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Sample records for air-filled pore space

  1. The pore space scramble

    NASA Astrophysics Data System (ADS)

    Gormally, Alexandra; Bentham, Michelle; Vermeylen, Saskia; Markusson, Nils

    2015-04-01

    Climate change and energy security continue to be the context of the transition to a secure, affordable and low carbon energy future, both in the UK and beyond. This is reflected in for example, binding climate policy targets at the EU level, the introduction of renewable energy targets, and has also led to an increasing interest in Carbon Capture and Storage (CCS) technology with its potential to help mitigate against the effects of CO2 emissions from fossil fuel burning. The UK has proposed a three phase strategy to integrate CCS into its energy system in the long term focussing on off-shore subsurface storage (DECC, 2014). The potential of CCS therefore, raises a number of challenging questions and issues surrounding the long-term storage of CO2 captured and injected into underground spaces and, alongside other novel uses of the subsurface, contributes to opening a new field for discussion on the governance of the subsurface. Such 'novel' uses of the subsurface have lead to it becoming an increasingly contested space in terms of its governance, with issues emerging around the role of ownership, liability and property rights of subsurface pore space. For instance, questions over the legal ownership of pore space have arisen with ambiguity over the legal standpoint of the surface owner and those wanting to utilise the pore space for gas storage, and suggestions of whether there are depths at which legal 'ownership' becomes obsolete (Barton, 2014). Here we propose to discuss this 'pore space scramble' and provide examples of the competing trajectories of different stakeholders, particularly in the off-shore context given its priority in the UK. We also propose to highlight the current ambiguity around property law of pore space in the UK with reference to approaches currently taken in different national contexts. Ultimately we delineate contrasting models of governance to illustrate the choices we face and consider the ethics of these models for the common good

  2. Resolving pore-space characteristics by rate-controlled porosimetry

    SciTech Connect

    Yuan, H.H.; Swanson, B.F.

    1989-03-01

    By monitoring the mercury capillary pressure in rate-controlled porosimetry (intrusion) experiments, new information regarding the pore space of a rock sample has been obtained. With this technique, called an apparatus for pore examination (APEX), it is now possible to resolve the pore space of a rock sample into two interconnected parts. One part identifies the individual pore systems (pore bodies), which are low-energy sumps or regions of low capillarity. The other part corresponds to the pore throats that interconnect with pore systems. New capillary-pressure curves have been obtained by partitioning the total capillary-pressure curve (normal capillary-pressure curve) into two subcurves: the subison capillary-pressure curve, which details the distribution of pore bodies, and the rison capillary-pressure curve, which details the distribution of pore throats. The authors present APEX data on Berea sandstone and San Andres dolomite that show the volume distribution of low-capillarity regions within the pore space of these rocks. These regions of low capillarity are the principal pore-space regions that trap the residual nonwetting phase upon imbibition of a strongly wetting fluid, as measured by toluene/air systems. The residual nonwetting-phase saturations as determined by the APEX method and by the toluene/air method are in excellent agreement. Thus, the detailed volume distribution of pore systems responsible for trapped nonwetting-phase saturation is determined from APEX measurements, which can have important implications for EOR.

  3. X-ray microtomography application in pore space reservoir rock.

    PubMed

    Oliveira, M F S; Lima, I; Borghi, L; Lopes, R T

    2012-07-01

    Characterization of porosity in carbonate rocks is important in the oil and gas industry since a major hydrocarbons field is formed by this lithology and they have a complex media porous. In this context, this research presents a study of the pore space in limestones rocks by x-ray microtomography. Total porosity, type of porosity and pore size distribution were evaluated from 3D high resolution images. Results show that carbonate rocks has a complex pore space system with different pores types at the same facies.

  4. The Dimension of the Pore Space in Sponges

    ERIC Educational Resources Information Center

    Silva, L. H. F.; Yamashita, M. T.

    2009-01-01

    A simple experiment to reveal the dimension of the pore space in sponges is proposed. This experiment is suitable for the first year of a physics or engineering course. The calculated dimension of the void space in a sponge of density 16 mg cm[superscript -3] was 2.948 [plus or minus] 0.008. (Contains 2 figures.)

  5. Carbon turnover in pore spaces - CIPS model approach

    NASA Astrophysics Data System (ADS)

    Kuka, Katrin

    2010-05-01

    The CIPS (Carbon turnover In Pore Spaces) model has been developed to overcome the constraints of conceptual pools and to get a better insight into the nature of carbon stabilization in soil (KUKA, 2007). This pure carbon turnover model was implemented in CANDY (CArbon and Nitrogen Dynamics) model system (Franko, 1995). The CIPS model did overcome the empirical pools taking into account soil structure effects. It is based on quality driven primary stabilisation mechanism (recalcitrance of SOM) and process driven secondary stabilisation mechanism (place of turnover) of SOM in soil. In addition to the division of SOM in the qualitative pools on the basis of chemical measurability, a dependence of the turnover conditions from the location of SOM in pore space is implemented taking into account different turnover conditions in the particular pore space and the accessibility for microbial biomass. The main assumption of the CIPS model is that the biological activity is not evenly distributed through the whole pore space. The pore space classes - micro, meso and macro pores - used in the model are marked by wilting point, field capacity and pore volume as a first approach. Because of the poor aeration in the micro pores they show very low biological activity leading to a strong protection of the carbon localized in this pore space. The biological active time (BAT) concept of the CANDY model was adapted to the CIPS model in order to calculate the distribution of biological activity for each pore space class. The reduction functions of the turnover active time concept of CANDY model, related to soil temperature, soil moisture, soil texture, relative air volume and distance to the soil surface are multiplied by the step width of calendar time producing the transformed time step as total BAT (BATtot). The calculated BATtot corresponds to the time that would be required under optimal conditions in the laboratory to perform the same turnover result as under the given

  6. Source Rock (shales) Pore Space Transformation during Hydrocarbon Generation

    NASA Astrophysics Data System (ADS)

    Giliazetdinova, D. R.; Korost, D. V.; Sudin, V. V.

    2015-12-01

    The main objective of this investigations is to study the factors controlling changes in rock structure during catagenetic transformation of organic matter. Hydrocarbon generation and primary migration can be controlled by numerous parameters; the most important are temperature, pressure, hydrocarbon composition, and organic matter type and content. Several experimental studies focused on the influence of these main parameters. However few dedicated works investigated how the primary structure characteristic and organic matter content affects the pore space transformation of rocks. For this purpose we simulated the primary migration processes in laboratory conditions (pyrolises and CT scanning) in order to observe the dynamics of pore space transformation. Our experiments demonstrate that after each stage of heating the rocks change their original morphology with the formation of new pores and conduits connecting the primary voids. The samples with relatively low content in organic matter revealed fewer changes in pore space morphology, in contrast to rocks rich in organic content. Our results also highlight that the newly formed pore structures are directly related with the original structure of the unaltered rocks and the primary connectivity of the organics. Most of the structural changes were observed during the sequential heating between 260 - 430 ° C; within this interval also occur the most intense reactions for hydrocarbons formation.

  7. 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

  8. Scaffold pore space modulation through intelligent design of dissolvable microparticles.

    PubMed

    Liebschner, Michael A K; Wettergreen, Matthew

    2012-01-01

    The goal of this area of research is to manipulate the pore space of scaffolds through the application of an intelligent design concept on dissolvable microparticles. To accomplish this goal, we developed an efficient and repeatable process for fabrication of microparticles from multiple materials using a combination of rapid prototyping (RP) and soft lithography. Phase changed 3D printing was used to create masters for PDMS molds. A photocrosslinkable polymer was then delivered into these molds to make geometrically complex 3D microparticles. This repeatable process has demonstrated to generate the objects with greater than 95% repeatability with complete pattern transfer. This process was illustrated for three different shapes of various complexities. The shapes were based on the extrusion of 2D shapes. This may allow simplification of the fabrication process in the future combined with a direct transfer of the findings. Altering the shapes of particles used for porous scaffold fabrication will allow for tailoring of the pore shapes, and therefore their biological function within a porous tissue engineering scaffold. Through permeation experiments, we have shown that the pore geometry may alter the permeability coefficient of scaffolds while influencing mechanical properties to a lesser extent. By selecting different porogen shapes, the nutrition transport and scaffold degradation can be significantly influenced with minimal effect on the mechanical integrity of the construct. In addition, the different shapes may allow a control of drug release by modifying their surface-to-volume ratio, which could modulate drug delivery over time. While soft lithography is currently used with photolithography, its high precision is offset by high cost of production. The employment of RP to a specific resolution offers a much less expensive alternative with increased throughput due to the speed of current RP systems.

  9. Chemomechanical evolution of pore space in carbonate microstructures upon dissolution: Linking pore geometry to bulk elasticity

    NASA Astrophysics Data System (ADS)

    Arson, C.; Vanorio, T.

    2015-10-01

    One of the challenges faced today in a variety of geophysical applications is the need to understand the changes of elastic properties due to time-variant chemomechanical processes. The objective of this work is to model carbonate rock elastic properties as functions of pore geometry changes that occur when the solid matrix is dissolved by carbon dioxide. We compared two carbonate microstructures: porous micrite ("mudstone") and grain-supported carbonate ("packstone"). We formulated a mathematical model that distinguishes the effects of microporosity and macroporosity on stiffness changes. We used measures of mechanical and chemical porosity changes recorded during injection tests to compute elastic moduli and compare them to moduli obtained from wave velocity measurements. In mudstones, both experimental and numerical results indicate that bulk moduli change by less than 5%. The evolution of elastic moduli is controlled by macropore enlargement. In packstones, model predictions underestimate changes of elastic moduli with total porosity by 10% to 80%. The total porosity variation is 60% to 75% smaller than the chemical porosity variation, which indicates that pore expansion due to dissolution is counterbalanced by pore shrinkage due to compaction. Packstone elastic properties are controlled by grain sliding. The methodology presented in this paper can be generalized to other chemomechanical processes studied in rocks, such as dislocations, glide, diffusive mass transfer, recrystallization, and precipitation.

  10. Modeling the Coupled Effects of Pore Space Geometry and Velocity on Colloid Transport and Retention

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent experimental and theoretical work has demonstrated that pore space geometry and hydrodynamics can play an important role in colloid retention under unfavorable attachment conditions. Computer models that only consider the average pore-water velocity and a single attachment rate coefficient a...

  11. Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

    PubMed Central

    Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; Marsh, Terence L.; Hildebrandt, Britton; Rivers, Mark L.

    2015-01-01

    Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C

  12. Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

    PubMed

    Negassa, Wakene C; Guber, Andrey K; Kravchenko, Alexandra N; Marsh, Terence L; Hildebrandt, Britton; Rivers, Mark L

    2015-01-01

    Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1) soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1) soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C

  13. Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

    SciTech Connect

    Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; Marsh, Terence L.; Hildebrandt, Britton; Rivers, Mark L.

    2015-07-01

    Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of

  14. Curvature effects on axisymmetric instability of conduction regime in a tall air-filled annulus

    NASA Astrophysics Data System (ADS)

    Pécheux, J.; Le Quéré, P.; Abcha, F.

    1994-10-01

    This paper numerically studies curvature effects on the instability of the conduction regime of natural convection in a tall air-filled differentially heated annulus of vertical aspect ratio 16 by integrating the two-dimensional axisymmetric Navier-Stokes equations in the Boussinesq approximation. The numerical algorithm combines a pseudospectral Chebyshev space discretization with a second-order time-stepping scheme. It is shown that, in contrast with linear stability analysis of the conduction solution, the time-periodic cross-roll instability does not take place in finite aspect ratio cavities for small values of the radius ratio. For all values of the radius ratio transition to unsteadiness occurs through supercritical Hopf bifurcations. Extensive computations show very complex behaviors of the unsteady solutions depending on the radius ratio. The nature of the reverse transition to steady state that occurs for increasing value of the Rayleigh number is also found to depend strongly on the value of the radius ratio.

  15. Mode-based microparticle conveyor belt in air-filled hollow-core photonic crystal fiber.

    PubMed

    Schmidt, Oliver A; Euser, Tijmen G; Russell, Philip St J

    2013-12-02

    We show how microparticles can be moved over long distances and precisely positioned in a low-loss air-filled hollow-core photonic crystal fiber using a coherent superposition of two co-propagating spatial modes, balanced by a backward-propagating fundamental mode. This creates a series of trapping positions spaced by half the beat-length between the forward-propagating modes (typically a fraction of a millimeter). The system allows a trapped microparticle to be moved along the fiber by continuously tuning the relative phase between the two forward-propagating modes. This mode-based optical conveyor belt combines long-range transport of microparticles with a positional accuracy of 1 µm. The technique also has potential uses in waveguide-based optofluidic systems.

  16. Autonomous generation of a thermoacoustic solitary wave in an air-filled tube

    NASA Astrophysics Data System (ADS)

    Shimizu, Dai; Sugimoto, Nobumasa

    2016-10-01

    Experiments are performed to demonstrate the autonomous generation of an acoustic solitary wave in an air-filled, looped tube with an array of Helmholtz resonators. The solitary wave is generated spontaneously due to thermoacoustic instability by a pair of stacks installed in the tube and subject to a temperature gradient axially. No external drivers are used to create initial disturbances. Once the solitary wave is generated, it keeps on propagating to circulate along the loop endlessly. The stacks, which are made of ceramics and of many pores of square cross section, are placed in the tube diametrically on exactly the opposite side of the loop, and they are sandwiched by hot and cold (ambient) heat exchangers. When the temperature gradient along both stacks is appropriate, pulses of smooth profiles are generated and propagated in both directions of the tube. From good agreements of not only the pressure profile measured but also the propagation speed with the theory, the pulse is identified as the acoustic solitary wave, and it can be called thermoacoustic solitary wave or thermoacoustic soliton corresponding to the soliton solution of the K-dV equation in one limit.

  17. 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

  18. FIB-SEM Tomography Probes the Mesoscale Pore Space of an Individual Catalytic Cracking Particle

    PubMed Central

    2016-01-01

    The overall performance of a catalyst particle strongly depends on the ability of mass transport through its pore space. Characterizing the three-dimensional structure of the macro- and mesopore space of a catalyst particle and establishing a correlation with transport efficiency is an essential step toward designing highly effective catalyst particles. In this work, a generally applicable workflow is presented to characterize the transport efficiency of individual catalyst particles. The developed workflow involves a multiscale characterization approach making use of a focused ion beam-scanning electron microscope (FIB-SEM). SEM imaging is performed on cross sections of 10.000 μm2, visualizing a set of catalyst particles, while FIB-SEM tomography visualized the pore space of a large number of 8 μm3 cubes (subvolumes) of individual catalyst particles. Geometrical parameters (porosity, pore connectivity, and heterogeneity) of the material were used to generate large numbers of virtual 3D volumes resembling the sample’s pore space characteristics, while being suitable for computationally demanding transport simulations. The transport ability, defined as the ratio of unhindered flow over hindered flow, is then determined via transport simulations through the virtual volumes. The simulation results are used as input for an upscaling routine based on an analogy with electrical networks, taking into account the spatial heterogeneity of the pore space over greater length scales. This novel approach is demonstrated for two distinct types of industrially manufactured fluid catalytic cracking (FCC) particles with zeolite Y as the active cracking component. Differences in physicochemical and catalytic properties were found to relate to differences in heterogeneities in the spatial porosity distribution. In addition to the characterization of existing FCC particles, our method of correlating pore space with transport efficiency does also allow for an up-front evaluation of

  19. Pore space connectivity and porosity using CT scans of tropical soils

    NASA Astrophysics Data System (ADS)

    Previatello da Silva, Livia; de Jong Van Lier, Quirijn

    2015-04-01

    Microtomography has been used in soil physics for characterization and allows non-destructive analysis with high-resolution, yielding a three-dimensional representation of pore space and fluid distribution. It also allows quantitative characterization of pore space, including pore size distribution, shape, connectivity, porosity, tortuosity, orientation, preferential pathways and is also possible predict the saturated hydraulic conductivity using Darcy's equation and a modified Poiseuille's equation. Connectivity of pore space is an important topological property of soil. Together with porosity and pore-size distribution, it governs transport of water, solutes and gases. In order to quantify and analyze pore space (quantifying connectivity of pores and porosity) of four tropical soils from Brazil with different texture and land use, undisturbed samples were collected in São Paulo State, Brazil, with PVC ring with 7.5 cm in height and diameter of 7.5 cm, depth of 10 - 30 cm from soil surface. Image acquisition was performed with a CT system Nikon XT H 225, with technical specifications of dual reflection-transmission target system including a 225 kV, 225 W high performance Xray source equipped with a reflection target with pot size of 3 μm combined with a nano-focus transmission module with a spot size of 1 μm. The images were acquired at specific energy level for each soil type, according to soil texture, and external copper filters were used in order to allow the attenuation of low frequency X-ray photons and passage of one monoenergetic beam. This step was performed aiming minimize artifacts such as beam hardening that may occur during the attenuation in the material interface with different densities within the same sample. Images were processed and analyzed using ImageJ/Fiji software. Retention curve (tension table and the pressure chamber methods), saturated hydraulic conductivity (constant head permeameter), granulometry, soil density and particle density

  20. 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.

  1. Three-dimensional pore space quantification of apple tissue using X-ray computed microtomography.

    PubMed

    Mendoza, Fernando; Verboven, Pieter; Mebatsion, Hibru K; Kerckhofs, Greet; Wevers, Martine; Nicolaï, Bart

    2007-08-01

    The microstructure and the connectivity of the pore space are important variables for better understanding of the complex gas transport phenomena that occur in plant tissues. In this study, we present an experimental procedure for image acquisition and image processing to quantitatively characterize in 3D the pore space of apple tissues (Malus domestica Borkh.) for two cultivars (Jonagold and Braeburn) taken from the fleshy part of the cortex using X-ray computer microtomography. Preliminary sensitivity analyses were performed to determine the effect of the resolution and the volume size (REV, representative elementary volume analysis) on the computed porosity of apple samples. For comparison among cultivars, geometrical properties such as porosity, specific surface area, number of disconnected pore volumes and their distribution parameters were extracted and analyzed in triplicate based on the 3D skeletonization of the pore space (medial axis analysis). The results showed that microtomography provides a resolution at the micrometer level to quantitatively analyze and characterize the 3D topology of the pore space in apple tissue. The computed porosity was confirmed to be highly dependent of the resolution used, and the minimum REV of the cortical flesh of apple fruit was estimated to be 1.3 mm(3). Comparisons among the two cultivars using a resolution of 8.5 mum with a minimum REV cube showed that in spite of the complexity and variability of the pore space network observed in Jonagold and Braeburn apples, the extracted parameters from the medial axis were significantly different (P-value < 0.05). Medial axis parameters showed potential to differentiate the microstructure between the two evaluated apple cultivars.

  2. Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

    DOE PAGES

    Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; ...

    2015-07-01

    Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and

  3. Microtomographic analysis of pore space in a virgin soddy-podzolic soil

    NASA Astrophysics Data System (ADS)

    Skvortsova, E. B.; Rozhkov, V. A.; Abrosimov, K. N.; Romanenko, K. A.; Khokhlov, S. F.; Khaidapova, D. D.; Klyueva, V. V.; Yudina, A. V.

    2016-11-01

    The method of X-ray microtomography was applied to study pore space of a virgin soddy-podzolic soil at the natural soil water content. The morphometric parameters of the pores of more than 100 μm in diameter were determined in the vertically oriented undisturbed soil monoliths ( d = 3 cm, h = 3-4 cm) from the genetic horizons of the most differentiated part of the soil profile (the AY, AEL, EL, BEL, BT1, and BT2 horizons). A tendency for the horizontal orientation of these pores was found in all the horizons, except for the humus (AY) horizon. Isolated vesicular pores of different sizes were abundant in the eluvial part of the profile. Numerous recent and relict phytogenic channels were found in the intraped mass of the BT2 horizon. Differently directed interfaces of structural units in the soil horizons were visualized. Cluster analysis was applied to estimate differences between the genetic horizons with respect to their textures, aggregate sizes, and shapes of pores as seen in vertical two-dimensional X-ray images.

  4. Imaging pore space in tight gas sandstone reservoir: insights from broad ion beam cross-sectioning

    NASA Astrophysics Data System (ADS)

    Desbois, G.; Enzmann, F.; Urai, J. L.; Baerle, C.; Kukla, P. A.; Konstanty, J.

    2010-06-01

    Monetization of tight gas reservoirs, which contain significant gas reserves world-wide, represents a challenge for the entire oil and gas industry. The development of new technologies to enhance tight gas reservoir productivity is strongly dependent on an improved understanding of the rock properties and especially the pore framework. Numerous methods are now available to characterize sandstone cores. However, the pore space characterization at pore scale remains difficult due to the fine pore size and delicate sample preparation, and has thus been mostly indirectly inferred until now. Here we propose a new method of ultra high-resolution petrography combining high resolution SEM and argon ion beam cross sectioning (BIB, Broad Ion Beam) which prepares smooth and damage free surfaces. We demonstrate this method using the example of Permian (Rotliegend) age tight gas sandstone core samples. The combination of Ar-beam cross-sectioning facility and high-resolution SEM imaging has the potential to result in a step change in the understanding of pore geometries, in terms of its morphology, spatial distribution and evolution based on the generation of unprecedented image quality and resolution enhancing the predictive reliability of image analysis.

  5. Factors affecting the pore space transformation during hydrocarbon generation in source rock (shales): laboratory experiment

    NASA Astrophysics Data System (ADS)

    Giliazetdinova, D. R.; Korost, D. V.

    2014-12-01

    Oil and gas generation is a set of processes which taking place in the interior, the processes can't be observable in nature. In the process of dumping the source rock, organic matter is transformed into a complex of high-molecular compounds - precursors of oil and gas (kerogen). Entering of a source column for specific thermobaric conditions, triggers the formation of low molecular weight hydrocarbon compounds. Generation of sufficient quantities of hydrocarbons leads to the primary fluid migration within the source rock. For the experiment were selected mainly siliceous-carbonate composition rocks from Domanic horizon South-Tatar arch. The main aim of experiment was heating the rocks in the pyrolyzer to temperatures which correspond katagenes stages. For monitoring changes in the morphology of the pore space X-ray microtomography method was used. As a result, when was made a study of the composition of mineral and organic content of the rocks, as well as textural and structural features, have been identified that the majority of the rock samples within the selected collection are identical. However, characteristics such as organic content and texture of rocks are different. Thus, the experiment was divided into two parts: 1) the study of the influence of organic matter content on the morphology of the rock in the process of thermal effects; 2) study the effect of texture on the primary migration processes for the same values of organic matter. Also, an additional experiment was conducted to study the dynamics of changes in the structure of the pore space. At each stage of the experiment morphology of altered rocks characterized by the formation of new pores and channels connecting the 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. At the second stage of the research also revealed that the conversion of the pore

  6. Selectivity of CO2 via pore space partition in zeolitic boron imidazolate frameworks.

    PubMed

    Zhang, Hai-Xia; Liu, Min; Xu, Guilan; Liu, Liyang; Zhang, Jian

    2016-02-28

    Reported here is a versatile method capable of generating pore space partition in zeolitic boron imidazolate frameworks (BIFs), which is based on the coexistence of presynthesized boron imidazolate complexes and charge balancing carboxylate ligands. Using this method, boron imidazolate complexes are used to form zeolitic nets, while the carboxylate serves to partition large channel spaces into multiple domains. The generality of this method is shown by two distinct boron imidazolate frameworks mimicking GIS (BIF-41) and ABW (BIF-42) zeotype topologies. BIF-41 shows high selectivity sorption of CO2 over N2.

  7. Induced polarization dependence on pore space geometry: Empirical observations and mechanistic predictions

    NASA Astrophysics Data System (ADS)

    Weller, A.; Slater, L. D.

    2015-12-01

    We use an extensive database to compare empirical observations and previously proposed empirical models against recently developed mechanistic formulations for the induced polarization (IP) response in porous media as a function of pore space geometry and interfacial chemistry. These comparisons support the argument that the pore-volume normalized internal surface (Spor) is the most important geometric parameter influencing the polarization. The specific polarizability derived from the empirical relationship between imaginary conductivity σ″ and Spor is independent of the porosity. By contrast, equivalent specific polarizability terms in recently proposed mechanistic models are found to be significantly correlated with porosity, and thus do not appear to represent an interfacial chemistry factor independent of the pore space geometry. Furthermore, the database shows no evidence for a significant decrease in the counterion mobility of clayey materials relative to clay-free materials, as postulated in recent studies. On the contrary, a single value of cp is consistent with no significant differences in ionic mobility given that all samples were saturated with a NaCl solution close to a common salinity of about 100 mS/m.

  8. Estimating pore-space gas hydrate saturations from well log acoustic data

    USGS Publications Warehouse

    Lee, Myung W.; Waite, William F.

    2008-01-01

    Relating pore-space gas hydrate saturation to sonic velocity data is important for remotely estimating gas hydrate concentration in sediment. In the present study, sonic velocities of gas hydrate–bearing sands are modeled using a three-phase Biot-type theory in which sand, gas hydrate, and pore fluid form three homogeneous, interwoven frameworks. This theory is developed using well log compressional and shear wave velocity data from the Mallik 5L-38 permafrost gas hydrate research well in Canada and applied to well log data from hydrate-bearing sands in the Alaskan permafrost, Gulf of Mexico, and northern Cascadia margin. Velocity-based gas hydrate saturation estimates are in good agreement with Nuclear Magneto Resonance and resistivity log estimates over the complete range of observed gas hydrate saturations.

  9. Three-Dimensional pore space and strain localization distribution in Majella limestone.

    NASA Astrophysics Data System (ADS)

    Ji, Yuntao; Hall, Stephen; Baud, Patrick; Wond, Teng-fong

    2015-04-01

    Brittle-ductile transition in porous rock is a topic of importance in many geological applications. Traditionally pore space in rock is characterized using optical and scanning electron microscopes (SEM). Advances in 3-dimensional imaging techniques such as X-ray computed tomography (CT) and laser scanning confocal microscopy have furnished enhanced perspective on pore geometry complexity. In particular, X-ray CT has been used widely for characterizing porous clastic rocks such as sandstone, whose void space is dominated by relatively equant pores connected by throats that are sufficiently large for direct imaging by X-ray microCT. However, standard techniques for CT imaging are not directly applicable to a carbonate rock because of the geometric complexity of its pore space. In this study, we first characterized the pore structure in Majella limestone. MicroCT data was partitioned into three distinct domains: macropores, solid grains and an intermediate domain made up of voxels of solid embedded with micropores below the resolution. A morphological analysis of the microCT images shows that both the solid and intermediate domains in Majella limestone are interconnected as it has been previously reported in a less porous limestone. We however show that the macroporosity in Majella limestone is fundamentally different, in that it has a percolative backbone which may contribute to significant enhancement of its permeability. We then present the first application of 3D-volumetric Digital Image Correlation (DIC) to a very porous limestone. If images of a rock sample are acquired before and after deformation, then DIC can be used to infer the displacement and strain fields. In our study, four Majella limestone samples were triaxially compressed at confining pressures ranging from 5 MPa to 25 MPa and another under hydrostatic conditions up to 60 MPa. For each of these five samples, two CT images were acquired before and after the deformation. We then used the Tomo

  10. Pore-space alteration in source rock (shales) during hydrocarbons generation: X-ray microtomography and pore-scale modelling study

    NASA Astrophysics Data System (ADS)

    Korost, Dmitry; Gerke, Kirill; Akhmanov, Grigory; Vasilyev, Roman; Čapek, Pavel; Karsanina, Marina; Nadezhkin, Dmitry

    2013-04-01

    Hydrocarbons (HC) are generated from solid organic matter (kerogen) due to thermocatalytic reactions. The rate of such reactions shows direct correlation with temperature and depends on the depth of source rock burial. Burial of sedimentary rock is also inevitably accompanied by its structural alteration owing to compaction, dehydration and re-crystallization. Processes of HC generation, primary migration and structural changes are inaccessible for direct observation in nature, but they can be studied in laboratory experiments. Modern technical facilities of laboratories make it possible to carry out experiments on HC generation from the organic-rich rocks at a completely new level (Kobchenko et al., 2011). Some new technologies, including X-ray microtomography and pore-scale modeling, allow us to carry out a step-by-step description of such processes and their development, and to study their reflection in alterations of rock structure. Experiments were carried out with a clayey-carbonate rock sample of the Domanic Formaition taken at a depth of 1939 m from borehole drilled in the central part of the Melekes depression (West Tatar arch, Russia). The rock chosen fits the very essential requirements for studying HC generation under laboratory conditions - high organic matter content and its low metamorphic grade. Our work aimed such a study in an undisturbed rock sample by heating it in nitrogen atmosphere based on a specified temperature regime in a RockEval6 analyzer and monitoring alterations in the pore space structure. Observations were carried out with a SkyScan-1172 X-ray microtomography scanner (resulting scan resolution of 1 µm). A cylinder, 4 mm in diameter, was prepared from the rock sample for the pyrolitic and microtomographic analyses. Scanning procedures were carried out in 5 runs. Temperature interval for each run had to match the most important stage of HC generation in the source rock, namely: (1) original structure; (2) 100-300

  11. Hybrid plasmonic microcavity with an air-filled gap for sensing applications

    NASA Astrophysics Data System (ADS)

    Zhang, Meng; Liu, Binbin; Wu, Genzhu; Chen, Daru

    2016-12-01

    In this paper, a novel hybrid plasmonic microcavity with air-filled regions in the low-permittivity dielectric gap is proposed for sensing applications. Compared with the conventional structure with homogeneous gap, the introduced air-filled regions could improve the key modal characteristics of the hybrid mode. Simulation results reveal that this kind of hybrid microcavity maintains low loss with high quality factor ∼3062, and high field confinement with small mode volume 0.891 μm3. Moreover, in the sensing applications, this hybrid microcavity features simultaneously large refractive index sensitivity of 100 nm/RIU (refractive index unit) and relatively high quality factor of 3062. Hence, it shows that the hybrid plasmonic microcavity has potential applications in ultra-compact refractive index sensor.

