assumed. Single phase macroscopic properties (porosity, permeability) are calculated and whenever possible are compared to experimental data. Using this information drainage and imbibition capillary pressure, and relative permeability curves are predicted and (whenever possible) compared to experimental data. The calculated information is grouped and compared to available literature information on typical behavior of tight formations. Capillary pressure curve for primary drainage process is predicted and compared to experimental mercury porosimetry in order to validate the virtual porous media by history matching. Relative permeability curves are also calculated and presented.

Variations in Multiscale (nano to mm) Porosity in the Eagle Ford Shale as a Function of Maturity through the Oil Window

NASA Astrophysics Data System (ADS)

Anovitz, L. M.; Cole, D. R.; Swift, A.; Sheets, J.; Elston, H. W.; Gutierrez, M. A.; Cook, A.; Chipera, S.; Littrell, K. C.; Mildner, D. F.; Wasbrough, M.

2013-12-01

Porosity and permeability are key variables that link the thermal-hydrologic, geomechanical and geochemical behavior in rock systems and are thus important input parameters for transport models. Recent neutron scattering studies have indicated that the scales of pore sizes in rocks extend over many orders of magnitude from nanometer pores with huge amounts of total surface area to large open fracture systems (multiscale porosity, cf. Anovitz et al., 2009, 2011, 2013a,b). However, despite a considerable amount of effort combining conventional rock petrophysics with more sophisticated neutron scattering and electron microscopy studies, the quantitative nature of this porosity in tight gas shales, especially at smaller scales and over larger rock volumes, remains largely unknown (Clarkson, 2011). We lack a quantitative understanding of the multiscale porosity regime (i.e., pore size, shape, and volume, pore size distribution, pore connectivity, pore wall roughness) in rocks. Nor is it understood how porosity is affected by regional variation, thermal changes across the oil window, and, most critically, hydraulic fracturing operations. In order to begin to provide a quantitative understanding of porosity at nanometer to core scales in these shale formations and how it relates to gas storage and recovery we have used a combination of small and ultrasmall angle neutron scattering measurments made on the GP-SANS instrument at ORNL/HFIR, and the NG3-SANS and BT5-USANS instruments and NIST/NCNR, with SEM/BSE and X-ray Computed Tomographic imaging to analyze the pore structure of both clay and carbonate-rich samples of the Eagle Ford Shale. The Eagle Ford Shale is a late Cretaceous unit underlying much of southeast Texas and probably adjacent sections of Mexico. It outcrops in an arc from north of Austin, through San Antonio and then west towards Kinney County. It is hydrocarbon rich, and buried portions straddle the oil window. The Eagle Ford is currently one of the most actively drilled oil and gas targets in the US. The first successful horizontal well was drilled in 2008, and 2522 permits were recorded (Texas railroad commission) by Sept 1, 2011. While the oil and gas reserves in the Eagle Ford have been known since the 1970's, prior to the invention of horizontal drilling/hydraulic fracturing it was not considered economic. Several important trends in the rock pore structure have been identified using our approach. Pore distributions are clearly fractal but, as was observed for the St. Peter sandstone (Anovitz et al., 2013a), are composed of several size distributions. Initial porosity is strongly anisotropic, as expected for shales. However, this decreases for shales, and disappears for carbonates with maturity. In both cases significant reduction occurs in total porosity, with most of the change coming at the finest scales (< ~ 10 nm), and an observable decrease at intermediate scales (near 100 nm) Research sponsored by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences, U.S. Department of Energy, and as part of the Center for Nanoscale Control of Geologic CO2, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science under U.S. Dept. of Energy (DOE) contract DE-AC02-05CH11231.

Methods for pore water extraction from unsaturated zone tuff, Yucca Mountain, Nevada

USGS Publications Warehouse

Scofield, K.M.

2006-01-01

Assessing the performance of the proposed high-level radioactive waste repository at Yucca Mountain, Nevada, requires an understanding of the chemistry of the water that moves through the host rock. The uniaxial compression method used to extract pore water from samples of tuffaceous borehole core was successful only for nonwelded tuff. An ultracentrifugation method was adopted to extract pore water from samples of the densely welded tuff of the proposed repository horizon. Tests were performed using both methods to determine the efficiency of pore water extraction and the potential effects on pore water chemistry. Test results indicate that uniaxial compression is most efficient for extracting pore water from nonwelded tuff, while ultracentrifugation is more successful in extracting pore water from densely welded tuff. Pore water splits collected from a single nonwelded tuff core during uniaxial compression tests have shown changes in pore water chemistry with increasing pressure for calcium, chloride, sulfate, and nitrate. Pore water samples collected from the intermediate pressure ranges should prevent the influence of re-dissolved, evaporative salts and the addition of ion-deficient water from clays and zeolites. Chemistry of pore water splits from welded and nonwelded tuffs using ultracentrifugation indicates that there is no substantial fractionation of solutes.

Modeling the relaxation dynamics of fluids in nanoporous materials

NASA Astrophysics Data System (ADS)

Edison, John R.

Mesoporous materials are being widely used in the chemical industry in various environmentally friendly separation processes and as catalysts. Our research can be broadly described as an effort to understand the behavior of fluids confined in such materials. More specifically we try to understand the influence of state variables like temperature and pore variables like size, shape, connectivity and structural heterogeneity on both the dynamic and equilibrium behavior of confined fluids. The dynamic processes associated with the approach to equilibrium are largely unexplored. It is important to look into the dynamic behavior for two reasons. First, confined fluids experience enhanced metastabilities and large equilibration times in certain classes of mesoporous materials, and the approach to the metastable/stable equilibrium is of tremendous interest. Secondly, understanding the transport resistances in a microscopic scale will help better engineer heterogeneous catalysts and separation processes. Here we present some of our preliminary studies on dynamics of fluids in ideal pore geometries. The tool that we have used extensively to investigate the relaxation dynamics of fluids in pores is the dynamic mean field theory (DMFT) as developed by Monson [P. A. Monson, J. Chem. Phys., 128, 084701 (2008)]. The theory is based on a lattice gas model of the system and can be viewed as a highly computationally efficient approximation to the dynamics averaged over an ensemble of Kawasaki dynamics Monte Carlo trajectories of the system. It provides a theory of the dynamics of the system consistent with the thermodynamics in mean field theory. The nucleation mechanisms associated with confined fluid phase transitions are emergent features in the calculations. We begin by describing the details of the theory and then present several applications of DMFT. First we present applications to three model pore networks (a) a network of slit pores with a single pore width; (b) a network of slit pores with two pore widths arranged in intersecting channels with a single pore width in each channel; (c) a network of slit pores with two pore widths forming an array of ink-bottles. The results illustrate the effects of pore connectivity upon the dynamics of vapor liquid phase transformations as well as on the mass transfer resistances to equilibration. We then present an application to a case where the solid-fluid interactions lead to partial wetting on a planar surface. The pore filling process in such systems features an asymmetric density distribution where a liquid droplet appears on one of the walls. We also present studies on systems where there is partial drying or drying associated with weakly attractive or repulsive interactions between the fluid and the pore walls. We describe the symmetries exhibited by the lattice model between pore filling for wetting states and pore emptying for drying states, for both the thermodynamics and dynamics. We then present an extension of DMFT to mixtures and present some examples that illustrate the utility of the approach. Finally we present an assessment the accuracy of the DMFT through comparisons with a higher order approximation based on the path probability method as well as Kawasaki dynamics.

Comparison of the diagenetic and reservoir quality evolution between the anticline crest and flank of an Upper Jurassic carbonate gas reservoir, Abu Dhabi, United Arab Emirates

NASA Astrophysics Data System (ADS)

Morad, Daniel; Nader, Fadi H.; Gasparrini, Marta; Morad, Sadoon; Rossi, Carlos; Marchionda, Elisabetta; Al Darmaki, Fatima; Martines, Marco; Hellevang, Helge

2018-05-01

This petrographic, stable isotopic and fluid inclusion microthermometric study of the Upper Jurassic limestones of an onshore field, Abu Dhabi, United Arab Emirates (UAE) compares diagenesis in flanks and crest of the anticline. The results revealed that the diagenetic and related reservoir quality evolution occurred during three phases, including: (i) eogenesis to mesogenesis 1, during which reservoir quality across the field was either deteriorated or preserved by calcite cementation presumably derived from marine or evolved marine pore waters. Improvement of reservoir quality was due to the formation of micropores by micritization of allochems and creation of moldic/intragranular pores by dissolution of peloids and skeletal fragments. (ii) Obduction of Oman ophiolites and formation of the anticline of the studied field was accompanied by cementation by saddle dolomite and blocky calcite. High homogenization temperatures (125-175 °C) and high salinity (19-26 wt% NaCl eq) of the fluid inclusions, negative δ18OVPDB values (-7.7 to -2.9‰), saddle shape of dolomite, and the presence of exotic cements (i.e. fluorite and sphalerite) suggest that these carbonates were formed by flux of hot basinal brines, probably related to this tectonic compression event. (iii) Mesogenesis 2 during subsidence subsequent to the obduction event, which resulted in extensive stylolitization and cementation by calcite. This calcite cement occluded most of the remaining moldic and inter-/intragranular pores of the flank limestones (water zone) whereas porosity was preserved in the crest. This study contributes to: (1) our understanding of differences in the impact of diagenesis on reservoir quality evolution in flanks and crests of anticlines, i.e. impact of hydrocarbon emplacement on diagenesis, and (2) relating various diagenetic processes to burial history and tectonic events of foreland basins in the Arabian Gulf area and elsewhere.

Orthogonal functionalization of nanoporous substrates: control of 3D surface functionality.

PubMed

Lazzara, Thomas D; Kliesch, Torben-Tobias; Janshoff, Andreas; Steinem, Claudia

2011-04-01

Anodic aluminum oxide (AAO) membranes with aligned, cylindrical, nonintersecting pores were selectively functionalized in order to create dual-functionality substrates with different pore-rim and pore-interior surface functionalities, using silane chemistry. We used a two-step process involving an evaporated thin gold film to protect the underlying surface functionality of the pore rims. Subsequent treatment with oxygen plasma of the modified AAO membrane removed the unprotected organic functional groups, i.e., the pore-interior surface. After gold removal, the substrate became optically transparent, and displayed two distinct surface functionalities, one at the pore-rim surface and another at the pore-interior surface. We achieved a selective hydrophobic functionalization with dodecyl-trichlorosilane of either the pore rims or the pore interiors. The deposition of planar lipid membranes on the functionalized areas by addition of small unilamellar vesicles occurred in a predetermined fashion. Small unilamellar vesicles only ruptured upon contact with the hydrophobic substrate regions forming solid supported hybrid bilayers. In addition, pore-rim functionalization with dodecyl-trichlorosilane allowed the formation of pore-spanning hybrid lipid membranes as a result of giant unilamellar vesicle rupture. Confocal laser scanning microscopy was employed to identify the selective spatial localization of the adsorbed fluorescently labeled lipids. The corresponding increase in the AAO refractive index due to lipid adsorption on the hydrophobic regions was monitored by optical waveguide spectroscopy. This simple orthogonal functionalization route is a promising method to control the three-dimensional surface functionality of nanoporous films. © 2011 American Chemical Society

A thermodynamic approach to alamethicin pore formation.

PubMed

Rahaman, Asif; Lazaridis, Themis

2014-01-01

The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8Å pore and the octamer in an 11Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted "barrel-stave" model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself. © 2013.

Numerical Investigation of Physicochemical Processes Occurring During Water Evaporation in the Surface Layer Pores of a Forest Combustible Material

NASA Astrophysics Data System (ADS)

Zhdanova, A. O.; Kuznetsov, G. V.; Strizhak, P. A.

2014-07-01

A numerical investigation of the physicochemical processes occurring during water evaporation from the pores of the surface layer of a forest combustible material has been carried out. The characteristic features of the suppression of the thermal decomposition reaction of a combustible material with water filling fullyits pores and formation of a water fi lm over its surface have been determined. The characteristic times of suppression of thermal decomposition reactions under various environmental conditions and the thickness and kinds of forest combustible material (birch leaves, pine and spruce needles, etc.) have been established.

Dynamics of water in the amphiphilic pore of amyloid β fibrils

NASA Astrophysics Data System (ADS)

GhattyVenkataKrishna, Pavan K.; Mostofian, Barmak

2013-09-01

Alzheimers disease related amyloid peptide, Aβ, forms a fibrillar structure through aggregation. The aggregate is stabilized by a salt bridge that is responsible for the formation of an amphiphilic pore that can accommodate water molecules. None of the reported structures of Aβ, however, contain water. We present results from molecular dynamics simulations on dimeric Aβ fibrils solvated in water. Water penetrates and fills the amphiphilic pore increasing its volume. We observe a thick wire of water that is translationally and rotationally stiff in comparison to bulk water and may be essential for the stabilization of the amyloid Aβ protein.

Anticorrosive Microbial Polysaccharides: Structure-Function Relationships

USDA-ARS?s Scientific Manuscript database

Water-soluble microbial polysaccharides are often implicated in biofilm formation and are believed to mediate cell-cell aggregation and adhesion to surfaces. Generally, biofilm formation is considered harmful or undesirable, as it leads to increased drag, plugging of pores, dimished heat transfer, ...

Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation.

PubMed

Shu, Qin; Krezel, Andrzej M; Cusumano, Zachary T; Pinkner, Jerome S; Klein, Roger; Hultgren, Scott J; Frieden, Carl

2016-06-28

Curli, consisting primarily of major structural subunit CsgA, are functional amyloids produced on the surface of Escherichia coli, as well as many other enteric bacteria, and are involved in cell colonization and biofilm formation. CsgE is a periplasmic accessory protein that plays a crucial role in curli biogenesis. CsgE binds to both CsgA and the nonameric pore protein CsgG. The CsgG-CsgE complex is the curli secretion channel and is essential for the formation of the curli fibril in vivo. To better understand the role of CsgE in curli formation, we have determined the solution NMR structure of a double mutant of CsgE (W48A/F79A) that appears to be similar to the wild-type (WT) protein in overall structure and function but does not form mixed oligomers at NMR concentrations similar to the WT. The well-converged structure of this mutant has a core scaffold composed of a layer of two α-helices and a layer of three-stranded antiparallel β-sheet with flexible N and C termini. The structure of CsgE fits well into the cryoelectron microscopy density map of the CsgG-CsgE complex. We highlight a striking feature of the electrostatic potential surface in CsgE structure and present an assembly model of the CsgG-CsgE complex. We suggest a structural mechanism of the interaction between CsgE and CsgA. Understanding curli formation can provide the information necessary to develop treatments and therapeutic agents for biofilm-related infections and may benefit the prevention and treatment of amyloid diseases. CsgE could establish a paradigm for the regulation of amyloidogenesis because of its unique role in curli formation.

Pore pressure migration during hydraulic stimulation due to permeability enhancement by low-pressure subcritical fracture slip

NASA Astrophysics Data System (ADS)

Mukuhira, Yusuke; Moriya, Hirokazu; Ito, Takatoshi; Asanuma, Hiroshi; Häring, Markus

2017-04-01

Understanding the details of pressure migration during hydraulic stimulation is important for the design of an energy extraction system and reservoir management, as well as for the mitigation of hazardous-induced seismicity. Based on microseismic and regional stress information, we estimated the pore pressure increase required to generate shear slip on an existing fracture during stimulation. Spatiotemporal analysis of pore pressure migration revealed that lower pore pressure migrates farther and faster and that higher pore pressure migrates more slowly. These phenomena can be explained by the relationship between fracture permeability and stress state criticality. Subcritical fractures experience shear slip following smaller increases of pore pressure and promote migration of pore pressure because of their enhanced permeability. The difference in migration rates between lower and higher pore pressures suggests that the optimum wellhead pressure is the one that can stimulate relatively permeable fractures, selectively. Its selection optimizes economic benefits and minimizes seismic risk.

Changes in Physical Properties of the Nankai Trough Megasplay Fault Induced by Earthquakes, Detected by Continuous Pressure Monitoring

NASA Astrophysics Data System (ADS)

Kinoshita, C.; Saffer, D.; Kopf, A.; Roesner, A.; Wallace, L. M.; Araki, E.; Kimura, T.; Machida, Y.; Kobayashi, R.; Davis, E.; Toczko, S.; Carr, S.

2018-02-01

One primary objective of Integrated Ocean Drilling Program Expedition 365, conducted as part of the Nankai Trough Seismogenic Zone Experiment, was to recover a temporary observatory emplaced to monitor formation pore fluid pressure and temperature within a splay fault in the Nankai subduction zone offshore SW Honshu, Japan. Here we use a 5.3 year time series of formation pore fluid pressure, and in particular the response to ocean tidal loading, to evaluate changes in pore pressure and formation and fluid elastic properties induced by earthquakes. Our analysis reveals 31 earthquake-induced perturbations. These are dominantly characterized by small transient increases in pressure (28 events) and decreases in ocean tidal loading efficiency (14 events) that reflect changes to formation or fluid compressibility. The observed perturbations follow a magnitude-distance threshold similar to that reported for earthquake-driven hydrological effects in other settings. To explore the mechanisms that cause these changes, we evaluate the expected static and dynamic strains from each earthquake. The expected static strains are too small to explain the observed pressure changes. In contrast, estimated dynamic strains correlate with the magnitude of changes in both pressure and loading efficiency. We propose potential mechanism for the changes and subsequent recovery, which is exsolution of dissolved gas in interstitial fluids in response to shaking.

Bubble Induced Disruption of a Planar Solid-Liquid Interface During Controlled Directional Solidification in a Microgravity Environment

NASA Technical Reports Server (NTRS)

Grugel, Richard N.; Brush, Lucien N.; Anilkumar, Amrutur V.

2013-01-01

Pore Formation and Mobility Investigation (PFMI) experiments were conducted in the microgravity environment aboard the International Space Station with the intent of better understanding the role entrained porosity/bubbles play during controlled directional solidification. The planar interface in a slowing growing succinonitrile - 0.24 wt% water alloy was being observed when a nitrogen bubble traversed the mushy zone and remained at the solid-liquid interface. Breakdown of the interface to shallow cells subsequently occurred, and was later evaluated using down-linked data from a nearby thermocouple. These results and other detrimental effects due to the presence of bubbles during solidification processing in a microgravity environment are presented and discussed.

Discovery of siderite in marine sediment: Source and effect of violent gas venting at the Tsanyao Mud Volcano, offshore SW Taiwan

NASA Astrophysics Data System (ADS)

Tseng, Y.; Lin, S.; Hsieh, I. C.; Lien, K. L.