  12. Response of air-filled ion chambers to high-intensity radiation pulses

    SciTech Connect

    Plum, M.; Brown, D.

    1993-06-01

    Ion chambers are one of the most popular types of detectors used for beam loss-monitor systems. To provide a foundation for the development of future loss-monitor systems, and to fully characterize the ion chambers in use at LAMPF, we have studied the response of air-filled cylindrical ion chambers to high-intensity, short-duration radiation pulses. The most intense pulses were about 180 rad in 250 ns (the equivalent steady-state dose rate was about 700 Mrad/h). We filled our chambers with nitrogen gas at 760 Torr and air at 600 Torr. The ion chambers were driven into extreme nonlinear response. We hope these data will be used to design loss-monitor systems based on air-filled ion chambers, thus eliminating the need for gas-flow systems and/or airtight ion chambers.

  13. Response of air-filled ion chambers to high-intensity radiation pulses

    SciTech Connect

    Plum, M.; Brown, D.

    1993-01-01

    Ion chambers are one of the most popular types of detectors used for beam loss-monitor systems. To provide a foundation for the development of future loss-monitor systems, and to fully characterize the ion chambers in use at LAMPF, we have studied the response of air-filled cylindrical ion chambers to high-intensity, short-duration radiation pulses. The most intense pulses were about 180 rad in 250 ns (the equivalent steady-state dose rate was about 700 Mrad/h). We filled our chambers with nitrogen gas at 760 Torr and air at 600 Torr. The ion chambers were driven into extreme nonlinear response. We hope these data will be used to design loss-monitor systems based on air-filled ion chambers, thus eliminating the need for gas-flow systems and/or airtight ion chambers.

  14. Inflation pressure effect on performance of air-filled wheelchair cushions.

    PubMed

    Krouskop, T A; Williams, R; Noble, P; Brown, J

    1986-02-01

    Air-filled wheelchair cushions are frequently used in the prevention of pressure sores. Their effectiveness in reducing interface pressures and in redistributing body weight (BW) appears dependent on their internal inflation pressure. This pilot study examines and defines this relationship. Interface pressures were measured with the TIPE (Texas Interface Pressure Evaluator) system for 14 subjects while sitting on each of three commercially available air-filled wheelchair cushions. This relationship between interface pressure and internal pressure was then determined for each of the three body-build categories. In each category the interface pressure displayed a higher degree of sensitivity to underinflation than to overinflation. A high correlation found between BW and internal air pressure (IAP), may be useful in the design of a customized pressure indicator system. The study documents the influence of IAP on seating pressure and supports the need for further research in the development of an indicator system that alerts users to under- or overinflation of the cushion.

  15. Blood and Interstitial flow in the hierarchical pore space architecture of bone tissue

    PubMed Central

    Cowin, Stephen C.; Cardoso, Luis

    2015-01-01

    There are two main types of fluid in bone tissue, blood and interstitial fluid. The chemical composition of these fluids varies with time and location in bone. Blood arrives through the arterial system containing oxygen and other nutrients and the blood components depart via the venous system containing less oxygen and reduced nutrition. Within the bone, as within other tissues, substances pass from the blood through the arterial walls into the interstitial fluid. The movement of the interstitial fluid carries these substances to the cells within the bone and, at the same time, carries off the waste materials from the cells. Bone tissue would not live without these fluid movements. The development of a model for poroelastic materials with hierarchical pore space architecture for the description of blood flow and interstitial fluid flow in living bone tissue is reviewed. The model is applied to the problem of determining the exchange of pore fluid between the vascular porosity and the lacunar-canalicular porosity in bone tissue due to cyclic mechanical loading and blood pressure. These results are basic to the understanding of interstitial flow in bone tissue that, in turn, is basic to understanding of nutrient transport from the vasculature to the bone cells buried in the bone tissue and to the process of mechanotransduction by these cells. PMID:25666410

  16. 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.

  17. Alterations in Pore-Space Morphology and Hydraulic Properties of Porous Media Resulting From Coupling of Flow and Reactive Transport

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, S.

    2013-12-01

    property of the remaining percolation cluster. By generating multiple realizations of the same process, and employing a Monte Carlo type simulation approach, we can develop relationships between macroscopic properties and the extent of pore blocking. We show that the classical porosity-permeability relationships such as the Kozeny-Carman equations are not adequate to describe the evolution of macroscopic flow properties of these dynamically evolving systems, and we also show that the initial pore-space morphology and subsequent pore-connectivity alterations strongly influence the relationship between porosity and permeability. We also use the approach described above to explain certain observed porosity-permeability relationships from laboratory experiments and field tests.

  18. Pore-space alteration in source rock (shales) during hydrocarbons generation: laboratory experiment

    NASA Astrophysics Data System (ADS)

    Giliazetdinova, D. R.; Korost, D. V.; Nadezhkin, D. V.

    2013-12-01

    Hydrocarbons (HC) are generated from solid organic matter (kerogen) due to thermocatalytic reactions. The rate of such reactions shows direct correlation with temperature and depends on the depth of source rock burial. Burial of sedimentary rock is also inevitably accompanied by its structural alteration owing to compaction, dehydration and re-crystallization. Processes of HC generation, primary migration and structural changes are inaccessible for direct observation in nature, but they can be studied in laboratory experiments. Experiment was carried out with a clayey-carbonate rock sample of the Domanik Horizon taken from boreholes drilled in the northeastern part of the south Tatar arch. The rock chosen fits the very essential requirements - high organic matter content and its low metamorphic grade. Our work aimed at laboratory modeling of HC generation in an undisturbed rock sample by its heating in nitrogen atmosphere based on a specified temperature regime and monitoring alterations in the pore space structure. Observations were carried out with a SkyScan-1172 X-ray microtomography scanner (resulting scan resolution of 1 μm). A cylinder, 44 mm in diameter, was prepared from the rock sample for the pyrolitic and microtomographic analyses. Scanning procedures were carried out in 5 runs. Temperature interval for each run had to match the most important stage of HC generation in the source rock, namely: (1) original structure; (2) 100-300°C - discharge of free and adsorbed HC and water; (3) 300-400°C - initial stage of HC formation owing to high-temperature pyrolysis of the solid organic matter and discharge of the chemically bound water; (4) 400-470°C - temperature interval fitting the most intense stage of HC formation; (5) 470-510°C - final stage of HC formation. Maximum sample heating in the experiment was determined as temperature of the onset of active decomposition of carbonates, i.e., in essence, irreversible metamorphism of the rock. Additional

  19. A micro-gap, air-filled ionisation chamber as a detector for criticality accident dosimetry.

    PubMed

    Murawski, Ł; Zielczyński, M; Golnik, N; Gryziński, M A

    2014-10-01

    A micro-gap air-filled ionisation chamber was designed for criticality dosimetry. The special feature of the chamber is its very small gap between electrodes of only 0.3 mm. This prevents ion recombination at high dose rates and minimises the influence of gas on secondary particles spectrum. The electrodes are made of polypropylene because of higher content of hydrogen in this material, when compared with soft tissue. The difference between neutron and gamma sensitivity in such chamber becomes practically negligible. The chamber's envelope contains two specially connected capacitors, one for polarising the electrodes and the other for collecting the ionisation charge.

  20. Transport and Fate of Bacteria in Porous Media: Coupled Effects of Chemical Conditions and Pore Space Geometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Experimental and theoretical studies were undertaken to explore the coupling effects of chemical conditions and pore space geometry on bacteria transport in porous media. The retention of Escherichia coli D21g was investigated in a series of batch and column experiments with solutions of different i...

  1. Development and Preliminary Application of High-Resolution Endoscopic Piv for Quantification of Flow Structure Within a Pore Space

    NASA Astrophysics Data System (ADS)

    Blois, G.; Sambrook Smith, G.; Best, J.; Hardy, R.; Lead, J.

    2008-12-01

    Most natural rivers have beds of loose, cohesionless sediment that form a porous bed, thus permitting significant interactions between the free flow above the bed and that within the pore spaces. Many unresolved problems in channel engineering and ecohydraulics are related to an incomplete understanding of this interstitial flow. For example, the mechanisms of pollutant transport and prediction of river bed morphodynamics may be strongly influenced by flow occurring within the pore spaces. While this lack of understanding has been widely acknowledged, the direct experimental investigation of flow within the pore spaces has been restricted by the practical difficulties in collecting such data. This has also created drawbacks in the numerical modeling of pore flow as there remains a dearth of robust experimental data with which to validate such models. In order to help address these issues, we present details of a new endoscopic PIV system designed to tackle some of the challenges highlighted above. The work presented in this paper is also being used to validate a numerical model that is being developed as part of this project. A fully endoscopic PIV system has been developed to collect velocity and turbulence data for flow within the pore space of a gravel bed. The system comprises a pulsed Nd:YAG laser that provides high intensity illumination for single exposure pairs of images on a high-resolution digital camera. The use of rigid endoscopes for both the laser light source and camera allows measurement of quasi-instantaneous flow fields by high-resolution PIV images (2352*1728 pixels). In the first instance, the endoscopic PIV system has been used to study flow within an artificial pore space model constructed from 38 and 51 mm diameter spheres, used to represent a simplified version of a natural gravel-bed river. Across-correlation processing approach has been applied to the PIV images and the processing parameters have been optimized for the experimental

  2. Characterization of granite matrix porosity and pore-space geometry by in situ and laboratory methods

    NASA Astrophysics Data System (ADS)

    Schild, M.; Siegesmund, S.; Vollbrecht, A.; Mazurek, M.

    2001-07-01

    Most available studies of interconnected matrix porosity of crystalline rocks are based on laboratory investigations; that is, work on samples that have undergone stress relaxation and were affected by drilling and sample preparation. The extrapolation of the results to in situ conditions is therefore associated with considerable uncertainty, and this was the motivation to conduct the `in situ Connected Porosity' experiment at the Grimsel Test Site (Central Swiss Alps). An acrylic resin doped with fluorescent agents was used to impregnate the microporous granitic matrix in situ around an injection borehole, and samples were obtained by overcoring. The 3-D structure of the pore-space, represented by microcracks, was studied by U-stage fluorescence microscopy. Petrophysical methods, including the determination of porosity, permeability and P-wave velocity, were also applied. Investigations were conducted both on samples that were impregnated in situ and on non-impregnated samples, so that natural features could be distinguished from artefacts. The investigated deformed granites display complex microcrack populations representing a polyphase deformation at varying conditions. The crack population is dominated by open cleavage cracks in mica and grain boundary cracks. The porosity of non-impregnated samples lies slightly above 1 per cent, which is 2-2.5 times higher than the in situ porosity obtained for impregnated samples. Measurements of seismic velocities (Vp) on spherical rock samples as a function of confining pressure, spatial direction and water saturation for both non-impregnated and impregnated samples provide further constraints on the distinction between natural and induced crack types. The main conclusions are that (1) an interconnected network of microcracks exists in the whole granitic matrix, irrespective of the distance to ductile and brittle shear zones, and (2) conventional laboratory methods overestimate the matrix porosity. Calculations of

  3. Interaction of finite-amplitude sound with air-filled porous materials

    NASA Technical Reports Server (NTRS)

    Nelson, D. A.

    1985-01-01

    The propagation of high intensity sound waves through an air-filled porus material was studied. The material is assumed: (1) to be rigid, incompressible, and homogeneous, and (2) to be adequately described by two properties: resistivity r and porosity. The resulting wave equation is still nonlinear, however, because of the u sgn(u) term in the resistivity. The equation is solved in the frequency domain as an infinite set of coupled inhomogeneous Helmholtz equations, one for each harmonic. An approximate but analytical solution leads to predictions of excess attenuation, saturation, and phase speed reduction for the fundamental component. A more general numerical solution is used to calculate the propagation curves for the higher harmonics. The u sgn(u) nonlinearity produces a cubic distortion pattern; when the input signal is a pure tone, only odd harmonic distortion products are generated.

  4. Measurements of two types of dilatational waves in an air-filled unconsolidated sand

    SciTech Connect

    Hickey, C.J.; Sabatier, J.M.

    1997-07-01

    This study consists of laboratory measurements of dilatational waves propagating through an air-filled unconsolidated sand. One excitation technique consists of a loudspeaker suspended in the air above the packing of sand. A second excitation technique uses a mechanical shaker in contact with the sand. The transmitted signals are received using microphones and geophones located at various depths within the sand. An interpretation based on measured phase speeds indicates that the transmitted energy from the suspended loudspeaker source is partitioned primarily but not exclusively into the type-II dilatational wave. This wave attenuates rapidly and is only detected at depths of less than about 15 cm for this particular sample. At the deeper depths the detected signal is associated with the type-I dilatational wave. The mechanical shaker produces only a type-I dilatational wave. Both the geophone and microphone sensors can detect both types of dilatational waves. {copyright} {ital 1997 Acoustical Society of America.}

  5. Flow patterns of natural convection in an air-filled vertical cavity

    NASA Astrophysics Data System (ADS)

    Wakitani, Shunichi

    1998-08-01

    Flow patterns of two-dimensional natural convection in a vertical air-filled tall cavity with differentially heated sidewalls are investigated. Numerical simulations based on a finite difference method are carried out for a wide range of Rayleigh numbers and aspect ratios from the onset of the steady multicellular flow, through the reverse transition to the unicellular pattern, to the unsteady multicellular flow. For aspect ratios (height/width) from 10 to 24, the various cellular structures characterized by the number of secondary cells are clarified from the simulations by means of gradually increasing Rayleigh number to 106. Unsteady multicellular solutions are found in some region of Rayleigh numbers less than those at which the reverse transition has occurred.

  6. Infilling of Pore Spaces in Mortar Using Electrically-Driven Solution Transport Systems

    NASA Astrophysics Data System (ADS)

    Morefield, Sean W.; Weiss, Charles A.; Malone, Philip G.; Hock, Vincent F.

    2010-05-01

    It has been widely established that all types of conventional concrete can be strengthened by reducing the porosity of the concrete matrix. Attempts to infill the pores by converting reactive phases such as calcium hydroxide into calcium carbonate have been partly successful, but the success of this approach has been limited by the amount of Ca(OH)2 produced in the hydration of the concrete and by the positions of the new crystalline phases that are formed. These limitations can be overcome by using a combination of electrophoresis to move particles into concrete pores and the use of ion transport to move new dissolved reactants into the concrete mass. Bench scale experiments have demonstrated that significant density and strength increases can be obtained by electrophoretically moving seed crystals of selected mineral phases such as calcite, aragonite, or vaterite into the larger pores in concrete and then using a low-voltage DC current to migrate in calcium and carbonate ions to grow the selected crystalline phases in masses sufficient to fill up both large and small pores. This can be done in such a way as to leave even the reactive phases such as Ca(OH)2 unaltered. The bulk pH of the concrete is not reduced in the mineralization process as it would be in simple carbonation. Pore in-filling using electrophoretic and electro-transport systems can potentially be of use in creating very high-density concrete for concrete pipes, and panels with lower porosity than can be obtained using carbonation or pressure infiltration.

  7. New insights to pore space morphologies in Boom Clay - results from 2D BIB-SEM investigations and mercury injection porosimetry

    NASA Astrophysics Data System (ADS)

    Hemes, S.; Desbois, G.; Urai, J. L.

    2012-04-01

    BIB-SEM investigations on Boom Clay (Mol-Dessel reference site for radioactive waste disposal, Belgium) of different grain sizes yield new insights to pore space morphologies and pore-size distributions down to the resolution of state-of-the-art SEM. Non-clay minerals embedded into a clay matrix form the overall fabric of the different samples investigated. We identified four main porous mineral phases: clay, pyrite, mica and fossils. Regardless of the origin and the grain-size distribution of samples, characteristic pore morphologies were found for each different mineral phase. Our approach allows segmenting pores with a practical pore resolution of 25-30 nm in pore size (equivalent radius, ER) resulting in total porosities of 10-20 % and log-normal pore-size distributions at the scale of observation. Detailed studies of segmented porosities within the clay matrices point to a power-law distribution of pore-areas over three orders of magnitude, interpreted as self-similarity of the pore space. Moreover, two classes of pore-sizes were distinguished within the clay-matrix: biggest pores were found within the first 100 nm from non-clay mineral grain-boundaries, whereas pores smaller than 100 nm (ER) are homogeneously distributed within the clay matrix. Our calculations show clearly that the median pore-size value of the biggest pores is linked to the grain size parameter, which suggests that the grain- size and the amount of non-clay minerals is controlling the contribution of the largest pore-size fraction to the overall porosity. Bulk porosities measured by mercury injection porosimetry (MIP) are between 26-33 %. The comparison of our microstructural investigations inferred by BIB-SEM with MIP data, indicates that a significant pore fraction is not detected by using the BIB-SEM method (about 10-15 % of the total porosity), corresponding to pores smaller than 30 nm (ER). However, the extrapolation of power-law pore-size distributions, inferred for pores within the

  8. 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.

  9. Remote magnetic resonance sounding for exploration of pore space microstructure and aquifer macrostructure

    NASA Astrophysics Data System (ADS)

    Shushakov, O. A.; Maryasov, A. G.; Strelnikova, A. B.

    2016-03-01

    Proton nuclear magnetic resonance is a type of nuclear magnetic resonance (NMR), which is widely used to detect hydrogen containing liquids, like water or hydrocarbons. The use of the Earth’s magnetic field allows remote detection of fluids sub surface without generating an independent magnetic field that is expensive and complex enough to apply. An important feature of NMR in the Earth’s field is that the signals produced by snow and ice are generally unobservable under experimental conditions created for liquid water prospecting. The characteristics of the RF response are associated with the molecular environment of the nuclei. This allows detecting NMR signals of water in pores of various size.

  10. Pore Formation and Mobility (PFMI): An International Space Station Glovebox Investigation

    NASA Technical Reports Server (NTRS)

    Grugel, R. N.; Anilkumar, A.; Jeter, L.; Luz, P.; Volz, M. P.; Spivey, R.; Smith, G.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    Porosity in the form of "bubbles and pipes" can occur during controlled directional solidification processing of metal alloys. It is detrimental to material properties and precludes obtaining meaningful scientific results. On Earth, density differences allow an initiated bubble can rise through the liquid and "pop" at the surface resulting in a sound casting. This is not likely to occur in a microgravity environment and, unfortunately, a number of experiments conducted in microgravity have suffered from porosity effects. The current investigation is a systematic effort towards understanding porosity formation and mobility during controlled directional solidification in a microgravity environment. This will be investigated by utilizing a transparent material, succinonitrile (SCN), in conjunction with a translating temperature gradient stage so that direct observation and recording of pore generation and mobility can be made. The talk will cover the porosity problem, the details of the proposed experiments and the experimental hardware, and the expectations from the microgravity experiments.

  11. Air-filled postcranial bones in theropod dinosaurs: physiological implications and the 'reptile'-bird transition.

    PubMed

    Benson, Roger B J; Butler, Richard J; Carrano, Matthew T; O'Connor, Patrick M

    2012-02-01

    Pneumatic (air-filled) postcranial bones are unique to birds among extant tetrapods. Unambiguous skeletal correlates of postcranial pneumaticity first appeared in the Late Triassic (approximately 210 million years ago), when they evolved independently in several groups of bird-line archosaurs (ornithodirans). These include the theropod dinosaurs (of which birds are extant representatives), the pterosaurs, and sauropodomorph dinosaurs. Postulated functions of skeletal pneumatisation include weight reduction in large-bodied or flying taxa, and density reduction resulting in energetic savings during foraging and locomotion. However, the influence of these hypotheses on the early evolution of pneumaticity has not been studied in detail previously. We review recent work on the significance of pneumaticity for understanding the biology of extinct ornithodirans, and present detailed new data on the proportion of the skeleton that was pneumatised in 131 non-avian theropods and Archaeopteryx. This includes all taxa known from significant postcranial remains. Pneumaticity of the cervical and anterior dorsal vertebrae occurred early in theropod evolution. This 'common pattern' was conserved on the line leading to birds, and is likely present in Archaeopteryx. Increases in skeletal pneumaticity occurred independently in as many as 12 lineages, highlighting a remarkably high number of parallel acquisitions of a bird-like feature among non-avian theropods. Using a quantitative comparative framework, we show that evolutionary increases in skeletal pneumaticity are significantly concentrated in lineages with large body size, suggesting that mass reduction in response to gravitational constraints at large body sizes influenced the early evolution of pneumaticity. However, the body size threshold for extensive pneumatisation is lower in theropod lineages more closely related to birds (maniraptorans). Thus, relaxation of the relationship between body size and pneumatisation preceded

  12. Relative permeability and the microscopic distribution of wetting and nonwetting phases in the pore space of Berea sandstone

    SciTech Connect

    Schlueter, E.M.; Cook, N.G.W. |; Witherspoon, P.A.; Myer, L.R.

    1994-04-01

    Experiments to study relative permeabilities of a partially saturated rock have been carried out in Berea sandstone using fluids that can be solidified in place. The effective permeability of the spaces not occupied by the wetting fluid (paraffin wax) or the nonwetting fluid (Wood`s metal), have been measured at various saturations after solidifying each of the phases. The tests were conducted on Berea sandstone samples that had an absolute permeability of about 600 md. The shape of the laboratory-derived relative permeability vs. saturation curves measured with the other phase solidified conforms well with typical curves obtained using conventional experimental methods. The corresponding wetting and nonwetting fluid distributions at different saturations are presented and analyzed in light of the role of the pore structure in the invasion process, and their impact on relative permeability and capillary pressure. Irreducible wetting and nonwetting phase fluid distributions are studied. The effect of clay minerals on permeability is also assessed.

  13. Modeling the space-time evolution of pore pressure in layered shallow covers

    NASA Astrophysics Data System (ADS)

    Salciarini, Diana; Cuomo, Sabatino; Castorino, Giuseppe; Fanelli, Giulia; Tamagnini, Claudio

    2015-04-01

    In most of the available models for the prediction of shallow landslide susceptibility, the potentially unstable soil cover is considered uniform and homogeneous, over an impervious underlying bedrock (see, e.g., Baum et al. 2008; Salciarini et al. 2006, 2012). However, in several case studies, this was proven to be unlikely, for example in the case of pyroclastic soil covers, where two clearly separated layers are detectable (Cascini et al., 2008, 2011). The possibility of taking into account the detailed configuration of the soil cover allows having a more accurate estimate of the potentially unstable volumes, which significantly modify the intensity of the considered phenomena. To take into account the possibility of having layers in the soil cover with different permeability, the existing routines of the TRIGRS code (Baum et al. 2008) devoted to the hydrologic process modeling have been modified. The closed-form solution by Srivastava & Yeh (1991) implemented into TRIGRS was substituted with the numerical solution of the mass balance equation governing the infiltration process. A parametric analysis was carried out by varying the permeability ratio between the two layers, with the aim of examining the influence of such parameter on the pore-pressure distribution along the vertical profile. As expected, as the permeability ratio increases, the underlying layer tends to behave as an impervious boundary. This increases the chance that only the most superficial soil layer fails. An analysis of the routine performance and efficiency was also done to investigate the response of the model with different tolerances and different time steps of the integration procedure, and different spatial discretizations along the vertical profile.

  14. A semi-analytical model for computation of capillary entry pressures and fluid configurations in uniformly-wet pore spaces from 2D rock images

    NASA Astrophysics Data System (ADS)

    Frette, O. I.; Helland, J. O.

    2010-08-01

    A novel semi-analytical model for computation of capillary entry pressures and associated fluid configurations in arbitrary, potentially non-convex, 2D pore space geometries at uniform wettability is developed. The model computes all possible centre positions of circular arcs, and physically sound criteria are implemented to determine the set of these arcs that correspond to geometrically allowed interfaces. Interfaces and pore boundary segments are connected to form closed boundaries of identified geometrical regions. These regions are classified as either oil regions, located in the wider parts of the pore space, or as water regions located in pore space constrictions. All possible region combinations are identified and evaluated for each radius value in an iterative procedure to determine the favourable entry radius and corresponding configuration based on minimisation of free energy. The model has been validated by comparison with known analytical solutions in idealised pore geometries. In cases where different analytical solutions are geometrically possible, the model generates several oil and water regions, and the valid solution is determined by the region combination that corresponds to the most favourable entry pressure, consistent with the analytical solution. Entry pressure radii and configurations are computed in strongly non-convex pore spaces extracted from an image of Bentheimer sandstone, which demonstrates that the model captures successfully well-known characteristics of capillary behaviour at different wetting conditions. The computations also demonstrate the importance of selecting the fluid configuration of minimum change in free energy. In some cases, a merged region formed by a combination of oil and water regions corresponds to the favourable entry configuration of oil, whereas in other cases, an individual oil region may correspond to the favourable oil entry configuration. It is also demonstrated that oil entry configurations may

  15. Visualising the equilibrium distribution and mobility of organic contaminants in soil using the chemical partitioning space.

    PubMed

    Wong, Fiona; Wania, Frank

    2011-06-01

    Assessing the behaviour of organic chemicals in soil is a complex task as it is governed by the physical chemical properties of the chemicals, the characteristics of the soil as well as the ambient conditions of the environment. The chemical partitioning space, defined by the air-water partition coefficient (K(AW)) and the soil organic carbon-water partition coefficient (K(OC)), was employed to visualize the equilibrium distribution of organic contaminants between the air-filled pores, the pore water and the solid phases of the bulk soil and the relative importance of the three transport processes removing contaminants from soil (evaporation, leaching and particle erosion). The partitioning properties of twenty neutral organic chemicals (i.e. herbicides, pharmaceuticals, polychlorinated biphenyls and volatile chemicals) were estimated using poly-parameter linear free energy relationships and superimposed onto these maps. This allows instantaneous estimation of the equilibrium phase distribution and mobility of neutral organic chemicals in soil. Although there is a link between the major phase and the dominant transport process, such that chemicals found in air-filled pore space are subject to evaporation, those in water-filled pore space undergo leaching and those in the sorbed phase are associated with particle erosion, the partitioning coefficient thresholds for distribution and mobility can often deviate by many orders of magnitude. In particular, even a small fraction of chemical in pore water or pore air allows for evaporation and leaching to dominate over solid phase transport. Multiple maps that represent soils that differ in the amount and type of soil organic matter, water saturation, temperature, depth of surface soil horizon, and mineral matters were evaluated.

  16. A microporous Cu-MOF with optimized open metal sites and pore spaces for high gas storage and active chemical fixation of CO2.

    PubMed

    Gao, Chao-Ying; Tian, Hong-Rui; Ai, Jing; Li, Lei-Jiao; Dang, Song; Lan, Ya-Qian; Sun, Zhong-Ming

    2016-09-25

    A microporous Cu-MOF with optimized open metal sites and pore space was constructed based on a designed bent ligand; it exhibits high-capacity multiple gas storage under atmospheric pressure and efficient catalytic activity for chemical fixation of CO2 under mild conditions.

  17. Soil atmosphere exchange of Carbonyl Sulfide (COS) regulated by diffusivity depending on water-filled pore space

    NASA Astrophysics Data System (ADS)

    van Diest, H.; Kesselmeier, J.

    2007-10-01

    The exchange of carbonyl sulfide (COS) between soil and the atmosphere was investigated for three arable soils from Germany, China and Finland and one forest soil from Siberia for parameterization in the relation to ambient carbonyl sulfide (COS) concentration, soil water content (WC) and air temperature. All investigated soils acted as significant sinks for COS. A clear and distinct uptake optimum was found for the German, Chinese, Finnish and Siberian soils at 11.5%, 9%, 11.5%, and 9% soil WC, respectively, indicating that the soil WC acts as an important biological and physical parameter for characterizing the exchange of COS between soils and the atmosphere. Different optima of deposition velocities (Vd) as observed for the Chinese, Finnish and Siberian boreal soil types in relation to their soil WC, aligned at 19% in relation to the water-filled pore space (WFPS), indicating the dominating role of gas diffusion. This interpretation was supported by the linear correlation between Vd and bulk density. We suggest that the uptake of COS depends on the diffusivity dominated by WFPS, a parameter depending on soil WC, soil structure and porosity of the soil.

  18. Soil atmosphere exchange of carbonyl sulfide (COS) regulated by diffusivity depending on water-filled pore space

    NASA Astrophysics Data System (ADS)

    van Diest, H.; Kesselmeier, J.

    2008-04-01

    The exchange of carbonyl sulfide (COS) between soil and the atmosphere was investigated for three arable soils from Germany, China and Finland and one forest soil from Siberia for parameterization in the relation to ambient carbonyl sulfide (COS) concentration, soil water content (WC) and air temperature. All investigated soils acted as sinks for COS. A clear and distinct uptake optimum was found for the German, Chinese, Finnish and Siberian soils at 11.5%, 9%, 11.5%, and 9% soil WC, respectively, indicating that the soil WC acts as an important biological and physical parameter for characterizing the exchange of COS between soils and the atmosphere. Different optima of deposition velocities (Vd) as observed for the Chinese, Finnish and Siberian boreal soil types in relation to their soil WC, aligned at 19% in relation to the water-filled pore space (WFPS), indicating the dominating role of gas diffusion. This interpretation was supported by the linear correlation between Vd and bulk density. We suggest that the uptake of COS depends on the diffusivity dominated by WFPS, a parameter depending on soil WC, soil structure and porosity of the soil.

  19. Three dimensional analysis of the pore space in fine-grained Boom Clay, using BIB-SEM (broad-ion beam scanning electron microscopy), combined with FIB (focused ion-beam) serial cross-sectioning, pore network modeling and Wood's metal injection

    NASA Astrophysics Data System (ADS)

    Hemes, Susanne; Klaver, Jop; Desbois, Guillaume; Urai, Janos

    2014-05-01

    The Boom Clay is, besides the Ypresian clays, one of the potential host rock materials for radioactive waste disposal in Belgium (Gens et al., 2003; Van Marcke & Laenen, 2005; Verhoef et al., 2011). To access parameters, which are relevant for the diffusion controlled transport of radionuclides in the material, such as porosity, pore connectivity and permeability, it is crucial to characterize the pore space at high resolution (nm-scale) and in 3D. Focused-ion-beam (FIB) serial cross-sectioning in combination with high resolution scanning electron microscopy (SEM), pore network modeling, Wood's metal injection and broad-ion-beam (BIB) milling, constitute a superior set of methods to characterize the 3D pore space in fine-grained, clayey materials, down to the nm-scale resolution. In the present study, we identified characteristic 3D pore space morphologies, determined the 3D volume porosity of the material and applied pore network extraction modeling (Dong and Blunt, 2009), to access the connectivity of the pore space and to discriminate between pore bodies and pore throats. Moreover, we used Wood's metal injection (WMI) in combination with BIB-SEM imaging to assess the pore connectivity at a larger scale and even higher resolution. The FIB-SEM results show a highly (~ 90 %) interconnected pore space in Boom Clay, down to the resolution of ~ 3E+03 nm³ (voxel-size), with a total volume porosity of ~ 20 %. Pore morphologies of large (> 5E+08 nm³), highly interconnected pores are complex, with high surface area to volume ratios (shape factors G ~ 0.01), whereas small (< 1E+06 nm³), often isolated pores are much more compact and show higher shape factors (G) up to 0.03. WMI in combination with BIB-SEM, down to a resolution of ~ 50 nm² pixel-size, indicates an interconnected porosity fraction of ~ 80 %, of a total measured 2D porosity of ~ 20 %. Determining and distinguishing between pore bodies and pore throats enables us to compare 3D FIB-SEM pore

  20. Nonlinear compression of high energy fiber amplifier pulses in air-filled hypocycloid-core Kagome fiber.

    PubMed

    Guichard, Florent; Giree, Achut; Zaouter, Yoann; Hanna, Marc; Machinet, Guillaume; Debord, Benoît; Gérôme, Frédéric; Dupriez, Pascal; Druon, Frédéric; Hönninger, Clemens; Mottay, Eric; Benabid, Fetah; Georges, Patrick

    2015-03-23

    We report on the generation of 34 fs and 50 µJ pulses from a high energy fiber amplifier system with nonlinear compression in an air-filled hypocycloid-core Kagome fiber. The unique properties of such fibers allow bridging the gap between solid core fibers-based and hollow capillary-based post-compression setups, thereby operating with pulse energies obtained with current state-of-the-art fiber systems. The overall transmission of the compression setup is over 70%. Together with Yb-doped fiber amplifier technologies, Kagome fibers therefore appear as a promising tool for efficient generation of pulses with durations below 50 fs, energies ranging from 10 to several hundreds of µJ, and high average powers.

  1. Changes in composition and pore space of sand rocks in the oil water contact zone (section YU1 3-4, Klyuchevskaya area, Tomsk region)

    NASA Astrophysics Data System (ADS)

    Nedolivko, N.; Perevertailo, T.; Pavlovec, T.

    2016-09-01

    The article provides an analysis of specific features in changes of rocks in the oil water contact zone. The object of study is the formation YU1 3-4 (J3o1) of Klyuchevskaya oil deposit (West Siberian oil-gas province, Tomsk region). The research data allow the authors to determine vertical zoning of the surface structure and identify the following zones: oil saturation (weak alteration), bitumen-content dissolution, non-bitumen-content dissolution, cementation, including rocks not affected by hydrocarbon deposit. The rocks under investigation are characterized by different changes in composition, pore space, as well as reservoir filtration and volumetric parameters. Detection of irregularity in distribution of void- pore space in oil-water contact zones is of great practical importance. It helps to avoid the errors in differential pressure drawdown and explain the origin of low-resistivity collectors.

  2. Structural factors affecting pore space transformation during hydrocarbon generation in source rock (shales): laboratory experiments and X-ray microtomography/SEM study

    NASA Astrophysics Data System (ADS)

    Giliazetdinova, Dina; Korost, Dmitry; Gerke, Kirill

    2015-04-01

    Oil and gas generation is a complex superposition of processes which take place in the interiors and are not readily observable in nature in human life time-frames. During burial of the source rocks organic matter is transformed into a mixture of high-molecular compounds - precursors of oil and gas (kerogen). Specific thermobaric conditions trigger formation of low molecular weight hydrocarbon compounds. Generation of sufficient quantities of hydrocarbons leads to the primary fluid migration. For series of our experiments we selected mainly siliceous-carbonate composition shale rocks from Domanic horizon of South-Tatar arch. Rock samples were heated in the pyrolyzer to temperatures closely corresponding to different catagenesis stages. X-ray microtomography method was used to monitor changes in the morphology of the pore space 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

  3. Bubble absorption by an air-filled helically-supported capillary channel

    NASA Astrophysics Data System (ADS)

    Beheshtipour, Negar; Thiessen, David

    2016-11-01

    Gas-liquid phase separation under microgravity conditions where buoyancy is not active represents a challenge for two-phase liquid-continuous space systems. Similar challenges are present in micro-scale electrochemical systems on Earth that generate gas bubbles in geometries where surface tension prevails over gravity. A possible ground-based application would be the removal of carbon dioxide bubbles from large aspect ratio channels in a direct-methanol fuel cell that could otherwise occlude the channel. In this study we use a 3-mm diameter stretched stainless-steel spring coated with a superhydrophobic layer to create a helically-supported capillary channel. Such a channel that is submerged in water and filled with air while vented to the atmosphere was found to absorb a stream of 2.5-mm diameter air bubbles at a rate of at least 36 bubbles/s. An optical detector and high-speed imaging system have been used to study bubble absorption dynamics. A significant finding is that the initial attachment of the bubble to the channel that involves the rupture of a thin film of water happens in less than 1 ms. The rapid rupture of the water film separating the bubble from the channel might be attributed to the roughness of the hydrophobic coating.

  4. Diagenetic patterns and pore space distribution along a platform to outer-shelf transect (Urgonian limestone, Barremian-Aptian, SE France)

    NASA Astrophysics Data System (ADS)

    Léonide, Philippe; Fournier, François; Reijmer, John J. G.; Vonhof, Hubert; Borgomano, Jean; Dijk, Jurrien; Rosenthal, Maelle; van Goethem, Manon; Cochard, Jean; Meulenaars, Karlien

    2014-06-01

    The Urgonian limestones of Late Barremian/Early Aptian from Provence (SE, France) are characterized by the occurrence of microporous limestones at regional scale alternating with tight carbonates. This study, based on petrographical (sediment texture, facies) and diagenetical analyses (cement stratigraphy, porosity and isotope geochemistry) of more than 800 limestone samples provides insight into the parameters controlling the genesis, preservation or occlusion of microporosity along an inner platform to outer shelf transect. The tight and microporous Urgonian limestones from Provence can be grouped into 5 rock-types based on textures, associated depositional environments, porosity and pore-type, being: (1) tight inner-platform: TIP; (2) porous inner platform: PIP; (3) tight outer platform: TOP; (4) porous outer platform: POP and (5) tight outer shelf: TOS. In tight (TIP, TOP and TOS types) limestones intergranular and intragranular pore spaces were entirely occluded by early marine and/or early meteoric cementation, whereas in microporous (PIP, POP) limestones a significant fraction of the intergranular macroporosity was preserved during early and shallow burial diagenesis. Micrite neomorphism (hybrid Ostwald ripening process) occurred during meteoric shallow burial diagenesis in PIP and POP limestones during the regional Durancian Uplift event (Albian-Lower Cenomanian). This process resulted in microporosity enhancement and preservation. Circulation of meteoric fluids during exhumation produces intercrystalline microporosity enhancement and moldic porosity development. The present study documents the important role that both early diagenetic and depositional cycles and long-term tectonic processes have on pore space evolution and distribution in Mesozoic platform carbonates.

  5. Intraoperative measurement of intraocular pressure in vitrectomized aphakic air-filled eyes using the Tono-Pen XL.

    PubMed

    Badrinath, S S; Vasudevan, R; Murugesan, R; Basti, S; Nicholson, A D; Singh, P; Gopal, L; Sharma, T; Rao, S B; Abraham, C

    1993-01-01

    The Tono-Pen XL (Bio-Rad, Santa Ana, CA) was compared with manometer readings for intraoperative measurement of intraocular pressure (IOP) in 40 eyes of 40 consecutive patients after vitrectomy, lensectomy, and fluid-air exchange. Tono-Pen readings corresponding to manometer readings of 10, 20, 30, 40, and 50 mmHg were obtained in a masked fashion with a randomized sequence of manometer readings. A correlation was obtained between the manometer and Tono-Pen readings (r = 0.96 in emmetropic eyes and r = 0.93 in myopic eyes). The regression curve that represents the calibration curve of Tono-Pen in terms of the manometer readings for air-filled vitrectomized eyes was obtained. Any Tono-Pen reading can be easily translated into the corresponding manometer reading by referring to the curve. The Tono-Pen can therefore be effectively used to accurately determine intraoperative IOP in eyes undergoing vitrectomy, lensectomy, and fluid-air exchange.

  6. On the air-filled effective porosity parameter of Rogers and Nielson's (1991) bulk radon diffusion coefficient in unsaturated soils.

    PubMed

    Saâdi, Zakaria

    2014-05-01

    The radon exhalation rate at the earth's surface from soil or rock with radium as its source is the main mechanism behind the radon activity concentrations observed in both indoor and outdoor environments. During the last two decades, many subsurface radon transport models have used Rogers and Nielson's formula for modeling the unsaturated soil bulk radon diffusion coefficient. This formula uses an "air-filled effective porosity" to account for radon adsorption and radon dissolution in the groundwater. This formula is reviewed here, and its hypotheses are examined for accuracy in dealing with subsurface radon transport problems. The author shows its limitations by comparing one dimensional steady-state analytical solutions of the two-phase (air/water) transport equation (Fick's law) with Rogers and Nielson's formula. For radon diffusion-dominated transport, the calculated Rogers and Nielson's radon exhalation rate is shown to be unrealistic as it is independent of the values of the radon adsorption and groundwater dissolution coefficients. For convective and diffusive transport, radon exhalation rates calculated using Fick's law and this formula agree only for high values of gas-phase velocity and groundwater saturation. However, these conditions are not usually met in most shallow subsurface environments where radon migration takes place under low gas phase velocities and low water saturation.

  7. Initially linear echo-spacing dependence of 1/T2 measurements in many porous media with pore-scale inhomogeneous fields.

    PubMed

    Fantazzini, Paola; Brown, Robert J S

    2005-12-01

    For a liquid sample with unrestricted diffusion in a constant magnetic field gradient g, the increase R in R2=1/T2 for CPMG measurements is 1/3(taugammag)2D, where gamma is magnetogyric ratio, tau is the half the echo spacing TE, and D is the diffusion constant. For measurements on samples of porous media with pore fluids and without externally applied gradients there may still be significant pore-scale local inhomogeneous fields due to susceptibility differences, whose contributions to R2 depend on tau. Here, diffusion is not unrestricted nor is the field gradient constant. One class of approaches to this problem is to use an "effective gradient" or some kind of average gradient. Then, R2 is often plotted against tau2, with the effective gradient determined from the slope of some of the early points. In many cases, a replot of R2 against tau instead of tau2 shows a substantial straight-line interval, often including the earliest available points. In earlier work [G.C. Borgia, R.J.S. Brown, P. Fantazzini, Phys. Rev. E 51 (1995) 2104; R.J.S. Brown, P. Fantazzini, Phys. Rev. B 47 (1993) 14823] these features were noted, and attention was called to the fact that very large changes in field and gradient are likely for a small part of the pore fluid over distances very much smaller than pore dimensions. A truncated Cauchy-Lorentz (C-L) distribution of local fields in the pore space was used to explain observations, giving reduced effects of diffusion because of the averaging properties of the C-L distribution, the truncation being at approximately +/-1/2chiB0, where chi is the susceptibility difference. It was also noted that, when there is a narrow range of pore size a, over a range of about 40 of the parameter xi=1/3chinua2/D, where nu is the frequency, R2 does not depend much on pore size a nor on diffusion constant D. Examples are shown where plots of R2 vs tau show better linear fits to the data for small tau values than do plots vs tau2. The present work shows

  8. Influence of confinement in controlled-pore glass on the layer spacing of smectic- A liquid crystals

    NASA Astrophysics Data System (ADS)

    Cordoyiannis, George; Zidanšek, Aleksander; Lahajnar, Gojmir; Kutnjak, Zdravko; Amenitsch, Heinz; Nounesis, George; Kralj, Samo

    2009-05-01

    A detailed x-ray scattering study has been performed in the temperature range of the smectic- A phase for the liquid crystal compounds dodecylcyanobiphenyl (12CB) and octylcyanobiphenyl (8CB) confined in different controlled-pore glasses (CPGs) characterized by their average void radius R . On decreasing the temperature in bulk samples the layer thickness is increasing for 12CB and decreasing for 8CB, respectively. In nontreated CPG samples the layers dilate significantly with respect to the bulk liquid crystal. In order to explain the layer thickness behavior on varying temperature and R , one has to take into account molecular details of the liquid crystalline samples as well as memory effects.

  9. Restoration of middle-ear input in fluid-filled middle ears by controlled introduction of air or a novel air-filled implant.

    PubMed

    Ravicz, Michael E; Chien, Wade W; Rosowski, John J

    2015-10-01

    The effect of small amounts of air on sound-induced umbo velocity in an otherwise saline-filled middle ear (ME) was investigated to examine the efficacy of a novel balloon-like air-filled ME implant suitable for patients with chronically non-aerated MEs. In this study, air bubbles or air-filled implants were introduced into saline-filled human cadaveric MEs. Umbo velocity, a convenient measure of ME response, served as an indicator of hearing sensitivity. Filling the ME with saline reduced umbo velocity by 25-30 dB at low frequencies and more at high frequencies, consistent with earlier work (Ravicz et al., Hear. Res. 195: 103-130 (2004)). Small amounts of air (∼30 μl) in the otherwise saline-filled ME increased umbo velocity substantially, to levels only 10-15 dB lower than in the dry ME, in a frequency- and location-dependent manner: air in contact with the tympanic membrane (TM) increased umbo velocity at all frequencies, while air located away from the TM increased umbo velocity only below about 500 Hz. The air-filled implant also affected umbo velocity in a manner similar to an air bubble of equivalent compliance. Inserting additional implants into the ME had the same effect as increasing air volume. These results suggest these middle-ear implants would significantly reduce conductive hearing loss in patients with chronically fluid-filled MEs.

  10. A conceptual model of pore-space blockage in mixed sediments using a new numerical approach, with implications for sediment bed stabilization

    NASA Astrophysics Data System (ADS)

    Bartzke, Gerhard; Huhn, Katrin

    2015-06-01

    In mixed sediment beds, erosion resistance can change relative to that of beds composed of a uniform sediment because of varying textural and/or other grain-size parameters, with effects on pore water flow that are difficult to quantify by means of analogue techniques. To overcome this difficulty, a three-dimensional numerical model was developed using a finite difference method (FDM) flow model coupled with a distinct element method (DEM) particle model. The main aim was to investigate, at a high spatial resolution, the physical processes occurring during the initiation of motion of single grains at the sediment-water interface and in the shallow subsurface of simplified sediment beds under different flow velocities. Increasing proportions of very fine sand (D50=0.08 mm) were mixed into a coarse sand matrix (D50=0.6 mm) to simulate mixed sediment beds, starting with a pure coarse sand bed in experiment 1 (0 wt% fines), and proceeding through experiment 2 (6.5 wt% fines), experiment 3 (10.5 wt% fines), and experiment 4 (28.7 wt% fines). All mixed beds were tested for their erosion behavior at predefined flow velocities varying in the range of U 1-5=10-30 cm/s. The experiments show that, with increasing fine content, the smaller particles increasingly fill the spaces between the larger particles. As a consequence, pore water inflow into the sediment is increasingly blocked, i.e., there is a decrease in pore water flow velocity and, hence, in the flow momentum available to entrain particles. These findings are portrayed in a new conceptual model of enhanced sediment bed stabilization.

  11. 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.

  12. SU-E-T-297: Dosimetric Assessment of An Air-Filled Balloon Applicator in HDR Vaginal Cuff Brachytherapy Using the Monte Carlo Method

    SciTech Connect

    Jiang, H; Lee, Y; Pokhrel, D; Badkul, R

    2015-06-15

    Purpose: As an alternative to cylindrical applicators, air inflated balloon applicators have been introduced into HDR vaginal cuff brachytherapy treatment to achieve sufficient dose to vagina mucosa as well as to spare rectum and bladder. In general, TG43 formulae based treatment planning systems do not take into account tissue inhomogeneity, and air in the balloon applicator can cause higher delivered dose to mucosa than treatment plan reported. We investigated dosimetric effect of air in balloon applicator using the Monte Carlo method. Methods: The thirteen-catheter Capri applicator with a Nucletron Ir-192 seed was modeled for various balloon diameters (2cm to 3.5cm) using the MCNP Monte Carlo code. Ir-192 seed was placed in both central and peripheral catheters to replicate real patient situations. Existence of charged particle equilibrium (CPE) with air balloon was evaluated by comparing kerma and dose at various distances (1mm to 70mm) from surface of air-filled applicator. Also mucosa dose by an air-filled applicator was compared with by a water-filled applicator to evaluate dosimetry accuracy of planning system without tissue inhomogeneity correction. Results: Beyond 1mm from air/tissue interface, the difference between kerma and dose was within 2%. CPE (or transient CPE) condition was deemed existent, and in this region no electron transport was necessary in Monte Carlo simulations. At 1mm or less, the deviation of dose from kerma became more apparent. Increase of dose to mucosa depended on diameter of air balloon. The increment of dose to mucosa was 2.5% and 4.3% on average for 2cm and 3.5cm applicators, respectively. Conclusion: After introduction of air balloon applicator, CPE fails only at the proximity of air/tissue interface. Although dose to mucosa is increased, there is no significant dosimetric difference (<5%) between air and water filled applicators. Tissue inhomogeneity correction is not necessary for air-filled applicators.

  13. Elastic anisotropy and pore space geometry of schlieren granite: direct 3-D measurements at high confining pressure combined with microfabric analysis

    NASA Astrophysics Data System (ADS)

    Staněk, Martin; Géraud, Yves; Lexa, Ondrej; Špaček, Petr; Ulrich, Stanislav; Diraison, Marc

    2013-07-01

    Pore space geometry of granitic rocks and its evolution with depth are key factors in large-scale seismics or in projects of enhanced geothermal systems or of deep hazardous waste repositories. In this study, we studied macroscopically anisotropic schlieren-bearing granite by experimental P-wave velocity (VP) measurements on spherical sample in 132 directions at seven different confining pressures in the range 0.1-400 MPa. In order to discriminate the phenomena affecting the rock elastic properties we analysed the orientation of microcracks and of grain boundaries and we measured the anisotropy of magnetic susceptibility of the rock. Three sets of microcracks were defined, with two of them linked to the massif exfoliation process and one to cooling contraction of the massif. During pressurization the measured mean VP and VP anisotropy degree at ambient pressure and at highest confinement (400 MPa) yielded 3.3 km s-1 and 24 per cent, and 6.2 km s-1 and 3 per cent, respectively. The associated VP anisotropy pattern was transversely isotropic and governed by the schlieren, with a minimum VP direction perpendicular to them and a girdle of high VP directions parallel to them. The highest change in VP was observed between 0.1 and 10 MPa, suggesting a significant closure of porosity below depths of 500 m. Change of the VP anisotropy pattern to orthorhombic together with increase of mean VP and VP anisotropy degree during depressurization was attributed to inelastic response of one of the sets of microcracks to the loading-unloading cycle.

  14. Geophysical signatures of carbonate rocks flooded with CO2-rich water: effect of the presence of oil in the pore space

    NASA Astrophysics Data System (ADS)

    Vialle, S.; Mavko, G. M.

    2012-04-01

    about 45% of oil in the pore space, as deduced from mass balances. After injection of the reactive fluid, P-wave velocities showed larger relative decreases in the clean sample, compared with the oil-bearing sample. To better understand the reason of such a difference, sample microstructure was observed under VP-SEM and confocal microscopy. Images revealed that oil was trapped in the micritic matrix, preventing its dissolution. Dissolution can thus only occur through the macropores and the spar cement. On the other hand, all the microstructure of the clean sample was affected by dissolution. Since micrite has been reported as a stiff component of the rock, inhibiting its leaching will lead to a lower relative decrease in P-wave velocity compared to the case where micrite can be leached.

  15. The Relationship Between Soil Air Filled Porosity and Soil Methane Oxidation is Almost Identical in Both Dry and Wet Temperate Eucalypt Forests

    NASA Astrophysics Data System (ADS)

    Fest, B. J.; Wardlaw, T.; Hinko-Najera, N.; Arndt, S. K.

    2015-12-01

    In order to gain a better understanding of the temporal variation in soil methane (CH4) exchange in temperate evergreen eucalypt forests in south-eastern Australia we measured soil CH4 exchange in high temporal resolution (every 2 hours or less) over two consecutive years (Wombat State Forest, Victoria, AUS) and over one year (Warra, Tasmania, AUS) in two temperate Eucalyptus obliqua (L. Her) forests with contrasting annual precipitation (Wombat State Forest = 870 mm yr-1, Warra = 1700 mm yr-1). Both forests were continuous CH4 sinks with the Victorian site having a sink strength of -1.79 kg CH4 ha-1 yr-1 and the Tasmanian site having a sink strength of -3.83 kg CH4 ha-1 yr-1. Our results show that CH4 uptake was strongly controlled by soil moisture at both sites and explained up to 90% of the temporal variability in CH4 uptake. Furthermore, when soil moisture was expressed as soil air filled porosity (AFP) we were able to predict the CH4 uptake of one site by the linear regression between AFP and CH4 uptake from the other site. Soil temperature only had an apparent control over seasonal variation in CH4 uptake during periods when soil moisture and soil temperature were closely correlated. The fluctuation of the generally low soil nitrogen levels did not influence soil CH4 uptake at either site.

  16. Soils, Pores, and NMR

    NASA Astrophysics Data System (ADS)

    Pohlmeier, Andreas; Haber-Pohlmeier, Sabina; Haber, Agnes; Sucre, Oscar; Stingaciu, Laura; Stapf, Siegfried; Blümich, Bernhard

    2010-05-01

    Within Cluster A, Partial Project A1, the pore space exploration by means of Nuclear Magnetic Resonance (NMR) plays a central role. NMR is especially convenient since it probes directly the state and dynamics of the substance of interest: water. First, NMR is applied as relaxometry, where the degree of saturation but also the pore geometry controls the NMR signature of natural porous systems. Examples are presented where soil samples from the Selhausen, Merzenhausen (silt loams), and Kaldenkirchen (sandy loam) test sites are investigated by means of Fast Field Cycling Relaxometry at different degrees of saturation. From the change of the relaxation time distributions with decreasing water content and by comparison with conventional water retention curves we conclude that the fraction of immobile water is characterized by T1 < 5 ms. Moreover, the dependence of the relaxation rate on magnetic field strength allows the identification of 2D diffusion at the interfaces as the mechanism which governs the relaxation process (Pohlmeier et al. 2009). T2 relaxation curves are frequently measured for the rapid characterization of soils by means of the CPMG echo train. Basically, they contain the same information about the pore systems like T1 curves, since mostly the overall relaxation is dominated by surface relaxivity and the surface/volume ratio of the pores. However, one must be aware that T2 relaxation is additionally affected by diffusion in internal gradients, and this can be overcome by using sufficiently short echo times and low magnetic fields (Stingaciu et al. 2009). Second, the logic continuation of conventional relaxation measurements is the 2-dimensional experiment, where prior to the final detection of the CPMG echo train an encoding period is applied. This can be T1-encoding by an inversion pulse, or T2 encoding by a sequence of 90 and 180° pulses. During the following evolution time the separately encoded signals can mix and this reveals information about

  17. Stability of two-dimensional (2D) natural convection flows in air-filled differentially heated cavities: 2D/3D disturbances

    NASA Astrophysics Data System (ADS)

    Xin, Shihe; Le Quéré, Patrick

    2012-06-01

    Following our previous two-dimensional (2D) studies of flows in differentially heated cavities filled with air, we studied the stability of 2D natural convection flows in these cavities with respect to 3D periodic perturbations. The basis of the numerical methods is a time-stepping code using the Chebyshev spectral collocation method and the direct Uzawa method for velocity-pressure coupling. Newton's iteration, Arnoldi's method and the continuation method have been used in order to, respectively, compute the 2D steady-state base solution, estimate the leading eigenmodes of the Jacobian and perform linear stability analysis. Differentially heated air-filled cavities of aspect ratios from 1 to 7 were investigated. Neutral curves (Rayleigh number versus wave number) have been obtained. It turned out that only for aspect ratio 7, 3D stationary instability occurs at slightly higher Rayleigh numbers than the onset of 2D time-dependent flow and that for other aspect ratios 3D instability always takes place before 2D time-dependent flows. 3D unstable modes are stationary and anti-centro-symmetric. 3D nonlinear simulations revealed that the corresponding pitchfork bifurcations are supercritical and that 3D instability leads only to weak flow in the third direction. Further 3D computations are also performed at higher Rayleigh number in order to understand the effects of the weak 3D fluid motion on the onset of time-dependent flow. 3D flow structures are responsible for the onset of time-dependent flow for aspect ratios 1, 2 and 3, while for larger aspect ratios they do not alter the transition scenario, which was observed in the 2D cases and that vertical boundary layers become unstable to traveling waves.

  18. SEM and FIB-SEM investigations on potential gas shales in the Dniepr-Donets Basin (Ukraine): pore space evolution in organic matter during thermal maturation

    NASA Astrophysics Data System (ADS)

    Misch, D.; Mendez-Martin, F.; Hawranek, G.; Onuk, P.; Gross, D.; Sachsenhofer, R. F.

    2016-02-01

    Porosity and permeability are essential parameters for reservoir rocks. Techniques developed for conventional reservoir rocks characterized by large pores, cannot be applied to study gas shales. Therefore, high resolution techniques are increasingly used to determine reservoir quality of shale gas plays. Within the frame of the recent study, Upper Visean black shales (“Rudov Beds”) from the Dniepr-Donets-Basin (DDB, Ukraine) were characterized by X-ray diffraction, conventional SEM imaging and FIB/BIB-SEM. According to SEM and FIB/BIB-SEM data, nanopores are not abundant in primary macerals (e.g., vitrinite) even in overmature rocks, whereas they develop within secondary organic matter (bitumen) formed mainly at gas window maturity. Frequently occurring sub-micrometre porosity, probably related to gas generation from bituminous organic matter, was detected within mudstones at a vitrinite reflectance > 2.0 % Rr. However, such pores have also been detected occasionally in solid bitumen at oil window maturity (0.9 % Rr). Authigenic nanoscale clay minerals and calcite occur within pyrobitumen at gas window maturity. Furthermore, Rudov Beds can be subdivided into mineralogical facies zones by SEM imaging and X-ray diffraction. A basin-centred, brittle siliceous facies is most likely caused by increased contribution from deeper water radiolaria and is separated from a marginal clayey and carbonate-rich facies.

  19. Soil methane oxidation in both dry and wet temperate eucalypt forests shows a near-identical relationship with soil air-filled porosity

    NASA Astrophysics Data System (ADS)

    Fest, Benedikt J.; Hinko-Najera, Nina; Wardlaw, Tim; Griffith, David W. T.; Livesley, Stephen J.; Arndt, Stefan K.