2016-12-01

Tsanyao mud volcano is a 400 meters high, 5 kilometers in diameter, a center crater of 50 meters width activing venting mud diapir. The gigantic size of mud volcano indicate massive transportation of material, i.e., gas, fluid, and breccia from deep to the sea floor in building up the mud volcano. The mud volcano is located at the upper slope of the accretionary wedge with a surrounding water depth of about xx m, offshore Southwestern Taiwan. On shore, a series of active mud volcanos also exist in a trend similar to those found offshore. In order to understand sources of gas, fluid, solid materials and the effect of gas migration and associate authigenic mineral formation, we have obtained multibeam bathymetry, water column echo sounding, together with sediment XRD and SEM and pore water composition of methane, sulfide, sulfate, chloride, potassium, lithium, boron, and water O-18 at the study mud volcano. We have observed more than 30 flares around the main cone within a perimeter of 10 square miles. δ13C values of methane in the pore water ranged from -30 to -50 ‰. The lower C13 ratios, together with high C2+/C1 ratios demonstrated that vent gas is mostly thermogenic in origin. Higher thermal gradient and water temperature indicated that cone top is unfavorable for gas-hydrate formation, however, gas hydrate may exist at a deeper part of the mud volcano system. High concentration of sulfide presence right near the sulfate-methane interface, a result of anoxic methane oxidation. However, low concentrations of pyrite in sediments indicated that AOM did not favor pyrite formation at depth. In addition, abundant siderite were found in the sediments collected in the mud volcano cone. Rapid consumption of sulfate through AOM reaction generated a condition favor the siderite fomation, instead of the typical pyrite formation commonly observed.

Pore-network model of evaporation-induced salt precipitation in porous media: The effect of correlations and heterogeneity

NASA Astrophysics Data System (ADS)

Dashtian, Hassan; Shokri, Nima; Sahimi, Muhammad

2018-02-01

Salt transport and precipitation in porous media constitute a set of complex and fascinating phenomena that are of considerable interest to several important problems, ranging from storage of CO2 in geological formations, to soil fertility, and protection of pavements and roads, as well as historical monuments. The phenomena occur at the pore scale and are greatly influenced by the heterogeneity of the pore space morphology. We present a pore-network (PN) model to study the phenomena. Vapor diffusion, capillary effect at the brine-vapor interface, flow of brine, and transport of salt and its precipitation in the pores that plug the pores partially or completely are all accounted for. The drying process is modeled by the invasion percolation, while transport of salt in brine is accounted for by the convective-diffusion equation. We demonstrate that the drying patterns, the clustering and connectivity of the pore throats in which salt precipitation occurs, the saturation distribution, and the drying rate are all strongly dependent upon the pore-size distribution, the correlations among the pore sizes, and the anisotropy of the pore space caused by stratification that most natural porous media contain. In particular, if the strata are more or less parallel to the direction of injection of the gas that dries out the pore space (air, for example) and/or causes salt precipitation (CO2, for example), the drying rate increases significantly. Moreover, salt tends to precipitate in clusters of neighboring pores that are parallel to the open surface of the porous medium.

THE EFFECT OF GAS HYDRATES DISSOCIATION AND DRILLING FLUIDS INVASION UPON BOREHOLE STABILITY IN OCEANIC GAS HYDRATES-BEARING SEDIMENT

NASA Astrophysics Data System (ADS)

Ning, F.; Wu, N.; Jiang, G.; Zhang, L.

2009-12-01

Under the condition of over-pressure drilling, the solid-phase and liquid-phase in drilling fluids immediately penetrate into the oceanic gas hydrates-bearing sediment, which causes the water content surrounding the borehole to increase largely. At the same time, the hydrates surrounding borehole maybe quickly decompose into water and gas because of the rapid change of temperature and pressure. The drilling practices prove that this two factors may change the rock characteristics of wellbore, such as rock strength, pore pressure, resistivity, etc., and then affect the logging response and evaluation, wellbore stability and well safty. The invasion of filtrate can lower the angle of friction and weaken the cohesion of hydrates-bearing sediment,which is same to the effect of invading into conventional oil and gas formation on borehole mechnical properties. The difference is that temperature isn’t considered in the invasion process of conventional formations while in hydrates-bearing sediments, it is a factor that can not be ignored. Temperature changes can result in hydrates dissociating, which has a great effect on mechanical properties of borehole. With the application of numerical simulation method, we studied the changes of pore pressure and variation of water content in the gas hydrates-bearing sediment caused by drilling fluid invasion under pressure differential and gas hydrate dissociation under temperature differential and analyzed their influence on borehole stability.The result of simulation indicated that the temperature near borehole increased quickly and changed hardly any after 6 min later. About 1m away from the borehole, the temperature of formation wasn’t affected by the temperature change of borehole. At the place near borehole, as gas hydrate dissociated dramatically and drilling fluid invaded quickly, the pore pressure increased promptly. The degree of increase depends on the permeability and speed of temperature rise of formation around bohole. If the formation has a low permeability and is heated quickly, the dissociated gas and water couldn’t flow away in time, which is likely to bring a hazard of excess pore pressure. Especially in the area near the wall of borehole, the increase degree of pore pressure is high than other area because the dissociation of gas hydrates is relatively violent and hydraulic gradient is bigger. We also studied the distribution of water saturation around borehole after 10min, 30min and 60min respectively. It revealed that along with the invasion of drilling fluid and dissociation of gas hydrate, the degree of water saturation increased gradually. The effect of gas hydrate dissociation and drilling fluids invasion on borehole stability is to weaken mechanical properties of wellbore and change the pore pressure, then changes the effective stress of gas hydrates-bearing sediment. So temperature, pressure in the borehole and filter loss of drilling fluids should be controlled strictly to prevent gas hydrates from decomposing largely and in order to keep the borehole stability in the gas hydrates-bearing formations.

Micro-CT Pore Scale Study Of Flow In Porous Media: Effect Of Voxel Resolution

NASA Astrophysics Data System (ADS)

Shah, S.; Gray, F.; Crawshaw, J.; Boek, E.

2014-12-01

In the last few years, pore scale studies have become the key to understanding the complex fluid flow processes in the fields of groundwater remediation, hydrocarbon recovery and environmental issues related to carbon storage and capture. A pore scale study is often comprised of two key procedures: 3D pore scale imaging and numerical modelling techniques. The essence of a pore scale study is to test the physics implemented in a model of complicated fluid flow processes at one scale (microscopic) and then apply the model to solve the problems associated with water resources and oil recovery at other scales (macroscopic and field). However, the process of up-scaling from the pore scale to the macroscopic scale has encountered many challenges due to both pore scale imaging and modelling techniques. Due to the technical limitations in the imaging method, there is always a compromise between the spatial (voxel) resolution and the physical volume of the sample (field of view, FOV) to be scanned by the imaging methods, specifically X-ray micro-CT (XMT) in our case In this study, a careful analysis was done to understand the effect of voxel size, using XMT to image the 3D pore space of a variety of porous media from sandstones to carbonates scanned at different voxel resolution (4.5 μm, 6.2 μm, 8.3 μm and 10.2 μm) but keeping the scanned FOV constant for all the samples. We systematically segment the micro-CT images into three phases, the macro-pore phase, an intermediate phase (unresolved micro-pores + grains) and the grain phase and then study the effect of voxel size on the structure of the macro-pore and the intermediate phases and the fluid flow properties using lattice-Boltzmann (LB) and pore network (PN) modelling methods. We have also applied a numerical coarsening algorithm (up-scale method) to reduce the computational power and time required to accurately predict the flow properties using the LB and PN method.

Membranes with functionalized carbon nanotube pores for selective transport

DOEpatents

Bakajin, Olgica; Noy, Aleksandr; Fornasiero, Francesco; Park, Hyung Gyu; Holt, Jason K; Kim, Sangil

2015-01-27

Provided herein composition and methods for nanoporous membranes comprising single walled, double walled, or multi-walled carbon nanotubes embedded in a matrix material. Average pore size of the carbon nanotube can be 6 nm or less. These membranes are a robust platform for the study of confined molecular transport, with applications in liquid and gas separations and chemical sensing including desalination, dialysis, and fabric formation.

Initial characterization of mudstone nanoporosity with small angle neutron scattering using caprocks from carbon sequestration sites.

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCray, John; Navarre-Sitchler, Alexis; Mouzakis, Katherine

Geological carbon sequestration relies on the principle that CO{sub 2} injected deep into the subsurface is unable to leak to the atmosphere. Structural trapping by a relatively impermeable caprock (often mudstone such as a shale) is the main trapping mechanism that is currently relied on for the first hundreds of years. Many of the pores of the caprock are of micrometer to nanometer scale. However, the distribution, geometry and volume of porosity at these scales are poorly characterized. Differences in pore shape and size can cause variation in capillary properties and fluid transport resulting in fluid pathways with different capillarymore » entry pressures in the same sample. Prediction of pore network properties for distinct geologic environments would result in significant advancement in our ability to model subsurface fluid flow. Specifically, prediction of fluid flow through caprocks of geologic CO{sub 2} sequestration reservoirs is a critical step in evaluating the risk of leakage to overlying aquifers. The micro- and nanoporosity was analyzed in four mudstones using small angle neutron scattering (SANS). These mudstones are caprocks of formations that are currently under study or being used for carbon sequestration projects and include the Marine Tuscaloosa Group, the Lower Tuscaloosa Group, the upper and lower shale members of the Kirtland Formation, and the Pennsylvanian Gothic shale. Total organic carbon varies from <0.3% to 4% by weight. Expandable clay contents range from 10% to {approx}40% in the Gothic shale and Kirtland Formation, respectively. Neutrons effectively scatter from interfaces between materials with differing scattering length density (i.e. minerals and pores). The intensity of scattered neutrons, I(Q), where Q is the scattering vector, gives information about the volume of pores and their arrangement in the sample. The slope of the scattering data when plotted as log I(Q) vs. log Q provides information about the fractality or geometry of the pore network. Results from this study, combined with high-resolution TEM imaging, provide insight into the differences in volume and geometry of porosity between these various mudstones.« less

Visualization of soil structure and pore structure modifications by pioneering ground beetles (Cicindelidae) in surface sediments of an artificial catchment

NASA Astrophysics Data System (ADS)

Badorreck, Annika; Gerke, Horst H.; Weller, Ulrich; Vontobel, Peter

2010-05-01

An artificial catchment was constructed to study initial soil and ecosystem development. As a key process, the pore structure dynamics in the soil at the surface strongly influences erosion, infiltration, matter dynamics, and vegetation establishment. Little is known, however, about the first macropore formation in the very early stage. This presentation focuses on observations of soil pore geometry and its effect on water flow at the surface comparing samples from three sites in the catchment and in an adjacent "younger" site composed of comparable sediments. The surface soil was sampled in cylindrical plastic rings (10 cm³) down to 2 cm depth in three replicates each site and six where caves from pioneering ground-dwelling beetles Cicindelidae were found. The samples were scanned with micro-X-ray computed tomography (at UFZ-Halle, Germany) with a resolution of 0.084 mm. The infiltration dynamics were visualized with neutronradiography (at Paul-Scherer-Institute, Switzerland) on slab-type soil samples in 2D. The micro-tomographies exhibit formation of surface sealing whose thickness and intensity vary with silt and clay content. The CT images show several coarser- and finer-textured micro-layers at the sample surfaces that were formed as a consequence of repeated washing in of finer particles in underlying coarser sediment. In micro-depressions, the uppermost layers consist of sorted fine sand and silt due to wind erosion. Similar as for desert pavements, a vesicular pore structure developed in these sediments on top, but also scattered in fine sand- and silt-enriched micro-layers. The ground-dwelling activity of Cicindelidae beetles greatly modifies the soil structure through forming caves in the first centimetres of the soil. Older collapsed caves, which form isolated pores within mixed zones, were also found. The infiltration rates were severely affected both, by surface crusts and activity of ground-dwelling beetles. The observations demonstrate relatively high abiotic and biotic dynamics of soil pore structure in the soil surface even during the very early development stages. The structure formation has potentially great effects on changing runoff and infiltration by forming sealing layers or preferential flow paths.

The Rapid Formation of Localized Compaction Bands Under Hydrostatic Load Leading to Pore-pressure Transients in Compacting Rocks

NASA Astrophysics Data System (ADS)

Faulkner, D.; Leclere, H.; Bedford, J. D.; Behnsen, J.; Wheeler, J.

2017-12-01

Compaction of porous rocks can occur uniformly or within localized deformation bands. The formation of compaction bands and their effects on deformation behaviour are poorly understood. Porosity may be primary and compaction can occur with burial, or it can be produced by metamorphic reactions with a solid volume reduction, that can then undergo collapse. We report results from hydrostatic compaction experiments on porous bassanite (CaSO4.0.5H2O) aggregates. Gypsum (CaSO4.2H2O) is first dehydrated under low effective pressure, 4 MPa, to produce a bassanite aggregate with a porosity of 27%. Compaction is induced by increasing confining pressure at rates from 0.001 MPa/s to 0.02 MPa/s while the sample is maintained at a temperature of 115°C. At slow compaction rates, porosity collapse proceeds smoothly. At higher compaction rates, sudden increases in the pore-fluid pressure occur with a magnitude of 5 MPa. Microstructural investigations using X-ray microtomography and SEM observations show that randomly oriented localized compaction features occur in all samples, where the bulk porosity of 18% outside the band is reduced to 5% inside the band. Previous work on deformation bands has suggested that localized compactive features only form under an elevated differential stress and not under a hydrostatic stress state. The magnitude of the pore-pressure pulses can be explained by the formation of compaction bands. The results indicate that the compaction bands can form by rapid (unstable) propagation across the sample above a critical strain rate, or quasi-statically at low compaction rates without pore-fluid pressure bursts. The absence of pore-fluid pressure bursts at slow compaction rates can be explained by viscous deformation of the bassanite aggregate around the tip of a propagating compaction band, relaxing stress, and promoting stable propagation. Conversely, at higher compaction rates, viscous deformation cannot relax the stress sufficiently and unstable, brittle propagation occurs. In nature, this type of compaction behaviour might result in a mechanism to produce pulses of pore pressure within porous rocks which might have a significant effect on the deformation behaviour at depth.

FIB and MIP: understanding nanoscale porosity in molecularly imprinted polymers via 3D FIB/SEM tomography.

PubMed

Neusser, G; Eppler, S; Bowen, J; Allender, C J; Walther, P; Mizaikoff, B; Kranz, C

2017-10-05

We present combined focused ion beam/scanning electron beam (FIB/SEM) tomography as innovative method for differentiating and visualizing the distribution and connectivity of pores within molecularly imprinted polymers (MIPs) and non-imprinted control polymers (NIPs). FIB/SEM tomography is used in cell biology for elucidating three-dimensional structures such as organelles, but has not yet been extensively applied for visualizing the heterogeneity of nanoscopic pore networks, interconnectivity, and tortuosity in polymers. To our best knowledge, the present study is the first application of this strategy for analyzing the nanoscale porosity of MIPs. MIPs imprinted for propranolol - and the corresponding NIPs - were investigated establishing FIB/SEM tomography as a viable future strategy complementing conventional isotherm studies. For visualizing and understanding the properties of pore networks in detail, polymer particles were stained with osmium tetroxide (OsO 4 ) vapor, and embedded in epoxy resin. Staining with OsO 4 provides excellent contrast during high-resolution SEM imaging. After optimizing the threshold to discriminate between the stained polymer matrix, and pores filled with epoxy resin, a 3D model of the sampled volume may be established for deriving not only the pore volume and pore surface area, but also to visualize the interconnectivity and tortuosity of the pores within the sampled polymer volume. Detailed studies using different types of cross-linkers and the effect of hydrolysis on the resulting polymer properties have been investigated. In comparison of MIP and NIP, it could be unambiguously shown that the interconnectivity of the visualized pores in MIPs is significantly higher vs. the non-imprinted polymer, and that the pore volume and pore area is 34% and approx. 35% higher within the MIP matrix. This confirms that the templating process not only induces selective binding sites, but indeed also affects the physical properties of such polymers down to the nanoscale, and that additional chemical modification, e.g., via hydrolysis clearly affects that nature of the polymer.

Evidence for dimer formation by an amphiphilic heptapeptide that mediates chloride and carboxyfluorescein release from liposomes

PubMed Central

Pajewski, Robert; Ferdani, Riccardo; Pajewska, Jolanta; Djedovič, Natasha; Schlesinger, Paul H.; Gokel, George W.

2008-01-01

Heptapeptides having dioctadecyl, N-terminal hydrocarbon chains insert in phospholipid bilayer membranes and form pores through which at least chloride ions pass. Although amphiphilic, these compounds do not typically form vesicles themselves. They insert in the bilayers of phospholipid vesicles and mediate the release of carboxyfluorescein. Hill analysis indicates that at least two molecules of the amphiphile are involved in pore formation. In CD2Cl2, dimer formation is detected by NMR chemical shift changes. The anion release activity of individual anion transporters is increased by linking them covalently at the C-terminus or, even more, by linking them at the N-terminus. Evidence is presented that either linked molecule releases chloride from liposomes more effectively and rapidly than the individual transporter molecule at a comparable concentration. PMID:15703797

Understanding and Shaping the Morphology of the Barrier Layer of Supported Porous Anodized Alumina on Gold Underlayers.

PubMed

Berger, Nele; Es-Souni, Mohammed

2016-07-12

Large-area ordered nanorod (NR) arrays of various functional materials can be easily and cost-effectively processed using on-substrate anodized porous aluminum oxide (PAO) films as templates. However, reproducibility in the processing of PAO films is still an issue because they are prone to delamination, and control of fabrication parameters such as electrolyte type and concentration and anodizing time is critical for making robust templates and subsequently mechanically reliable NR arrays. In the present work, we systematically investigate the effects of the fabrication parameters on pore base morphology, devise a method to avoid delamination, and control void formation under the barrier layer of PAO films on gold underlayers. Via systematic control of the anodization parameters, particularly the anodization current density and time, we follow the different stages of void development and discuss their formation mechanisms. The practical aspect of this work demonstrates how void size can be controlled and how void formation can be utilized to control the shape of NR bases for improving the mechanical stability of the NRs.

Understanding and Controlling Nanoscale Morphology in Self-Assembled Semiconducting Materials

NASA Astrophysics Data System (ADS)

Kang, Hyeyeon

Self-assembled semiconducting materials have been rapidly developed for a range of applications. This work aims to control the morphology of nanostructured semiconductors to understand how their functions arise from the structural properties. The first part of this dissertation focuses on the formation of a bulk-heterojunction (BHJ) in the active layer of organic photovoltaics (OPV). A BHJ is a bicontinuous interpenetrating network of organic components. The phase separation of the electron donor and the acceptor is required to achieve a BHJ structure in the nanostructured morphology, which promotes an efficient charge transportation. The use of solvent additive is one of the strategies to control the spontaneous phase separation during the film formation. Low vapor pressure solvent additives are introduced to a polymer casting solution in a sequentially processed OPV system, to study the swelling effect on the phase separation. In particular, the change in crystallinity and vertical mixing will be intensively studied upon polymer swelling. As another strategy, we introduce a molecular structure change to fullerene derivatives. A small structural variation leads to a large enough contrast of their surface energy, which is attributed to different vertical phase separation in the active layer. It eventually allows us to examine photovoltaic performance and device physics. In the second part, mesoporous inorganic films are investigated by preparation from a nanocrystal solution or sol-gel precursors for solar energy applications. Mesoporous nanocrystal-based titania is synthesized for inorganic/organic hybrid solar cells. The effect of surface modification is examined by anchoring a fullerene derivative on to titania surface. 3D interconnected mesoporous tantalum nitride films are prepared via sol-gel method as photoanodes in solar water splitting. The simple synthetic method using polymer template enables us to successfully prepare nitride films with excellent pore periodicity. The porous tantalum nitride film is examined with photoelectrochemical measurement to investigate the correlation between nanostructuring and photocatalytic activity. For the final part of this dissertation, porous cobalt ferrite and cadmium sulfide films are studied using ellipsometric porosimetry. Understanding the nature of their pores allows us to tune the intrinsic properties of the materials or prove the newly designed synthetic method.

Growth of aragonite calcium carbonate nanorods in the biomimetic anodic aluminum oxide template

NASA Astrophysics Data System (ADS)

Lee, Inho; Han, Haksoo; Lee, Sang-Yup

2010-04-01

In this study, a biomimetic template was prepared and applied for growing calcium carbonate (CaCO 3) nanorods whose shape and polymorphism were controlled. A biomimetic template was prepared by adsorbing catalytic dipeptides into the pores of an anodic aluminum oxide (AAO) membrane. Using this peptide-adsorbed template, mineralization and aggregation of CaCO 3 was carried out to form large nanorods in the pores. The nanorods were aragonite and had a structure similar to nanoneedle assembly. This aragonite nanorod formation was driven by both the AAO template and catalytic function of dipeptides. The AAO membrane pores promoted generation of aragonite polymorph and guided nanorod formation by guiding the nanorod growth. The catalytic dipeptides promoted the aggregation and further dehydration of calcium species to form large nanorods. Functions of the AAO template and catalytic dipeptides were verified through several control experiments. This biomimetic approach makes possible the production of functional inorganic materials with controlled shapes and crystalline structures.

Cytotoxic T Cells Use Mechanical Force to Potentiate Target Cell Killing.

PubMed

Basu, Roshni; Whitlock, Benjamin M; Husson, Julien; Le Floc'h, Audrey; Jin, Weiyang; Oyler-Yaniv, Alon; Dotiwala, Farokh; Giannone, Gregory; Hivroz, Claire; Biais, Nicolas; Lieberman, Judy; Kam, Lance C; Huse, Morgan

2016-03-24

The immunological synapse formed between a cytotoxic T lymphocyte (CTL) and an infected or transformed target cell is a physically active structure capable of exerting mechanical force. Here, we investigated whether synaptic forces promote the destruction of target cells. CTLs kill by secreting toxic proteases and the pore forming protein perforin into the synapse. Biophysical experiments revealed a striking correlation between the magnitude of force exertion across the synapse and the speed of perforin pore formation on the target cell, implying that force potentiates cytotoxicity by enhancing perforin activity. Consistent with this interpretation, we found that increasing target cell tension augmented pore formation by perforin and killing by CTLs. Our data also indicate that CTLs coordinate perforin release and force exertion in space and time. These results reveal an unappreciated physical dimension to lymphocyte function and demonstrate that cells use mechanical forces to control the activity of outgoing chemical signals. Copyright © 2016 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ullah, Ghanim; Demuro, Angelo; Parker, Ian

Amyloid beta (Aβ) oligomers associated with Alzheimer’s disease (AD) form Ca 2+-permeable plasma membrane pores, leading to a disruption of the otherwise well-controlled intracellular calcium (Ca 2+) homeostasis. The resultant up-regulation of intracellular Ca 2+ concentration has detrimental implications for memory formation and cell survival. The gating kinetics and Ca 2+ permeability of Aβ pores are not well understood. We have used computational modeling in conjunction with the ability of optical patch-clamping for massively parallel imaging of Ca 2+ flux through thousands of pores in the cell membrane of Xenopus oocytes to elucidate the kinetic properties of Aβ pores. Themore » fluorescence time-series data from individual pores were idealized and used to develop data-driven Markov chain models for the kinetics of the Aβ pore at different stages of its evolution. Our study provides the first demonstration of developing Markov chain models for ion channel gating that are driven by optical-patch clamp data with the advantage of experiments being performed under close to physiological conditions. As a result, we demonstrate the up-regulation of gating of various Ca 2+ release channels due to Aβ pores and show that the extent and spatial range of such up-regulation increases as Aβ pores with low open probability and Ca 2+ permeability transition into those with high open probability and Ca 2+ permeability.« less

Molecular understanding of osmosis in semipermeable membranes.

PubMed

Raghunathan, A V; Aluru, N R

2006-07-14

We investigate single-file osmosis of water through a semipermeable membrane with an uncharged, a positively and a negatively charged nanopore. Molecular dynamics simulations indicate that the osmotic flux through a negatively charged pore (J_) is higher compared to the osmotic flux in a positively charged pore (J+) followed by the osmotic flux in the uncharged pore (J(0)), i.e., J_ > J+ > J(0). The molecular mechanisms governing osmosis, steady state osmosis, and the observed osmotic flux dependence on the nanopore charge are explained by computing all the molecular interactions involved and identifying the molecular interactions that play an important role during and after osmosis. This study helps in a fundamental understanding of osmosis and in the design of advanced nanoporous membranes for various applications of osmosis.

Relationship between pore geometric characteristics and SIP/NMR parameters observed for mudstones

NASA Astrophysics Data System (ADS)

Robinson, J.; Slater, L. D.; Keating, K.; Parker, B. L.; Robinson, T.

2017-12-01

The reliable estimation of permeability remains one of the most challenging problems in hydrogeological characterization. Cost effective, non-invasive geophysical methods such as spectral induced polarization (SIP) and nuclear magnetic resonance (NMR) offer an alternative to traditional sampling methods as they are sensitive to the mineral surfaces and pore spaces that control permeability. We performed extensive physical characterization, SIP and NMR geophysical measurements on fractured rock cores extracted from a mudstone site in an effort to compare 1) the pore size characterization determined from traditional and geophysical methods and 2) the performance of permeability models based on these methods. We focus on two physical characterizations that are well-correlated with hydraulic properties: the pore volume normalized surface area (Spor) and an interconnected pore diameter (Λ). We find the SIP polarization magnitude and relaxation time are better correlated with Spor than Λ, the best correlation of these SIP measures for our sample dataset was found with Spor divided by the electrical formation factor (F). NMR parameters are, similarly, better correlated with Spor than Λ. We implement previously proposed mechanistic and empirical permeability models using SIP and NMR parameters. A sandstone-calibrated SIP model using a polarization magnitude does not perform well while a SIP model using a mean relaxation time performs better in part by more sufficiently accounting for the effects of fluid chemistry. A sandstone-calibrated NMR permeability model using an average measure of the relaxation time does not perform well, presumably due to small pore sizes which are either not connected or contain water of limited mobility. An NMR model based on the laboratory determined portions of the bound versus mobile portions of the relaxation distribution performed reasonably well. While limitations exist, there are many opportunities to use geophysical data to predict permeability in mudstone formations.

Soil architecture relationships with dynamic soil physical processes: a conceptual study using natural, artificial, and 3D-printed soil cores

NASA Astrophysics Data System (ADS)

Lamandé, Mathieu; Schjønning, Per; Dal Ferro, Nicola; Morari, Francesco

2017-04-01

Pore system architecture is a key feature for understanding physical, biological and chemical processes in soils. Development of visualisation technics, especially x-ray CT, during recent years has been useful in describing the complex relationships between soil architecture and soil functions. We believe that combining visualization with physical models is a step further towards a better understanding of these relationships. We conducted a concept study using natural, artificial and 3D-printed soil cores. Eight natural soil cores (100 cm3) were sampled in a cultivated stagnic Luvisol at two depths (topsoil and subsoil), representing contrasting soil pore systems. Cylinders (100 cm3) were produced from plastic or from autoclaved aerated concrete. Holes of diameters 1.5 and 3 mm were drilled in the cylinder direction for the plastic cylinder and for one of the AAC cylinders. All natural and artificial cores were scanned in a micro x-ray CT scanner at a resolution of 35 µm. The reconstructed image of each soil core was printed with 3D multijet printing technology at a resolution of 29 µm. In some reconstructed digital volumes of the natural soil cores, pores of different sizes (equivalent diameter of 35, 70, 100, and 200 µm) were removed before additional 3D printing. Effective air-filled porosity, Darcian air permeability, and oxygen diffusion were measured on all natural, artificial and printed cores. The comparison of the natural and the artificial cores emphasized the difference in pore architecture between topsoil (sponge like) and subsoil (dominated by large vertical macropores). This study showed the high potential of using printed soil cores for understanding soil pore functions. The results confirm the suitability of the Ball model partitioning the pore system into arterial, marginal and remote pores to describe effects of soil structure on gas transport.

Pore structure characterization of Chang-7 tight sandstone using MICP combined with N2GA techniques and its geological control factors

NASA Astrophysics Data System (ADS)

Cao, Zhe; Liu, Guangdi; Zhan, Hongbin; Li, Chaozheng; You, Yuan; Yang, Chengyu; Jiang, Hang

2016-11-01

Understanding the pore networks of unconventional tight reservoirs such as tight sandstones and shales is crucial for extracting oil/gas from such reservoirs. Mercury injection capillary pressure (MICP) and N2 gas adsorption (N2GA) are performed to evaluate pore structure of Chang-7 tight sandstone. Thin section observation, scanning electron microscope, grain size analysis, mineral composition analysis, and porosity measurement are applied to investigate geological control factors of pore structure. Grain size is positively correlated with detrital mineral content and grain size standard deviation while negatively related to clay content. Detrital mineral content and grain size are positively correlated with porosity, pore throat radius and withdrawal efficiency and negatively related to capillary pressure and pore-to-throat size ratio; while interstitial material is negatively correlated with above mentioned factors. Well sorted sediments with high debris usually possess strong compaction resistance to preserve original pores. Although many inter-crystalline pores are produced in clay minerals, this type of pores is not the most important contributor to porosity. Besides this, pore shape determined by N2GA hysteresis loop is consistent with SEM observation on clay inter-crystalline pores while BJH pore volume is positively related with clay content, suggesting N2GA is suitable for describing clay inter-crystalline pores in tight sandstones.

Pore structure characterization of Chang-7 tight sandstone using MICP combined with N2GA techniques and its geological control factors

PubMed Central

Cao, Zhe; Liu, Guangdi; Zhan, Hongbin; Li, Chaozheng; You, Yuan; Yang, Chengyu; Jiang, Hang

2016-01-01

Understanding the pore networks of unconventional tight reservoirs such as tight sandstones and shales is crucial for extracting oil/gas from such reservoirs. Mercury injection capillary pressure (MICP) and N2 gas adsorption (N2GA) are performed to evaluate pore structure of Chang-7 tight sandstone. Thin section observation, scanning electron microscope, grain size analysis, mineral composition analysis, and porosity measurement are applied to investigate geological control factors of pore structure. Grain size is positively correlated with detrital mineral content and grain size standard deviation while negatively related to clay content. Detrital mineral content and grain size are positively correlated with porosity, pore throat radius and withdrawal efficiency and negatively related to capillary pressure and pore-to-throat size ratio; while interstitial material is negatively correlated with above mentioned factors. Well sorted sediments with high debris usually possess strong compaction resistance to preserve original pores. Although many inter-crystalline pores are produced in clay minerals, this type of pores is not the most important contributor to porosity. Besides this, pore shape determined by N2GA hysteresis loop is consistent with SEM observation on clay inter-crystalline pores while BJH pore volume is positively related with clay content, suggesting N2GA is suitable for describing clay inter-crystalline pores in tight sandstones. PMID:27830731

Influence of ester-modified lipids on bilayer structure.

PubMed

Villanueva, Diana Y; Lim, Joseph B; Klauda, Jeffery B

2013-11-19

Lipid membranes function as barriers for cells to prevent unwanted chemicals from entering the cell and wanted chemicals from leaving. Because of their hydrophobic interior, membranes do not allow water to penetrate beyond the headgroup region. We performed molecular simulations to examine the effects of ester-modified lipids, which contain ester groups along their hydrocarbon chains, on bilayer structure. We chose two lipids from those presented in Menger et al. [J. Am. Chem. Soc. 2006, 128, 14034] with ester groups in (1) the upper half of the lipid chain (MEPC) and (2) the middle and end of the lipid chain (MGPC). MGPC (30%)/POPC bilayers formed stable water pores of diameter 5-7 Å, but MGPC (22%)/POPC and MEPC (30%)/POPC bilayers did not form these defects. These pores were similar to those formed during electroporation; i.e., the head groups lined the pore and allowed water and ions to transport across the bilayer. However, we found that lateral organization of the MGPC lipids into clusters, instead of an electric field or charge disparity as in electroporation, was essential for pore formation. On the basis of this, we propose an overall mechanism for pore formation. The similarities between the ester-modified lipids and byproducts of lipid peroxidation with multiple hydrophilic groups in the middle of the chain suggest that free radical reactions with unsaturated lipids and sterols result in fundamental changes that may be similar to what is seen in bilayers with ester-modified lipids.

The Effect of Boron on the Low Cycle Fatigue Behavior of Disk Alloy KM4

NASA Technical Reports Server (NTRS)

Gabb, Timothy; Gayda, John; Sweeney, Joseph

2000-01-01

The durability of powder metallurgy nickel base superalloys employed as compressor and turbine disks is often limited by low cycle fatigue (LCF) crack initiation and crack growth from highly stressed surface locations (corners, holes, etc.). Crack growth induced by dwells at high stresses during aerospace engine operation can be particularly severe. Supersolvus solution heat treatments can be used to produce coarse grain sizes approaching ASTM 6 for improved resistance to dwell fatigue crack growth. However, the coarse grain sizes reduce yield strength, which can lower LCF initiation life. These high temperature heat treatments also can encourage pores to form. In the advanced General Electric disk superalloy KM4, such pores can initiate fatigue cracks that limit LCF initiation life. Hot isostatic pressing (HIP) during the supersolvus solution heat treatment has been shown to improve LCF initiation life in KM4, as the HIP pressure minimizes formation of the pores. Reduction of boron levels in KM4 has also been shown to increase LCF initiation life after a conventional supersolvus heat treatment, again possibly due to effects on the formation tendencies of these pores. However, the effects of reduced boron levels on microstructure, pore characteristics, and LCF failure modes in KM4 still need to be fully quantified. The objective of this study was to determine the effect of boron level on the microstructure, porosity, LCF behavior, and failure modes of supersolvus heat treated KM4.

Numerous nanopores developed in organo-clay complexes during the shale formations

NASA Astrophysics Data System (ADS)

Wang, Q.; Wang, T.; Lu, H.; Liao, J.

2017-12-01

Shale gas as new energy resource is either stored in nano pores and microfractures or absorbed on the surface of kerogen and clay aggregate (Chalmers et al., 2012). Nano pores developed in organic matters is very important, because these organic pores have better connectivity than inorganic pores (Loucks et al., 2012) and can form an effective pore system where shale gas flows dominantly (Curtis et al., 2010). In order to figure out how the organic pores is affected by shale compositions, we conduct in-situ FE-SEM and EDS analysis on organic-rich Longmaxi shales. The data indicate that 1) organic matter, mixed with clay minerals, can form an organo-clay complex containing many nanopores; 2)furthermore, larger organic pores are developed in organo-clay complexes with higher clay content than in those with lower clay content(Wang et al., 2017). It seems that the presence of organo-clay complex raises the heterogeneous than pure organic matters. Organo-clay complex may bring in lots of intergranular nanopores between organic matter and clay minerals. Another potential interpretation is that clay minerals may influence kerogen thermal decomposition, generation of hydrocarbons and thus the development of organic pores. The presence of numerous nanopores in organo-clay complexes may promote the connectivity of the pore network and enhance the hydrocarbon production efficiency for shale gas field.

Analyzing and modeling the kinetics of amyloid beta pores associated with Alzheimer’s disease pathology

DOE PAGES

Ullah, Ghanim; Demuro, Angelo; Parker, Ian; ...