    2017-01-01

    Well-drained, aerated soils are important sinks for atmospheric methane (CH4) via the process of CH4 oxidation by methane-oxidising bacteria (MOB). This terrestrial CH4 sink may contribute towards climate change mitigation, but the impact of changing soil moisture and temperature regimes on CH4 uptake is not well understood in all ecosystems. Soils in temperate forest ecosystems are the greatest terrestrial CH4 sink globally. Under predicted climate change scenarios, temperate eucalypt forests in south-eastern Australia are predicted to experience rapid and extreme changes in rainfall patterns, temperatures and wild fires. To investigate the influence of environmental drivers on seasonal and inter-annual variation of soil-atmosphere CH4 exchange, we measured soil-atmosphere CH4 exchange at high-temporal resolution (< 2 h) in a dry temperate eucalypt forest in Victoria (Wombat State Forest, precipitation 870 mm yr-1) and in a wet temperature eucalypt forest in Tasmania (Warra Long-Term Ecological Research site, 1700 mm yr-1). Both forest soil systems were continuous CH4 sinks of -1.79 kg CH4 ha-1 yr-1 in Victoria and -3.83 kg CH4 ha-1 yr-1 in Tasmania. Soil CH4 uptake showed substantial temporal variation and was strongly controlled by soil moisture at both forest sites. Soil CH4 uptake increased when soil moisture decreased and this relationship explained up to 90 % of the temporal variability. Furthermore, the relationship between soil moisture and soil CH4 flux was near-identical at both forest sites when soil moisture was expressed as soil air-filled porosity (AFP). Soil temperature only had a minor influence on soil CH4 uptake. Soil nitrogen concentrations were generally low and fluctuations in nitrogen availability did not influence soil CH4 uptake at either forest site. Our data suggest that soil MOB activity in the two forests was similar and that differences in soil CH4 exchange between the two forests were related to differences in soil moisture and

  20. Hyperbolic regions in flows through three-dimensional pore structures.

    PubMed

    Hyman, Jeffrey D; Winter, C Larrabee

    2013-12-01

    Finite time Lyapunov exponents are used to determine expanding, contracting, and hyperbolic regions in computational simulations of laminar steady-state fluid flows within realistic three dimensional pore structures embedded within an impermeable matrix. These regions correspond approximately to pores where flow converges (contraction) or diverges (expansion), and to throats between pores where the flow mixes (hyperbolic). The regions are sparse and disjoint from one another, occupying only a small percentage of the pore space. Nonetheless, nearly every percolating fluid particle trajectory passes through several hyperbolic regions indicating that the effects of in-pore mixing are distributed throughout an entire pore structure. Furthermore, the observed range of fluid dynamics evidences two scales of heterogeneity within each of these flow fields. There is a larger scale that affects dispersion of fluid particle trajectories across the connected network of pores and a relatively small scale of nonuniform distributions of velocities within an individual pore.

  1. Protein crystal nucleation in pores

    PubMed Central

    Nanev, Christo N.; Saridakis, Emmanuel; Chayen, Naomi E.

    2017-01-01

    The most powerful method for protein structure determination is X-ray crystallography which relies on the availability of high quality crystals. Obtaining protein crystals is a major bottleneck, and inducing their nucleation is of crucial importance in this field. An effective method to form crystals is to introduce nucleation-inducing heterologous materials into the crystallization solution. Porous materials are exceptionally effective at inducing nucleation. It is shown here that a combined diffusion-adsorption effect can increase protein concentration inside pores, which enables crystal nucleation even under conditions where heterogeneous nucleation on flat surfaces is absent. Provided the pore is sufficiently narrow, protein molecules approach its walls and adsorb more frequently than they can escape. The decrease in the nucleation energy barrier is calculated, exhibiting its quantitative dependence on the confinement space and the energy of interaction with the pore walls. These results provide a detailed explanation of the effectiveness of porous materials for nucleation of protein crystals, and will be useful for optimal design of such materials. PMID:28091515

  2. Velocities in Solar Pores

    NASA Astrophysics Data System (ADS)

    Balasubramaniam, K. S.; Keil, S. L.; Smaldone, L. A.

    1996-05-01

    We investigate the three dimensional structure of solar pores and their surroundings using high spatial and spectral resolution data. We present evidence that surface velocities decrease around pores with a corresponding increase in the line-of-sight (LOS) velocities. LOS velocities in pores increase with the strength of the magnetic field. Surface velocities show convergence toward a weak downflow which appear to trace boundaries resembling meso-granular and super granular flows. The observed magnetic fields in the pores appear near these boundaries. We analyze the vertical velocity structure in pores and show that they generally have downflows decreasing exponentially with height, with a scale height of about 90 km. Evidence is also presented for the expanding nature of flux tubes. Finally we describe a phenomenological model for pores. This work was supported by AFOSR Task 2311G3. LAS was partially supported by the Progetto Nazionale Astrofisica e Fisica Cosmica of MURST and Scambi Internazionali of the Universita degli Studi di Napoli Frederico II. National Solar Observatory, NOAO, is operated for the National Science Foundation by AURA, Inc.

  3. An integral-free expression for short-term changes in fault stability due to pore pressure induced when a point load is placed on the pervious boundary of a porous elastic half space containing a fault

    NASA Astrophysics Data System (ADS)

    Chander, Ramesh; Tomar, S. K.

    2014-10-01

    A concentrated load with step-function time behaviour is placed normal to the planar, pervious boundary of a porous elastic half space (PEHS) with compressible constituents. A planar fault exists in the PEHS in such a way that the poroelastic behaviour of the medium is unhindered. We derive an approximate but integral-free expression for CFSCPP, i.e., changes in fault stability due to changes in pore pressure, at a point not too far off the line along which the load acts. But, in the interest of simplicity, the main discussion is focussed on a consideration of CFSCPP at a point P located on the fault at depth z directly beneath the load. It is convenient to introduce dimensionless time t D directly proportional to real time t. The constant of proportionality is 4 c/ z 2, where c is hydraulic diffusivity. The derived approximate expression gives results with an accuracy of greater than 99% for limited values of t D after the load is imposed. We learn from the derived expression that, for a given z, fault stability undergoes an initial sudden decrease commensurate with the undrained pore pressure induced in the PEHS. This is followed by a more gradual decrease in fault stability with increasing t D until a minimum is reached. The real time t to minimum fault stability increases with z. The magnitude of CFSCPP decreases with z as z -2 for a given t D in the permissible range. The derived expression and the inferences based on it should be useful during earth science investigations of the possible hazards due to reactivation of a pre-existing shallow fault when a civil engineering project involving imposition of a heavy load on the earth's surface is to be executed nearby. They should be useful also for investigations if a shallow earthquake occurs near such a project soon after its execution.

  4. Capillary Properties of Model Pores.

    NASA Astrophysics Data System (ADS)

    Walsh, Tim J.

    Available from UMI in association with The British Library. Liquid menisci in small pores exhibit a curved surface across which there is a significant pressure difference. In the past it has been difficult to calculate the curvatures, of this class of menisci. Some recent studies have shown that a relatively straightforward, but hitherto neglected, method originated by Mayer & Stowe (1965) and Princen (1969a) can be applied to analyse wedging menisci. However, the method has lacked a comprehensive experimental verification. This investigation follows on from the previously limited studies. A standardised method for the application of the analysis is described, the results from which are compared to observations made using modified experimental procedures. The behaviour of the capillary surfaces formed in several model pores are analysed with the method. The model systems studied are rectangular ducts, the pores formed by a rod in an angled corner, by two contacting rods and a plate and the space between a rod and a plate. For the latter two shapes the analysis is extended to include systems of mixed wettability which have a particular bearing on enhanced oil recovery operations. Experiments in which curvatures are inferred from observations of capillary rise, are performed using two comparative techniques. An involved procedure confirms predictions of meniscus curvature to within 0.3%. Use of a more straightforward, through less accurate, technique enables variations of curvature with tube shape or contact angle(s) to be conveniently studied. Results obtained are excellent and confirm the theory within the determined experimental errors. (Abstract shortened by UMI.).

  5. Pore pressure embrittlement in a volcanic edifice

    NASA Astrophysics Data System (ADS)

    Farquharson, Jamie; Heap, Michael J.; Baud, Patrick; Reuschlé, Thierry; Varley, Nick R.

    2016-01-01

    The failure mode of porous rock in compression—dilatant or compactant—is largely governed by the overlying lithostatic pressure and the pressure of pore fluids within the rock (Wong, Solid Earth 102:3009-3025, 1997), both of which are subject to change in space and time within a volcanic edifice. While lithostatic pressure will tend to increase monotonously with depth due to the progressive accumulation of erupted products, pore pressures are prone to fluctuations (during periods of volcanic unrest, for example). An increase in pore fluid pressure can result in rock fracture, even at depths where the lithostatic pressure would otherwise preclude such dilatant behaviour—a process termed pore fluid-induced embrittlement. We explore this phenomenon through a series of targeted triaxial experiments on typical edifice-forming andesites (from Volcán de Colima, Mexico). We first show that increasing pore pressure over a range of timescales (on the order of 1 min to 1 day) can culminate in brittle failure of otherwise intact rock. Irrespective of the pore pressure increase rate, we record comparable accelerations in acoustic emission and strain prior to macroscopic failure. We further show that oscillating pore fluid pressures can cause iterative and cumulative damage, ultimately resulting in brittle failure under relatively low effective mean stress conditions. We find that macroscopic failure occurs once a critical threshold of damage is surpassed, suggesting that only small increases in pore pressure may be necessary to trigger failure in previously damaged rocks. Finally, we observe that inelastic compaction of volcanic rock (as we may expect in much of the deep edifice) can be overprinted by shear fractures due to this mechanism of embrittlement. Pore fluid-induced embrittlement of edifice rock during volcanic unrest is anticipated to be highest closer to the conduit and, as a result, may assist in the development of a fractured halo zone surrounding the

  6. Low pore connectivity in natural rock.

    PubMed

    Hu, Qinhong; Ewing, Robert P; Dultz, Stefan

    2012-05-15

    As repositories for CO(2) and radioactive waste, as oil and gas reservoirs, and as contaminated sites needing remediation, rock formations play a central role in energy and environmental management. The connectivity of the rock's porespace strongly affects fluid flow and solute transport. This work examines pore connectivity and its implications for fluid flow and chemical transport. Three experimental approaches (imbibition, tracer concentration profiles, and imaging) were used in combination with network modeling. In the imbibition results, three types of imbibition slope [log (cumulative imbibition) vs. log (imbibition time)] were found: the classical 0.5, plus 0.26, and 0.26 transitioning to 0.5. The imbibition slope of 0.26 seen in Indiana sandstone, metagraywacke, and Barnett shale indicates low pore connectivity, in contrast to the slope of 0.5 seen in the well-connected Berea sandstone. In the tracer profile work, rocks exhibited different distances to the plateau porosity, consistent with the pore connectivity from the imbibition tests. Injection of a molten metal into connected pore spaces, followed by 2-D imaging of the solidified alloy in polished thin sections, allowed direct assessment of pore structure and lateral connection in the rock samples. Pore-scale network modeling gave results consistent with measurements, confirming pore connectivity as the underlying cause of both anomalous behaviors: imbibition slope not having the classical value of 0.5, and accessible porosity being a function of distance from the edge. A poorly connected porespace will exhibit anomalous behavior in fluid flow and chemical transport, such as a lower imbibition slope (in air-water system) and diffusion rate than expected from classical behavior.

  7. Low Pore Connectivity in Natural Rock

    SciTech Connect

    Hu, Qinhong; Ewing, Robert P.; Dultz, Stefan

    2012-05-15

    As repositories for CO₂ and radioactive waste, as oil and gas reservoirs, and as contaminated sites needing remediation, rock formations play a central role in energy and environmental management. The connectivity of the rock's porespace strongly affects fluid flow and solute transport. This work examines pore connectivity and its implications for fluid flow and chemical transport. Three experimental approaches (imbibition, tracer concentration profiles, and imaging) were used in combination with network modeling. In the imbibition results, three types of imbibition slope [log (cumulative imbibition) vs. log (imbibition time)] were found: the classical 0.5, plus 0.26, and 0.26 transitioning to 0.5. The imbibition slope of 0.26 seen in Indiana sandstone, metagraywacke, and Barnett shale indicates low pore connectivity, in contrast to the slope of 0.5 seen in the well-connected Berea sandstone. In the tracer profile work, rocks exhibited different distances to the plateau porosity, consistent with the pore connectivity from the imbibition tests. Injection of a molten metal into connected pore spaces, followed by 2-D imaging of the solidified alloy in polished thin sections, allowed direct assessment of pore structure and lateral connection in the rock samples. Pore-scale network modeling gave results consistent with measurements, confirming pore connectivity as the underlying cause of both anomalous behaviors: imbibition slope not having the classical value of 0.5, and accessible porosity being a function of distance from the edge. A poorly connected porespace will exhibit anomalous behavior in fluid flow and chemical transport, such as a lower imbibition slope (in air–water system) and diffusion rate than expected from classical behavior.

  8. Magnetic-resonance pore imaging of nonsymmetric microscopic pore shapes

    NASA Astrophysics Data System (ADS)

    Hertel, Stefan Andreas; Wang, Xindi; Hosking, Peter; Simpson, M. Cather; Hunter, Mark; Galvosas, Petrik

    2015-07-01

    Imaging of the microstructure of porous media such as biological tissue or porous solids is of high interest in health science and technology, engineering and material science. Magnetic resonance pore imaging (MRPI) is a recent technique based on nuclear magnetic resonance (NMR) which allows us to acquire images of the average pore shape in a given sample. Here we provide details on the experimental design, challenges, and requirements of MRPI, including its calibration procedures. Utilizing a laser-machined phantom sample, we present images of microscopic pores with a hemiequilateral triangular shape even in the presence of NMR relaxation effects at the pore walls. We therefore show that MRPI is applicable to porous samples without a priori knowledge about their pore shape and symmetry. Furthermore, we introduce "MRPI mapping," which combines MRPI with conventional magnetic resonance imaging (MRI). This enables one to resolve microscopic pore sizes and shapes spatially, thus expanding the application of MRPI to samples with heterogeneous distributions of pores.

  9. Model Pores of Molecular Dimension

    PubMed Central

    Quinn, J. A.; Anderson, J. L.; Ho, W. S.; Petzny, W. J.

    1972-01-01

    Extremely uniform pores of near molecular dimension can be formed by the irradiation-etching technique first demonstrated by Price and Walker. The technique has now been developed to the stage where it can be used to fabricate model membranes for examining the various steric, hydrodynamic, and electrodynamic phenomena encountered in transport through molecular-size pores. Methods for preparing and characterizing membranes with pores as small as 25 A (radius) are described in this paper. Results on pore size determination via Knudsen gas flow and electrolyte conduction are compared. Pore wall modification by monolayer deposition is also discussed. PMID:4339801

  10. 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.

  11. Drainage Studies Using Pore-Scale Approaches

    NASA Astrophysics Data System (ADS)

    Liu, E. B.; Reed, A. H.; Hilpert, M.

    2007-12-01

    The process of drainage has wide spread applications in soil hydrology, irrigation, and the remediation of contaminants in the subsurface. In this paper, we present the comparison of experimental and pore-scale modeling results for drainage. Using a HD-500 microCT system, X-ray tomographic images (21 micron voxels) of saturation during a drainage experiment were obtained in a porous medium consisting of 20/30 mesh (590- 840 microns) Accusand. Utilizing the segmented microtomographic images of the pore space, we modeled drainage using two pore-scale approaches: (1) the pore-morphology-based simulator (PMBS) developed by Hilpert and Miller (2001), and (2) a Lattice Boltzmann (LB) model. Invasion pathways and pressure-saturation relations obtained from both the PMBS and the LB model were compared with those obtained from experiments. The results of PMBS modeling displayed good agreement with experimental observations, except at high suction and low water saturation values, where both CT resolution and model assumptions become an issue. The LB model is currently being refined, and the results of these simulations will also be presented.

  12. Pore Scale Analysis of Oil Shale/Sands Pyrolysis

    SciTech Connect

    Lin, Chen-Luh; Miller, Jan

    2011-03-01

    There are important questions concerning the quality and volume of pore space that is created when oil shale is pyrolyzed for the purpose of producing shale oil. In this report, 1.9 cm diameter cores of Mahogany oil shale were pyrolyzed at different temperatures and heating rates. Detailed 3D imaging of core samples was done using multiscale X-ray computed tomography (CT) before and after pyrolysis to establish the pore structure. The pore structure of the unreacted material was not clear. Selected images of a core pyrolyzed at 400oC were obtained at voxel resolutions from 39 microns (Οm) to 60 nanometers (nm). Some of the pore space created during pyrolysis was clearly visible at these resolutions and it was possible to distinguish between the reaction products and the host shale rock. The pore structure deduced from the images was used in Lattice Boltzmann simulations to calculate the permeability in the pore space. The permeabilities of the pyrolyzed samples of the silicate-rich zone were on the order of millidarcies, while the permeabilities of the kerogen-rich zone after pyrolysis were very anisotropic and about four orders of magnitude higher.

  13. Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria.

    PubMed

    Wolf, Alexandra B; Vos, Michiel; de Boer, Wietse; Kowalchuk, George A

    2013-01-01

    The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.

  14. X-ray CT analysis of pore structure in sand

    NASA Astrophysics Data System (ADS)

    Mukunoki, Toshifumi; Miyata, Yoshihisa; Mikami, Kazuaki; Shiota, Erika

    2016-06-01

    The development of microfocused X-ray computed tomography (CT) devices enables digital imaging analysis at the pore scale. The applications of these devices are diverse in soil mechanics, geotechnical and geoenvironmental engineering, petroleum engineering, and agricultural engineering. In particular, the imaging of the pore space in porous media has contributed to numerical simulations for single-phase and multiphase flows or contaminant transport through the pore structure as three-dimensional image data. These obtained results are affected by the pore diameter; therefore, it is necessary to verify the image preprocessing for the image analysis and to validate the pore diameters obtained from the CT image data. Moreover, it is meaningful to produce the physical parameters in a representative element volume (REV) and significant to define the dimension of the REV. This paper describes the underlying method of image processing and analysis and discusses the physical properties of Toyoura sand for the verification of the image analysis based on the definition of the REV. On the basis of the obtained verification results, a pore-diameter analysis can be conducted and validated by a comparison with the experimental work and image analysis. The pore diameter is deduced from Young-Laplace's law and a water retention test for the drainage process. The results from previous study and perforated-pore diameter originally proposed in this study, called the voxel-percolation method (VPM), are compared in this paper. In addition, the limitations of the REV, the definition of the pore diameter, and the effectiveness of the VPM for an assessment of the pore diameter are discussed.

  15. Hydrate formation and growth in pores

    NASA Astrophysics Data System (ADS)

    Jung, Jong-Won; Santamarina, J. Carlos

    2012-04-01

    Gas hydrates consist of guest gas molecules encaged in water cages. Methane hydrate forms in marine and permafrost sediments. In this study, we use optical, mechanical and electrical measurements to monitor hydrate formation and growth in small pores to better understand the hydrate pore habit in hydrate-bearing sediments. Hydrate formation in capillary tubes exposes the complex and dynamic interactions between nucleation, gas diffusion and gas solubility. The observation of hydrate growth in a droplet between transparent plates shows that the hydrate shell does not grow homogeneously but advances in the form of lobes that invade the water phase; in fact, the hydrate shell must be discontinuous and possibly cracked to justify the relatively fast growth rates observed in these experiments. Volume expansion during hydrate formation causes water to flow out of menisci; expelled water either spreads on the surface of water-wet substrates and forms a thin hydrate sheet, or remains next to menisci when substrates are oil-wet. Hydrate formation is accompanied by ion exclusion, yet, there is an overall increase in electrical resistance during hydrate formation. Hydrate growth may become salt-limited in trapped water conditions; in this case, aqueous brine and gas CH4 may be separated by hydrate and the three-phase system remains stable within the pore space of sediments.

  16. Triggered pore-forming agents

    DOEpatents

    Bayley, Hagan; Walker, Barbara J.; Chang, Chung-yu; Niblack, Brett; Panchal, Rekha

    1998-01-01

    An inactive pore-forming agent which is activated to lytic function by a condition such as pH, light, heat, reducing potential, or metal ion concentration, or substance such as a protease, at the surface of a cell.

  17. Nanoscale Pore Imaging and Pore Scale Fluid Flow Modeling in Chalk

    SciTech Connect

    Tomutsa, Liviu; Silin, Dmitriy

    2004-08-19

    For many rocks of high economic interest such as chalk, diatomite, tight gas sands or coal, nanometer scale resolution is needed to resolve the 3D-pore structure, which controls the flow and trapping of fluids in the rocks. Such resolutions cannot be achieved with existing tomographic technologies. A new 3D imaging method, based on serial sectioning and using the Focused Ion Beam (FIB) technology has been developed. FIB allows for the milling of layers as thin as 10 nanometers by using accelerated Ga+ ions to sputter atoms from the sample surface. After each milling step, as a new surface is exposed, a 2D image of this surface is generated. Next, the 2D images are stacked to reconstruct the 3D pore or grain structure. Resolutions as high as 10 nm are achievable using such a technique. A new robust method of pore-scale fluid flow modeling has been developed and applied to sandstone and chalk samples. The method uses direct morphological analysis of the pore space to characterize the petrophysical properties of diverse formations. Not only petrophysical properties (porosity, permeability, relative permeability and capillary pressures) can be computed but also flow processes, such as those encountered in various IOR approaches, can be simulated. Petrophysical properties computed with the new method using the new FIB data will be presented. Present study is a part of the development of an Electronic Core Laboratory at LBNL/UCB.

  18. Pore scale dynamics underlying the motion of drainage fronts in porous media

    NASA Astrophysics Data System (ADS)

    Moebius, Franziska; Or, Dani

    2014-11-01

    Fluid displacement fronts in porous media exhibit a peculiar duality; the seemingly regular macroscopic motion of the front is propelled by numerous and irregular pore scale interfacial jumps. These pore scale events shape emergent front morphology, affect phase entrapment behind a front, and are likely important for colloidal mobilization and solute dispersion at the front. We present an experimental study focusing on drainage fluid front invasion dynamics through sintered glass beads using a high-speed camera and rapid capillary pressure measurements to resolve pore scale invasion events over a wide range of boundary conditions (flow rates and gravitational influences). We distinguished three types of "pores": geometrical pores deduced from image analyses; individual pore invasion volumes imaged during displacement; and pore volumes deduced from capillary pressure fluctuations during constant withdrawal rates. The resulting pore volume distributions were remarkably similar for slow drainage rates. Invaded pore volumes were not affected by gravitational forces, however with increased viscous forces (higher displacement rates) the fraction of small invaded volumes increased. Capillary pressure fluctuations were exponentially distributed in agreement with findings from previous studies. The distribution of pressure fluctuations exhibited a distinct cutoff concurrent with the onset of simultaneous invasion events. The study highlights the different manifestation of "pores" and their sensitivity to external (macroscopic) boundary conditions. The remarkable similarity of geometrical and pressure-deduced pore spaces offers opportunities for deducing pore size distribution dynamically.

  19. Development of a closed pore insulation material

    NASA Technical Reports Server (NTRS)

    Tobin, A.; Feldman, C.; Russak, M.; Reichman, J.

    1973-01-01

    A closed pore ceramic foam insulation material (CPI) has been developed that offers possibilities for use as a reusable external heat shield for the NASA manned space shuttle. The outstanding characteristics of CPI are: (1) negligible water absorption due to a noninterconnecting network of cells; (2) high emittance at room and elevated temperature; (3) ability to survive at least 10 simulated reentry cycles to 1500 K using radiant heat lamps to simulate the reentry heat fluxes; (4) ability to survive, with no change in properties or appearance, at least 10 simulated plasma arc jet cycles to 1500 K (with the exception of some stress cracks induced either by the unduly severe nature of the initial arc splash heating pulse or by improper mechanical holding of the specimen in the test fixture); (5) strength (flexure); and (6) a low thermal conductivity throughout the temperature range of interest for the space shuttle.

  20. Gas Hydrate and Pore Pressure

    NASA Astrophysics Data System (ADS)

    Tinivella, Umberta; Giustiniani, Michela

    2014-05-01

    Many efforts have been devoted to quantify excess pore pressures related to gas hydrate dissociation in marine sediments below the BSR using several approaches. Dissociation of gas hydrates in proximity of the BSR, in response to a change in the physical environment (i.e., temperature and/or pressure regime), can liberate excess gas incrising the local pore fluid pressure in the sediment, so decreasing the effective normal stress. So, gas hydrate dissociation may lead to excess pore pressure resulting in sediment deformation or failure, such as submarine landslides, sediment slumping, pockmarks and mud volcanoes, soft-sediment deformation and giant hummocks. Moreover, excess pore pressure may be the result of gas hydrate dissociation due to continuous sedimentation, tectonic uplift, sea level fall, heating or inhibitor injection. In order to detect the presence of the overpressure below the BSR, we propose two approachs. The fist approach models the BSR depth versus pore pressure; in fact, if the free gas below the BSR is in overpressure condition, the base of the gas hydrate stability is deeper with respect to the hydrostatic case. This effect causes a discrepancy between seismic and theoretical BSR depths. The second approach models the velocities versus gas hydrate and free gas concentrations and pore pressure, considering the approximation of the Biot theory in case of low frequency, i.e. seismic frequency. Knowing the P and S seismic velocity from seismic data analysis, it is possibile to jointly estimate the gas hydrate and free gas concentrations and the pore pressure regime. Alternatively, if the S-wave velocity is not availbale (due to lack of OBS/OBC data), an AVO analysis can be performed in order to extract information about Poisson ratio. Our modeling suggests that the areas characterized by shallow waters (i.e., areas in which human infrastructures, such as pipelines, are present) are significantly affected by the presence of overpressure condition

  1. Stochastic generation of explicit pore structures by thresholding Gaussian random fields

    SciTech Connect

    Hyman, Jeffrey D.; Winter, C. Larrabee

    2014-11-15

    We provide a description and computational investigation of an efficient method to stochastically generate realistic pore structures. Smolarkiewicz and Winter introduced this specific method in pores resolving simulation of Darcy flows (Smolarkiewicz and Winter, 2010 [1]) without giving a complete formal description or analysis of the method, or indicating how to control the parameterization of the ensemble. We address both issues in this paper. The method consists of two steps. First, a realization of a correlated Gaussian field, or topography, is produced by convolving a prescribed kernel with an initial field of independent, identically distributed random variables. The intrinsic length scales of the kernel determine the correlation structure of the topography. Next, a sample pore space is generated by applying a level threshold to the Gaussian field realization: points are assigned to the void phase or the solid phase depending on whether the topography over them is above or below the threshold. Hence, the topology and geometry of the pore space depend on the form of the kernel and the level threshold. Manipulating these two user prescribed quantities allows good control of pore space observables, in particular the Minkowski functionals. Extensions of the method to generate media with multiple pore structures and preferential flow directions are also discussed. To demonstrate its usefulness, the method is used to generate a pore space with physical and hydrological properties similar to a sample of Berea sandstone. -- Graphical abstract: -- Highlights: •An efficient method to stochastically generate realistic pore structures is provided. •Samples are generated by applying a level threshold to a Gaussian field realization. •Two user prescribed quantities determine the topology and geometry of the pore space. •Multiple pore structures and preferential flow directions can be produced. •A pore space based on Berea sandstone is generated.

  2. Geostatistical Modeling of Pore Velocity

    SciTech Connect

    Devary, J.L.; Doctor, P.G.

    1981-06-01

    A significant part of evaluating a geologic formation as a nuclear waste repository involves the modeling of contaminant transport in the surrounding media in the event the repository is breached. The commonly used contaminant transport models are deterministic. However, the spatial variability of hydrologic field parameters introduces uncertainties into contaminant transport predictions. This paper discusses the application of geostatistical techniques to the modeling of spatially varying hydrologic field parameters required as input to contaminant transport analyses. Kriging estimation techniques were applied to Hanford Reservation field data to calculate hydraulic conductivity and the ground-water potential gradients. These quantities were statistically combined to estimate the groundwater pore velocity and to characterize the pore velocity estimation error. Combining geostatistical modeling techniques with product error propagation techniques results in an effective stochastic characterization of groundwater pore velocity, a hydrologic parameter required for contaminant transport analyses.

  3. 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.

  4. Restricted Transport in Small Pores

    PubMed Central

    Anderson, John L.; Quinn, John A.

    1974-01-01

    The basic hydrodynamic equations governing transport in submicron pores are reexamined. Conditions necessary for a simplified, one-dimensional treatment of the diffusion/convection process are established. Steric restrictions and Brownian motion are incorporated directly into the resulting model. Currently available fluid mechanical results are used to evaluate an upper limit on hindered diffusion; this limit is valid for small particle-to-pore ratios. Extensions of the analysis are shown to depend on numerical solutions of the related hydrodynamic problem, that of asymmetrical particle motion in a bounded fluid. PMID:4813157

  5. PORE CONNECTIVITY, EPISODIC FLOW, AND UNSATURATED DIFFUSION IN FRACTURED TUFF

    SciTech Connect

    Q. Hu; R.P. Ewing; L. Tomutsa; M.J. Singleton

    2006-02-21

    We use an integrated approach consisting of experiments and complementary pore-scale network modeling to investigate the occurrence of sparsely connected pore spaces in rock matrices at Yucca Mountain, Nevada, and their implications for matrix diffusion. Imbibition results indicate that pore spaces in devitrified tuff are not well-connected, and that this lack of connectivity is further compounded by episodic flow in fractured devitrified tuff with low matrix permeability. A rigorous methodology for investigating chemical transport in fractured rock under episodic conditions, employing a suite of both sorbing and non-sorbing tracers (including radionuclides U-235, Np-237, and Pu-242), has been developed and implemented. In addition, gas diffusion and synchrotron microtomography techniques have been under development to examine the scaling issues of diffusion and pore connectivity. Preliminary results from experiments and modeling work are presented in this paper, confirming the need to reexamine our understanding of matrix diffusion and to evaluate the impact on diffusive radionuclide retardation of episodic fracture flow and low pore connectivity.