2015-09-08

Amyloid beta (Aβ) oligomers associated with Alzheimer’s disease (AD) form Ca 2+-permeable plasma membrane pores, leading to a disruption of the otherwise well-controlled intracellular calcium (Ca 2+) homeostasis. The resultant up-regulation of intracellular Ca 2+ concentration has detrimental implications for memory formation and cell survival. The gating kinetics and Ca 2+ permeability of Aβ pores are not well understood. We have used computational modeling in conjunction with the ability of optical patch-clamping for massively parallel imaging of Ca 2+ flux through thousands of pores in the cell membrane of Xenopus oocytes to elucidate the kinetic properties of Aβ pores. Themore » fluorescence time-series data from individual pores were idealized and used to develop data-driven Markov chain models for the kinetics of the Aβ pore at different stages of its evolution. Our study provides the first demonstration of developing Markov chain models for ion channel gating that are driven by optical-patch clamp data with the advantage of experiments being performed under close to physiological conditions. As a result, we demonstrate the up-regulation of gating of various Ca 2+ release channels due to Aβ pores and show that the extent and spatial range of such up-regulation increases as Aβ pores with low open probability and Ca 2+ permeability transition into those with high open probability and Ca 2+ permeability.« less

The effects of salt, particle and pore size on the process of carbon dioxide hydrate formation: A critical review

NASA Astrophysics Data System (ADS)

Ghaedi, Hosein; Ayoub, Muhammad; Bhat, A. H.; Mahmood, Syed Mohammad; Akbari, Saeed; Murshid, Ghulam

2016-11-01

Hydration is an alternative method for CO2 capture. In doing so, some researchers use porous media on an experimental scale. This paper tries to gather the researches on the formation of CO2 hydrate in different types of porous media such as silica sand, quartz sand, Toyoura, pumice, and fire hardened red clay. This review has attempted to examine the effects of salt and particle sizes as two major factors on the induction time, water to hydrate conversion, gas uptake (or gas consumption), and the rate of CO2 hydrate formation. By performing a critical assessment of previous research works, it was observed that the figure for the gas uptake (or gas consumption) and water to hydrate conversion in porous media was decreased by increasing the particle size provided that the pore size was constant. Although, salt can play a role in hydrate formation as the thermodynamic inhibitor, the results show that salt can be regarded as the kinetic growth inhibitor and kinetic promoter. Because of the fact that the gas uptake in seawater is lower than pure water at the end of experiment, the salt can act as a kinetic growth inhibitor. However, since gas uptake (after the nucleation period and for a short period) and the initial rate of hydrate formation in saline water were more than that of pure water, salt can play a promoter role in the kinetic reaction, too. Besides these, in the case of pure water and within a certain particle size, the amount of the hydrate formation rate has been seen to be greater in smaller particles (provided that the pore size is constant), however this has not been observed for seawater.

Methane and CO2 Adsorption Capacities of Kerogen in the Eagle Ford Shale from Molecular Simulation.

PubMed

Psarras, Peter; Holmes, Randall; Vishal, Vikram; Wilcox, Jennifer

2017-08-15

Over the past decade, the United States has become a world leader in natural gas production, thanks in part to a large-fold increase in recovery from unconventional resources, i.e., shale rock and tight oil reservoirs. In an attempt to help mitigate climate change, these depleted formations are being considered for their long-term CO 2 storage potential. Because of the variability in mineral and structural composition from one formation to the next (even within the same region), it is imperative to understand the adsorption behavior of CH 4 and CO 2 in the context of specific conditions and pore surface chemistry, i.e., relative total organic content (TOC), clay, and surface functionality. This study examines two Eagle Ford shale samples, both recovered from shale that was extracted at depths of approximately 3800 m and having low clay content (i.e., less than 5%) and similar mineral compositions but distinct TOCs (i.e., 2% and 5%, respectively). Experimentally validated models of kerogen were used to the estimate CH 4 and CO 2 adsorption capacities. The pore size distributions modeled were derived from low-pressure adsorption isotherm data using CO 2 and N 2 as probe gases for micropores and mesopores, respectively. Given the presence of water in these natural systems, the role of surface chemistry on modeled kerogen pore surfaces was investigated. Several functional groups associated with surface-dissociated water were considered. Pressure conditions from 10 to 50 bar were investigated using grand canonical Monte Carlo simulations along with typical outgassing temperatures used in many shale characterization and adsorption studies (i.e., 60 and 250 °C). Both CO 2 and N 2 were used as probe gases to determine the total pore volume available for gas adsorption spanning pore diameters ranging from 0.3 to 30 nm. The impacts of surface chemistry, outgassing temperature, and the inclusion of nanopores with diameters of less than 1.5 nm were determined for applications of CH 4 and CO 2 storage from samples of the gas-producing region of the Eagle Ford Shale. At 50 bar and temperatures of 60 and 250 °C, CH 4 adsorption increased across all surface chemistries considered by 60% and 2-fold, respectively. In the case of CO 2 , the surface chemistry played a role at both 10 and 50 bar. For instance, at temperatures of 60 and 250 °C, CO 2 adsorption increased across all surface chemistries by 6-fold and just over 2-fold, respectively. It was also found that at both 10 and 50 bar, if too low an outgassing temperature is used, this may lead to a 2-fold underestimation of gas in place. Finally, neglecting to include pores with diameters of less than 1.5 nm has the potential to underestimate pore volume by up to 28%. Taking into consideration these aspects of kerogen and shale characterization in general will lead to improvements in estimating the CH 4 and CO 2 storage potential of gas shales.

Microstructure and permeability of the Whitby Mudstone (UK) as an analogue for the Posidonia shale (NL)

NASA Astrophysics Data System (ADS)

Houben, Maartje; Barnhoorn, Auke; Drury, Martyn; Peach, Colin; Spiers, Christopher

2015-04-01

In order to make gas productivity from a shale economically interesting we should find ways to better connect the in-situ pore network to the natural occurring and mechanical induced fractures in the rock. When trying to improve gas productivity a first aim is to understand gas storage and gas flow potential through the rock by investigating the microstructure and measure the matrix porosity and permeability of the unfractured shales. Using a combination of methods we have characterized the porosity and permeability of the Jet Dogger section of the Whitby Mudstone Formation (UK), which we use as an analogue for the Posidonia Shale (NL). The Posidonia shale is a possible unconventional source for gas in Northern Europe. A combination of Precision Ion Polishing (PIPS) and Scanning Electron Microscopy (SEM) has been used to investigate the microstructure and the pores. Microstructurally the circa 8 meter thick Jet section of the Whitby Mudstone Formation can be subdivided into a fossil rich (>15 %) top half with an organic matter content of 7-10% and a sub-mm laminated (alternating clay-rich, carbonate-rich, not necessarily fossils, layers) lower half were the organic matter content varies from 0.3-16%. In addition, any possible flow in the rock has to go through the fine-grained clay matrix (all grains < 2 μm) due to the fact that all larger grains are completely surround by this matrix. Visible PIPS-SEM porosity (pore diameter > 100 nm) is in the order of 0.5-2.5% and is not connected in 2D. Furthermore, overall more than 40% of the visible porosity is present within the clay matrix (sometimes even up to 80%). Porosity and pore size distributions for pores with smaller diameters (2 < diameter < 100 nm) were determined using Ar and N2 gas adsorption. The adsorption porosity was in the order of 1-5%, were we found 1-2.5% porosity for the top half of the section and 2-5% porosity for the bottom half. Ar gas permeability of the samples was measured on 1-inch diameter cores using Ar-gas-permeametry with a pressure step of 0.2 MPa. The permeability measured was in the order of 2•10-19 - 1•10-17 m2 at a confining pressure of 0.8 MPa. The top half of the section (less porous) showed a slightly lower permeability (2•10-19 -3•10-18 m2) than the lower half of the Jet Dogger section (1•10-18 - 1•10-17m2). The PIPS-SEM porosity is apparently unconnected on the scale used for imaging and any flow through these rocks has to go through the clay matrix. A connected network of nano-scale pores connected to the micro-scale (PIPS-SEM) pores should be present because of the fact that we measured a through flow of gas. Relationships between the permeability and Ar-porosity and permeability and microstructure were, however, not systematic.

Electrochemical Impedance Spectroscopy for Real-Time Detection of Lipid Membrane Damage Based on a Porous Self-Assembly Monolayer Support.

PubMed

Zhang, Meng; Zhai, Qingyu; Wan, Liping; Chen, Li; Peng, Yu; Deng, Chunyan; Xiang, Juan; Yan, Jiawei

2018-06-19

Layer-by-layer dissolution and permeable pore formation are two typical membrane damage pathways, which induce membrane function disorder and result in serious disease, such as Alzheimer's disease, Keshan disease, Sickle-cell disease, and so on. To effectively distinguish and sensitively monitor these two typical membrane damage pathways, a facile electrochemical impedance strategy was developed on a porous self-assembly monolayer (pSAM) supported bilayer lipid membrane (BLM). The pSAM was prepared by selectively electrochemical reductive desorption of the mercaptopropionic acid in a mixed mercaptopropionic acid/11-mercaptoundecanoic acid self-assembled monolayer, which created plenty of nanopores with tens of nanometers in diameter and several nanometers in height (defined as inner-pores). The ultralow aspect ratio of the inner-pores was advantageous to the mass transfer of electrochemical probe [Fe(CN) 6 ] 3-/4- , simplifying the equivalent electric circuit for electrochemical impedance spectroscopy analysis at the electrode/membrane interface. [Fe(CN) 6 ] 3-/4- transferring from the bulk solution into the inner-pore induce significant changes of the interfacial impedance properties, improving the detection sensitivity. Based on these, the different membrane damage pathways were effectively distinguished and sensitively monitored with the normalized resistance-capacitance changes of inner-pore-related parameters including the electrolyte resistance within the pore length ( R pore ) and the metal/inner-pore interfacial capacitance ( C pore ) and the charge-transfer resistance ( R ct-in ) at the metal/inner-pore interface.

Porous silicon technology for integrated microsystems

NASA Astrophysics Data System (ADS)

Wallner, Jin Zheng

With the development of micro systems, there is an increasing demand for integrable porous materials. In addition to those conventional applications, such as filtration, wicking, and insulating, many new micro devices, including micro reactors, sensors, actuators, and optical components, can benefit from porous materials. Conventional porous materials, such as ceramics and polymers, however, cannot meet the challenges posed by micro systems, due to their incompatibility with standard micro-fabrication processes. In an effort to produce porous materials that can be used in micro systems, porous silicon (PS) generated by anodization of single crystalline silicon has been investigated. In this work, the PS formation process has been extensively studied and characterized as a function of substrate type, crystal orientation, doping concentration, current density and surfactant concentration and type. Anodization conditions have been optimized for producing very thick porous silicon layers with uniform pore size, and for obtaining ideal pore morphologies. Three different types of porous silicon materials: meso porous silicon, macro porous silicon with straight pores, and macro porous silicon with tortuous pores, have been successfully produced. Regular pore arrays with controllable pore size in the range of 2mum to 6mum have been demonstrated as well. Localized PS formation has been achieved by using oxide/nitride/polysilicon stack as masking materials, which can withstand anodization in hydrofluoric acid up to twenty hours. A special etching cell with electrolytic liquid backside contact along with two process flows has been developed to enable the fabrication of thick macro porous silicon membranes with though wafer pores. For device assembly, Si-Au and In-Au bonding technologies have been developed. Very low bonding temperature (˜200°C) and thick/soft bonding layers (˜6mum) have been achieved by In-Au bonding technology, which is able to compensate the potentially rough surface on the porous silicon sample without introducing significant thermal stress. (Abstract shortened by UMI.)

Microporous nanofibrous fibrin-based scaffolds for craniofacial bone tissue engineering

NASA Astrophysics Data System (ADS)

Osathanon, Thanaphum

The fibrotic response of the body to synthetic polymers limits their success in tissue engineering and other applications. Though porous polymers have demonstrated improved healing, difficulty in controlling their pore sizes and pore interconnections has clouded the understanding of this phenomenon. In this study, a novel method to fabricate natural polymer/calcium phosphate composite scaffolds and immobilized alkaline phosphatase fibrin scaffolds with tightly controllable pore size, pore interconnection has been investigated. Microporous, nanofibrous fibrin scaffolds (FS) were fabricated using sphere-templating method. Calcium phosphate/fibrin composite scaffolds were created by solution deposition of calcium phosphate on fibrin surfaces or by direct incorporation of nanocrystalline hydroxyapatite (nHA). The SEM results showed that fibrin scaffolds exhibited a highly porous and interconnected structure. Osteoblast-like cells, obtained from murine calvaria, attached, spread and showed a polygonal morphology on the surface of the biomaterial. Multiple cell layers and fibrillar matrix deposition were observed. Moreover, cells seeded on mineralized fibrin scaffolds (MFS) exhibited significantly higher alkaline phosphatase activity as well as osteoblast marker gene expression compared to FS and nHA incorporated fibrin scaffolds (nHA/FS). These fibrin-based scaffolds were degraded both in vitro and in vivo. Furthermore, these scaffolds promoted bone formation in a mouse calvarial defect model and the bone formation was enhanced by addition of rhBMP-2. The second approach was to immobilize alkaline phosphatase (ALP) on fibrin scaffolds. ALP enzyme was covalently immobilized on the microporous nanofibrous fibrin scaffolds using 1-ethyl-3-(dimethylaminopropyl)carbodiimide hydrochloride (EDC). The SEM results demonstrated mineral deposition on immobilized ALP fibrin scaffolds (ALP/FS) when incubated in medium supplemented with beta-glycerophosphate, suggesting that the immobilized ALP enzyme was active. Mineral deposition was also observed in cells seeded on immobilized ALP/FS. Furthermore, cells seeded on immobilized ALP/FS exhibited higher osteoblast marker gene expression compared to those on control FS. Upon implantation in mouse calvarial defect, the immobilized ALP/FS treated group had slightly higher bone volume in the defect compared to empty defect control and FS alone. In conclusion, the enhanced biological responses both in vitro and in vivo demonstrated the potential application of these novel microporous nanofibrous fibrin-based scaffolds for bone tissue engineering.

Do Shale Pore Throats Have a Threshold Diameter for Oil Storage?

PubMed Central

Zou, Caineng; Jin, Xu; Zhu, Rukai; Gong, Guangming; Sun, Liang; Dai, Jinxing; Meng, Depeng; Wang, Xiaoqi; Li, Jianming; Wu, Songtao; Liu, Xiaodan; Wu, Juntao; Jiang, Lei

2015-01-01

In this work, a nanoporous template with a controllable channel diameter was used to simulate the oil storage ability of shale pore throats. On the basis of the wetting behaviours at the nanoscale solid-liquid interfaces, the seepage of oil in nano-channels of different diameters was examined to accurately and systematically determine the effect of the pore diameter on the oil storage capacity. The results indicated that the lower threshold for oil storage was a pore throat of 20 nm, under certain conditions. This proposed pore size threshold provides novel, evidence-based criteria for estimating the geological reserves, recoverable reserves and economically recoverable reserves of shale oil. This new understanding of shale oil processes could revolutionize the related industries. PMID:26314637

Do Shale Pore Throats Have a Threshold Diameter for Oil Storage?

PubMed

Zou, Caineng; Jin, Xu; Zhu, Rukai; Gong, Guangming; Sun, Liang; Dai, Jinxing; Meng, Depeng; Wang, Xiaoqi; Li, Jianming; Wu, Songtao; Liu, Xiaodan; Wu, Juntao; Jiang, Lei

2015-08-28

In this work, a nanoporous template with a controllable channel diameter was used to simulate the oil storage ability of shale pore throats. On the basis of the wetting behaviours at the nanoscale solid-liquid interfaces, the seepage of oil in nano-channels of different diameters was examined to accurately and systematically determine the effect of the pore diameter on the oil storage capacity. The results indicated that the lower threshold for oil storage was a pore throat of 20 nm, under certain conditions. This proposed pore size threshold provides novel, evidence-based criteria for estimating the geological reserves, recoverable reserves and economically recoverable reserves of shale oil. This new understanding of shale oil processes could revolutionize the related industries.

A biodegradable vascularizing membrane: a feasibility study.

PubMed

Kaushiva, Anchal; Turzhitsky, Vladimir M; Darmoc, Marissa; Backman, Vadim; Ameer, Guillermo A

2007-09-01

Regenerative medicine and in vivo biosensor applications require the formation of mature vascular networks for long-term success. This study investigated whether biodegradable porous membranes could induce the formation of a vascularized fibrous capsule and, if so, the effect of degradation kinetics on neovascularization. Poly(l-lactic acid) (PLLA) and poly(dl-lactic-co-glycolic) acid (PLGA) membranes were created by a solvent casting/salt leaching method. Specifically, PLLA, PLGA 75:25 and PLGA 50:50 polymers were used to vary degradation kinetics. The membranes were designed to have an average 60mum pore diameter, as this pore size has been shown to be optimal for inducing blood vessel formation around nondegradable polymer materials. Membrane samples were imaged by scanning electron microscopy at several time points during in vitro degradation to assess any changes in pore structure. The in vivo performance of the membranes was assessed in Sprague-Dawley rats by measuring vascularization within the fibrous capsule that forms adjacent to implants. The vascular density within 100microm of the membranes was compared with that seen in normal tissue, and to that surrounding the commercially available vascularizing membrane TheraCyte. The hemoglobin content of tissue containing the membranes was measured by four-dimensional elastic light scattering as a novel method to assess tissue perfusion. Results from this study show that slow-degrading membranes induce greater amounts of neovascularization and a thinner fibrous capsule relative to fast degrading membranes. These results may be due both to an initially increased number of macrophages surrounding the slower degrading membranes and to the maintenance of their initial pore structure.

Mechanical Degradation of Porous NiTi Alloys Under Static and Cyclic Loading

NASA Astrophysics Data System (ADS)

Hosseini, Seyyed Alireza

2017-12-01

Pore characteristics and morphology have significant effect on mechanical behavior of porous NiTi specimens. In this research, porous NiTi with different pore sizes, shapes and morphology were produced by powder metallurgy methods using space-holder materials. The effect of the pore characteristics on the mechanical properties was investigated by static and cyclic compression tests at body temperature. The results show that specimens with low porosity and isolated pores exhibit more mechanical strength and recoverable strain. The specimen with 36% porosity produced without space holder could preserve its properties up to 10% strain and its strain recovery was complete after cyclic compression tests. On the other hand, the specimens produced by a urea space holder with more than 60% interconnected porosity show rapid degradation of their scaffolds. The highly porous specimens degraded even below 5% strain due to crack formation and propagation in the thin pore walls. For highly porous specimens produced by a NaCl space holder, the pores are partially interconnected with a cubic shape; nevertheless, their mechanical behavior is close to low-porosity specimens.

Confinement-Driven Phase Separation of Quantum Liquid Mixtures

NASA Astrophysics Data System (ADS)

Prisk, T. R.; Pantalei, C.; Kaiser, H.; Sokol, P. E.

2012-08-01

We report small-angle neutron scattering studies of liquid helium mixtures confined in Mobil Crystalline Material-41 (MCM-41), a porous silica glass with narrow cylindrical nanopores (d=3.4nm). MCM-41 is an ideal model adsorbent for fundamental studies of gas sorption in porous media because its monodisperse pores are arranged in a 2D triangular lattice. The small-angle scattering consists of a series of diffraction peaks whose intensities are determined by how the imbibed liquid fills the pores. Pure He4 adsorbed in the pores show classic, layer-by-layer film growth as a function of pore filling, leaving the long range symmetry of the system intact. In contrast, the adsorption of He3-He4 mixtures produces a structure incommensurate with the pore lattice. Neither capillary condensation nor preferential adsorption of one helium isotope to the pore walls can provide the symmetry-breaking mechanism. The scattering is consistent with the formation of randomly distributed liquid-liquid microdomains ˜2.3nm in size, providing evidence that confinement in a nanometer scale capillary can drive local phase separation in quantum liquid mixtures.

Pom121 links two essential subcomplexes of the nuclear pore complex core to the membrane

PubMed Central

Mitchell, Jana M.; Mansfeld, Jörg; Capitanio, Juliana; Kutay, Ulrike

2010-01-01

Nuclear pore complexes (NPCs) control the movement of molecules across the nuclear envelope (NE). We investigated the molecular interactions that exist at the interface between the NPC scaffold and the pore membrane. We show that key players mediating these interactions in mammalian cells are the nucleoporins Nup155 and Nup160. Nup155 depletion massively alters NE structure, causing a dramatic decrease in NPC numbers and the improper targeting of membrane proteins to the inner nuclear membrane. The role of Nup155 in assembly is likely closely linked to events at the membrane as we show that Nup155 interacts with pore membrane proteins Pom121 and NDC1. Furthermore, we demonstrate that the N terminus of Pom121 directly binds the β-propeller regions of Nup155 and Nup160. We propose a model in which the interactions of Pom121 with Nup155 and Nup160 are predicted to assist in the formation of the nuclear pore and the anchoring of the NPC to the pore membrane. PMID:20974814

Correlation of Thermally Induced Pores with Microstructural Features Using High Energy X-rays

NASA Astrophysics Data System (ADS)

Menasche, David B.; Shade, Paul A.; Lind, Jonathan; Li, Shiu Fai; Bernier, Joel V.; Kenesei, Peter; Schuren, Jay C.; Suter, Robert M.

2016-11-01

Combined application of a near-field High Energy Diffraction Microscopy measurement of crystal lattice orientation fields and a tomographic measurement of pore distributions in a sintered nickel-based superalloy sample allows pore locations to be correlated with microstructural features. Measurements were carried out at the Advanced Photon Source beamline 1-ID using an X-ray energy of 65 keV for each of the measurement modes. The nickel superalloy sample was prepared in such a way as to generate significant thermally induced porosity. A three-dimensionally resolved orientation map is directly overlaid with the tomographically determined pore map through a careful registration procedure. The data are shown to reliably reproduce the expected correlations between specific microstructural features (triple lines and quadruple nodes) and pore positions. With the statistics afforded by the 3D data set, we conclude that within statistical limits, pore formation does not depend on the relative orientations of the grains. The experimental procedures and analysis tools illustrated are being applied to a variety of materials problems in which local heterogeneities can affect materials properties.

Cohesiveness tunes assembly and morphology of FG nucleoporin domain meshworks – Implications for nuclear pore permeability

PubMed Central

Eisele, Nico B.; Labokha, Aksana A.; Frey, Steffen; Görlich, Dirk; Richter, Ralf P.

2013-01-01

Nuclear pore complexes control the exchange of macromolecules between the cytoplasm and the nucleus. A selective permeability barrier that arises from a supramolecular assembly of intrinsically unfolded nucleoporin domains rich in phenylalanine-glycine dipeptides (FG domains) fills the nuclear pore. There is increasing evidence that selective transport requires cohesive FG domain interactions. To understand the functional roles of cohesive interactions, we studied monolayers of end-grafted FG domains as a bottom-up nanoscale model system of the permeability barrier. Based on detailed physicochemical analysis of the model films and comparison of the data with polymer theory, we propose that cohesiveness is tuned to promote rapid assembly of the permeability barrier and to generate a stable and compact pore-filling meshwork with a small mesh size. Our results highlight the functional importance of weak interactions, typically a few kBT per chain, and contribute important information to understand the mechanism of size-selective transport. PMID:24138862

Pore Distribution Characteristics of the Igneous Reservoirs in the Eastern Sag of the Liaohe Depression

NASA Astrophysics Data System (ADS)

Zongli, Liu; Zhuwen, Wang; Dapeng, Zhou; Shuqin, Zhao; Min, Xiang

2017-05-01

In the Es3 formation (third section of the Shahejie) of the Eastern sag section of the Liaohe Depression, basalt and trachyte are predominant in the igneous rock. The reservoir consists of complex reservoir space types. Based on the porosity bins of nuclear magnetic logging and the porosity distribution of electric imaging logging, the pores' sizes and distribution, as well as the mutual connectivity of the reservoir, were analyzed. Also, the characteristics of the different reservoirs were summarized. In regards to the oil reservoirs, large pores (PS>10) were found to account for the majority of the reservoir spaces, and the pore distribution was concentrated and well connected. However, for the poor oil reservoirs, the large and small pores were found to alternate, and the pore distribution was scattered and poorly connected. Within the dry layers, the smaller pores (PS<10) were predominant. The pore distributions were found to be influenced by lithology, facies, and tectonism. The reservoirs of the pyroclastic flow of the explosive facies had good connectivity, and the interlayer heterogeneity was relatively weak. This reservoir's pore distributions were found to be mainly dominated by the larger pores (PS10-PS13), which displayed a concentrated distribution mainly in one porosity bin. Therefore, it was taken as a favorable facie belt in the eastern sag of the Liaohe Depression. The examination of the pore distribution characteristics of the igneous rock was the key to the evaluation of the properties and effectiveness of the igneous reservoirs in this study, which potentially has great significance to the future exploration and development of igneous rock.

Natural stimulus responsive scaffolds/cells for bone tissue engineering: influence of lysozyme upon scaffold degradation and osteogenic differentiation of cultured marrow stromal cells induced by CaP coatings.

PubMed

Martins, Ana M; Pham, Quynh P; Malafaya, Patrícia B; Raphael, Robert M; Kasper, F Kurtis; Reis, Rui L; Mikos, Antonios G

2009-08-01

This work proposes the use of nonporous, smart, and stimulus responsive chitosan-based scaffolds for bone tissue engineering applications. The overall vision is to use biodegradable scaffolds based on chitosan and starch that present properties that will be regulated by bone regeneration, with the capability of gradual in situ pore formation. Biomimetic calcium phosphate (CaP) coatings were used as a strategy to incorporate lysozyme at the surface of chitosan-based materials with the main objective of controlling and tailoring their degradation profile as a function of immersion time. To confirm the concept, degradation tests with a lysozyme concentration similar to that incorporated into CaP chitosan-based scaffolds were used to study the degradation of the scaffolds and the formation of pores as a function of immersion time. Degradation studies with lysozyme (1.5 g/L) showed the formation of pores, indicating an increase of porosity ( approximately 5-55% up to 21 days) resulting in porous three-dimensional structures with interconnected pores. Additional studies investigated the influence of a CaP biomimetic coating on osteogenic differentiation of rat marrow stromal cells (MSCs) and showed enhanced differentiation of rat MSCs seeded on the CaP-coated chitosan-based scaffolds with lysozyme incorporated. At all culture times, CaP-coated chitosan-based scaffolds with incorporated lysozyme demonstrated greater osteogenic differentiation of MSCs, bone matrix production, and mineralization as demonstrated by calcium deposition measurements, compared with controls (uncoated scaffolds). The ability of these CaP-coated chitosan-based scaffolds with incorporated lysozyme to create an interconnected pore network in situ coupled with the demonstrated positive effect of these scaffolds upon osteogenic differentiation of MSCs and mineralized matrix production illustrates the strong potential of these scaffolds for application in bone tissue engineering strategies.

Conductivity affects nanosecond electrical pulse induced pressure transient formation

NASA Astrophysics Data System (ADS)

Roth, Caleb C.; Barnes, Ronald A.; Ibey, Bennett L.; Beier, Hope T.; Glickman, Randolph D.

2016-03-01

Nanoporation occurs in cells exposed to high amplitude short duration (< 1μs) electrical pulses. The biophysical mechanism(s) responsible for nanoporation is unknown although several theories exist. Current theories focus exclusively on the electrical field, citing electrostriction, water dipole alignment and/or electrodeformation as the primary mechanisms for pore formation. Our group has shown that mechanical forces of substantial magnitude are also generated during nsEP exposures. We hypothesize that these mechanical forces may contribute to pore formation. In this paper, we report that alteration of the conductivity of the exposure solution also altered the level of mechanical forces generated during a nsEP exposure. By reducing the conductivity of the exposure solutions, we found that we could completely eliminate any pressure transients normally created by nsEP exposure. The data collected for this proceeding does not definitively show that the pressure transients previously identified contribute to nanoporation; however; it indicates that conductivity influences both survival and pressure transient formation.

Gas hydrate formation rates from dissolved-phase methane in porous laboratory specimens

USGS Publications Warehouse

Waite, William F.; Spangenberg, E.K.

2013-01-01

Marine sands highly saturated with gas hydrates are potential energy resources, likely forming from methane dissolved in pore water. Laboratory fabrication of gas hydrate-bearing sands formed from dissolved-phase methane usually requires 1–2 months to attain the high hydrate saturations characteristic of naturally occurring energy resource targets. A series of gas hydrate formation tests, in which methane-supersaturated water circulates through 100, 240, and 200,000 cm3 vessels containing glass beads or unconsolidated sand, show that the rate-limiting step is dissolving gaseous-phase methane into the circulating water to form methane-supersaturated fluid. This implies that laboratory and natural hydrate formation rates are primarily limited by methane availability. Developing effective techniques for dissolving gaseous methane into water will increase formation rates above our observed (1 ± 0.5) × 10−7 mol of methane consumed for hydrate formation per minute per cubic centimeter of pore space, which corresponds to a hydrate saturation increase of 2 ± 1% per day, regardless of specimen size.

Characterization of Biogenic Gas and Mineral Formation Process by Denitrification in Porous Media

NASA Astrophysics Data System (ADS)

Hall, C. A.; Kim, D.; Mahabadi, N.; van Paassen, L. A.

2017-12-01

Biologically mediated processes have been regarded and developed as an alternative approach to traditional ground improvement techniques. Denitrification has been investigated as a potential ground improvement process towards liquefaction hazard mitigation. During denitrification, microorganisms reduce nitrate to dinitrogen gas and facilitate calcium carbonate precipitation as a by-product under adequate environmental conditions. The formation of dinitrogen gas desaturates soils and allows for potential pore pressure dampening during earthquake events. While, precipitation of calcium carbonate can improve the mechanical properties by filling the voids and cementing soil particles. As a result of small changes in gas and mineral phases, the mechanical properties of soils can be significantly affected. Prior research has primarily focused on quantitative analysis of overall residual calcium carbonate mineral and biogenic gas products in lab-scale porous media. However, the distribution of these products at the pore-scale has not been well-investigated. In this research, denitrification is activated in a microfluidic chip simulating a homogenous pore structure. The denitrification process is monitored by sequential image capture, where gas and mineral phase changes are evaluated by image processing. Analysis of these images correspond with previous findings, which demonstrate that biogenic gas behaviour at the pore scale is affected by the balance between reaction, diffusion, and convection rates.

Carbon Dioxide Sealing Capacity: Textural or Compositional Controls?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cranganu, Constantin; Soleymani, Hamidreza; Sadiqua, Soleymani

2013-11-30

This research project is aiming to assess the carbon dioxide sealing capacity of most common seal-rocks, such as shales and non-fractured limestones, by analyzing the role of textural and compositional parameters of those rocks. We hypothesize that sealing capacity is controlled by textural and/or compositional pa-rameters of caprocks. In this research, we seek to evaluate the importance of textural and compositional parameters affecting the sealing capacity of caprocks. The conceptu-al framework involves two testable end-member hypotheses concerning the sealing ca-pacity of carbon dioxide reservoir caprocks. Better understanding of the elements controlling sealing quality will advance our knowledge regarding the sealingmore » capacity of shales and carbonates. Due to relatively low permeability, shale and non-fractured carbonate units are considered relatively imper-meable formations which can retard reservoir fluid flow by forming high capillary pres-sure. Similarly, these unites can constitute reliable seals for carbon dioxide capture and sequestration purposes. This project is a part of the comprehensive project with the final aim of studying the caprock sealing properties and the relationship between microscopic and macroscopic characteristics of seal rocks in depleted gas fields of Oklahoma Pan-handle. Through this study we examined various seal rock characteristics to infer about their respective effects on sealing capacity in special case of replacing reservoir fluid with super critical carbon dioxide (scCO{sub 2}). To assess the effect of textural and compositional properties on scCO{sub 2} maximum reten-tion column height we collected 30 representative core samples in caprock formations in three counties (Cimarron, Texas, Beaver) in Oklahoma Panhandle. Core samples were collected from various seal formations (e.g., Cherokee, Keys, Morrowan) at different depths. We studied the compositional and textural properties of the core samples using several techniques. Mercury Injection Porosimetry (MIP), Scanning Electron Microsco-py SEM, and Sedigraph measurements are used to assess the pore-throat-size distribu-tion, sorting, texture, and grain size of the samples. Also, displacement pressure at 10% mercury saturation (Pd) and graphically derived threshold pressure (Pc) were deter-mined by MIP technique. SEM images were used for qualitative study of the minerals and pores texture of the core samples. Moreover, EDS (Energy Dispersive X-Ray Spec-trometer), BET specific surface area, and Total Organic Carbon (TOC) measurements were performed to study various parameters and their possible effects on sealing capaci-ty of the samples. We found that shales have the relatively higher average sealing threshold pressure (Pc) than carbonate and sandstone samples. Based on these observations, shale formations could be considered as a promising caprock in terms of retarding scCO{sub 2} flow and leak-age into above formations. We hypothesized that certain characteristics of shales (e.g., 3 fine pore size, pore size distribution, high specific surface area, and strong physical chemical interaction between wetting phase and mineral surface) make them an effi-cient caprock for sealing super critical CO{sub 2}. We found that the displacement pressure at 10% mercury saturation could not be the ultimate representative of the sealing capacity of the rock sample. On the other hand, we believe that graphical method, introduced by Cranganu (2004) is a better indicator of the true sealing capacity. Based on statistical analysis of our samples from Oklahoma Panhandle we assessed the effects of each group of properties (textural and compositional) on maximum supercriti-cal CO{sub 2} height that can be hold by the caprock. We conclude that there is a relatively strong positive relationship (+.40 to +.69) between supercritical CO{sub 2} column height based on Pc and hard/ soft mineral content index (ratio of minerals with Mohs hardness more than 5 over minerals with Mohs hardness less than 5) in both shales and limestone samples. Average median pore radius and porosity display a strong negative correlation with supercritical CO{sub 2} retention column height. Also, increasing bulk density is positive-ly correlated with the supercritical CO{sub 2} retention column height. One of the most im-portant factors affecting sealing capacity and consequently the height of supercritical CO{sub 2} column is sorting of the pore throats. We observed a strong positive correlation be-tween pore throat sorting and height of CO{sub 2} retention column, especially in shales. This correlation could not be observed in limestone samples. It suggests that the pore throat sorting is more controlling the sealing capacity in shales and shales with well sorted pore throats are the most reliable lithology as seal. We observed that Brunauer–Emmett–Teller (BET) surface area shows a very strong correlation with CO{sub 2} retention column height in limestone samples while BET surface area did not display significant correlation in shales. Pore structure based on SEM mi-crographs exhibits strong correlation with CO{sub 2} retention column height in limestones. Both intercrystalline and vuggy structures have negative correlations while intergranu-lar texture has positive correlation in limestone with respect to CO{sub 2} retention column height. Textural effects observed on SEM micrographs did not show statistically signifi-cant correlation with supercritical CO{sub 2} retention column height in shale samples. Finally, we showed that increasing hard/soft mineral index is strongly correlated with the displacement pressure in limestone samples. Vuggy texture displays a relatively strong and negative correlation with displacement pressure values at 10% mercury satu-ration in shale samples.« less

Enzymes immobilized in mesoporous silica: a physical-chemical perspective.

PubMed

Carlsson, Nils; Gustafsson, Hanna; Thörn, Christian; Olsson, Lisbeth; Holmberg, Krister; Åkerman, Björn

2014-03-01

Mesoporous materials as support for immobilized enzymes have been explored extensively during the last two decades, primarily not only for biocatalysis applications, but also for biosensing, biofuels and enzyme-controlled drug delivery. The activity of the immobilized enzymes inside the pores is often different compared to that of the free enzymes, and an important challenge is to understand how the immobilization affects the enzymes in order to design immobilization conditions that lead to optimal enzyme activity. This review summarizes methods that can be used to understand how material properties can be linked to changes in enzyme activity. Real-time monitoring of the immobilization process and techniques that demonstrate that the enzymes are located inside the pores is discussed by contrasting them to the common practice of indirectly measuring the depletion of the protein concentration or enzyme activity in the surrounding bulk phase. We propose that pore filling (pore volume fraction occupied by proteins) is the best standard for comparing the amount of immobilized enzymes at the molecular level, and present equations to calculate pore filling from the more commonly reported immobilized mass. Methods to detect changes in enzyme structure upon immobilization and to study the microenvironment inside the pores are discussed in detail. Combining the knowledge generated from these methodologies should aid in rationally designing biocatalyst based on enzymes immobilized in mesoporous materials. © 2013 Elsevier B.V. All rights reserved.

Pore-Scale Investigation on Stress-Dependent Characteristics of Granular Packs and Their Impact on Multiphase Fluid Distribution

NASA Astrophysics Data System (ADS)

Torrealba, V.; Karpyn, Z.; Yoon, H.; Hart, D. B.; Klise, K. A.