  6. Pore Connectivity, Episodic Flow, and Unsaturated Diffusion in Fractured Tuff

    SciTech Connect

    Hu, Q; Ewing, R P; Tomutsa, L; Singleton, M J

    2006-01-30

    We use an integrated approach consisting of experiments and complementary pore-scale network modeling to investigate the occurrence of sparsely connected pore spaces in rock matrices at Yucca Mountain, Nevada, and its implication to matrix diffusion. Imbibition results indicate that pore spaces in devitrified tuff are not well-connected, and that this lack of connectivity is further compounded by episodic flow in fractured devitrified tuff with low matrix permeability. A rigorous methodology for investigating chemical transport in fractured rock under episodic conditions, employing a suite of both sorbing and non-sorbing tracers (including radionuclides U-235, Np-237, and Pu-242), has been developed and implemented. In addition, gas diffusion and synchrotron microtomography techniques have been under development to examine the scaling issues of diffusion and pore connectivity. Preliminary results from experiments and modeling work are presented in this paper, in order to reexamine our understanding of matrix diffusion and to evaluate the impact on diffusive radionuclide retardation of episodic fracture flow and low pore connectivity.

  7. GATED PORES IN THE FERRITIN PROTEIN NANOCAGE

    PubMed Central

    Theil, Elizabeth C.; Liu, Xiaofeng S.; Tosha, Takehiko

    2008-01-01

    Synopsis and pictogram: Gated pores in the ferritin family of protein nanocages, illustrated in the pictogram, control transfer of ferrous iron into and out of the cages by regulating contact between hydrated ferric oxide mineral inside the protein cage, and reductants such as FMNH2 on the outside. The structural and functional homology between the gated ion channel proteins in inaccessible membranes and gated ferritin pores in the stable, water soluble nanoprotein, make studies of ferritin pores models for gated pores in many ion channel proteins. Properties of ferritin gated pores, which control rates of FMNH2 reduction of ferric iron in hydrated oxide minerals inside the protein nanocage, are discussed in terms of the conserved pore gate residues (arginine 72-apspartate 122 and leucine 110-leucine 134), of pore sensitivity to heat at temperatures 30 °C below that of the nanocage itself, and of pore sensitivity to physiological changes in urea (1–10 mM). Conditions which alter ferritin pore structure/function in solution, coupled with the high evolutionary conservation of the pore gates, suggest the presence of molecular regulators in vivo that recognize the pore gates and hold them either closed or open, depending on biological iron need. The apparent homology between ferrous ion transport through gated pores in the ferritin nanocage and ion transport through gated pores in ion channel proteins embedded in cell membranes, make studies of water soluble ferritin and the pore gating folding/unfolding a useful model for other gated pores. PMID:19262678

  8. Smectic pores and defect cores

    PubMed Central

    Matsumoto, Elisabetta A.; Kamien, Randall D.; Santangelo, Christian D.

    2012-01-01

    Riemann's minimal surfaces, a one-parameter family of minimal surfaces, describe a bicontinuous lamellar system with pores connecting alternating layers. We demonstrate explicitly that Riemann's minimal surfaces are composed of a nonlinear sum of two oppositely handed helicoids. PMID:24098846

  9. Membrane pores induced by magainin

    SciTech Connect

    Ludtke, S.J.; He, Ke; Heller, W.T.

    1996-10-29

    Magainin, found in the skin of Xenopus laevis, belongs to a broad class of antimicrobial peptides which kill bacteria by permeabilizing the cytoplasmic membrane but do not lyse eukaryotic cells. The 23-residue peptide has been shown to form an amphiphilic helix when associated with membranes. However, its molecular mechanism of action has been controversial. Oriented circular dichroism has detected helical magainin oriented perpendicular to the plane of the membrane at high peptide concentrations, but Raman, fluorescence, differential scanning calorimetry, and NMR all indicate that the peptide is associated with the head groups of the lipid bilayer. Here we show that neutron in-plane scattering detects pores formed by magainin 2 in membranes only when a substantial fraction of the peptide is oriented perpendicular to the membrane. The pores are almost twice as large as the alamethicin pores. On the basis of the in-plane scattering data, we propose a toroidal (or wormhole) model, which differs from the barrel-stave model of alamethicin in that the lipid bends back on itself like the inside of a torus. The bending requires a lateral expansion in the head group region of the bilayer. Magainin monomers play the role of fillers in the expansion region thereby stabilizing the pore. This molecular configuration is consistent with all published magainin data. 33 refs., 5 figs.

  10. Triggered pore-forming agents

    DOEpatents

    Bayley, H.; Walker, B.J.; Chang, C.Y.; Niblack, B.; Panchal, R.

    1998-07-07

    An inactive pore-forming agent is revealed which is activated to lytic function by a condition such as pH, light, heat, reducing potential, or metal ion concentration, or substance such as a protease, at the surface of a cell. 30 figs.

  11. Heterogeneous melting of methane confined in nano-pores.

    PubMed

    Dundar, E; Boulet, P; Wexler, C; Firlej, L; Llewellyn, Ph; Kuchta, B

    2016-10-14

    The melting transition of methane adsorbed in nanopores has been studied and compared in two types of structures: carbon slits pores and square shaped channels. We show that the nano-confinement not only modifies the temperatures of phase transformation but also induces strong space heterogeneity of the adsorbate. We emphasize the role of the structural heterogeneity on the mechanism of melting: in nanometric pores, each adsorbed layer exhibits different mechanisms of structural transformation and the notion of a unique transition temperature is not well defined.

  12. Heterogeneous melting of methane confined in nano-pores

    NASA Astrophysics Data System (ADS)

    Dundar, E.; Boulet, P.; Wexler, C.; Firlej, L.; Llewellyn, Ph.; Kuchta, B.

    2016-10-01

    The melting transition of methane adsorbed in nanopores has been studied and compared in two types of structures: carbon slits pores and square shaped channels. We show that the nano-confinement not only modifies the temperatures of phase transformation but also induces strong space heterogeneity of the adsorbate. We emphasize the role of the structural heterogeneity on the mechanism of melting: in nanometric pores, each adsorbed layer exhibits different mechanisms of structural transformation and the notion of a unique transition temperature is not well defined.

  13. Slow Desorption of Phenanthrene from Silica Particles: Influence of Pore Size, Pore Water, and Aging Time

    SciTech Connect

    Huesemann, Michael H.; Fortman, Timothy J.; Riley, Robert G.; Thompson, Christopher J.; Wang, Zheming; Truex, Michael J.; Peyton, Brent M.

    2006-01-16

    When micro-porous and meso-porous silica particles were exposed to aqueous phenanthrene solutions for various durations it was observed that sorbed-phase phenanthrene concentrations increased with aging time only for meso-porous but not micro-porous silicas. Desorption equilibrium was reached almost instantaneously for the micro-porous particles while both the rate and extent of desorption decreased with increasing aging time for the meso-porous silicas. These findings indicate that phenanthrene can be sequestered within the internal pore-space of meso-porous silicas while the internal surfaces of micro-porous silicas are not accessible to phenanthrene sorption, possibly due to the presence of physi- or chemi-sorbed water that may sterically hinder the diffusion of phenanthrene inside water-filled micro-pores. By contrast, the internal surfaces of these micro-porous silicas are accessible to phenanthrene when aging methods are employed which assure that pores are devoid of physi-sorbed water. Consequently, when phenanthrene was incorporated into these particles using either supercritical CO2 or via solvent soaking, the aqueous desorption kinetics were extremely slow indicating effective sequestration of phenanthrene inside micro-porous particles. Finally, a two-compartment conceptual model is used to interpret the experimental findings.

  14. Precipitation in pores: A geochemical frontier

    DOE PAGES

    Stack, Andrew G.

    2015-07-29

    This article's purpose is to review some of the recent research in which geochemists have examined precipitation of solid phases in porous media, particularly in pores a few nanometers in diameter (nanopores). While this is a “review,” it is actually more forward-looking in that the list of things about this phenomenon that we do not know or cannot control at this time is likely longer than what we do know and can control. For example, there are three directly contradictory theories on how to predict how precipitation proceeds in a medium of varying pore size, as will be discussed below.more » The confusion on this subject likely stems from the complexity of the phenomenon itself: One can easily clog a porous medium by inducing a rapid, homogeneous precipitation directly from solution, or have limited precipitation occur that does not affect permeability or even porosity substantially. It is more difficult to engineer mineral precipitation in order to obtain a specific outcome, such as filling all available pore space over a targeted area for the purposes of contaminant sequestration. However, breakthrough discoveries could occur in the next five to ten years that enhance our ability to predict robustly and finely control precipitation in porous media by understanding how porosity and permeability evolve in response to system perturbations. These discoveries will likely stem (at least in part) from advances in our ability to 1) perform and interpret X-ray/neutron scattering experiments that reveal the extent of precipitation and its locales within porous media (Anovitz and Cole 2015, this volume), and 2) utilize increasingly powerful simulations to test concepts and models about the evolution of porosity and permeability as precipitation occurs (Steefel et al. 2015, this volume). A further important technique to isolate specific phenomena and understand reactivity is also microfluidics cell experiments that allow specific control of flow paths and fluid

  15. Precipitation in pores: A geochemical frontier

    SciTech Connect

    Stack, Andrew G.

    2015-07-29

    This article's purpose is to review some of the recent research in which geochemists have examined precipitation of solid phases in porous media, particularly in pores a few nanometers in diameter (nanopores). While this is a “review,” it is actually more forward-looking in that the list of things about this phenomenon that we do not know or cannot control at this time is likely longer than what we do know and can control. For example, there are three directly contradictory theories on how to predict how precipitation proceeds in a medium of varying pore size, as will be discussed below. The confusion on this subject likely stems from the complexity of the phenomenon itself: One can easily clog a porous medium by inducing a rapid, homogeneous precipitation directly from solution, or have limited precipitation occur that does not affect permeability or even porosity substantially. It is more difficult to engineer mineral precipitation in order to obtain a specific outcome, such as filling all available pore space over a targeted area for the purposes of contaminant sequestration. However, breakthrough discoveries could occur in the next five to ten years that enhance our ability to predict robustly and finely control precipitation in porous media by understanding how porosity and permeability evolve in response to system perturbations. These discoveries will likely stem (at least in part) from advances in our ability to 1) perform and interpret X-ray/neutron scattering experiments that reveal the extent of precipitation and its locales within porous media (Anovitz and Cole 2015, this volume), and 2) utilize increasingly powerful simulations to test concepts and models about the evolution of porosity and permeability as precipitation occurs (Steefel et al. 2015, this volume). A further important technique to isolate specific phenomena and understand reactivity is also microfluidics cell experiments that allow specific control of flow paths and fluid velocities

  16. A quantitative investigation of the effect of pore morphology on soil aggregate stability

    NASA Astrophysics Data System (ADS)

    Papadopoulos, A.

    2009-04-01

    Soil structure determines the operating environment for all physical, chemical and biological processes within the soil. Soil aggregate stability is an important measure for assessing soil structure quality. Non-destructive tomography techniques such as X-ray Computed Tomography (CT) offer great opportunities to quantitatively investigate the soil porous architecture which can provide important information for understanding soil processes and function in a multi-scale manner. For instance, the intra-aggregate pore space is of great importance for microbial activity, the sequestration of organic carbon and water flow. This paper investigates the effect of pore morphology on soil aggregate stability. Apparent porosity, pore size distribution, average pore size and fractal perimeter dimension (pore roughness) were measured from the images of the reconstructed 2-D image stacks. A new theoretical concept of soil aggregate stability is proposed. A strong relationship was observed between soil aggregate stability and pore morphological complexity.

  17. Pore-Scale X-ray Micro-CT Imaging and Analysis of Oil Shales

    NASA Astrophysics Data System (ADS)

    Saif, T.

    2015-12-01

    The pore structure and the connectivity of the pore space during the pyrolysis of oil shales are important characteristics which determine hydrocarbon flow behaviour and ultimate recovery. We study the effect of temperature on the evolution of pore space and subsequent permeability on five oil shale samples: (1) Vernal Utah United States, (2) El Lajjun Al Karak Jordan, (3) Gladstone Queensland Australia (4) Fushun China and (5) Kimmerdige United Kingdom. Oil Shale cores of 5mm in diameter were pyrolized at 300, 400 and 500 °C. 3D imaging of 5mm diameter core samples was performed at 1μm voxel resolution using X-ray micro computed tomography (CT) and the evolution of the pore structures were characterized. The experimental results indicate that the thermal decomposition of kerogen at high temperatures is a major factor causing micro-scale changes in the internal structure of oil shales. At the early stage of pyrolysis, micron-scale heterogeneous pores were formed and with a further increase in temperature, the pores expanded and became interconnected by fractures. Permeability for each oil shale sample at each temperature was computed by simulation directly on the image voxels and by pore network extraction and simulation. Future work will investigate different samples and pursue insitu micro-CT imaging of oil shale pyrolysis to characterize the time evolution of the pore space.

  18. DESIGN INFORMATION ON FINE PORE AERATION SYSTEMS

    EPA Science Inventory

    Field studies were conducted over several years at municipal wastewater treatment plants employing line pore diffused aeration systems. These studies were designed to produce reliable information on the performance and operational requirements of fine pore devices under process ...

  19. 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.

  20. Silver Nanoparticle Transport Through Soil: Illuminating the Pore-Scale Processes

    NASA Astrophysics Data System (ADS)

    Molnar, I. L.; Willson, C. S.; Gerhard, J.; O'Carroll, D. M.

    2015-12-01

    For nanoparticle transport through soil, the pore-scale (i.e., tens to hundreds of grains and pores) is a crucial intermediate scale which links nanoparticle-surface interactions with field-scale transport behaviour. However, very little information exists on how nanoparticles behave within real three-dimensional pore spaces. As a result, pore-scale processes are poorly characterized for nanoparticle systems and, subsequently, continuum-scale transport models struggle to describe commonly observed 'anomalous' behaviour such as extended tailing. This knowledge gap is due to two primary factors: an inability to experimentally observe nanoparticles within real pore spaces, and the computationally expensive models required to simulate nanoparticle movement. However, due to recent advances in Synchrotron X-Ray Computed Microtomography (SXCMT), it is now possible to quantify in-situ pore-scale nanoparticle concentrations during transport through real 3-dimensional porous media [1]. Employing this SXCMT quantification method to examine real nanoparticle/soil transport experiments has yielded new insights into the pore-scale processes governing nanoparticle transport. By coupling SXCMT nanoparticle quantification method with Computational Fluid Dynamics (CFD) simulations we are able to construct a better picture of how nanoparticles flow through real pore spaces. This talk presents SXCMT/CFD analyses of three silver nanoparticle transport experiments. Silver nanoparticles were flushed through three different sands to characterize the influence of grain distribution and retention rates on pore-scale flow and transport processes. These CFD/SXCMT analyses illuminate how processes such as temporary hydraulic retention govern nanoparticle transport. In addition, the observed distributions of pore water velocities and nanoparticle mass flow rates challenge the standard conceptual model of nanoparticle transport, suggesting that pore-scale processes require explicit consideration

  1. Pore formation by Cry toxins.

    PubMed

    Soberón, Mario; Pardo, Liliana; Muñóz-Garay, Carlos; Sánchez, Jorge; Gómez, Isabel; Porta, Helena; Bravo, Alejandra

    2010-01-01

    Bacillus thuringiensis (Bt) bacteria produce insecticidal Cry and Cyt proteins used in the biological control of different insect pests. In this review, we will focus on the 3d-Cry toxins that represent the biggest group of Cry proteins and also on Cyt toxins. The 3d-Cry toxins are pore-forming toxins that induce cell death by forming ionic pores into the membrane of the midgut epithelial cells in their target insect. The initial steps in the mode of action include ingestion of the protoxin, activation by midgut proteases to produce the toxin fragment and the interaction with the primary cadherin receptor. The interaction of the monomeric CrylA toxin with the cadherin receptor promotes an extra proteolytic cleavage, where helix alpha-1 of domain I is eliminated and the toxin oligomerization is induced, forming a structure of 250 kDa. The oligomeric structure binds to a secondary receptor, aminopeptidase N or alkaline phosphatase. The secondary receptor drives the toxin into detergent resistant membrane microdomains formingpores that cause osmotic shock, burst of the midgut cells and insect death. Regarding to Cyt toxins, these proteins have a synergistic effect on the toxicity of some Cry toxins. Cyt proteins are also proteolytic activated in the midgut lumen of their target, they bind to some phospholipids present in the mosquito midgut cells. The proposed mechanism of synergism between Cry and Cyt toxins is that Cyt1Aa function as a receptor for Cry toxins. The Cyt1A inserts into midgut epithelium membrane and exposes protein regions that are recognized by Cry11Aa. It was demonstrated that this interaction facilitates the oligomerization of Cry11Aa and also its pore formation activity.

  2. A fast and robust new pore-network extraction method based on hybrid median axis and maximal inscribed ball techniques

    NASA Astrophysics Data System (ADS)

    Timofey, Sizonenko; Karsanina, Marina; Byuk, Irina; Gerke, Kirill

    2016-04-01

    To characterize pore structure relevant to single and multi-phase flow modelling it is of special interest to extract topology of the pore space. This is usually achieved using so-called pore-network models. Such models are useful not only to characterize pore space and pore size distributions, but also provide means to simulate flow and transport with very limited computational resources compared to other pore-scale modelling techniques. The main drawback of the pore-network approach is that they have first to simplify the pore space geometry. This crucial step is both time consuming and prone to numerous errors. Two most popular methods based on median axis or inscribed maximal balls have their own strong sides and disadvantages. To address aforementioned problems related to pore-network extraction here we propose a novel method utilizing the advantages of both popular approaches. Combining two algorithms resulted in much faster and robust extraction methodology. Moreover, we have found that accurate topology representation requires extension of the conventional pore-body and pore-throat classification. We test our new methodology using pore structures with "analytical solutions" such as different sphere packs. In addition, we rigorously compare it against inscribed maximal balls methodology's results using numerous 3D images of sandstone and carbonate rocks, soils and some other porous materials. Another verification includes permeability calculations which are also compared both against lab data and voxel based pore-scale modelling simulations. This work was partially supported by RFBR grant 15-34-20989 (X-ray tomography and image fusion) and RSF grant 14-17-00658 (image segmentation and pore-scale modelling).

  3. pH controlled gating of toxic protein pores by dendrimers

    NASA Astrophysics Data System (ADS)

    Mandal, Taraknath; Kanchi, Subbarao; Ayappa, K. G.; Maiti, Prabal K.

    2016-06-01

    Designing effective nanoscale blockers for membrane inserted pores formed by pore forming toxins, which are expressed by several virulent bacterial strains, on a target cell membrane is a challenging and active area of research. Here we demonstrate that PAMAM dendrimers can act as effective pH controlled gating devices once the pore has been formed. We have used fully atomistic molecular dynamics (MD) simulations to characterize the cytolysin A (ClyA) protein pores modified with fifth generation (G5) PAMAM dendrimers. Our results show that the PAMAM dendrimer, in either its protonated (P) or non-protonated (NP) states can spontaneously enter the protein lumen. Protonated dendrimers interact strongly with the negatively charged protein pore lumen. As a consequence, P dendrimers assume a more expanded configuration efficiently blocking the pore when compared with the more compact configuration adopted by the neutral NP dendrimers creating a greater void space for the passage of water and ions. To quantify the effective blockage of the protein pore, we have calculated the pore conductance as well as the residence times by applying a weak force on the ions/water. Ionic currents are reduced by 91% for the P dendrimers and 31% for the NP dendrimers. The preferential binding of Cl- counter ions to the P dendrimer creates a zone of high Cl- concentration in the vicinity of the internalized dendrimer and a high concentration of K+ ions in the transmembrane region of the pore lumen. In addition to steric effects, this induced charge segregation for the P dendrimer effectively blocks ionic transport through the pore. Our investigation shows that the bio-compatible PAMAM dendrimers can potentially be used to develop therapeutic protocols based on the pH sensitive gating of pores formed by pore forming toxins to mitigate bacterial infections.Designing effective nanoscale blockers for membrane inserted pores formed by pore forming toxins, which are expressed by several virulent

  4. Intercomparison of 3D pore-scale flow and solute transport simulation methods

    SciTech Connect

    Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.; Pasquali, Andrea; Schonherr, Martin; Kim, Kyungjoo; Perego, Mauro; Parks, Michael L.; Trask, Nathaniel; Balhoff, Matthew T.; Richmond, Marshall C.; Geier, Martin; Krafczyk, Manfred; Luo, Li -Shi; Tartakovsky, Alexandre M.; Scheibe, Timothy D.

    2015-09-28

    In this study, multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include (1) methods that explicitly model the three-dimensional geometry of pore spaces and (2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based on the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides support

  5. Saturation-dependent solute dispersivity in porous media: Pore-scale processes

    NASA Astrophysics Data System (ADS)

    Raoof, A.; Hassanizadeh, S. M.

    2013-04-01

    It is known that in variably saturated porous media, dispersion coefficient depends on Darcy velocity and water saturation. In one-dimensional flow, it is commonly assumed that the dispersion coefficient is a linear function of velocity. The coefficient of proportionality, called the dispersivity, is considered to depend on saturation. However, there is not much known about its dependence on saturation. In this study, we investigate, using a pore network model, how the longitudinal dispersivity varies nonlinearly with saturation. We schematize the porous medium as a network of pore bodies and pore throats with finite volumes. The pore space is modeled using the multidirectional pore-network concept, which allows for a distribution of pore coordination numbers. This topological property together with the distribution of pore sizes are used to mimic the microstructure of real porous media. The dispersivity is calculated by solving the mass balance equations for solute concentration in all network elements and averaging the concentrations over a large number of pores. We have introduced a new formulation of solute transport within pore space, where we account for different compartments of residual water within drained pores. This formulation makes it possible to capture the effect of limited mixing due to partial filling of the pores under variably saturated conditions. We found that dispersivity increases with the decrease in saturation, it reaches a maximum value, and then decreases with further decrease in saturation. To show the capability of our formulation to properly capture the effect of saturation on solute dispersion, we applied it to model the results of a reported experimental study.

  6. Benchmark Study of 3D Pore-scale Flow and Solute Transport Simulation Methods

    NASA Astrophysics Data System (ADS)

    Scheibe, T. D.; Yang, X.; Mehmani, Y.; Perkins, W. A.; Pasquali, A.; Schoenherr, M.; Kim, K.; Perego, M.; Parks, M. L.; Trask, N.; Balhoff, M.; Richmond, M. C.; Geier, M.; Krafczyk, M.; Luo, L. S.; Tartakovsky, A. M.

    2015-12-01

    Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that benchmark study to include additional models of the first type based on the immersed-boundary method (IMB), lattice Boltzmann method (LBM), and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries in the manner of PNMs has not been fully determined. We apply all five approaches (FVM-based CFD, IMB, LBM, SPH and PNM) to simulate pore-scale velocity distributions and nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The benchmark study was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides support for confidence in a variety of pore-scale modeling methods, and motivates further development and application of pore-scale simulation methods.

  7. Intercomparison of 3D pore-scale flow and solute transport simulation methods

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.; Pasquali, Andrea; Schönherr, Martin; Kim, Kyungjoo; Perego, Mauro; Parks, Michael L.; Trask, Nathaniel; Balhoff, Matthew T.; Richmond, Marshall C.; Geier, Martin; Krafczyk, Manfred; Luo, Li-Shi; Tartakovsky, Alexandre M.; Scheibe, Timothy D.

    2016-09-01

    Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based on the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides support for confidence

  8. Transmembrane Pores Formed by Human Antimicrobial Peptide LL-37

    SciTech Connect

    Qian, Shuo

    2011-01-01

    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 observed 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.

  9. Origin of melting point depression for rare gas solids confined in carbon pores.

    PubMed

    Morishige, Kunimitsu; Kataoka, Takaaki

    2015-07-21

    To obtain insights into the mechanism of the melting-point depression of rare gas solids confined in crystalline carbon pores, we examined the freezing and melting behavior of Xe and Ar confined to the crystalline pores of ordered mesoporous carbons as well as compressed exfoliated graphite compared to the amorphous pores of ordered mesoporous silicas, by means of X-ray diffraction. For the Xe and Ar confined to the crystalline carbon pores, there was no appreciable thermal hysteresis between freezing and melting. Furthermore, the position of the main diffraction peak did not change appreciably on freezing and melting. This strongly suggests that the liquids confined in the carbon pores form a multilayered structure parallel to the smooth walls. For the Xe and Ar confined to the amorphous silica pores, on the other hand, the position of the main diffraction peak shifted into higher scattering angle on freezing suggested that the density of the confined solid is distinctly larger than for the confined liquid. Using compressed exfoliated graphite with carbon walls of higher crystallinity, we observed that three-dimensional (3D) microcrystals of Xe confined in the slit-shaped pores melted to leave the unmelted bilayers on the pore walls below the bulk triple point. The lattice spacing of the 3D microcrystals confined is larger by ∼0.7% than that of the bilayer next to the pore walls in the vicinity of the melting point.

  10. Origin of melting point depression for rare gas solids confined in carbon pores

    SciTech Connect

    Morishige, Kunimitsu Kataoka, Takaaki

    2015-07-21

    To obtain insights into the mechanism of the melting-point depression of rare gas solids confined in crystalline carbon pores, we examined the freezing and melting behavior of Xe and Ar confined to the crystalline pores of ordered mesoporous carbons as well as compressed exfoliated graphite compared to the amorphous pores of ordered mesoporous silicas, by means of X-ray diffraction. For the Xe and Ar confined to the crystalline carbon pores, there was no appreciable thermal hysteresis between freezing and melting. Furthermore, the position of the main diffraction peak did not change appreciably on freezing and melting. This strongly suggests that the liquids confined in the carbon pores form a multilayered structure parallel to the smooth walls. For the Xe and Ar confined to the amorphous silica pores, on the other hand, the position of the main diffraction peak shifted into higher scattering angle on freezing suggested that the density of the confined solid is distinctly larger than for the confined liquid. Using compressed exfoliated graphite with carbon walls of higher crystallinity, we observed that three-dimensional (3D) microcrystals of Xe confined in the slit-shaped pores melted to leave the unmelted bilayers on the pore walls below the bulk triple point. The lattice spacing of the 3D microcrystals confined is larger by ∼0.7% than that of the bilayer next to the pore walls in the vicinity of the melting point.

  11. Study into the correlation of dominant pore throat size and SIP relaxation frequency

    NASA Astrophysics Data System (ADS)

    Kruschwitz, Sabine; Prinz, Carsten; Zimathies, Annett

    2016-12-01

    There is currently a debate within the SIP community about the characteristic textural length scale controlling relaxation time of consolidated porous media. One idea is that the relaxation time is dominated by the pore throat size distribution or more specifically the modal pore throat size as determined in mercury intrusion capillary pressure tests. Recently new studies on inverting pore size distributions from SIP data were published implying that the relaxation mechanisms and controlling length scale are well understood. In contrast new analytical model studies based on the Marshall-Madden membrane polarization theory suggested that two relaxation processes might compete: the one along the short narrow pore (the throat) with one across the wider pore in case the narrow pores become relatively long. This paper presents a first systematically focused study into the relationship of pore throat sizes and SIP relaxation times. The generality of predicted trends is investigated across a wide range of materials differing considerably in chemical composition, specific surface and pore space characteristics. Three different groups of relaxation behaviors can be clearly distinguished. The different behaviors are related to clay content and type, carbonate content, size of the grains and the wide pores in the samples.

  12. Origin of melting point depression for rare gas solids confined in carbon pores

    NASA Astrophysics Data System (ADS)

    Morishige, Kunimitsu; Kataoka, Takaaki

    2015-07-01

    To obtain insights into the mechanism of the melting-point depression of rare gas solids confined in crystalline carbon pores, we examined the freezing and melting behavior of Xe and Ar confined to the crystalline pores of ordered mesoporous carbons as well as compressed exfoliated graphite compared to the amorphous pores of ordered mesoporous silicas, by means of X-ray diffraction. For the Xe and Ar confined to the crystalline carbon pores, there was no appreciable thermal hysteresis between freezing and melting. Furthermore, the position of the main diffraction peak did not change appreciably on freezing and melting. This strongly suggests that the liquids confined in the carbon pores form a multilayered structure parallel to the smooth walls. For the Xe and Ar confined to the amorphous silica pores, on the other hand, the position of the main diffraction peak shifted into higher scattering angle on freezing suggested that the density of the confined solid is distinctly larger than for the confined liquid. Using compressed exfoliated graphite with carbon walls of higher crystallinity, we observed that three-dimensional (3D) microcrystals of Xe confined in the slit-shaped pores melted to leave the unmelted bilayers on the pore walls below the bulk triple point. The lattice spacing of the 3D microcrystals confined is larger by ˜0.7% than that of the bilayer next to the pore walls in the vicinity of the melting point.