2013-12-01

The pore-scale dynamics that govern multiphase flow under variable stress conditions are not well understood. This lack of fundamental understanding limits our ability to quantitatively predict multiphase flow and fluid distributions in natural geologic systems. In this research, we focus on pore-scale, single and multiphase flow properties that impact displacement mechanisms and residual trapping of non-wetting phase under varying stress conditions. X-ray micro-tomography is used to image pore structures and distribution of wetting and non-wetting fluids in water-wet synthetic granular packs, under dynamic load. Micro-tomography images are also used to determine structural features such as medial axis, surface area, and pore body and throat distribution; while the corresponding transport properties are determined from Lattice-Boltzmann simulations performed on lattice replicas of the imaged specimens. Results are used to investigate how inter-granular deformation mechanisms affect fluid displacement and residual trapping at the pore-scale. This will improve our understanding of the dynamic interaction of mechanical deformation and fluid flow during enhanced oil recovery and geologic CO2 sequestration. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Effects of Coke Calcination Level on Pore Structure in Carbon Anodes

NASA Astrophysics Data System (ADS)

Fang, Ning; Xue, Jilai; Lang, Guanghui; Bao, Chongai; Gao, Shoulei

2016-02-01

Effects of coke calcination levels on pore structure of carbon anodes have been investigated. Bench anodes were prepared by 3 types of cokes with 4 calcination temperatures (800°C, 900°C, 1000°C and 1100°C). The cokes and anodes were characterized using hydrostatic method, air permeability determination, mercury porosimetry, image analysis and confocal microscopy (CSLM). The cokes with different calcination levels are almost the same in LC values (19-20 Å) and real density (1.967-1.985 g/cm3), while the anode containing coke calcined at 900°C has the lowest open porosity and air permeability. Pore size distribution (represented by Anode H sample) can be roughly divided into two ranges: small and medium pores in diameter of 10-400 μm and large pores of 400-580 μm. For the anode containing coke calcined at 800°C, a number of long, narrow pores in the pore size range of 400-580 μm are presented among cokes particles. Formation of these elongated pores may be attributed to coke shrinkages during the anode baking process, which may develop cracking in the anode under cell operations. More small or medium rounded pores with pore size range of 10-400 μm emerge in the anodes with coke calcination temperatures of 900°C, 1000°C and 1100°C, which may be generated due to release of volatiles from the carbon anode during baking. For the anode containing coke calcined at 1100°C, it is found that many rounded pores often closely surround large coke particles, which have potential to form elongated, narrow pores.

Influence of the doping type and level on the morphology of porous Si formed by galvanic etching

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pyatilova, O. V., E-mail: 5ilova87@gmail.com; Gavrilov, S. A.; Shilyaeva, Yu. I.

The formation of porous silicon (por-Si) layers by the galvanic etching of single-crystal Si samples (doped with boron or phosphorus) in an HF/C{sub 2}H{sub 5}OH/H{sub 2}O{sub 2} solution is investigated. The por-Si layers are analyzed by the capillary condensation of nitrogen and scanning electron microscopy (SEM). The dependences of the morphological characteristics of por-Si (pore diameter, specific surface area, pore volume, and thickness of the pore walls), which determine the por-Si combustion kinetics, on the dopant type and initial wafer resistivity are established.

Determination of pore-scale hydrate phase equilibria in sediments using lab-on-a-chip technology.

PubMed

Almenningen, Stian; Flatlandsmo, Josef; Kovscek, Anthony R; Ersland, Geir; Fernø, Martin A

2017-11-21

We present an experimental protocol for fast determination of hydrate stability in porous media for a range of pressure and temperature (P, T) conditions. Using a lab-on-a-chip approach, we gain direct optical access to dynamic pore-scale hydrate formation and dissociation events to study the hydrate phase equilibria in sediments. Optical pore-scale observations of phase behavior reproduce the theoretical hydrate stability line with methane gas and distilled water, and demonstrate the accuracy of the new method. The procedure is applicable for any kind of hydrate transitions in sediments, and may be used to map gas hydrate stability zones in nature.

Textile properties of synthetic prolapse mesh in response to uniaxial loading.

PubMed

Barone, William R; Moalli, Pamela A; Abramowitch, Steven D

2016-09-01

Although synthetic mesh is associated with superior anatomic outcomes for the repair of pelvic organ prolapse, the benefits of mesh have been questioned because of the relatively high complication rates. To date, the mechanisms that result in such complications are poorly understood, yet the textile characteristics of mesh products are believed to play an important role. Interestingly, the pore diameter of synthetic mesh has been shown to impact the host response after hernia repair greatly, and such findings have served as design criteria for prolapse meshes, with larger pores viewed as more favorable. Although pore size and porosity are well-characterized before implantation, the changes in these textile properties after implantation are unclear; the application of mechanical forces has the potential to greatly alter pore geometries in vivo. Understanding the impact of mechanical loading on the textile properties of mesh is essential for the development of more effective devices for prolapse repair. The objective of this study was to determine the effect of tensile loading and pore orientation on mesh porosity and pore dimensions. In this study, the porosity and pore diameter of 4 currently available prolapse meshes were examined in response to uniaxial tensile loads of 0.1, 5, and 10 N while mimicking clinical loading conditions. The textile properties were compared with those observed for the unloaded mesh. Meshes included Gynemesh PS (Ethicon, Somerville, NJ), UltraPro (Artisyn; Ethicon), Restorelle (Coloplast, Minneapolis, MN), and Alyte Y-mesh (Bard, Covington, GA). In addition to the various pore geometries, 3 orientations of Restorelle (0-, 5-, 45-degree offset) and 2 orientations of UltraPro (0-, 90-degree offset) were examined. In response to uniaxial loading, both porosity and pore diameter dramatically decreased for most mesh products. The application of 5 N led to reductions in porosity for nearly all groups, with values decreasing by as much as 87% (P < .05). On loading to 10 N of force, nearly all mesh products that were tested were found to have porosities that approached 0% and 0 pores with diameters >1 mm. In this study, it was shown that the pore size of current prolapse meshes dramatically decreases in response to mechanical loading. These findings suggest that prolapse meshes, which are more likely to experience tensile forces in vivo relative to hernia repair meshes, have pores that are unfavorable for tissue integration after surgical tensioning and/or loading in urogynecologic surgeries. Such decreases in pore geometry support the hypothesis that regional increases in the concentration of mesh leads to an enhanced local foreign body response. Although pore deformation in transvaginal meshes requires further characterization, the findings presented here provide a mechanical understanding that can be used to recognize potential areas of concern for complex mesh geometries. Understanding mesh mechanics in response to surgical and in vivo loading conditions may provide improved design criteria for mesh and a refinement of surgical techniques, ultimately leading to better patient outcomes. Copyright © 2016 Elsevier Inc. All rights reserved.

Effects of Stretching Speed on Mechanical Rupture of Phospholipid/Cholesterol Bilayers: Molecular Dynamics Simulation

PubMed Central

Shigematsu, Taiki; Koshiyama, Kenichiro; Wada, Shigeo

2015-01-01

Rupture of biological cell membrane under mechanical stresses is critical for cell viability. It is triggered by local rearrangements of membrane molecules. We investigated the effects of stretching speed on mechanical rupture of phospholipid/cholesterol bilayers using unsteady molecular dynamics simulations. We focused on pore formation, the trigger of rupture, in a 40 mol% cholesterol-including bilayer. The unsteady stretching was modeled by proportional and temporal scaling of atom positions at stretching speeds from 0.025 to 30 m/s. The effects of the stretching speed on the critical areal strain, where the pore forms, is composed of two regimes. At low speeds (<1.0 m/s), the critical areal strain is insensitive to speed, whereas it significantly increases at higher speeds. Also, the strain is larger than that of a pure bilayer, regardless of the stretching speeds, which qualitatively agrees with available experimental data. Transient recovery of the cholesterol and phospholipid molecular orientations was evident at lower speeds, suggesting the formation of a stretch-induced interdigitated gel-like phase. However, this recovery was not confirmed at higher speeds or for the pure bilayer. The different responses of the molecular orientations may help explain the two regimes for the effect of stretching speed on pore formation. PMID:26471872

Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin.

PubMed

Leung, Carl; Dudkina, Natalya V; Lukoyanova, Natalya; Hodel, Adrian W; Farabella, Irene; Pandurangan, Arun P; Jahan, Nasrin; Pires Damaso, Mafalda; Osmanović, Dino; Reboul, Cyril F; Dunstone, Michelle A; Andrew, Peter W; Lonnen, Rana; Topf, Maya; Saibil, Helen R; Hoogenboom, Bart W

2014-12-02

Membrane attack complex/perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins constitute a major superfamily of pore-forming proteins that act as bacterial virulence factors and effectors in immune defence. Upon binding to the membrane, they convert from the soluble monomeric form to oligomeric, membrane-inserted pores. Using real-time atomic force microscopy (AFM), electron microscopy (EM), and atomic structure fitting, we have mapped the structure and assembly pathways of a bacterial CDC in unprecedented detail and accuracy, focussing on suilysin from Streptococcus suis. We show that suilysin assembly is a noncooperative process that is terminated before the protein inserts into the membrane. The resulting ring-shaped pores and kinetically trapped arc-shaped assemblies are all seen to perforate the membrane, as also visible by the ejection of its lipids. Membrane insertion requires a concerted conformational change of the monomeric subunits, with a marked expansion in pore diameter due to large changes in subunit structure and packing.

Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin

PubMed Central

Lukoyanova, Natalya; Hodel, Adrian W; Farabella, Irene; Pandurangan, Arun P; Jahan, Nasrin; Pires Damaso, Mafalda; Osmanović, Dino; Reboul, Cyril F; Dunstone, Michelle A; Andrew, Peter W; Lonnen, Rana; Topf, Maya

2014-01-01

Membrane attack complex/perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins constitute a major superfamily of pore-forming proteins that act as bacterial virulence factors and effectors in immune defence. Upon binding to the membrane, they convert from the soluble monomeric form to oligomeric, membrane-inserted pores. Using real-time atomic force microscopy (AFM), electron microscopy (EM), and atomic structure fitting, we have mapped the structure and assembly pathways of a bacterial CDC in unprecedented detail and accuracy, focussing on suilysin from Streptococcus suis. We show that suilysin assembly is a noncooperative process that is terminated before the protein inserts into the membrane. The resulting ring-shaped pores and kinetically trapped arc-shaped assemblies are all seen to perforate the membrane, as also visible by the ejection of its lipids. Membrane insertion requires a concerted conformational change of the monomeric subunits, with a marked expansion in pore diameter due to large changes in subunit structure and packing. DOI: http://dx.doi.org/10.7554/eLife.04247.001 PMID:25457051

Analysis of quasi-periodic pore-network structure of centric marine diatom frustules

NASA Astrophysics Data System (ADS)

Cohoon, Gregory A.; Alvarez, Christine E.; Meyers, Keith; Deheyn, Dimitri D.; Hildebrand, Mark; Kieu, Khanh; Norwood, Robert A.

2015-03-01

Diatoms are a common type of phytoplankton characterized by their silica exoskeleton known as a frustule. The diatom frustule is composed of two valves and a series of connecting girdle bands. Each diatom species has a unique frustule shape and valves in particular species display an intricate pattern of pores resembling a photonic crystal structure. We used several numerical techniques to analyze the periodic and quasi-periodic valve pore-network structure in diatoms of the Coscinodiscophyceae order. We quantitatively identify defect locations and pore spacing in the valve and use this information to better understand the optical and biological properties of the diatom.

Cavitation and pore blocking in nanoporous glasses.

PubMed

Reichenbach, C; Kalies, G; Enke, D; Klank, D

2011-09-06

In gas adsorption studies, porous glasses are frequently referred to as model materials for highly disordered mesopore systems. Numerous works suggest that an accurate interpretation of physisorption isotherms requires a complete understanding of network effects upon adsorption and desorption, respectively. The present article deals with nitrogen and argon adsorption at different temperatures (77 and 87 K) performed on a series of novel nanoporous glasses (NPG) with different mean pore widths. NPG samples contain smaller mesopores and significantly higher microporosity than porous Vycor glass or controlled pore glass. Since the mean pore width of NPG can be tuned sensitively, the evolution of adsorption characteristics with respect to a broadening pore network can be investigated starting from the narrowest nanopore width. With an increasing mean pore width, a H2-type hysteresis develops gradually which finally transforms into a H1-type. In this connection, a transition from a cavitation-induced desorption toward desorption controlled by pore blocking can be observed. Furthermore, we find concrete hints for a pore size dependence of the relative pressure of cavitation in highly disordered pore systems. By comparing nitrogen and argon adsorption, a comprehensive insight into adsorption mechanisms in novel disordered materials is provided. © 2011 American Chemical Society

Nanoporous Polymer Films of Cyanate Ester Resins Designed by Using Ionic Liquids as Porogens.

PubMed

Fainleib, Alexander; Vashchuk, Alina; Starostenko, Olga; Grigoryeva, Olga; Rogalsky, Sergiy; Nguyen, Thi-Thanh-Tam; Grande, Daniel

2017-12-01

Novel nanoporous film materials of thermostable cyanate ester resins (CERs) were generated by polycyclotrimerization of dicyanate ester of bisphenol E in the presence of varying amounts (from 20 to 40 wt%) of an ionic liquid (IL), i.e., 1-heptylpyridinium tetrafluoroborate, followed by its quantitative extraction after complete CER network formation. The completion of CER formation and IL extraction was assessed using gel fraction content determination, FTIR, 1 H NMR, and energy-dispersive X-ray spectroscopy (EDX). SEM and DSC-based thermoporometry analyses demonstrated the formation of nanoporous structures after IL removal from CER networks, thus showing the effective role of IL as a porogen. Pore sizes varied from ~20 to ~180 nm with an average pore diameter of around 45-60 nm depending on the initial IL content. The thermal stability of nanoporous CER-based films was investigated by thermogravimetric analysis.

Nanoporous Polymer Films of Cyanate Ester Resins Designed by Using Ionic Liquids as Porogens

NASA Astrophysics Data System (ADS)

Fainleib, Alexander; Vashchuk, Alina; Starostenko, Olga; Grigoryeva, Olga; Rogalsky, Sergiy; Nguyen, Thi-Thanh-Tam; Grande, Daniel

2017-02-01

Novel nanoporous film materials of thermostable cyanate ester resins (CERs) were generated by polycyclotrimerization of dicyanate ester of bisphenol E in the presence of varying amounts (from 20 to 40 wt%) of an ionic liquid (IL), i.e., 1-heptylpyridinium tetrafluoroborate, followed by its quantitative extraction after complete CER network formation. The completion of CER formation and IL extraction was assessed using gel fraction content determination, FTIR, 1H NMR, and energy-dispersive X-ray spectroscopy (EDX). SEM and DSC-based thermoporometry analyses demonstrated the formation of nanoporous structures after IL removal from CER networks, thus showing the effective role of IL as a porogen. Pore sizes varied from 20 to 180 nm with an average pore diameter of around 45-60 nm depending on the initial IL content. The thermal stability of nanoporous CER-based films was investigated by thermogravimetric analysis.

The Effect of Experimental Weathering on the Multiscale Pore Structure of Granites: A (U)SANS, Imaging Analysis

NASA Astrophysics Data System (ADS)

Anovitz, L. M.; Sheets, J.; Gu, X.; Brantley, S.; Cole, D. R.; Ilton, E. S.; Mildner, D. F. R.; Littrell, K. C.; Gagnon, C.

2017-12-01

The microstructure and evolution of pore space is a critically important factor controlling fluid flow properties in geological formations, including the migration and retention of water, gas and hydrocarbons, sequestration of wastes, the formation of ore deposits, and the evolution of metamorphic terranes. As noted by Navarre-Sitchler et al. (2013), pristine igneous bedrock does not usually contain significant water. However, infiltration of meteoric water causes the rock to begin to disaggregate, increasing the porosity and surface area. In many igneous rocks this process is enhanced by oxidation. However, the mechanisms of porosity formation during weathering are poorly understood, and we cannot accurately extrapolate laboratory reaction rates to the field in predictive numerical models. While there are many methods for interrogating pore structure, it is difficult to satisfactorily describe textural and porosity changes in rock samples using direct imaging techniques because of the wide variation in length scales involved. A combination of SANS, USANS and imaging is, however, well suited to this task. The weathering process in granite is especially complex. While more mafic rocks tend to alter diffusively, forming altered rims, stresses caused by oxidation of ferromagnesian minerals—particularly biotites—tend to cause granites to spall. In order to better understand the effects of oxidation on the weathering process we have performed a series of experiments on granite cores approximately 5/8" in diameter by 5/8" long. These have been reacted in a solution of Se6+ at 200°C for periods of 1, 2, 4, 8, 16, 32, 64, 256 and 438 days. The reaction of Se6+ to Se4+ is very oxidizing relative to that of the Fe2+ in the granite, the solution contained enough to buffer twice the ferrous iron expected in the rock sample, and no secondary phases are expected to form. Because of the geometry these are expected to form oxidized rims that grow with time prior to failure, and the reactive porosity and micro-stress-fractures are easily discernable and quantifiable by (U)SANS. Annular Cd masks were used to isolate core and rim processes during the (U)SANS analyses. These were supplemented by SEM analyses. Results suggest that reactive stresses play a significant role in the evolution of porosity during weathering.

Bacillus thuringiensis: A story of a successful bioinsecticide

PubMed Central

Bravo, Alejandra; Likitvivatanavong, Supaporn; Gill, Sarjeet S.; Soberón, Mario

2013-01-01

Bacillus thuringiensis (Bt) bacteria are insect pathogens that rely on insecticidal pore forming proteins known as Cry and Cyt toxins to kill their insect larval hosts. At least four different non-structurally related families of proteins form the Cry toxin group of toxins. The expression of certain Cry toxins in transgenic crops has contributed to an efficient control of insect pests resulting in a significant reduction in chemical insecticide use. The mode of action of the three domain Cry toxin family involves sequential interaction of these toxins with several insect midgut proteins facilitating the formation of a pre-pore oligomer structure and subsequent membrane insertion that leads to the killing of midgut insect cells by osmotic shock. In this manuscript we review recent progress in understanding the mode of action of this family of proteins in lepidopteran, dipteran and coleopteran insects. Interestingly, similar Cry-binding proteins have been identified in the three insect orders, as cadherin, aminopeptidase-N and alkaline phosphatase suggesting a conserved mode of action. Also, recent data on insect responses to Cry toxin attack is discussed. Finally, we review the different Bt based products, including transgenic crops, that are currently used in agriculture. PMID:21376122

Compositional Determination of Shale with Simultaneous Neutron and X-ray Tomography

NASA Astrophysics Data System (ADS)

LaManna, J.; Hussey, D. S.; Baltic, E.; Jacobson, D. L.

2017-12-01

Understanding the distribution of organic material, mineral inclusions, and porosity are critical to properly model the flow of fluids through rock formations in applications ranging from hydraulic fracturing and gas extraction, CO2 sequestration, geothermal power, and aquifer management. Typically, this information is obtained on the pore scale using destructive techniques such as focused ion beam scanning electron microscopy. Neutrons and X-rays provide non-destructive, complementary probes to gain three-dimensional distributions of porosity, minerals, and organic content along with fluid interactions in fractures and pore networks on the core scale. By capturing both neutron and X-ray tomography simultaneously it is possible to capture slowly dynamic or stochastic processes with both imaging modes. To facilitate this, NIST offers a system for simultaneous neutron and X-ray tomography at the Center for Neutron Research. This instrument provides neutron and X-ray beams capable of penetrating through pressure vessels to image the specimen inside at relevant geological conditions at resolutions ranging from 15 micrometers to 100 micrometers. This talk will discuss current efforts at identifying mineral and organic content and fracture and wettability in shales relevant to gas extraction.