  13. A thermodynamic approach to Alamethicin pore formation

    PubMed Central

    Rahaman, Asif; Lazaridis, Themis

    2013-01-01

    The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11 Å 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 6 Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8 Å pore and the octamer in an 11 Å 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. PMID:24071593

  14. 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.

  15. A thermodynamic approach to alamethicin pore formation.

    PubMed

    Rahaman, Asif; Lazaridis, Themis

    2014-05-01

    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.

  16. Armillaria luteobubalina mycelium develops air pores that conduct oxygen to rhizomorph clusters.

    PubMed

    Pareek, Mamta; Allaway, William G; Ashford, Anne E

    2006-01-01

    Armillaria luteobubalina produces air pores in culture. They consist of two parts: a basal region of tissue elevated to form a mound covered with a rind continuous with that of the colony, but perforated; and an apical region of long parallel hyphae, cemented together by scattered patches of extracellular material. This forms a hydrophobic structure that is elevated above the general level of the mycelial crust and does not easily become waterlogged. Air pores develop near the inoculum plug shortly after inoculation, arising directly from the mycelium, and rhizomorphs are initiated from them. The air pore contains a complex system of gas space connecting the atmosphere with the central canal of each rhizomorph. The tissue beneath the melanised colony crust also contains gas space, especially near air pores. This is also connected with the gas space of each rhizomorph and of each air pore. Measurements with oxygen electrodes show that air pores and their associated rhizomorphs conduct oxygen. The average oxygen conductance of a group of air pores with associated rhizomorphs, within agar blocks, but with rhizomorph apices cut off, was about 700 x 10(-12) m3s(-1), equivalent to about 200 x 10(-12) m3s(-1) for each air-pore. We conclude that the air pores conduct oxygen into the gas space below the pigmented mycelium of the colony, where the rhizomorphs - which also conduct oxygen - originate. A. luteobubalina thus has a complex aerating system which allows efficient diffusion of oxygen into rhizomorphs, and this is likely to facilitate extension of inoculum into low-oxygen environments.

  17. Fungal colonization in soils with different management histories: modeling growth in three-dimensional pore volumes.

    PubMed

    Kravchenko, Alexandra; Falconer, Ruth E; Grinev, Dmitri; Otten, Wilfred

    2011-06-01

    Despite the importance of fungi in soil functioning they have received comparatively little attention, and our understanding of fungal interactions and communities is lacking. This study aims to combine a physiologically based model of fungal growth with digitized images of internal pore volume of samples of undisturbed soil from contrasting management practices to determine the effect of physical structure on fungal growth dynamics. We quantified pore geometries of the undisturbed-soil samples from two contrasting agricultural practices, conventionally plowed (chisel plow) (CT) and no till (NT), and from native-species vegetation land use on land that was taken out of production in 1989 (NS). Then we modeled invasion of a fungal species within the soil samples and evaluated the role of soil structure on the progress of fungal colonization of the soil pore space. The size of the studied pores was > or =110 microm. The dynamics of fungal invasion was quantified through parameters of a mathematical model fitted to the fungal invasion curves. Results indicated that NT had substantially lower porosity and connectivity than CT and NS soils. For example, the largest connected pore volume occupied 79% and 88% of pore space in CT and NS treatments, respectively, while it only occupied 45% in NT. Likewise, the proportion of pore space available to fungal colonization was much greater in NS and CT than in NT treatment, and the dynamics of the fungal invasion differed among the treatments. The relative rate of fungal invasion at the onset of simulation was higher in NT samples, while the invasion followed a more sigmoidal pattern with relatively slow invasion rates at the initial time steps in NS and CT samples. Simulations allowed us to elucidate the contribution of physical structure to the rates and magnitudes of fungal invasion processes. It appeared that fragmented pore space disadvantaged fungal invasion in soils under long-term no-till, while large connected pores in

  18. Fine structures at pore boundary

    NASA Astrophysics Data System (ADS)

    Bharti, L.; Quintero Noda, C.; Joshi, C.; Rakesh, S.; Pandya, A.

    2016-10-01

    We present high resolution observations of fine structures at pore boundaries. The inner part of granules towards umbra show dark striations which evolve into a filamentary structure with dark core and `Y' shape at the head of the filaments. These filaments migrate into the umbra similar to penumbral filaments. These filaments show higher temperature, lower magnetic field strength and more inclined field compared to the background umbra. The optical depth stratification of physical quantities suggests their similarity with penumbral filaments. However, line-of-sight velocity pattern is different from penumbral filaments where they show downflows in the deeper layers of the atmosphere while the higher layers show upflows. These observations show filamentation in a simple magnetic configuration.

  19. Open-pore polyurethane product

    DOEpatents

    Jefferson, R.T.; Salyer, I.O.

    1974-02-17

    The method is described of producing an open-pore polyurethane foam having a porosity of at least 50% and a density of 0.1 to 0.5 g per cu cm, and which consists of coherent spherical particles of less than 10 mu diam separated by interconnected interstices. It is useful as a filter and oil absorbent. The product is admirably adapted to scavenging of crude oil from the surface of seawater by preferential wicking. The oil-soaked product may then be compressed to recover the oil or burned for disposal. The crosslinked polyurethane structures are remarkably solvent and heat-resistance as compared with known thermoplastic structures. Because of their relative inertness, they are useful filters for gasoline and other hydrocarbon compounds. (7 claims)

  20. Nuclear Pore Proteins and Cancer

    PubMed Central

    Xu, Songli; Powers, Maureen A.

    2009-01-01

    Nucleocytoplasmic trafficking of macromolecules, a highly specific and tightly regulated process, occurs exclusively through the Nuclear Pore Complex. This immense structure is assembled from approximately 30 proteins, termed nucleoporins. Here we discuss the four nucleoporins that have been linked to cancers, either through elevated expression in tumors (Nup88) or through involvement in chromosomal translocations that encode chimeric fusion proteins (Tpr, Nup98, Nup214). In each case we consider the normal function of the nucleoporin and its translocation partners, as well as what is known about their mechanistic contributions to carcinogenesis, particularly in leukemias. Studies of nucleoporin-linked cancers have revealed novel mechanisms of oncogenesis and. in the future, should continue to expand our understanding of cancer biology. PMID:19577736

  1. Pore connectivity, electrical conductivity, and partial water saturation: Network simulations

    NASA Astrophysics Data System (ADS)

    Li, M.; Tang, Y. B.; Bernabé, Y.; Zhao, J. Z.; Li, X. F.; Bai, X. Y.; Zhang, L. H.

    2015-06-01

    The electrical conductivity of brine-saturated rock is predominantly dependent on the geometry and topology of the pore space. When a resistive second phase (e.g., air in the vadose zone and oil/gas in hydrocarbon reservoirs) displaces the brine, the geometry and topology of the pore space occupied by the electrically conductive phase are changed. We investigated the effect of these changes on the electrical conductivity of rock partially saturated with brine. We simulated drainage and imbibition as invasion and bond percolation processes, respectively, in pipe networks assumed to be perfectly water-wet. The simulations included the formation of a water film in the pipes invaded by the nonwetting fluid. During simulated drainage/imbibition, we measured the changes in resistivity index as well as a number of relevant microstructural parameters describing the portion of the pore space saturated with water. Except Euler topological number, all quantities considered here showed a significant level of "universality," i.e., insensitivity to the type of lattice used (simple cubic, body-centered cubic, or face-centered cubic). Hence, the coordination number of the pore network appears to be a more effective measure of connectivity than Euler number. In general, the simulated resistivity index did not obey Archie's simple power law. In log-log scale, the resistivity index curves displayed a substantial downward or upward curvature depending on the presence or absence of a water film. Our network simulations compared relatively well with experimental data sets, which were obtained using experimental conditions and procedures consistent with the simulations. Finally, we verified that the connectivity/heterogeneity model proposed by Bernabé et al. (2011) could be extended to the partial brine saturation case when water films were not present.

  2. Modeling the interaction of ultrasound with pores

    NASA Technical Reports Server (NTRS)

    Lu, Yichi; Wadley, Haydn N. G.; Parthasarathi, Sanjai

    1991-01-01

    Factors that affect ultrasonic velocity sensing of density during consolidation of metal powders are examined. A comparison is made between experimental results obtained during the final stage of densification and the predictions of models that assume either a spherical or a spheroidal pore shape. It is found that for measurements made at low frequencies during the final stage of densification, relative density (pore fraction) and pore shape are the two most important factors determining the ultrasonic velocity, the effect of pore size is negligible.

  3. Nanoscale pore formation dynamics during aluminum anodization.

    PubMed

    Thamida, Sunil Kumar; Chang, Hsueh-Chia

    2002-03-01

    A theoretical analysis of nanoscale pore formation during anodization reveals its fundamental instability mechanism to be a field focusing phenomenon when perturbations on the minima of the two oxide interfaces are in phase. Lateral leakage of the layer potential at high wave number introduces a layer tension effect that balances the previous destabilizing effect to produce a long-wave instability and a selected pore separation that scales linearly with respect to voltage. At pH higher than 1.77, pores do not form due to a very thick barrier layer. A weakly nonlinear theory based on long-wave expansion of double free surface problem yields two coupled interface evolution equations that can be reduced to one without altering the dispersion relationship by assuming an equal and in-phase amplitude for the two interfaces. This interface evolution equation faithfully reproduces the initial pore ordering and their dynamics. A hodograph transformation technique is then used to determine the interior dimension of the well-developed pores in two dimensions. The ratio of pore diameter to pore separation is found to be a factor independent of voltage but varies with the pH of the electrolyte. Both the predicted pH range where pores are formed and the predicted pore dimensions are favorably compared to experimental data. (c) 2002 American Institute of Physics.

  4. Application of a pore-scale reactive transport model to a natural analog for reaction-induced pore alterations

    DOE PAGES

    Yoon, Hongkyu; Major, Jonathan; Dewers, Thomas; ...

    2017-01-05

    Dissolved CO2 in the subsurface resulting from geological CO2 storage may react with minerals in fractured rocks, confined aquifers, or faults, resulting in mineral precipitation and dissolution. The overall rate of reaction can be affected by coupled processes including hydrodynamics, transport, and reactions at the (sub) pore-scale. In this work pore-scale modeling of coupled fluid flow, reactive transport, and heterogeneous reactions at the mineral surface is applied to account for permeability alterations caused by precipitation-induced pore-blocking. This paper is motivated by observations of CO2 seeps from a natural CO2 sequestration analog, Crystal Geyser, Utah. Observations along the surface exposure ofmore » the Little Grand Wash fault indicate the lateral migration of CO2 seep sites (i.e., alteration zones) of 10–50 m width with spacing on the order of ~100 m over time. Sandstone permeability in alteration zones is reduced by 3–4 orders of magnitude by carbonate cementation compared to unaltered zones. One granular porous medium and one fracture network systems are used to conceptually represent permeable porous media and locations of conduits controlled by fault-segment intersections and/or topography, respectively. Simulation cases accounted for a range of reaction regimes characterized by the Damköhler (Da) and Peclet (Pe) numbers. Pore-scale simulation results demonstrate that combinations of transport (Pe), geochemical conditions (Da), solution chemistry, and pore and fracture configurations contributed to match key patterns observed in the field of how calcite precipitation alters flow paths by pore plugging. This comparison of simulation results with field observations reveals mechanistic explanations of the lateral migration and enhances our understanding of subsurface processes associated with the CO2 injection. In addition, permeability and porosity relations are constructed from pore-scale simulations which account for a range of

  5. Changes in the pore network structure of Hanford sediment after reaction with caustic tank wastes.

    PubMed

    Crandell, L E; Peters, C A; Um, W; Jones, K W; Lindquist, W B

    2012-04-01

    At the former nuclear weapon production site in Hanford, WA, caustic radioactive tank waste leaks into subsurface sediments and causes dissolution of quartz and aluminosilicate minerals, and precipitation of sodalite and cancrinite. This work examines changes in pore structure due to these reactions in a previously-conducted column experiment. The column was sectioned and 2D images of the pore space were generated using backscattered electron microscopy and energy dispersive X-ray spectroscopy. A pre-precipitation scenario was created by digitally removing mineral matter identified as secondary precipitates. Porosity, determined by segmenting the images to distinguish pore space from mineral matter, was up to 0.11 less after reaction. Erosion-dilation analysis was used to compute pore and throat size distributions. Images with precipitation had more small and fewer large pores. Precipitation decreased throat sizes and the abundance of large throats. These findings agree with previous findings based on 3D X-ray CMT imaging, observing decreased porosity, clogging of small throats, and little change in large throats. However, 2D imaging found an increase in small pores, mainly in intragranular regions or below the resolution of the 3D images. Also, an increase in large pores observed via 3D imaging was not observed in the 2D analysis. Changes in flow conducting throats that are the key permeability-controlling features were observed in both methods.

  6. Changes in the pore network structure of Hanford sediment after reaction with caustic tank wastes

    SciTech Connect

    Crandell, L. E.; Peters, Catherine A.; Um, Wooyong; Jones, Keith W.; Lindquist, W.Brent

    2012-04-01

    At the former nuclear weapon production site in Hanford, WA, caustic radioactive tank waste leaks into subsurface sediments and causes dissolution of quartz and aluminosilicate minerals, and precipitation of sodalite and cancrinite. This work examines changes in pore structure due to these reactions in a previously-conducted column experiment. The column was sectioned and 2D images of the pore space were generated using backscattered electron microscopy and energy dispersive X-ray spectroscopy. A pre-precipitation scenario was created by digitally removing mineral matter identified as secondary precipitates. Porosity, determined by segmenting the images to distinguish pore space from mineral matter, was up to 0.11 less after reaction. Erosion-dilation analysis was used to compute pore and throat size distributions. Images with precipitation had more small and fewer large pores. Precipitation decreased throat sizes and the abundance of large throats. These findings agree with previous findings based on 3D X-ray CMT imaging, observing decreased porosity, clogging of small throats, and little change in large throats. However, 2D imaging found an increase in small pores, mainly in intragranular regions or below the resolution of the 3D images. Also, an increase in large pores observed via 3D imaging was not observed in the 2D analysis. Changes in flow conducting throats that are the key permeability-controlling features were observed in both methods.

  7. Effective pore-scale dispersion upscaling with a correlated continuous time random walk approach

    NASA Astrophysics Data System (ADS)

    Le Borgne, T.; Bolster, D.; Dentz, M.; de Anna, P.; Tartakovsky, A.

    2011-12-01

    We investigate the upscaling of dispersion from a pore-scale analysis of Lagrangian velocities. A key challenge in the upscaling procedure is to relate the temporal evolution of spreading to the pore-scale velocity field properties. We test the hypothesis that one can represent Lagrangian velocities at the pore scale as a Markov process in space. The resulting effective transport model is a continuous time random walk (CTRW) characterized by a correlated random time increment, here denoted as correlated CTRW. We consider a simplified sinusoidal wavy channel model as well as a more complex heterogeneous pore space. For both systems, the predictions of the correlated CTRW model, with parameters defined from the velocity field properties (both distribution and correlation), are found to be in good agreement with results from direct pore-scale simulations over preasymptotic and asymptotic times. In this framework, the nontrivial dependence of dispersion on the pore boundary fluctuations is shown to be related to the competition between distribution and correlation effects. In particular, explicit inclusion of spatial velocity correlation in the effective CTRW model is found to be important to represent incomplete mixing in the pore throats.

  8. Microtomography and pore-scale modeling of two-phase Fluid Distribution

    SciTech Connect

    Silin, D.; Tomutsa, L.; Benson, S.; Patzek, T.

    2010-10-19

    Synchrotron-based X-ray microtomography (micro CT) at the Advanced Light Source (ALS) line 8.3.2 at the Lawrence Berkeley National Laboratory produces three-dimensional micron-scale-resolution digital images of the pore space of the reservoir rock along with the spacial distribution of the fluids. Pore-scale visualization of carbon dioxide flooding experiments performed at a reservoir pressure demonstrates that the injected gas fills some pores and pore clusters, and entirely bypasses the others. Using 3D digital images of the pore space as input data, the method of maximal inscribed spheres (MIS) predicts two-phase fluid distribution in capillary equilibrium. Verification against the tomography images shows a good agreement between the computed fluid distribution in the pores and the experimental data. The model-predicted capillary pressure curves and tomography-based porosimetry distributions compared favorably with the mercury injection data. Thus, micro CT in combination with modeling based on the MIS is a viable approach to study the pore-scale mechanisms of CO{sub 2} injection into an aquifer, as well as more general multi-phase flows.

  9. Numerical Simulation on Hydromechanical Coupling in Porous Media Adopting Three-Dimensional Pore-Scale Model

    PubMed Central

    Liu, Jianjun; Song, Rui; Cui, Mengmeng

    2014-01-01

    A novel approach of simulating hydromechanical coupling in pore-scale models of porous media is presented in this paper. Parameters of the sandstone samples, such as the stress-strain curve, Poisson's ratio, and permeability under different pore pressure and confining pressure, are tested in laboratory scale. The micro-CT scanner is employed to scan the samples for three-dimensional images, as input to construct the model. Accordingly, four physical models possessing the same pore and rock matrix characteristics as the natural sandstones are developed. Based on the micro-CT images, the three-dimensional finite element models of both rock matrix and pore space are established by MIMICS and ICEM software platform. Navier-Stokes equation and elastic constitutive equation are used as the mathematical model for simulation. A hydromechanical coupling analysis in pore-scale finite element model of porous media is simulated by ANSYS and CFX software. Hereby, permeability of sandstone samples under different pore pressure and confining pressure has been predicted. The simulation results agree well with the benchmark data. Through reproducing its stress state underground, the prediction accuracy of the porous rock permeability in pore-scale simulation is promoted. Consequently, the effects of pore pressure and confining pressure on permeability are revealed from the microscopic view. PMID:24955384

  10. Numerical simulation on hydromechanical coupling in porous media adopting three-dimensional pore-scale model.

    PubMed

    Liu, Jianjun; Song, Rui; Cui, Mengmeng

    2014-01-01

    A novel approach of simulating hydromechanical coupling in pore-scale models of porous media is presented in this paper. Parameters of the sandstone samples, such as the stress-strain curve, Poisson's ratio, and permeability under different pore pressure and confining pressure, are tested in laboratory scale. The micro-CT scanner is employed to scan the samples for three-dimensional images, as input to construct the model. Accordingly, four physical models possessing the same pore and rock matrix characteristics as the natural sandstones are developed. Based on the micro-CT images, the three-dimensional finite element models of both rock matrix and pore space are established by MIMICS and ICEM software platform. Navier-Stokes equation and elastic constitutive equation are used as the mathematical model for simulation. A hydromechanical coupling analysis in pore-scale finite element model of porous media is simulated by ANSYS and CFX software. Hereby, permeability of sandstone samples under different pore pressure and confining pressure has been predicted. The simulation results agree well with the benchmark data. Through reproducing its stress state underground, the prediction accuracy of the porous rock permeability in pore-scale simulation is promoted. Consequently, the effects of pore pressure and confining pressure on permeability are revealed from the microscopic view.

  11. Pore-size distribution in loamy soils: A comparison between microtomographic and capillarimetric determination methods

    NASA Astrophysics Data System (ADS)

    Shein, E. V.; Skvortsova, E. B.; Dembovetskii, A. V.; Abrosimov, K. N.; Il'in, L. I.; Shnyrev, N. A.

    2016-03-01

    Pore-size distribution in a soddy-podzolic silt loamy soil developing from mantle loesslike loam (Eutric Albic Retisol (Loamic, Cutanic)) was calculated from the water retention curve according to Jurin's equation and directly determined in microtomographic experiments. Rounded macropores with the diameter of their sections from 75 to 1000 μm predominate in horizontal sections if the studied soil samples. A larger part of the soil pores (>30-35%) belongs to micro- and nanopores, and they cannot be quantitatively determined by the tomographic method, because their sizes are smaller than the detection limit of the applied X-ray microtomography (8.75 μm per pixel). This leads to a significantly larger pore volume determined from the water retention curve in comparison with the "tomographic" pore volume. A comparative analysis of pore-size distribution curves obtained by these methods shows that the major regularities of the pore-size distribution in the range from 30 to 5000 μm are similar in both cases. Fine macropores and, partly, mesopores predominate. Common characteristics of the pore-size distribution curves obtained by these methods, including the coincidence of the peaks, attest to the validity of classical approaches, according to which the hydrology of soil pore space can be perceived as a physical model of cylindrical capillaries of different sizes with capillary-sorbed water.

  12. 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.

  13. Large pore size nanoporous materials from the self-assembly of asymmetric bottlebrush block copolymers.

    PubMed

    Bolton, Justin; Bailey, Travis S; Rzayev, Javid

    2011-03-09

    Asymmetric polystyrene-polylactide (PS-PLA) bottlebrush block copolymers have been shown to self-assemble into a cylindrical morphology with large domain spacings. PLA cylinders can be selectively etched out of the shear-aligned polymer monoliths to generate nanoporous materials with an average cylindrical pore diameter of 55 nm. The remaining bottlebrush backbone provides a functional, hydrophilic coating inside the nanopores. This methodology significantly expands the range of pore sizes attainable in block copolymer based nanoporous materials.

  14. A New Path through the Nuclear Pore.

    PubMed

    Gozalo, Alejandro; Capelson, Maya

    2016-11-17

    Knowing the configuration of the nuclear pore is essential for appreciating the underlying mechanisms of nucleo-cytoplasmic communication. Now, Fernandez-Martinez et al. present a high-resolution structure of the cytoplasmic nuclear pore-mRNA export holo-complex, challenging our textbook depiction of this massive membrane-embedded complex.

  15. 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.

  16. Fluctuation of surface charge in membrane pores.

    PubMed Central

    Bashford, C Lindsay; Alder, Glenn M; Pasternak, Charles A

    2002-01-01

    Surface charge in track-etched polyethylene terephthalate (PET) membranes with narrow pores has been probed with a fluorescent cationic dye (3,3'-diethyloxacarbocyanine iodide (diO-C2-(3))) using confocal microscopy. Staining of negatively charged PET membranes with diO-C2-(3) is a useful measure of surface charge for the following reasons: 1) the dye inhibits K(+) currents through the pores and reduces their selectivity for cations; 2) it inhibits [3H]-choline+ transport and promotes 36Cl- transport across the membrane in a pH- and ionic-strength-dependent fashion; and 3) staining of pores by diO-C2-(3) is reduced by low pH and by the presence of divalent cations such as Ca2+ and Zn2+. Measurement of the time dependence of cyanine staining of pores shows fluctuations of fluorescence intensity that occur on the same time scale as do fluctuations of ionic current in such pores. These data support our earlier proposal that fluctuations in ionic current across pores in synthetic and biological membranes reflect fluctuations in the surface charge of the pore walls in addition to molecular changes in pore proteins. PMID:11916860

  17. Petrophysical and magnetic pore network anisotropy of some cretaceous sandstone from Tushka Basin, Egypt

    NASA Astrophysics Data System (ADS)

    Nabawy, Bassem S.; Rochette, Pierre; Géraud, Yves

    2009-04-01

    Pore magnetic fabric is a well-established technique for the determination of pore elongation and preferred directions for migration of the interstitial fluids. This study further exemplify this technique on a set of the Nubia sandstones through a comparison with the pore anisotropy obtained from measuring permeability in three orthogonal directions in a gaz permeameter. The Nubia sandstones are represented in Tushka area (South Egypt) by quartz arenite of large porosity (29-40 per cent) which was measured on thin sections parallel and perpendicular to the bedding plane and petrophysically by helium pycnometry and ferrofluid injection at 1 bar pressure. Petrographically, there is a detectable difference between the porosity values in the bedding plane and in the perpendicular direction indicating inhomogeneity in the pore space network distribution. The petrophysical studies indicate large porosity and permeability values with some differences between the helium and ferrofluid porosity due to presence of micro pore spaces not accessible for the ferrofluid molecules having relatively high diameters and injected at low pressure. An overall agreement is observed between the permeability anisotropy and the magnetic grain and pore fabrics (magnetic anisotropy measured before and after ferrofluid injection). The three fabrics are mainly dominated by a bedding parallel foliation. In a few cases maximum permeability appears to be perpendicular to bedding. Within the bedding plane, maximum pore elongation direction from ferrofluid injection is NNW for Adindan and Kesieba formations and NW for Abu Simbil Formation. The maximum pore elongation direction for Abu Ballas samples showed a direction fluctuating around the E-W direction, the main fault trends in Tushka area. The pore fabric of Abu Ballas formation seems therefore to be structurally controlled, while it would be originated from palaeocurrent directions in the other formations.

  18. Review of pore network modelling of porous media: Experimental characterisations, network constructions and applications to reactive transport

    NASA Astrophysics Data System (ADS)

    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.

  19. 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.

  20. Analytical applications for pore-forming proteins.

    PubMed

    Kasianowicz, John J; Balijepalli, Arvind K; Ettedgui, Jessica; Forstater, Jacob H; Wang, Haiyan; Zhang, Huisheng; Robertson, Joseph W F

    2016-03-01

    Proteinaceous nanometer-scale pores are ubiquitous in biology. The canonical ionic channels (e.g., those that transport Na(+), K(+), Ca(2+), and Cl(-) across cell membranes) play key roles in many cellular processes, including nerve and muscle activity. Another class of channels includes bacterial pore-forming toxins, which disrupt cell function, and can lead to cell death. We describe here the recent development of these toxins for a wide range of biological sensing applications. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.

  1. Control of pore size in epoxy systems.

    SciTech Connect

    Sawyer, Patricia Sue; Lenhart, Joseph Ludlow; Lee, Elizabeth; Kallam, Alekhya; Majumdar, Partha; Dirk, Shawn M.; Gubbins, Nathan; Chisholm, Bret J.; Celina, Mathias Christopher; Bahr, James; Klein, Robert J.

    2009-01-01

    Both conventional and combinatorial approaches were used to study the pore formation process in epoxy based polymer systems. Sandia National Laboratories conducted the initial work and collaborated with North Dakota State University (NDSU) using a combinatorial research approach to produce a library of novel monomers and crosslinkers capable of forming porous polymers. The library was screened to determine the physical factors that control porosity, such as porogen loading, polymer-porogen interactions, and polymer crosslink density. We have identified the physical and chemical factors that control the average porosity, pore size, and pore size distribution within epoxy based systems.

  2. High temperature ion channels and pores

    NASA Technical Reports Server (NTRS)

    Kang, Xiaofeng (Inventor); Gu, Li Qun (Inventor); Cheley, Stephen (Inventor); Bayley, Hagan (Inventor)

    2011-01-01

    The present invention includes an apparatus, system and method for stochastic sensing of an analyte to a protein pore. The protein pore may be an engineer protein pore, such as an ion channel at temperatures above 55.degree. C. and even as high as near 100.degree. C. The analyte may be any reactive analyte, including chemical weapons, environmental toxins and pharmaceuticals. The analyte covalently bonds to the sensor element to produce a detectable electrical current signal. Possible signals include change in electrical current. Detection of the signal allows identification of the analyte and determination of its concentration in a sample solution. Multiple analytes present in the same solution may also be detected.

  3. Quantitative characterization of pore structure of several biochars with 3D imaging.

    PubMed

    Hyväluoma, Jari; Kulju, Sampo; Hannula, Markus; Wikberg, Hanne; Källi, Anssi; Rasa, Kimmo

    2017-03-24

    Pore space characteristics of biochars may vary depending on the used raw material and processing technology. Pore structure has significant effects on the water retention properties of biochar amended soils. In this work, several biochars were characterized with three-dimensional imaging and image analysis. X-ray computed microtomography was used to image biochars at resolution of 1.14 μm and the obtained images were analysed for porosity, pore size distribution, specific surface area and structural anisotropy. In addition, random walk simulations were used to relate structural anisotropy to diffusive transport. Image analysis showed that considerable part of the biochar volume consist of pores in size range relevant to hydrological processes and storage of plant available water. Porosity and pore size distribution were found to depend on the biochar type and the structural anisotopy analysis showed that used raw material considerably affects the pore characteristics at micrometre scale. Therefore, attention should be paid to raw material selection and quality in applications requiring optimized pore structure.

  4. Block copolymer structures in nano-pores

    NASA Astrophysics Data System (ADS)

    Pinna, Marco; Guo, Xiaohu; Zvelindovsky, Andrei

    2010-03-01

    We present results of coarse-grained computer modelling of block copolymer systems in cylindrical and spherical nanopores on Cell Dynamics Simulation. We study both cylindrical and spherical pores and systematically investigate structures formed by lamellar, cylinders and spherical block copolymer systems for various pore radii and affinity of block copolymer blocks to the pore walls. The obtained structures include: standing lamellae and cylinders, ``onions,'' cylinder ``knitting balls,'' ``golf-ball,'' layered spherical, ``virus''-like and mixed morphologies with T-junctions and U-type defects [1]. Kinetics of the structure formation and the differences with planar films are discussed. Our simulations suggest that novel porous nano-containers can be formed by confining block copolymers in pores of different geometries [1,2]. [4pt] [1] M. Pinna, X. Guo, A.V. Zvelindovsky, Polymer 49, 2797 (2008).[0pt] [2] M. Pinna, X. Guo, A.V. Zvelindovsky, J. Chem. Phys. 131, 214902 (2009).