Metastable Prepores in Tension-Free Lipid Bilayers

NASA Astrophysics Data System (ADS)

Ting, Christina L.; Awasthi, Neha; Müller, Marcus; Hub, Jochen S.

2018-03-01

The formation and closure of aqueous pores in lipid bilayers is a key step in various biophysical processes. Large pores are well described by classical nucleation theory, but the free-energy landscape of small, biologically relevant pores has remained largely unexplored. The existence of small and metastable "prepores" was hypothesized decades ago from electroporation experiments, but resolving metastable prepores from theoretical models remained challenging. Using two complementary methods—atomistic simulations and self-consistent field theory of a minimal lipid model—we determine the parameters for which metastable prepores occur in lipid membranes. Both methods consistently suggest that pore metastability depends on the relative volume ratio between the lipid head group and lipid tails: lipids with a larger head-group volume fraction (or shorter saturated tails) form metastable prepores, whereas lipids with a smaller head-group volume fraction (or longer unsaturated tails) form unstable prepores.

Molecular transport through large-diameter DNA nanopores

NASA Astrophysics Data System (ADS)

Krishnan, Swati; Ziegler, Daniela; Arnaut, Vera; Martin, Thomas G.; Kapsner, Korbinian; Henneberg, Katharina; Bausch, Andreas R.; Dietz, Hendrik; Simmel, Friedrich C.

2016-09-01

DNA-based nanopores are synthetic biomolecular membrane pores, whose geometry and chemical functionality can be tuned using the tools of DNA nanotechnology, making them promising molecular devices for applications in single-molecule biosensing and synthetic biology. Here we introduce a large DNA membrane channel with an ~4 nm diameter pore, which has stable electrical properties and spontaneously inserts into flat lipid bilayer membranes. Membrane incorporation is facilitated by a large number of hydrophobic functionalizations or, alternatively, streptavidin linkages between biotinylated channels and lipids. The channel displays an Ohmic conductance of ~3 nS, consistent with its size, and allows electrically driven translocation of single-stranded and double-stranded DNA analytes. Using confocal microscopy and a dye influx assay, we demonstrate the spontaneous formation of membrane pores in giant unilamellar vesicles. Pores can be created both in an outside-in and an inside-out configuration.

Early diagenesis and authigenic mineral formation in mobile muds of the Changjiang Estuary and adjacent shelf

NASA Astrophysics Data System (ADS)

Zhao, Bin; Yao, Peng; Bianchi, Thomas S.; Xu, Yahong; Liu, Hui; Mi, Tiezhu; Zhang, Xiao-Hua; Liu, Jiwen; Yu, Zhigang

2017-08-01

Large-river delta-front estuaries (LDEs) and their adjacent shelf margins are sites of dynamic diagenetic processes that play a significant role in coastal biogeochemical cycling. In this study, we used dissolved inorganic carbon (DIC), redox sensitive elements (Fe2 + and Mn2 +), dissolved inorganic nitrogen (DIN) nutrients (NH4+, NO3-, and NO2-), major cations and anions (K+, Ca2 +, Mg2 +, SO42 -, and Cl-) in bottom-water and sediment pore-waters, to investigate the early chemical diagenesis and authigenic mineral formation in mobile-mud deposits of the Changjiang Estuary and adjacent inner shelf of the East China Sea (ECS). Vertical profiles of DIC and NH4+ in pore-waters had similar trends at most sites, showing a significant increase with depth near the Changjiang Estuary and being relatively constant at offshore sites. Higher pore-water DIC and NH4+ concentrations were observed in nearshore sites in winter, which were likely attributed to exposure of deeper deposits by winter coastal erosion. Nitrification was observed at most sites, and AOB (ammonia-oxidizing bacteria) played a leading role in ammonia oxidation in the study areas. The nitrification-denitrification was likely important in contributing to the loss of DIN in offshore sites during summer. Large inputs of organic carbon (OC) and terrestrial materials from Changjiang River resulted in intense sulfate reduction and Fe and Mn reduction in nearshore sites. Lower C/N and C/S ratios coupled with an apparent decrease in pore-water Ca2 + and Mg2+ concentrations with depth near the Changjiang Estuary, which indicated that authigenic carbonate formation occurs in these sediments. Decreases in K+ and Mg2 + with depth reflected that reverse weathering was an important process of authigenic mineral formation in these sediments. We conclude that adsorption process, seasonal erosion-redeposition, and summer hypoxic conditions of bottom-waters may play an important role in early diagenesis processes and remineralization of SOC in the Changjiang LDE.

Authigenic Carbonate Formation on the Peru Margin; New Insights from IODP Site 1230

NASA Astrophysics Data System (ADS)

Abdullajintakam, S.; Naehr, T. H.

2015-12-01

Fluid seepage of reduced organic compounds such as methane impacts the geology and biology of the seabed by inducing complex, microbially mediated biogeochemical processes. Authigenic carbonates serve as one of the few permanent records of these of dynamic biogeochemical interactions that involve methanogenesis, methanotrophy, sulfate reduction and carbonate precipitation. Meister et al. (2007) investigated deep-sea dolomite formation at Sites 1227-1229 on the Peru margin, where dolomite precipitation occurs in association with organic carbon-rich continental margin sediments. Geochemical and petrographic studies indicated episodic dolomite precipitation at a dynamic sulfate methane transition zone (SMTZ). Variations in δ13C values of these dolomites between +15‰ and -15‰ were attributed to non-steady state conditions as a result of the upward and downward migration of the SMTZ. Our study aims to better understand the biogeochemical processes associated with authigenic carbonate precipitation in this dynamic deep-sea setting. We focused our efforts on IODP Site 1230, which is a gas-hydrate-bearing site that shows sulphate consumption within the uppermost 10 m below the seafloor as well as high methane production. Using a multi proxy approach, we combined X-ray diffraction, stable isotope geochemistry, and trace metal analysis of authigenic carbonates to elucidate conditions for authigenic carbonate formation. Results from Site 1230 are compared to Sites 1227 and 1229, which lacks gas hydrates and is characterized by high pore water sulfate and low methane concentrations. This study contributes to a more comprehensive understanding of authigenic carbonate formation and associated biogeochemical processes in continental margin sediments. Meister, P., Mckenzie, J. A., Vasconcelos, C., Bernasconi, S., Frank, M., Gutjhar, M. and SCHRAG, D. P. (2007), Dolomite formation in the dynamic deep biosphere: results from the Peru Margin. Sedimentology, 54: 1007-1032.

Review of pore network modelling of porous media: Experimental characterisations, network constructions and applications to reactive transport.

PubMed

Xiong, Qingrong; Baychev, Todor G; Jivkov, Andrey P

2016-09-01

Pore network models have been applied widely for simulating a variety of different physical and chemical processes, including phase exchange, non-Newtonian displacement, non-Darcy flow, reactive transport and thermodynamically consistent oil layers. The realism of such modelling, i.e. the credibility of their predictions, depends to a large extent on the quality of the correspondence between the pore space of a given medium and the pore network constructed as its representation. The main experimental techniques for pore space characterisation, including direct imaging, mercury intrusion porosimetry and gas adsorption, are firstly summarised. A review of the main pore network construction techniques is then presented. Particular focus is given on how such constructions are adapted to the data from experimentally characterised pore systems. Current applications of pore network models are considered, with special emphasis on the effects of adsorption, dissolution and precipitation, as well as biomass growth, on transport coefficients. Pore network models are found to be a valuable tool for understanding and predicting meso-scale phenomena, linking single pore processes, where other techniques are more accurate, and the homogenised continuum porous media, used by engineering community. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Impact of spatially correlated pore-scale heterogeneity on drying porous media

NASA Astrophysics Data System (ADS)

Borgman, Oshri; Fantinel, Paolo; Lühder, Wieland; Goehring, Lucas; Holtzman, Ran

2017-07-01

We study the effect of spatially-correlated heterogeneity on isothermal drying of porous media. We combine a minimal pore-scale model with microfluidic experiments with the same pore geometry. Our simulated drying behavior compares favorably with experiments, considering the large sensitivity of the emergent behavior to the uncertainty associated with even small manufacturing errors. We show that increasing the correlation length in particle sizes promotes preferential drying of clusters of large pores, prolonging liquid connectivity and surface wetness and thus higher drying rates for longer periods. Our findings improve our quantitative understanding of how pore-scale heterogeneity impacts drying, which plays a role in a wide range of processes ranging from fuel cells to curing of paints and cements to global budgets of energy, water and solutes in soils.

Petrophysical laboratory invertigations of carbon dioxide storage in a subsurface saline aquifer in Ketzin/Germany within the scope of CO2SINK

NASA Astrophysics Data System (ADS)

Zemke, K.; Kummmerow, J.; Wandrey, M.; Co2SINK Group

2009-04-01

Since June of 2008 carbon dioxide has been injected into a saline aquifer at the Ketzin test site [Würdemann et al., this volume]. The food grade CO2 is injected into a sandstone zone of the Stuttgart formation at ca. 650 m depth at 35°C reservoir temperature and 62 bar reservoir pressure. With the injection of CO2 into the geological formation, chemical and physical reservoir characteristics are changed depending on pressure, temperature, fluid chemistry and rock composition. Fluid-rock interaction could comprise dissolution of non-resistant minerals in CO2-bearing pore fluids, cementing of the pore space by precipitating substances from the pore fluid, drying and disintegration of clay minerals and thus influence of the composition and activities of the deep biosphere. To testing the injection behaviour of CO2 in water saturated rock and to evaluate the geophysical signature depending on the thermodynamic conditions, flow experiments with water and CO2 have been performed on cores of the Stuttgart formation from different locations including new wells of ketzin test site. The studied core material is an unconsolidated fine-grained sandstone with porosity values from 15 to 32 %. Permeability, electrical resistivity, and sonic wave velocities and their changes with pressure, saturation and time have been studied under simulated in situ conditions. The flow experiments conducted over several weeks with brine and CO2 showed no significant changes of resistivity and velocity and a slightly decreasing permeability. Pore fluid analysis showed mobilization of clay and some other components. A main objective of the CO2Sink laboratory program is the assessment of the effect of long-term CO2 exposure on reservoir rocks to predict the long-term behaviour of geological CO2 storage. For this CO2 exposure experiments reservoir rock samples were exposed to CO2 saturated reservoir fluid in corrosion-resistant high pressure vessels under in situ temperature and pressure conditions over a period of several months. Before and after the CO2 exposure experiment cyclic measurements of physical properties were carried out on these cores in a mechanical testing system. After experimental runs of up to 3 months no significant changes in flow and petrophysical data were observed. [For the microbilogical studies see Wandrey et al., this volume.] To study the impact of fluid-rock interactions on petrophysical parameters, porosity and pore radii distribution have been investigated before and after the experiment by NMR relaxation and mercury-injection. NMR measurements on rock core plugs saturated with brine may return valuable information on the porous structure of the rock core. The distribution of NMR-T2 values (CPMG) reflects the pore sizes within the rock core. NMR pore size is a derivative of the ratio pore surface/volume. The mercury injection pore size is an area-equivalent diameter of the throats connecting the pore system. Most of the tested samples show in the NMR measurements a slightly increasing porosity and a higher part of large pores. The mercury measurements and thin- section for microstructural characterisation after the CO2 exposure will be done at a later date.

Estimation of activation energy for electroporation and pore growth rate in liquid crystalline and gel phases of lipid bilayers using molecular dynamics simulations.

PubMed

Majhi, Amit Kumar; Kanchi, Subbarao; Venkataraman, V; Ayappa, K G; Maiti, Prabal K

2015-11-28

Molecular dynamics simulations of electroporation in POPC and DPPC lipid bilayers have been carried out at different temperatures ranging from 230 K to 350 K for varying electric fields. The dynamics of pore formation, including threshold field, pore initiation time, pore growth rate, and pore closure rate after the field is switched off, was studied in both the gel and liquid crystalline (Lα) phases of the bilayers. Using an Arrhenius model of pore initiation kinetics, the activation energy for pore opening was estimated to be 25.6 kJ mol(-1) and 32.6 kJ mol(-1) in the Lα phase of POPC and DPPC lipids respectively at a field strength of 0.32 V nm(-1). The activation energy decreases to 24.2 kJ mol(-1) and 23.7 kJ mol(-1) respectively at a higher field strength of 1.1 V nm(-1). At temperatures below the melting point, the activation energy in the gel phase of POPC and DPPC increases to 28.8 kJ mol(-1) and 34.4 kJ mol(-1) respectively at the same field of 1.1 V nm(-1). The pore closing time was found to be higher in the gel than in the Lα phase. The pore growth rate increases linearly with temperature and quadratically with field, consistent with viscosity limited growth models.

A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores

PubMed Central

Yoo, Jejoong; Jackson, Meyer B.; Cui, Qiang

2013-01-01

To establish the validity of continuum mechanics models quantitatively for the analysis of membrane remodeling processes, we compare the shape and energies of the membrane fusion pore predicted by coarse-grained (MARTINI) and continuum mechanics models. The results at these distinct levels of resolution give surprisingly consistent descriptions for the shape of the fusion pore, and the deviation between the continuum and coarse-grained models becomes notable only when the radius of curvature approaches the thickness of a monolayer. Although slow relaxation beyond microseconds is observed in different perturbative simulations, the key structural features (e.g., dimension and shape of the fusion pore near the pore center) are consistent among independent simulations. These observations provide solid support for the use of coarse-grained and continuum models in the analysis of membrane remodeling. The combined coarse-grained and continuum analysis confirms the recent prediction of continuum models that the fusion pore is a metastable structure and that its optimal shape is neither toroidal nor catenoidal. Moreover, our results help reveal a new, to our knowledge, bowing feature in which the bilayers close to the pore axis separate more from one another than those at greater distances from the pore axis; bowing helps reduce the curvature and therefore stabilizes the fusion pore structure. The spread of the bilayer deformations over distances of hundreds of nanometers and the substantial reduction in energy of fusion pore formation provided by this spread indicate that membrane fusion can be enhanced by allowing a larger area of membrane to participate and be deformed. PMID:23442963

Porosity change after gypsum crust formation on macro-porous limestones

NASA Astrophysics Data System (ADS)

Dewanckele, Jan; Cnudde, Veerle; de Kock, Tim; Boone, Marijn; Boone, Matthieu; van Hoorebeke, Luc; Jacobs, Patric

2010-05-01

The deterioration of stone is a complex process in which physical, biological and chemical mechanisms are involved. In this research, pore structure changes inside two types of porous limestone were analyzed before, during and after strong acid tests with SO2. Sulphatation and crust formation phenomena on natural building stones exposed to a polluted environment, are largely described in literature. As far as rocks rich in calcium carbonate are concerned, the main processes involved are the dissolution of the calcium carbonate and the formation of gypsum (CaSO4.2H2O) in presence of an acid atmosphere. The low mobility of this newly formed salt favours its accumulation in porous materials and at the surface of less porous media. The main actor in the process of gypsum crystallization on limestone is the aggressive sulphur dioxide gas (SO2). In this study, the Savonnières and Euville limestone were subjected to tests with a strong acid. According to the standard EN 13919:2002E, samples were put in acid environment for 21 days. At the bottom of the container a mixture of 500 ± 10 ml H2SO3 and 150 ± 10 ml de-mineralized H2O was added. No airborne particles or oxides of nitrogen (NOx) were added. Before exposure, after 6 days in the polluted environment and at the end of the test, the two samples were scanned with X-ray computed tomography (X-ray CT) at the Centre for X-ray Tomography at Ghent University, Belgium (UGCT; www.ugct.ugent.be). This visualization technique allows 2D and 3D reconstructions on a micrometer scale of the internal structure of an object without damaging the material. It thus enables to scan the same sample in a sequential way. In order to obtain information about the sample's interior of which the characteristics can be compared before, during and after the test, the same scanning parameters (exposure time, amount of frames, energy, etc.) were used. In addition, the same adjustments like beam hardening correction, normalizing, ring and spot filter, etc. were applied for the reconstruction. Total porosity, open and closed porosity and radial porosity were calculated for each sample by using the in-house developed software program Morpho+. The analysis of the various scans revealed that the Euville limestone developed a distinct gypsum crust, behind which a secondary porous layer of 100 μm thickness had developed. Inside the sample the porosity decreased by infilling of the large pore spaces with gypsum. However, after 6 days exposure the total porosity of the sample increased from 5.70% to 8.45%. In this case, the formation of secondary porosity behind the newly formed exterior gypsum layer prevailed upon the crystallizing of gypsum inside the pores located in the sample's interior. Also, the firstly formed gypsum crystals prevented the further interaction of the sulphuric acid with the stone material. After 21 days, the total porosity of the sample still reached 8.45%. The results of the radial porosity measurements were also the same after 6 and 21 days, indicating that the secondary porosity and the filling of pores inside the samples were stabilized. On the other hand, the gypsum crust on the Savonnières limestone was less visible. No secondary formed porous layer was measured and the total porosity decreased from 12.10% to 10.94% after 6 days and further to 10.31% at the end of the test. The decrease of porosity was still measurable at a depth of 500 μm inside the sample. The combination of micro-CT, image analysis and induced weathering tests are a promising combination of tools and techniques that allow for a better understanding of gypsum crust formation and pore structure change just behind the crust and deeper inside the rock sample.

Effect of Dihedral Angle and Porosity on Percolating-Sealing Capacity of Texturally Equilibrated Rock Salt

NASA Astrophysics Data System (ADS)

Ghanbarzadeh, S.; Hesse, M. A.; Prodanovic, M.; Gardner, J. E.