  5. OBSERVATIONS OF SAUSAGE MODES IN MAGNETIC PORES

    SciTech Connect

    Morton, R. J.; Erdelyi, R.; Jess, D. B.; Mathioudakis, M. E-mail: Robertus@sheffield.ac.uk

    2011-03-10

    We present here evidence for the observation of the magnetohydrodynamic (MHD) sausage modes in magnetic pores in the solar photosphere. Further evidence for the omnipresent nature of acoustic global modes is also found. The empirical decomposition method of wave analysis is used to identify the oscillations detected through a 4170 A 'blue continuum' filter observed with the Rapid Oscillations in the Solar Atmosphere (ROSA) instrument. Out of phase, periodic behavior in pore size and intensity is used as an indicator of the presence of magnetoacoustic sausage oscillations. Multiple signatures of the magnetoacoustic sausage mode are found in a number of pores. The periods range from as short as 30 s up to 450 s. A number of the magnetoacoustic sausage mode oscillations found have periods of 3 and 5 minutes, similar to the acoustic global modes of the solar interior. It is proposed that these global oscillations could be the driver of the sausage-type magnetoacoustic MHD wave modes in pores.

  6. Pore-scale controls on calcite dissolution rates from flow-through laboratory and numerical experiments.

    PubMed

    Molins, Sergi; Trebotich, David; Yang, Li; Ajo-Franklin, Jonathan B; Ligocki, Terry J; Shen, Chaopeng; Steefel, Carl I

    2014-07-01

    A combination of experimental, imaging, and modeling techniques were applied to investigate the pore-scale transport and surface reaction controls on calcite dissolution under elevated pCO2 conditions. The laboratory experiment consisted of the injection of a solution at 4 bar pCO2 into a capillary tube packed with crushed calcite. A high resolution pore-scale numerical model was used to simulate the experiment based on a computational domain consisting of reactive calcite, pore space, and the capillary wall constructed from volumetric X-ray microtomography images. Simulated pore-scale effluent concentrations were higher than those measured by a factor of 1.8, with the largest component of the discrepancy related to uncertainties in the reaction rate model and its parameters. However, part of the discrepancy was apparently due to mass transport limitations to reactive surfaces, which were most pronounced near the inlet where larger diffusive boundary layers formed around grains and in slow-flowing pore spaces that exchanged mass by diffusion with fast flow paths. Although minor, the difference between pore- and continuum-scale results due to transport controls was discernible with the highly accurate methods employed and is expected to be more significant where heterogeneity is greater, as in natural subsurface materials.

  7. Pore-network study of bubble growth in porous media driven by heat transfer

    SciTech Connect

    Satik, C.; Yortsos, Y.C.

    1996-05-01

    We present experimental and theoretical investigations of vapor phase growth in pore-network models of porous media. Visualization experiments of boiling of ethyl alcohol in horizontal etched-glass micromodels were conducted. The vapor phase was observed to grow into a disordered pattern following a sequence of pressurization and pore-filling steps. At sufficiently small cluster sizes, growth occurred `one pore at a time,` leading to invasion percolation patterns. Single-bubble (cluster) growth was next simulated with a pore-network simulator that includes heat transfer (convection and conduction), and capillary and viscous forces, although not gravity. A boundary in the parameter space was delineated that separates patterns of growth dictated solely by capillarity (invasion percolation) from other patterns. The region of validity of invasion percolation was found to decrease as the supersaturation (heat flux), the capillary number, the thermal diffusivity, and the vapor cluster size increase. Implications to continuum models are discussed. 33 refs., 9 figs.

  8. Visualization of enzyme activities inside earthworm pores

    NASA Astrophysics Data System (ADS)

    Hoang, Duyen; Razavi, Bahar S.

    2015-04-01

    In extremely dynamic microhabitats as bio-pores made by earthworm, the in situ enzyme activities are assumed as a footprint of complex biotic interactions. Our study focused on the effect of earthworm on the enzyme activities inside bio-pores and visualizing the differences between bio-pores and earthworm-free soil by zymography technique (Spohn and Kuzyakov, 2013). For the first time, we aimed at quantitative imaging of enzyme activities in bio-pores. Lumbricus terrestris L. was placed into transparent box (15×20×15cm). After two weeks when bio-pore systems were formed by earthworms, we visualized in situ enzyme activities of five hydrolytic enzymes (β-glucosidase, cellobiohydrolase, chitinase, xylanase, leucine-aminopeptidase, and phosphatase. Zymography showed higher activity of β-glucosidase, chitinase, xylanase and phosphatase in biopores comparing to bulk soil. However, the differences in activity of cellobiohydrolase and leucine aminopeptidase between bio-pore and bulk soil were less pronounced. This demonstrated an applicability of zymography approach to monitor and to distinguish the in situ activity of hydrolytic enzymes in soil biopores.

  9. Deposition nucleation viewed as homogeneous or immersion freezing in pores and cavities

    NASA Astrophysics Data System (ADS)

    Marcolli, C.

    2013-06-01

    , these will condense preferentially in pores before a coating on the surface of the particles is formed. A pore partially filled with condensed species attracts water at lower RHw than an empty pore, but the aqueous solution that forms in the pore will freeze at a higher RHi than pure water. The ice nucleation ability of pores completely filled with condensed organic species might be totally impeded. Pores might also be important for preactivation, the capability of a particle to nucleate ice at lower RHi in subsequent experiments when compared to the first initial ice nucleation event. Preactivation has often been explained by persistence of ice embryos at specific sites like dislocations, steps, kinks or pores. However, it is not clear how such features can preserve an ice embryo at RHi < 100%. Rather, ice embryos could be preserved when embedded in water. To keep liquid water at RHw well below 100%, narrow pores are needed but to avoid a strong melting point depression large pores are favorable. A narrow pore opening and a large inner volume are combined in "ink bottle" pores. Such "ink bottle" pores would be suited to preserve ice at RHi < 100% and can arise e.g. in spaces between aggregated particles.

  10. More Than a Pore: The Interplay of Pore-Forming Proteins and Lipid Membranes.

    PubMed

    Ros, Uris; García-Sáez, Ana J

    2015-06-01

    Pore-forming proteins (PFPs) punch holes in their target cell membrane to alter their permeability. Permeabilization of lipid membranes by PFPs has received special attention to study the basic molecular mechanisms of protein insertion into membranes and the development of biotechnological tools. PFPs act through a general multi-step mechanism that involves (i) membrane partitioning, (ii) insertion into the hydrophobic core of the bilayer, (iii) oligomerization, and (iv) pore formation. Interestingly, PFPs and membranes show a dynamic interplay. As PFPs are usually produced as soluble proteins, they require a large conformational change for membrane insertion. Moreover, membrane structure is modified upon PFPs insertion. In this context, the toroidal pore model has been proposed to describe a pore architecture in which not only protein molecules but also lipids are directly involved in the structure. Here, we discuss how PFPs and lipids cooperate and remodel each other to achieve pore formation, and explore new evidences of protein-lipid pore structures.

  11. Determining the Zeta Potential of Porous Membranes Using Electrolyte Conductivity inside Pores.

    PubMed

    Fievet, P.; Szymczyk, A.; Labbez, C.; Aoubiza, B.; Simon, C.; Foissy, A.; Pagetti, J.

    2001-03-15

    The zeta potential is an important and reliable indicator of the surface charge of membranes, and knowledge of it is essential for the design and operation of membrane processes. The zeta potential cannot be measured directly, but must be deduced from experiments by means of a model. The possibility of determining the zeta potential of porous membranes from measurements of the electrolyte conductivity inside pores (lambda(pore)) is investigated in the case of a ceramic microfiltration membrane. To this end, experimental measurements of the electrical resistance in pores are performed with the membrane filled with KCl solutions of various pHs and concentrations. lambda(pore) is deduced from these experiments. The farther the pH is from the isoelectric point and/or the lower the salt concentration is, the higher the ratio of the electrolyte conductivity inside pores to the bulk conductivity is, due to a more important contribution of the surface conduction. Zeta potentials are calculated from lambda(pore) values by means of a space charge model and compared to those calculated from streaming potential measurements. It is found that the isoelectric points are very close and that zeta potential values for both methods are in quite good agreement. The differences observed in zeta potentials could be due to the fact that the space charge model does not consider the surface conductivity in the inner part of the double layer. Measurements of the electrolyte conductivity within the membrane pores are proved to be a well-adapted procedure for the determination of the zeta potential in situations where the contribution of the surface conduction is significant, i.e., for small and charged pores. Copyright 2001 Academic Press.

  12. Use of Computed Microtomography to Visualize and Quantify Pore-Scale Transport Processes

    NASA Astrophysics Data System (ADS)

    Altman, S. J.; Rivers, M.; Peplinski, W. J.; Lucero, D. A.

    2001-05-01

    Pore-scale transport processes are critical to the understanding of oil and gas reservoirs, groundwater transport and toxic and radioactive waste migration. For example, at certain sites where deep geological repositories are being studied for nuclear waste storage, diffusion in fractured crystalline rocks is thought to be an important factor in retarding radionuclide transport. Presently, there is little direct observation of heterogeneous diffusion processes in crystalline rocks as it is mostly studied by field tracer tests or bulk laboratory measurements. Computed microtomography (CMT) is being applied at GSECARS (GeoSoilEnviro Consortium for Advanced Radiation Sources) at the Argonne National Laboratory Advanced Photon Source to better understand pore-space transport processes. The technique is being applied to 1-cm diameter, crystalline rock cores from underground experimental rock laboratories in Sweden, Switzerland and Japan. Approximately 20 micron resolution in three-dimensions is achieved on these cores. The CMT images of the natural samples show pore space, but the contrast in some samples is relatively poor because the required X-ray energy was high in order to penetrate the samples. The pore space is enhanced by digital subtraction tomography. In this method, the rock is saturated with high atomic number fluid (CsCl or KI solution) and images are taken with the X-ray energy below and above the cesium or iodine K absorption edge. The difference image shows only the solution, which is present in the accessible pore space and thus reveals potential fluid transport pathways. In addition to imaging the pore space, this method can detect minerals to which the cesium sorbs and differentiate between felsic and mafic minerals in the samples. New work will concentrate on real time experiments to measure transport properties. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy

  13. Isolated pores dissected from human two-pore channel 2 are functional

    PubMed Central

    Penny, Christopher J.; Rahman, Taufiq; Sula, Altin; Miles, Andrew J.; Wallace, B. A.; Patel, Sandip

    2016-01-01

    Multi-domain voltage-gated ion channels appear to have evolved through sequential rounds of intragenic duplication from a primordial one-domain precursor. Whereas modularity within one-domain symmetrical channels is established, little is known about the roles of individual regions within more complex asymmetrical channels where the domains have undergone substantial divergence. Here we isolated and characterised both of the divergent pore regions from human TPC2, a two-domain channel that holds a key intermediate position in the evolution of voltage-gated ion channels. In HeLa cells, each pore localised to the ER and caused Ca2+ depletion, whereas an ER-targeted pore mutated at a residue that inactivates full-length TPC2 did not. Additionally, one of the pores expressed at high levels in E. coli. When purified, it formed a stable, folded tetramer. Liposomes reconstituted with the pore supported Ca2+ and Na+ uptake that was inhibited by known blockers of full-length channels. Computational modelling of the pore corroborated cationic permeability and drug interaction. Therefore, despite divergence, both pores are constitutively active in the absence of their partners and retain several properties of the wild-type pore. Such symmetrical ‘pore-only’ proteins derived from divergent channel domains may therefore provide tractable tools for probing the functional architecture of complex ion channels. PMID:27941820

  14. Relating salt marsh pore water geochemistry patterns to vegetation zones and hydrologic influences

    NASA Astrophysics Data System (ADS)

    Moffett, Kevan B.; Gorelick, Steven M.

    2016-03-01

    Physical, chemical, and biological factors influence vegetation zonation in salt marshes and other wetlands, but connections among these factors could be better understood. If salt marsh vegetation and marsh pore water geochemistry coorganize, e.g., via continuous plant water uptake and persistently unsaturated sediments controlling vegetation zone-specific pore water geochemistry, this could complement known physical mechanisms of marsh self-organization. A high-resolution survey of pore water geochemistry was conducted among five salt marsh vegetation zones at the same intertidal elevation. Sampling transects were arrayed both parallel and perpendicular to tidal channels. Pore water geochemistry patterns were both horizontally differentiated, corresponding to vegetation zonation, and vertically differentiated, relating to root influences. The geochemical patterns across the site were less broadly related to marsh hydrology than to vegetation zonation. Mechanisms contributing to geochemical differentiation included: root-induced oxidation and nutrient (P) depletion, surface and creek-bank sediment flushing by rainfall or tides, evapotranspiration creating aerated pore space for partial sediment flushing in some areas while persistently saturated conditions hindered pore water renewal in others, and evapoconcentration of pore water solutes overall. The concentrated pore waters draining to the tidal creeks accounted for 41% of ebb tide solutes (median of 14 elements), including being a potentially toxic source of Ni but a slight sink for Zn, at least during the short, winter study period in southern San Francisco Bay. Heterogeneous vegetation effects on pore water geochemistry are not only significant locally within the marsh but may broadly influence marsh-estuary solute exchange and ecology.

  15. Final Report, DE-FG02-92ER14261, Pore Scale Geometric and Fluid Distribution Analysis

    SciTech Connect

    W. Brent Lindquist

    2005-01-21

    The elucidation of the relationship between pore scale structure and fluid flow in porous media is a fundamental problem of long standing interest. Incomplete characterization of medium properties continues to be a limiting factor in accurate field scale simulations. The accomplishments of this grant have kept us at the forefront in investigating the applicability of X-ray computed microtomography (XCMT) as a tool for contributing to the understanding of this relationship. Specific accomplishments have been achieved in four areas: - development of numerical algorithms (largely in the field of computational geometry) to provide automated recognition of and measurements on features of interest in the pore space. These algorithms have been embodied in a software package, 3DMA-Rock. - application of these algorithms to extensive studies of the pore space of sandstones. - application of these algorithms to studies of fluid (oil/water) partitioning in the pore space of Berea sandstone and polyethylene models. - technology transfer.

  16. Using synchrotron X-ray microtomography to characterize the pore network of reservoir rocks: A case study on carbonates

    NASA Astrophysics Data System (ADS)

    Arzilli, F.; Cilona, A.; Mancini, L.; Tondi, E.

    2016-09-01

    In this work we propose a new methodology to calculate pore connectivity in granular rocks. This method is useful to characterize the pore networks of natural and laboratory compaction bands (CBs), and compare them with the host rock pore network. Data were collected using the synchrotron X-ray microtomography technique and quantitative analyses were carried out using the Pore3D software library. The porosity was calculated from segmented tridimensional images of deformed and pristine rocks. A process of skeletonization of the pore space was used to obtain the number of connected pores within the rock volume. By analyzing the skeletons the differences between natural and laboratory CBs were highlighted. The natural CB has a lower porosity than to the laboratory one. In natural CBs, the grain contacts appear welded, whereas laboratory CBs show irregular pore shape. Moreover, we assessed for the first time how pore connectivity evolves as a function of deformation, documenting the mechanism responsible for pore connectivity drop within the CBs.

  17. Intercomparison of 3D pore-scale flow and solute transport simulation methods

    DOE PAGES

    Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.; ...

    2015-09-28

    In this study, multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include (1) methods that explicitly model the three-dimensional geometry of pore spaces and (2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the firstmore » type based on the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides

  18. Hydrochromic Approaches to Mapping Human Sweat Pores.

    PubMed

    Park, Dong-Hoon; Park, Bum Jun; Kim, Jong-Man

    2016-06-21

    Hydrochromic materials, which undergo changes in their light absorption and/or emission properties in response to water, have been extensively investigated as humidity sensors. Recent advances in the design of these materials have led to novel applications, including monitoring the water content of organic solvents, water-jet-based rewritable printing on paper, and hydrochromic mapping of human sweat pores. Our interest in this area has focused on the design of hydrochromic materials for human sweat pore mapping. We recognized that materials appropriate for this purpose must have balanced sensitivities to water. Specifically, while they should not undergo light absorption and/or emission transitions under ambient moisture conditions, the materials must have sufficiently high hydrochromic sensitivities that they display responses to water secreted from human sweat pores. In this Account, we describe investigations that we have carried out to develop hydrochromic substances that are suitable for human sweat pore mapping. Polydiacetylenes (PDAs) have been extensively investigated as sensor matrices because of their stimulus-responsive color change property. We found that incorporation of headgroups composed of hygroscopic ions such as cesium or rubidium and carboxylate counterions enables PDAs to undergo a blue-to-red colorimetric transition as well as a fluorescence turn-on response to water. Very intriguingly, the small quantities of water secreted from human sweat pores were found to be sufficient to trigger fluorescence turn-on responses of the hydrochromic PDAs, allowing precise mapping of human sweat pores. Since the hygroscopic ion-containing PDAs developed in the initial stage display a colorimetric transition under ambient conditions that exist during humid summer periods, a new system was designed. A PDA containing an imidazolium ion was found to be stable under all ambient conditions and showed temperature-dependent hydrochromism corresponding to a

  19. Analysis of a spatially deconvolved solar pore

    NASA Astrophysics Data System (ADS)

    Quintero Noda, C.; Shimizu, T.; Ruiz Cobo, B.; Suematsu, Y.; Katsukawa, Y.; Ichimoto, K.

    2016-08-01

    Solar pores are active regions with large magnetic field strengths and apparent simple magnetic configurations. Their properties resemble the ones found for the sunspot umbra although pores do not show penumbra. Therefore, solar pores present themselves as an intriguing phenomenon that is not completely understood. We examine in this work a solar pore observed with Hinode/SP using two state of the art techniques. The first one is the spatial deconvolution of the spectropolarimetric data that allows removing the stray light contamination induced by the spatial point spread function of the telescope. The second one is the inversion of the Stokes profiles assuming local thermodynamic equilibrium that let us to infer the atmospheric physical parameters. After applying these techniques, we found that the spatial deconvolution method does not introduce artefacts, even at the edges of the magnetic structure, where large horizontal gradients are detected on the atmospheric parameters. Moreover, we also describe the physical properties of the magnetic structure at different heights finding that, in the inner part of the solar pore, the temperature is lower than outside, the magnetic field strength is larger than 2 kG and unipolar, and the line-of-sight velocity is almost null. At neighbouring pixels, we found low magnetic field strengths of same polarity and strong downward motions that only occur at the low photosphere, below the continuum optical depth log τ = -1. Finally, we studied the spatial relation between different atmospheric parameters at different heights corroborating the physical properties described before.

  20. Modeling tissue growth within nonwoven scaffolds pores.

    PubMed

    Edwards, Sharon L; Church, Jeffrey S; Alexander, David L J; Russell, Stephen J; Ingham, Eileen; Ramshaw, John A M; Werkmeister, Jerome A

    2011-02-01

    In this study we present a novel approach for predicting tissue growth within the pores of fibrous tissue engineering scaffolds. Thin nonwoven polyethylene terephthalate scaffolds were prepared to characterize tissue growth within scaffold pores, by mouse NR6 fibroblast cells. On the basis of measurements of tissue lengths at fiber crossovers and along fiber segments, mathematical models were determined during the proliferative phase of cell growth. Tissue growth at fiber crossovers decreased with increasing interfiber angle, with exponential relationships determined on day 6 and 10 of culture. Analysis of tissue growth along fiber segments determined two growth profiles, one with enhanced growth as a result of increased tissue lengths near the fiber crossover, achieved in the latter stage of culture. Derived mathematical models were used in the development of a software program to visualize predicted tissue growth within a pore. This study identifies key pore parameters that contribute toward tissue growth, and suggests models for predicting this growth, based on fibroblast cells. Such models may be used in aiding scaffold design, for optimum pore infiltration during the tissue engineering process.

  1. Modeling branching pore structures in membrane filters

    NASA Astrophysics Data System (ADS)

    Sanaei, Pejman; Cummings, Linda J.

    2016-11-01

    Membrane filters are in widespread industrial use, and mathematical models to predict their efficacy are potentially very useful, as such models can suggest design modifications to improve filter performance and lifetime. Many models have been proposed to describe particle capture by membrane filters and the associated fluid dynamics, but most such models are based on a very simple structure in which the pores of the membrane are assumed to be simple circularly-cylindrical tubes spanning the depth of the membrane. Real membranes used in applications usually have much more complex geometry, with interconnected pores which may branch and bifurcate. Pores are also typically larger on the upstream side of the membrane than on the downstream side. We present an idealized mathematical model, in which a membrane consists of a series of bifurcating pores, which decrease in size as the membrane is traversed. Feed solution is forced through the membrane by applied pressure, and particles are removed from the feed either by sieving, or by particle adsorption within pores (which shrinks them). Thus the membrane's permeability decreases as the filtration progresses, ultimately falling to zero. We discuss how filtration efficiency depends on the characteristics of the branching structure. Partial support from NSF DMS 1261596 is gratefully acknowledged.

  2. 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.

  3. Broad pore channels as molecular highways in nanoporous catalysts: Multiscale modeling, optimization and applications

    NASA Astrophysics Data System (ADS)

    Wang, Gang

    the total volume of the catalyst) and keeping broad pore channel walls (consisting of the same mesoporous catalytic material) 33mum thick. For autothermal reforming of methane, the gain in overall catalytic activity could be improved by a factor of 1.5-1.8, by the introduction of broad pore channels with a size of 1 mum, and occupying an optimized fraction of space. The H 2/CO ratio could be tuned as well: a large channel volume fraction generally favors a high H2/CO ratio.

  4. Modeling of N2 adsorption in MCM-41 materials: hexagonal pores versus cylindrical pores.

    PubMed

    Ustinov, Eugene A

    2009-07-07

    Low-temperature nitrogen adsorption in hexagonal pores and equivalent cylindrical pores is analyzed using nonlocal density functional theory extended to amorphous solids (NLDFT-AS). It is found that, despite significant difference of the density distribution over the cross-section of the pore, the capillary condensation/evaporation pressure is not considerably affected by the pore shape being slightly lower in the case of hexagonal geometry. However, the condensation/evaporation step in the hexagonal pore is slightly larger than that in the equivalent cylindrical pore because in the latter case the pore wall surface area and, hence, the amount adsorbed at pressures below the evaporation pressure are underestimated by 5%. We show that a dimensionless parameter defined as the ratio of the condensation/evaporation step and the upper value of the amount adsorbed at the condensation/evaporation pressure can be used as an additional criterion of the correct choice of the gas-solid molecular parameters along with the dependence of condensation/evaporation pressure on the pore diameter. Application of the criteria to experimental data on nitrogen adsorption on a series of MCM-41 silica at 77 K corroborates some evidence that the capillary condensation occurs at equilibrium conditions.

  5. Chromatographic performance of large-pore versus small-pore columns in micellar liquid chromatography.

    PubMed

    McCormick, Timothy J; Foley, Joe P; Lloyd, David K

    2003-02-25

    Micellar liquid chromatography (MLC) is useful in bioanalysis because proteinaceous biofluids can be directly injected onto the column. The technique has been limited in part because of the apparently weak eluting power of micellar mobile phases. It has recently been shown [Anal. Chem. 72 (2000) 294] that this may be overcome by the use of large pore size stationary phases. In this work, large-pore (1000 A) C(18) stationary phases were evaluated relative to conventional small-pore (100 A) C(18) stationary phases for the direct sample injection of drugs in plasma. Furthermore, the difference between the large and small pore phases in gradient elution separations of mixtures of widely varying hydrophobicities was investigated. Large-pore stationary phases were found to be very effective for eluting moderately to highly hydrophobic compounds such as ibuprofen, crotamiton, propranolol, and dodecanophenone, which were highly retained on the small-pore stationary phases typically used in MLC. The advantages of direct introduction of biological samples (drugs in plasma) and rapid column re-equilibration after gradient elution in MLC were maintained with large-pore phases. Finally, recoveries, precision, linearity, and detection limits for the determination of quinidine and DPC 961 in spiked bovine plasma were somewhat better using MLC with wide pore phases.

  6. Foam invasion through a single pore.

    PubMed

    Delbos, Aline; Pitois, Olivier

    2011-07-01

    We investigate experimentally the behavior of liquid foams pumped at a given flow rate through a single pore, in the situation where the pore diameter is smaller than the bubble diameter. Results reveal that foam invasion can be observed only within a restricted range of values for the dimensionless flow rate and the foam liquid fraction. Within this foam invasion regime, the liquid content of invading foams is measured to be three times higher than the initial liquid content. Outside this regime, both gas alone and liquid alone invasion regimes can be observed. The gas invasion regime results from the rupture of foam films during local T1, during bubble rearrangements events induced by foam flow, whereas the liquid invasion regime is allowed by the formation of a stable cluster of jammed bubbles at the pore's opening.

  7. Moving Magnetic Features around a Pore

    NASA Astrophysics Data System (ADS)

    Kaithakkal, A. J.; Riethmüller, T. L.; Solanki, S. K.; Lagg, A.; Barthol, P.; Gandorfer, A.; Gizon, L.; Hirzberger, J.; vanNoort, M.; Blanco Rodríguez, J.; Del Toro Iniesta, J. C.; Orozco Suárez, D.; Schmidt, W.; Martínez Pillet, V.; Knölker, M.

    2017-03-01

    Spectropolarimetric observations from Sunrise/IMaX, obtained in 2013 June, are used for a statistical analysis to determine the physical properties of moving magnetic features (MMFs) observed near a pore. MMFs of the same and opposite polarity, with respect to the pore, are found to stream from its border at an average speed of 1.3 km s‑1 and 1.2 km s‑1, respectively, with mainly same-polarity MMFs found further away from the pore. MMFs of both polarities are found to harbor rather weak, inclined magnetic fields. Opposite-polarity MMFs are blueshifted, whereas same-polarity MMFs do not show any preference for up- or downflows. Most of the MMFs are found to be of sub-arcsecond size and carry a mean flux of ∼1.2 × 1017 Mx.

  8. 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.

  9. Pore-by-pore capillary pressure measurements using X-ray microtomography at reservoir conditions: Curvature, snap-off, and remobilization of residual CO2

    NASA Astrophysics Data System (ADS)

    Andrew, Matthew; Bijeljic, Branko; Blunt, Martin J.

    2014-11-01

    X-ray microtomography was used to image the shape and size of residual ganglia of supercritical CO2 at resolutions of 3.5 and 2 μm and at representative subsurface conditions of temperature and pressure. The capillary pressure for each ganglion was found by measuring the curvature of the CO2-brine interface, while the pore structure was parameterized using distance maps of the pore space. The formation of the residual clusters by snap-off was examined by comparing the ganglion capillary pressure to local pore topography. The capillary pressure was found to be inversely proportional to the radius of the largest restriction (throat) surrounding the ganglion, which validates the imbibition mechanisms used in pore-network modeling. The potential mobilization of residual ganglia was assessed using a reformulation of both the capillary (Ncmacro) and Bond numbers (Nbmacro), rigorously based on a balance of pore-scale forces, with the majority of ganglia remobilized at Ncmacro around 1. Buoyancy forces were found to be small in this system (Nbmacro << 1), meaning the gravitational remobilization of CO2 after residual trapping would be extremely difficult.

  10. Assessing Coating Reliability Through Pore Architecture Evaluation

    NASA Astrophysics Data System (ADS)

    Paul, S.

    2010-06-01

    Plasma-sprayed thermal barrier coatings (TBCs) exhibit many interlamellar pores, voids, and microcracks. These microstructural features are primarily responsible for the low global stiffness and the low thermal conductivity commonly exhibited by such coatings. The pore architecture thus has an important influence on such thermophysical properties. In the present work, the effect of heat treatment (at temperatures up to 1400 °C, for times of up to 20 h) on the pore architecture of detached YSZ top coats with different impurity levels have been characterized by mercury intrusion porosimetry and gas-sorption techniques. Stiffness and thermal conductivity were also monitored to assess the effect of change in pore architecture on properties. While the overall porosity level remained relatively unaffected (at around 10-12%) after the heat treatments concerned, there were substantial changes in the pore size distribution and the (surface-connected) specific surface area. Fine pores (<~50 nm) rapidly disappeared, while the specific surface area dropped dramatically, particularly at high-treatment temperatures (~1400 °C). These changes are thought to be associated with intrasplat microcrack healing, improved intersplat bonding and increased contact area, leading to disappearance of much of the fine porosity. These microstructural changes are reflected in sharply increased stiffness and thermal conductivity. Increase in thermal conductivity and stiffness were found to be more pronounced for coatings with higher impurity content (particularly alumina and silica). Reliability issues surrounding such increase in thermal conductivity and stiffness are discussed along with a brief note on the effect of impurities on TBC life.