2013-12-01

Salt deposits in sedimentary basins have long been considered to be a seal against fluid penetration. However, experimental, theoretical and field evidence suggests brine (and oil) can wet salt crystal surfaces at higher pressures and temperatures, which can form a percolating network. This network may act as flow conduits even at low porosities. The aim of this work is to investigate the effects of dihedral angle and porosity on the formation of percolating paths in different salt network lattices. However, previous studies considered only simple homogeneous and isotropic geometries. This work extends the analysis to realistic salt textures by presenting a novel numerical method to describe the texturally equilibrated pore shapes in polycrystalline rock salt and brine systems. First, a theoretical interfacial topology was formulated to minimize the interfacial surface between brine and salt. Then, the resulting nonlinear system of ordinary differential equations was solved using the Newton-Raphson method. Results show that the formation of connected fluid channels is more probable in lower dihedral angles and at higher porosities. The connectivity of the pore network is hysteretic, because the connection and disconnection at the pore throats for processes with increasing or decreasing porosities occur at different porosities. In porous media with anisotropic solids, pores initially connect in the direction of the shorter crystal axis and only at much higher porosities in the other directions. Consequently, even an infinitesimal elongation of the crystal shape can give rise to very strong anisotropy in permeability of the pore network. Also, fluid flow was simulated in the resulting pore network to calculate permeability, capillary entry pressure and velocity field. This work enabled us to investigate the opening of pore space and sealing capacity of rock salts. The obtained pore geometries determine a wide range of petrophysical properties such as permeability and capillary entry pressure. This expanded knowledge of the salt textural behavior vs. depth could also improve drilling operations in salt. Second, a series of experiments in different P-T conditions was carried out to investigate the actual shape of equilibrated channels in salt. The synthetic salt samples were scanned at the High Resolution X-ray CT Facility at the Department of Geological Science, the University of Texas at Austin with resolution in 1-6 micron range. The experimental results show both equilibrated (tubular pores) and non-equilibrated (planar features) in salt structure. Image processing was carried out by two open source software programs: ImageJ, which is a public domain Java image processing program, and 3DMA-Rock, which is a software package for quantitative analyzing of the pore space in three-dimensional X-ray computed microtomographic images of rock. We obtain medial axis and medial surface of the pore space, as well as find and characterize the corresponding pore-throat network. We also report permeability of the pore space computed using Palabos software.

Energy Dissipation in Calico Hills Tuff due to Pore Collapse

NASA Astrophysics Data System (ADS)

Lockner, D. A.; Morrow, C. A.

2008-12-01

Laboratory tests indicate that the weakest portions of the Calico Hills tuff formation are at or near yield stress under in situ conditions and that the energy expended during incremental loading can be more than 90 percent irrecoverable. The Calico Hills tuff underlies the Yucca Mountain waste repository site at a depth of 400 to 500 m within the unsaturated zone. The formation is highly variable in the degree of both vitrification and zeolitization. Since 1980, a number of boreholes penetrated this formation to provide site characterization for the YM repository. In the past, standard strength measurements were conducted on core samples from the drillholes. However, a significant sampling bias occurred in that tests were preferentially conducted on highly vitrified, higher-strength samples. In fact, the most recent holes were drilled with a dry coring technique that would pulverize the weakest layers, leaving none of this material for testing. We have re-examined Calico Hills samples preserved at the YM Core Facility and selected the least vitrified examples (some cores exceeded 50 percent porosity) for mechanical testing. Three basic tests were performed: (i) hydrostatic crushing tests (to 350 MPa), (ii) standard triaxial deformation tests at constant effective confining pressure (to 70 MPa), and (iii) plane strain tests with initial conditions similar to in situ stresses. In all cases, constant pore pressure of 10 MPa was maintained using argon gas as a pore fluid and pore volume loss was monitored during deformation. The strongest samples typically failed along discrete fractures in agreement with standard Mohr-Coulomb failure. The weaker, high porosity samples, however, would fail by pure pore collapse or by a combined shear-induced compaction mechanism similar to failure mechanisms described for porous sandstones and carbonates. In the plane-strain experiments, energy dissipation due to pore collapse was determined for eventual input into dynamic wave calculations. These calculations will simulate ground accelerations at the YM repository due to propagation of high-amplitude compressional waves generated by scenario earthquakes. As an example, in one typical test on a sample with 43 percent starting porosity, an axial stress increase of 25 MPa resulted from 6 percent shortening and energy dissipation (due to grain crushing and pore collapse) of approximately 1.5x106 J/m3. Under proper conditions, this dissipation mechanism could represent a significant absorption of radiated seismic energy and the possible shielding of the repository from extreme ground shaking.

Evaluation of accessible mineral surface areas for improved prediction of mineral reaction rates in porous media

NASA Astrophysics Data System (ADS)

Beckingham, Lauren E.; Steefel, Carl I.; Swift, Alexander M.; Voltolini, Marco; Yang, Li; Anovitz, Lawrence M.; Sheets, Julia M.; Cole, David R.; Kneafsey, Timothy J.; Mitnick, Elizabeth H.; Zhang, Shuo; Landrot, Gautier; Ajo-Franklin, Jonathan B.; DePaolo, Donald J.; Mito, Saeko; Xue, Ziqiu

2017-05-01

The rates of mineral dissolution reactions in porous media are difficult to predict, in part because of a lack of understanding of mineral reactive surface area in natural porous media. Common estimates of mineral reactive surface area used in reactive transport models for porous media are typically ad hoc and often based on average grain size, increased to account for surface roughness or decreased by several orders of magnitude to account for reduced surface reactivity of field as opposed to laboratory samples. In this study, accessible mineral surface areas are determined for a sample from the reservoir formation at the Nagaoka pilot CO2 injection site (Japan) using a multi-scale image analysis based on synchrotron X-ray microCT, SEM QEMSCAN, XRD, SANS, and FIB-SEM. This analysis not only accounts for accessibility of mineral surfaces to macro-pores, but also accessibility through connected micro-pores in smectite, the most abundant clay mineral in this sample. While the imaging analysis reveals that most of the micro- and macro-pores are well connected, some pore regions are unconnected and thus inaccessible to fluid flow and diffusion. To evaluate whether mineral accessible surface area accurately reflects reactive surface area a flow-through core experiment is performed and modeled at the continuum scale. The core experiment is performed under conditions replicating the pilot site and the evolution of effluent solutes in the aqueous phase is tracked. Various reactive surface area models are evaluated for their ability to capture the observed effluent chemistry, beginning with parameter values determined as a best fit to a disaggregated sediment experiment (Beckingham et al., 2016) described previously. Simulations that assume that all mineral surfaces are accessible (as in the disaggregated sediment experiment) over-predict the observed mineral reaction rates, suggesting that a reduction of RSA by a factor of 10-20 is required to match the core flood experimental data. While the fit of the effluent chemistry (and inferred mineral dissolution rates) greatly improve when the pore-accessible mineral surface areas are used, it was also necessary to include highly reactive glass phases to match the experimental observations, in agreement with conclusions from the disaggregated sediment experiment. It is hypothesized here that the 10-20 reduction in reactive surface areas based on the limited pore accessibility of reactive phases in core flood experiment may be reasonable for poorly sorted and cemented sediments like those at the Nagaoka site, although this reflects pore rather than larger scale heterogeneity.

Formation factor in Bentheimer and Fontainebleau sandstones: Theory compared with pore-scale numerical simulations

NASA Astrophysics Data System (ADS)

Ghanbarian, Behzad; Berg, Carl F.

2017-09-01

Accurate quantification of formation resistivity factor F (also called formation factor) provides useful insight into connectivity and pore space topology in fully saturated porous media. In particular the formation factor has been extensively used to estimate permeability in reservoir rocks. One of the widely applied models to estimate F is Archie's law (F = ϕ- m in which ϕ is total porosity and m is cementation exponent) that is known to be valid in rocks with negligible clay content, such as clean sandstones. In this study we compare formation factors determined by percolation and effective-medium theories as well as Archie's law with numerical simulations of electrical resistivity on digital rock models. These digital models represent Bentheimer and Fontainebleau sandstones and are derived either by reconstruction or directly from micro-tomographic images. Results show that the universal quadratic power law from percolation theory accurately estimates the calculated formation factor values in network models over the entire range of porosity. However, it crosses over to the linear scaling from the effective-medium approximation at the porosity of 0.75 in grid models. We also show that the effect of critical porosity, disregarded in Archie's law, is nontrivial, and the Archie model inaccurately estimates the formation factor in low-porosity homogeneous sandstones.

Strength and acoustic properties of Ottawa sand containing laboratory-formed methane gas hydrate

USGS Publications Warehouse

Winters, William J.; Waite, William F.; Mason, David H.

2004-01-01

Although gas hydrate occurs in a wide variety of sediment types and is present and even pervasive at some locations on continental margins, little is known about how it forms naturally. Physical properties of the resultant gas hydrate-sediment mixtures, data needed for input into models that predict location and quantity of in situ hydrate are also lacking. Not only do properties of the host materials influence the type and quantity of hydrate formed and whether a particular deposit may be an economic resource or a geohazard, the properties of the natural sediment are also subsequently changed by the formation of gas hydrate in the pore space. The magnitude of the change is primarily related to the amount and the weighted inter-particle distribution of the hydrate deposits in relation to the actual sediment grains. Our goal is to understand the interaction between natural sediments and gas hydrate formation in order to quantify physical properties that are useful to predictive models.

Cytotoxic Helix-Rich Oligomer Formation by Melittin and Pancreatic Polypeptide

PubMed Central

Singh, Pradeep K.; Ghosh, Dhiman; Tewari, Debanjan; Mohite, Ganesh M.; Carvalho, Edmund; Jha, Narendra Nath; Jacob, Reeba S.; Sahay, Shruti; Banerjee, Rinti; Bera, Amal K.; Maji, Samir K.

2015-01-01

Conversion of amyloid fibrils by many peptides/proteins involves cytotoxic helix-rich oligomers. However, their toxicity and biophysical studies remain largely unknown due to their highly dynamic nature. To address this, we chose two helical peptides (melittin, Mel and pancreatic polypeptide, PP) and studied their aggregation and toxicity. Mel converted its random coil structure to oligomeric helical structure upon binding to heparin; however, PP remained as helix after oligomerization. Interestingly, similar to Parkinson’s associated α-synuclein (AS) oligomers, Mel and PP also showed tinctorial properties, higher hydrophobic surface exposure, cellular toxicity and membrane pore formation after oligomerization in the presence of heparin. We suggest that helix-rich oligomers with exposed hydrophobic surface are highly cytotoxic to cells irrespective of their disease association. Moreover as Mel and PP (in the presence of heparin) instantly self-assemble into stable helix-rich amyloidogenic oligomers; they could be represented as models for understanding the biophysical and cytotoxic properties of helix-rich intermediates in detail. PMID:25803428

Modern and late Holocene dolomite formation: Manito Lake, Saskatchewan, Canada

NASA Astrophysics Data System (ADS)

Last, Fawn M.; Last, William M.; Halden, Norman M.

2012-12-01

Major advances have occurred in our understanding of modern dolomite formation and penecontemporaneous dolomitization over the past several decades. Manito Lake, located in west-central Saskatchewan, Canada, is a large (65 km2), deep (zmax: 22 m) perennial saline (~ 45 ppt TDS) lake in which modern and late Holocene dolomite coexists with other endogenic and authigenic carbonate precipitates, including aragonite, monohydrocalcite, calcite, and Mg-calcite. Like many other lacustrine dolomites, Manito Lake dolomite is microcrystalline (less than 1 μm to 5 μm), Ca-rich and poor to moderately ordered. It occurs as relatively pure hardgrounds and as a component of nearshore microbialites. It also forms isopachous cements in consolidated siliciclastic shoreline sediments. Manito Lake dolomite is most likely forming by mainly biomediated precipitation at or near the sediment-water interface (i) in pore spaces of coarse siliciclastic sediments (i.e., beachrock), (ii) as fine laminae associated with microbialites, and (iii) as a major component of mudstone hardgrounds and pavements.

Numerical models of pore pressure and stress changes along basement faults due to wastewater injection: Applications to the 2014 Milan, Kansas Earthquake

USGS Publications Warehouse

Hearn, Elizabeth H.; Koltermann, Christine; Rubinstein, Justin R.

2018-01-01

We have developed groundwater flow models to explore the possible relationship between wastewater injection and the 12 November 2014 Mw 4.8 Milan, Kansas earthquake. We calculate pore pressure increases in the uppermost crust using a suite of models in which hydraulic properties of the Arbuckle Formation and the Milan earthquake fault zone, the Milan earthquake hypocenter depth, and fault zone geometry are varied. Given pre‐earthquake injection volumes and reasonable hydrogeologic properties, significantly increasing pore pressure at the Milan hypocenter requires that most flow occur through a conductive channel (i.e., the lower Arbuckle and the fault zone) rather than a conductive 3‐D volume. For a range of reasonable lower Arbuckle and fault zone hydraulic parameters, the modeled pore pressure increase at the Milan hypocenter exceeds a minimum triggering threshold of 0.01 MPa at the time of the earthquake. Critical factors include injection into the base of the Arbuckle Formation and proximity of the injection point to a narrow fault damage zone or conductive fracture in the pre‐Cambrian basement with a hydraulic diffusivity of about 3–30 m2/s. The maximum pore pressure increase we obtain at the Milan hypocenter before the earthquake is 0.06 MPa. This suggests that the Milan earthquake occurred on a fault segment that was critically stressed prior to significant wastewater injection in the area. Given continued wastewater injection into the upper Arbuckle in the Milan region, assessment of the middle Arbuckle as a hydraulic barrier remains an important research priority.

Effect of membrane characteristics on the performance of membrane bioreactors for oily wastewater treatment.

PubMed

Mafirad, S; Mehrnia, M R; Sarrafzadeh, M H

2011-01-01

Influence of membrane material and pore size on the performance of a submerged membrane bioreactor (sMBR) for oily wastewater treatment was investigated. The sMBR had a working volume of about 19 L with flat sheet modules at the same hydrodynamic conditions. Five types of micro- and ultra-polymeric membranes containing cellulose acetate (CA), cellulose nitrate (CN), polyamide (PA), polyvinylidene difluoride (PVDF) and polyethersulfone (PES) were used and their filtration performance in terms of permeability, permeate quality and fouling intensity were evaluated. Characterization of the membranes was done by performing some analysis such as pore size distribution; contact angle and scanning electronic microscopy (SEM) microphotograph on all membranes. The quality of permeates from each membrane was identified by measuring chemical oxygen demand (COD). The results showed more irreversible fouling intensity for membranes with larger pore size which can be due to more permeation of bioparticles and colloids inside the pores. Membrane characteristics have a major role in the preliminary time of the filtration before cake layer formation so that the PA with the highest hydrophilicity had the lowest permeability decline by fouling in this period. Also, the PVDF and PES membranes had better performance according to better permeate quality in the preliminary time of the filtration related to smaller pore size and also their better fouling resistance and chemical stability properties. However, all membranes resulted in the same permeability and permeate quality after cake layer formation. An overall efficiency of about 95% in COD removal was obtained for oily wastewater treatment by the membranes used in this study.

Topological Transitions in Mitochondrial Membranes controlled by Apoptotic Proteins

NASA Astrophysics Data System (ADS)

Hwee Lai, Ghee; Sanders, Lori K.; Mishra, Abhijit; Schmidt, Nathan W.; Wong, Gerard C. L.; Ivashyna, Olena; Schlesinger, Paul H.

2010-03-01

The Bcl-2 family comprises pro-apoptotic proteins, capable of permeabilizing the mitochondrial membrane, and anti-apoptotic members interacting in an antagonistic fashion to regulate programmed cell death (apoptosis). They offer potential therapeutic targets to re-engage cellular suicide in tumor cells but the extensive network of implicated protein-protein interactions has impeded full understanding of the decision pathway. We show, using synchrotron x-ray diffraction, that pro-apoptotic proteins interact with mitochondrial-like model membranes to generate saddle-splay (negative Gaussian) curvature topologically required for pore formation, while anti-apoptotic proteins can deactivate curvature generation by molecules drastically different from Bcl-2 family members and offer evidence for membrane-curvature mediated interactions general enough to affect very disparate systems.

Pore opening dynamics in the exocytosis of serotonin

NASA Astrophysics Data System (ADS)

Ramirez-Santiago, Guillermo; Cercos, Montserrat G.; Martinez-Valencia, Alejandro; Salinas Hernandez, Israel; Rodríguez-Sosa, Leonardo; de-Miguel, Francisco F.

2015-03-01

The current view of the exocytosis of transmitter molecules is that it starts with the formation of a fusion pore that connects the intravesicular and the extracellular spaces, and is completed by the release of the rest of the transmitter contained in the vesicle upon the full fusion and collapse of the vesicle with the plasma membrane. However, under certain circumstances, a rapid closure of the pore before the full vesicle fusion produces only a partial release of the transmitter. Here we show that whole release of the transmitter occurs through fusion pores that remain opened for tens of milliseconds without vesicle collapse. This was demonstrated through amperometric measurements of serotonin release from electrodense vesicles in the axon of leech Retzius neurons and mathematical modelling. By modeling transmitter release with a diffusion equation subjected to boundary conditions that are defined by the experiment, we showed that those pores with a fast half rise time constant remained opened and allowed the full quantum release without vesicle collapse, whereas pores with a slow rise time constant closed rapidly, thus producing partial release. We conclude that a full transmitter release may occur through the fusion pore in the absence of vesicle collapse. This work was founded by a DGAPA-UNAM grants IN200914 and IN118410 CONACYT GRANT 130031, and CONACyT doctoral fellowships.

Experimental Investigation on Pore Structure Characterization of Concrete Exposed to Water and Chlorides

PubMed Central

Liu, Jun; Tang, Kaifeng; Qiu, Qiwen; Pan, Dong; Lei, Zongru; Xing, Feng

2014-01-01

In this paper, the pore structure characterization of concrete exposed to deionised water and 5% NaCl solution was evaluated using mercury intrusion porosity (MIP), scanning electron microscopy (SEM) and X-ray diffraction (XRD). The effects of calcium leaching, fly ash incorporation, and chloride ions on the evolution of pore structure characteristics were investigated. The results demonstrate that: (i) in ordinary concrete without any fly ash, the leaching effect of the cement products is more evident than the cement hydration effect. From the experimental data, Ca(OH)2 is leached considerably with the increase in immersion time. The pore structure of concrete can also be affected by the formation of an oriented structure of water in concrete materials; (ii) incorporation of fly ash makes a difference for the performance of concrete submersed in solutions as the total porosity and the pore connectivity can be lower. Especially when the dosage of fly ash is up to 30%, the pores with the diameter of larger than 100 nm show significant decrease. It demonstrates that the pore properties are improved by fly ash, which enhances the resistance against the calcium leaching; (iii) chlorides have a significant impact on microstructure of concrete materials because of the chemical interactions between the chlorides and cement hydrates. PMID:28788204