  11. Hydrophobic pore array surfaces: wetting and interaction forces in water/ethanol mixtures.

    PubMed

    Hansson, Petra M; Hormozan, Yashar; Brandner, Birgit D; Linnros, Jan; Claesson, Per M; Swerin, Agne; Schoelkopf, Joachim; Gane, Patrick A C; Thormann, Esben

    2013-04-15

    Interactions between and wetting behavior of structured hydrophobic surfaces using different concentrations of water/ethanol mixtures have been investigated. Silica surfaces consisting of pore arrays with different pore spacings and pore depths were made hydrophobic by silanization. Their static and dynamic contact angles were found to be independent of the pore depth while fewer pores on the surface, i.e. a closer resemblance to a flat surface, gave a lower contact angle. As expected, a higher amount of ethanol facilitated wetting on all the surfaces tested. Confocal Raman microscopy measurements proved both water and ethanol to penetrate into the pores. AFM colloidal probe force measurements clearly showed that formation of air cavitation was hindered between the hydrophobic surfaces in presence of ethanol, and an increase in ethanol concentration was followed by a smaller jump-in distance and a weaker adhesion force. On separation, an immediate jump-out of contact occurred. The measured forces were interpreted as being due to capillary condensation of ethanol between the surfaces giving rise to very unstable cavities immediately rupturing on surface separation.

  12. On Pore Dynamics and Calcite Solubility in Carbonaceous Aquifers used in Energy Storage Applications

    NASA Astrophysics Data System (ADS)

    Tilley, Bs; Brady, Ds; Ueckert, M.; Baumann, T.

    2015-11-01

    Geothermal energy harvesting applications use deep groundwater aquifers to store harvested energy. The impact of this additional energy to the aquifer chemistry is crucial for long-term operation. Gaseous CO2 is added to the injected water to compensate potential precipitates of carbonates and to prevent structural changes to the aquifer. Both of these effects affect the local chemical equilibrium of the aquifer, and we consider a long-wave model of this process for a single axisymmetric pore where gaseous CO2 concentration, temperature, fluid flow and hydrochemistry modify the pore radius in space and time. Substrates are composed of calcite and dolomite, whose composition evolution is part of the full pore problem. During oscillatory flow conditions, concentration levels of the dissolved species can be sufficient to overcome elevated temperature levels and promote pore closure for sufficiently thin pores. We identify the conditions under which this pore closure takes place. Support from the Bavarian State Ministry for the Economy is gratefully acknowledged.

  13. A pore-scale model of two-phase flow in water-wet rock

    SciTech Connect

    Silin, Dmitriy; Patzek, Tad

    2009-02-01

    A finite-difference discretization of Stokes equations is used to simulate flow in the pore space of natural rocks. Numerical solutions are obtained using the method of artificial compressibility. In conjunction with Maximal Inscribed Spheres method, these computations produce relative permeability curves. The results of computations are in agreement with laboratory measurements.

  14. Active Polymer Translocation through Flickering Pores

    NASA Astrophysics Data System (ADS)

    Cohen, Jack A.; Chaudhuri, Abhishek; Golestanian, Ramin

    2011-12-01

    Single file translocation of a homopolymer through an active channel under the presence of a driving force is studied using Langevin dynamics simulation. It is shown that a channel with sticky walls and oscillating width could lead to significantly more efficient translocation as compared to a static channel that has a width equal to the mean width of the oscillating pore. The gain in translocation exhibits a strong dependence on the stickiness of the pore, which could allow the polymer translocation process to be highly selective.

  15. Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains

    DOE PAGES

    Bailey, Vanessa L.; Smith, A. P.; Tfaily, Malak; ...

    2017-01-11

    Spatial isolation of soil organic carbon (SOC) in different sized pores may be a mechanism by which otherwise labile carbon (C) could be protected in soils. When soil water content increases, the hydrologic connectivity of soil pores also increases, allowing greater transport of SOC and other resources from protected locations, to microbially colonized locations more favorable to decomposition. The heterogeneous distribution of specialized decomposers, C, and other resources throughout the soil indicates that the metabolism or persistence of soil C compounds is highly dependent on short-distance transport processes. The objective of this research was to characterize the complexity of Cmore » in pore waters held at weak and strong water tensions (effectively soil solution held behind coarse- and fine-pore throats, respectively) and evaluate the microbial decomposability of these pore waters. We saturated intact soil cores and extracted pore waters with increasing suction pressures to sequentially sample pore waters from increasingly fine pore domains. Ultrahigh resolution mass spectrometry of the SOC was used to profile the major biochemical classes (i.e., lipids, proteins, lignin, carbohydrates, and condensed aromatics) of compounds present in the pore waters; some of these samples were then used as substrates for growth of Cellvibrio japonicus (DSMZ 16018), Streptomyces cellulosae (ATCC® 25439™), and Trichoderma reseei (QM6a) in 7 day incubations. The soluble C in finer pores was more complex than the soluble C in coarser pores, and the incubations revealed that the more complex C in these fine pores is not recalcitrant. The decomposition of this complex C led to greater losses of C through respiration than the simpler C from coarser pore waters. Our research suggests that soils that experience repeated cycles of drying and wetting may be accompanied by repeated cycles of increased CO2 fluxes that are driven by i) the transport of C from protected pools into

  16. Pore-Scale Modeling of Pore Structure Effects on P-Wave Scattering Attenuation in Dry Rocks

    PubMed Central

    Li, Tianyang; Qiu, Hao; Wang, Feifei

    2015-01-01

    Underground rocks usually have complex pore system with a variety of pore types and a wide range of pore size. The effects of pore structure on elastic wave attenuation cannot be neglected. We investigated the pore structure effects on P-wave scattering attenuation in dry rocks by pore-scale modeling based on the wave theory and the similarity principle. Our modeling results indicate that pore size, pore shape (such as aspect ratio), and pore density are important factors influencing P-wave scattering attenuation in porous rocks, and can explain the variation of scattering attenuation at the same porosity. From the perspective of scattering attenuation, porous rocks can safely suit to the long wavelength assumption when the ratio of wavelength to pore size is larger than 15. Under the long wavelength condition, the scattering attenuation coefficient increases as a power function as the pore density increases, and it increases exponentially with the increase in aspect ratio. For a certain porosity, rocks with smaller aspect ratio and/or larger pore size have stronger scattering attenuation. When the pore aspect ratio is larger than 0.5, the variation of scattering attenuation at the same porosity is dominantly caused by pore size and almost independent of the pore aspect ratio. These results lay a foundation for pore structure inversion from elastic wave responses in porous rocks. PMID:25961729

  17. Pore-scale modeling of pore structure effects on P-wave scattering attenuation in dry rocks.

    PubMed

    Wang, Zizhen; Wang, Ruihe; Li, Tianyang; Qiu, Hao; Wang, Feifei

    2015-01-01

    Underground rocks usually have complex pore system with a variety of pore types and a wide range of pore size. The effects of pore structure on elastic wave attenuation cannot be neglected. We investigated the pore structure effects on P-wave scattering attenuation in dry rocks by pore-scale modeling based on the wave theory and the similarity principle. Our modeling results indicate that pore size, pore shape (such as aspect ratio), and pore density are important factors influencing P-wave scattering attenuation in porous rocks, and can explain the variation of scattering attenuation at the same porosity. From the perspective of scattering attenuation, porous rocks can safely suit to the long wavelength assumption when the ratio of wavelength to pore size is larger than 15. Under the long wavelength condition, the scattering attenuation coefficient increases as a power function as the pore density increases, and it increases exponentially with the increase in aspect ratio. For a certain porosity, rocks with smaller aspect ratio and/or larger pore size have stronger scattering attenuation. When the pore aspect ratio is larger than 0.5, the variation of scattering attenuation at the same porosity is dominantly caused by pore size and almost independent of the pore aspect ratio. These results lay a foundation for pore structure inversion from elastic wave responses in porous rocks.

  18. Controlling the Pore Size of Mesoporous Carbon Thin Films through Thermal and Solvent Annealing.

    PubMed

    Zhou, Zhengping; Liu, Guoliang

    2017-02-02

    Herein an approach to controlling the pore size of mesoporous carbon thin films from metal-free polyacrylonitrile-containing block copolymers is described. A high-molecular-weight poly(acrylonitrile-block-methyl methacrylate) (PAN-b-PMMA) is synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization. The authors systematically investigate the self-assembly behavior of PAN-b-PMMA thin films during thermal and solvent annealing, as well as the pore size of mesoporous carbon thin films after pyrolysis. The as-spin-coated PAN-b-PMMA is microphase-separated into uniformly spaced globular nanostructures, and these globular nanostructures evolve into various morphologies after thermal or solvent annealing. Surprisingly, through thermal annealing and subsequent pyrolysis of PAN-b-PMMA into mesoporous carbon thin films, the pore size and center-to-center spacing increase significantly with thermal annealing temperature, different from most block copolymers. In addition, the choice of solvent in solvent annealing strongly influences the block copolymer nanostructure and the pore size of mesoporous carbon thin films. The discoveries herein provide a simple strategy to control the pore size of mesoporous carbon thin films by tuning thermal or solvent annealing conditions, instead of synthesizing a series of block copolymers of various molecular weights and compositions.

  19. In-situ X-ray Synchrotron Microtomography: Real Time Pore Structure Evolution during Olivine Carbonation

    NASA Astrophysics Data System (ADS)

    Zhu, W.; Fusseis, F.; Lisabeth, H. P.; Xiao, X.

    2013-12-01

    Mineral carbonation has been proposed as a promising method for long-term, secure sequestration of carbon dioxide. In porous rocks, fluid-rock interactions can significantly alter the pore space and thus exert important controls over the rate and extent of carbonation. We constructed an x-ray transparent pressure cell [Fusseis et al., 2013] to investigate the real time pore structure evolution during mineral carbonation in porous olivine aggregates. In each experiment, a sintered olivine sample was subjected to a confining pressure of 13 MPa and a pore pressure of 10 MPa, with a sodium bicarbonate solution (NaHCO3 at 1.5 M) as pore fluid. At these pressure conditions, the cell was heated to 473 K. Constant pressure and temperature conditions were maintained during the length of the experiments, lasting 72-120 hours. Using a polychromatic beam in the 2-BM upstream hutch at the Advanced Photon Source, 3-dimensional (3-D) microtomography data were collected in 20 seconds with 30-minute interval. A novel phase retrieval reconstruction algorithm [Paganin et al., 2002] was used to reconstruct microtomographic datasets with a voxel size of ~1.1 micron. The microtomography images at different stages of the carbonation process reveal progressive growth of new crystals in the pore space. Integration of a x-ray transparent pressure vessel with flow through capacity and 3-D microtomography provides a novel research direction of studying the coupled chemo-hydro-thermal-mechanical processes in rocks.

  20. Acoustical properties of air-saturated porous material with periodically distributed dead-end pores.

    PubMed

    Leclaire, P; Umnova, O; Dupont, T; Panneton, R

    2015-04-01

    A theoretical and numerical study of the sound propagation in air-saturated porous media with straight main pores bearing lateral cavities (dead-ends) is presented. The lateral cavities are located at "nodes" periodically spaced along each main pore. The effect of periodicity in the distribution of the lateral cavities is studied, and the low frequency limit valid for the closely spaced dead-ends is considered separately. It is shown that the absorption coefficient and transmission loss are influenced by the viscous and thermal losses in the main pores as well as their perforation rate. The presence of long or short dead-ends significantly alters the acoustical properties of the material and can increase significantly the absorption at low frequencies (a few hundred hertz). These depend strongly on the geometry (diameter and length) of the dead-ends, on their number per node, and on the periodicity along the propagation axis. These effects are primarily due to low sound speed in the main pores and to thermal losses in the dead-end pores. The model predictions are compared with experimental results. Possible designs of materials of a few cm thicknesses displaying enhanced low frequency absorption at a few hundred hertz are proposed.

  1. Characterization of PSD of activated carbons by using slit and triangular pore geometries

    NASA Astrophysics Data System (ADS)

    Azevedo, D. C. S.; Rios, R. B.; López, R. H.; Torres, A. E. B.; Cavalcante, C. L.; Toso, J. P.; Zgrablich, G.

    2010-06-01

    A mixed geometry model for activated carbons, representing the porous space as a collection of an undetermined proportion of slit and triangular pores, is developed, evaluated theoretically and applied to the characterization of a controlled series of samples of activated carbon obtained from the same precursor material. A method is proposed for the determination of the Pore Size Distribution (PSD) for such a mixed geometry model, leading to the unique determination of the proportion of pores of the two geometries fitting adsorption data. By using the Grand Canonical Monte Carlo (GCMC) simulation method in the continuum space, families of N2 adsorption isotherms are generated both for slit and triangular geometry corresponding to different pore sizes. The problem of the uniqueness in the determination of the PSD by fitting an adsorption isotherm using the mixed geometry model is then discussed and the effects of the addition of triangular pores on the PSD are analyzed by performing a test where the adsorption isotherm corresponding to the known PSD is generated and used as the "experimental" isotherm. It is found that a pure slit geometry model would widen the PSD and shift it to smaller sizes, whereas a pure triangular geometry model would produce the opposite effect. The slit and triangular geometry families of isotherms are finally used to the fit experimental N 2 adsorption data corresponding to a family of activated carbons obtained from coconut shells through a one-step chemical activation process with phosphoric acid in air, allowing for the determination of the micropore volume, the proportion of slit and triangular pores and the PSD corresponding to the mixed geometry. The same experimental data were fit using both the conventional slit pore model and the mixed geometry model. From the analysis of the effect of different preparation procedures on the resulting PSDs, it is concluded that the proposed mixed geometry model may probably better capture the

  2. Changes in pore geometry and relative permeability caused by carbonate precipitation in porous media.

    PubMed

    Jiang, Fei; Tsuji, Takeshi

    2014-11-01

    The CO_{2} behavior within the reservoirs of carbon capture and storage projects is usually predicted from large-scale simulations of the reservoir. A key parameter in reservoir simulation is relative permeability. However, mineral precipitation alters the pore structure over time, and leads correspondingly to permeability changing with time. In this study, we numerically investigate the influence of carbonate precipitation on relative permeability during CO_{2} storage. The pore spaces in rock samples were extracted by high-resolution microcomputed tomography (CT) scanned images. The fluid velocity field within the three-dimensional pore spaces was calculated by the lattice Boltzmann method, while reactive transport with calcite deposition was modeled by an advection-reaction formulation solved by the finite volume method. To increase the computational efficiency and reduce the processing time, we adopted a graphics processing unit parallel computing technique. The relative permeability of the sample rock was then calculated by a highly optimized two-phase lattice Boltzmann model. We also proposed two pore clogging models. In the first model, the clogging processes are modeled by transforming fluid nodes to solid nodes based on their precipitated mass level. In the second model, the porosity is artificially reduced by adjusting the gray scale threshold of the CT images. The developed method accurately simulates the mineralization process observed in laboratory experiment. Precipitation-induced evolution of pore structure significantly influenced the absolute permeability. The relative permeability, however, was much more influenced by pore reduction in the nonwetting phase than in the wetting phase. The output of the structural changes in pore geometry by this model could be input to CO_{2} reservoir simulators to investigate the outcome of sequestered CO_{2}.

  3. A streamline splitting pore-network approach for computationally inexpensive and accurate simulation of transport in porous media

    SciTech Connect

    Mehmani, Yashar; Oostrom, Martinus; Balhoff, Matthew

    2014-03-20

    Several approaches have been developed in the literature for solving flow and transport at the pore-scale. Some authors use a direct modeling approach where the fundamental flow and transport equations are solved on the actual pore-space geometry. Such direct modeling, while very accurate, comes at a great computational cost. Network models are computationally more efficient because the pore-space morphology is approximated. Typically, a mixed cell method (MCM) is employed for solving the flow and transport system which assumes pore-level perfect mixing. This assumption is invalid at moderate to high Peclet regimes. In this work, a novel Eulerian perspective on modeling flow and transport at the pore-scale is developed. The new streamline splitting method (SSM) allows for circumventing the pore-level perfect mixing assumption, while maintaining the computational efficiency of pore-network models. SSM was verified with direct simulations and excellent matches were obtained against micromodel experiments across a wide range of pore-structure and fluid-flow parameters. The increase in the computational cost from MCM to SSM is shown to be minimal, while the accuracy of SSM is much higher than that of MCM and comparable to direct modeling approaches. Therefore, SSM can be regarded as an appropriate balance between incorporating detailed physics and controlling computational cost. The truly predictive capability of the model allows for the study of pore-level interactions of fluid flow and transport in different porous materials. In this paper, we apply SSM and MCM to study the effects of pore-level mixing on transverse dispersion in 3D disordered granular media.

  4. Mathematical model of an air-filled alpha stirling refrigerator

    NASA Astrophysics Data System (ADS)

    McFarlane, Patrick; Semperlotti, Fabio; Sen, Mihir

    2013-10-01

    This work develops a mathematical model for an alpha Stirling refrigerator with air as the working fluid and will be useful in optimizing the mechanical design of these machines. Two pistons cyclically compress and expand air while moving sinusoidally in separate chambers connected by a regenerator, thus creating a temperature difference across the system. A complete non-linear mathematical model of the machine, including air thermodynamics, and heat transfer from the walls, as well as heat transfer and fluid resistance in the regenerator, is developed. Non-dimensional groups are derived, and the mathematical model is numerically solved. The heat transfer and work are found for both chambers, and the coefficient of performance of each chamber is calculated. Important design parameters are varied and their effect on refrigerator performance determined. This sensitivity analysis, which shows what the significant parameters are, is a useful tool for the design of practical Stirling refrigeration systems.

  5. Molecular Sensing with an Artificial Pore

    NASA Astrophysics Data System (ADS)

    Saleh, Omar A.

    2002-03-01

    While microfluidic systems are routinely integrated with optical schemes to measure biological macromolecules, there are relatively few examples of experiments in which electronic techniques are used. There are, however, good reasons to perform electronic measurements- macromolecules do not need to be fluorescently tagged, and different parameters of the analyte can be investigated. To begin to take advantage of these differences, we have developed a chip-based device that uses resistive sensing of a micro-fabricated pore to characterize solutions of particles. The device can perform size-based differentiation of polydisperse solutions of colloids with a precision of 10 nm in diameter^*. This level of precision could be utilized to perform simple binding or immuno-assays whereby the attachment of the appropriate ligand to a receptor immobilized on the colloid surface causes a detectable increase in the colloid’s diameter. Furthermore, the relatively simple design can easily be scaled up to create arrays of pores on a single chip, thus adding the capability to perform multiple assays in parallel. Finally, reductions in pore size have allowed us to detect successfully single molecules of lambda-phage DNA passing through the pore. This particular achievement represents a first step towards a host of bio-molecular sensing applications. ^*O. A. Saleh and L. L. Sohn, Rev. Sci. Instrum. 72, 4449 (2001)

  6. Channel gating pore: a new therapeutic target.

    PubMed

    Kornilov, Polina; Peretz, Asher; Attali, Bernard

    2013-09-01

    Each subunit of voltage-gated cation channels comprises a voltage-sensing domain and a pore region. In a paper recently published in Cell Research, Li et al. showed that the gating charge pathway of the voltage sensor of the KCNQ2 K+ channel can accommodate small opener molecules and offer a new target to treat hyperexcitability disorders.

  7. Pore-Forming Toxins Trigger the Purge.

    PubMed

    Bonfini, Alessandro; Buchon, Nicolas

    2016-12-14

    The intestinal epithelium responds to pathogens by coordinating microbial elimination with tissue repair, both required to survive an infection. In this issue of Cell Host & Microbe, Lee et al. (2016) discover a rapid and evolutionarily conserved response to pore-forming toxins in the gut, involving cytoplasm ejection and enterocyte regrowth.

  8. The evolution of pore connectivity in volcanic rocks

    NASA Astrophysics Data System (ADS)

    Colombier, Mathieu; Wadsworth, Fabian B.; Gurioli, Lucia; Scheu, Bettina; Kueppers, Ulrich; Di Muro, Andrea; Dingwell, Donald B.

    2017-03-01

    Pore connectivity is a measure of the fraction of pore space (vesicles, voids or cracks) in a material that is interconnected on the system length scale. Pore connectivity is fundamentally related to permeability, which has been shown to control magma outgassing and the explosive potential of magma during ascent in the shallowest part of the crust. Here, we compile a database of connectivity and porosity from published sources and supplement this with additional measurements, using natural volcanic rocks produced in a broad range of eruptive styles and with a range of bulk composition. The database comprises 2715 pairs of connectivity C and porosity ϕ values for rocks from 35 volcanoes as well as 116 products of experimental work. For 535 volcanic rock samples, the permeability k was also measured. Data from experimental studies constrain the general features of the relationship between C and ϕ associated with both vesiculation and densification processes, which can then be used to interpret natural data. To a first order, we show that a suite of rocks originating from effusive eruptive behaviour can be distinguished from rocks originating from explosive eruptive behaviour using C and ϕ. We observe that on this basis, a particularly clear distinction can be made between scoria formed in fire-fountains and that formed in Strombolian activity. With increasing ϕ, the onset of connectivity occurs at the percolation threshold ϕc which in turn can be hugely variable. We demonstrate that C is an excellent metric for constraining ϕc in suites of porous rocks formed in a common process and discuss the range of ϕc values recorded in volcanic rocks. The percolation threshold is key to understanding the onset of permeability, outgassing and compaction in shallow magmas. We show that this threshold is dramatically different in rocks formed during densification processes than in rocks formed in vesiculating processes and propose that this value is the biggest factor in

  9. Long-term Differences in Tillage and Land Use Affect Intra-aggregate Pore Heterogeneity

    SciTech Connect

    Kravchenko, A.N.; Wang, A.N.W.; Smucker, A.J.M.; Rivers, M.L.

    2012-10-25

    Recent advances in computed tomography provide measurement tools to study internal structures of soil aggregates at micrometer resolutions and to improve our understanding of specific mechanisms of various soil processes. Fractal analysis is one of the data analysis tools that can be helpful in evaluating heterogeneity of the intra-aggregate internal structures. The goal of this study was to examine how long-term tillage and land use differences affect intra-aggregate pore heterogeneity. The specific objectives were: (i) to develop an approach to enhance utility of box-counting fractal dimension in characterizing intra-aggregate pore heterogeneity; (ii) to examine intra-aggregate pores in macro-aggregates (4-6 mm in size) using the computed tomography scanning and fractal analysis, and (iii) to compare heterogeneity of intra-aggregate pore space in aggregates from loamy Alfisol soil subjected to 20 yr of contrasting management practices, namely, conventional tillage (chisel plow) (CT), no-till (NT), and native succession vegetation (NS). Three-dimensional images of the intact aggregates were obtained with a resolution of 14.6 {micro}m at the Advanced Photon Source, Argonne National Laboratory, Argonne, IL. Proposed box-counting fractal dimension normalization was successfully implemented to estimate heterogeneity of pore voxel distributions without bias associated with different porosities in soil aggregates. The aggregates from all three studied treatments had higher porosity associated with large (>100 {micro}m) pores present in their centers than in their exteriors. Pores 15 to 60 {micro}m were equally abundant throughout entire aggregates but their distributions were more heterogeneous in aggregate interiors. The CT aggregates had greater numbers of pores 15 to 60 {micro}m than NT and NS. Distribution of pore voxels belonging to large pores was most heterogeneous in the aggregates from NS, followed by NT and by CT. This result was consistent with presence of

  10. Chemical sensing and imaging in microfluidic pore network structures relevant to natural carbon cycling and industrial carbon sequestration

    SciTech Connect

    Grate, Jay W.; Zhang, Changyong; Wilkins, Michael J.; Warner, Marvin G.; Anheier, Norman C.; Suter, Jonathan D.; Kelly, Ryan T.; Oostrom, Martinus

    2013-06-11

    Energy and climate change represent significant factors in global security. Atmospheric carbon dioxide levels, while global in scope, are influenced by pore-scale phenomena in the subsurface. We are developing tools to visualize and investigate processes in pore network microfluidic structures with transparent covers as representations of normally-opaque porous media. In situ fluorescent oxygen sensing methods and fluorescent cellulosic materials are being used to investigate processes related to terrestrial carbon cycling involving cellulytic respiring microorganisms. These structures also enable visualization of water displacement from pore spaces by hydrophobic fluids, including carbon dioxide, in studies related to carbon sequestration.

  11. Chemical sensing and imaging in microfluidic pore network structures relevant to natural carbon cycling and industrial carbon sequestration

    NASA Astrophysics Data System (ADS)

    Grate, Jay W.; Zhang, Changyong; Wilkins, Michael; Warner, Marvin G.; Anheier, Norm C.; Suter, Jonathan; Kelly, Ryan; Oostrom, Mart

    2013-06-01

    Energy and climate change represent significant factors in global security. Atmospheric carbon dioxide levels, while global in scope, are influenced by pore-scale phenomena in the subsurface. We are developing tools to visualize and investigate processes in pore network microfluidic structures that serve as representations of normally-opaque porous media. These structures enable, for example, visualization of water displacement from pore spaces by hydrophobic fluids, including carbon dioxide, in studies related to carbon sequestration. In situ fluorescent oxygen sensing methods and fluorescent cellulosic materials are being used to investigate processes related to terrestrial carbon cycling involving cellulolytic respiring microorganisms.

  12. Nuclear magnetic resonance pore size determination for unconsolidated sediments with strong internal gradients

    NASA Astrophysics Data System (ADS)

    Duschl, M.; Pohlmeier, A. J.; Galvosas, P.; Vereecken, H.

    2014-12-01

    Water distribution and flow within porous media are mainly controlled by the pore space structure. Well established methods for the determination of pore sizes like multistep outflow and gas adsorption isotherms (BET) are often time consuming, expensive, or produce toxic waste. As an alternative fast and non-destructive technique, nuclear magnetic resonance (NMR) is used because it probes hydrogen and therefore the dynamics and interactions of water. Pore space is most easily characterized by NMR relaxometry where the total relaxation rate is controlled by the surface relaxivity ρ of the porous medium in combination with the surface-to-volume ratio (S/V) [1]. Furthermore, there are contributions of molecular diffusion through local magnetic field gradients which are created by susceptibility differences between solid and liquid phases [2] as well as by paramagnetic impurities [3]. Hence, surface to volume ratios and surface relaxivities of porous media cannot be measured individually with NMR relaxometry. Therefore, NMR diffusion measurements are applied to probe the S/V of pores without other contributions. In this study, we demonstrate that NMR diffusion measurements are feasible to determine the S/V ratio of the pore space of quartz sand coated with goethite (α-FeOOH) as paramagnetic impurity. Our findings were compared to BET measurements and we found no dependence of the S/V on the coating density with NMR diffusion and a clear dependence between coating density and S/V with krypton BET measurements. Possible explanations are the different characteristic length scales on which the pore space is probed, and the intrinsic fractal nature of porous media [4] together with the roughness of the pore surface on a nm-scale due to the coating process. After isolating the additional contribution of the paramagnetic impurities to the NMR relaxation and the calibration of the NMR relaxation signal for each coating density it was possible to use fast relaxometry

  13. PolyA Single Strand DNA Translocation Through an Alpha-Hemolysin Pore Stem

    NASA Technical Reports Server (NTRS)

    OKeeffe, James; Cozmuta, Ioana; Stolc, Viktor

    2003-01-01

    A new model for the polymer-pore interaction energy is introduced, based on an atomic-scale description of coulombic polymer-pore interaction. The enhanced drift velocity, experimentally observed for short polymers, is successfully accounted for, using this interaction energy model. For R/R(sub 0)>4 (R(sub 0)=7 angstroms) the translocation velocity approaches the free space drift velocity v(sub 0). This motivates the need to appropriately derivatize artificial nanopores, where R>R(sub 0).

  14. Macroscopic parameters from simulations of pore scale flow

    SciTech Connect

    Blunt, M.; King, P. )

    1990-10-15

    We simulate two-phase flow in a porous medium, which is represented by random, isotropic two- and three-dimensional networks containing up to 80 000 interconnected pore spaces. The simulations are sufficiently large that macroscopic properties of the flow may be determined. For unstable viscous floods, we show that the displacements are compact with a fractal interface between the fluids. The fractal dimension is found as a function of viscosity ratio. For invasion percolation, where the displacement is controlled by capillary forces, and for viscous fingering, we calculate relative permeabilities in an averaged two-phase Darcy equation, which we show are functions of mean saturation. The relative permeabilities also depend on flow rate, which means that the two-phase Darcy equation is nonlinear, even with microscopic linear Poiseuille flow.

  15. Method for determining pore pressure and horizontal effective stress from overburden and effective vertical stresses

    SciTech Connect

    Holbrook, P.; Robertson, H.A.; Hauck, M.L.

    1990-01-01

    This patent describes a method for determining pore pressure in an in-situ subsurface formation. It comprises: causing a well logging tool to traverse an earth borehole between the earth's surface and the subsurface formation; determining the total overburden stress resulting from the integrated weight of material overlying the subsurface formation between the earth's surface and the subsurface formation. The overburden stress determining step being a function of the density of the solid rock portion and of the density of the fluid filling the pore spaces in the the overlying materials as measured, at least in part, by the well logging tool; determining the vertical effective stress in the subsurface formation from porosity logs. The porosity logs being generated by the well logging tool as the tool traverses the earth borehole through the subsurface formation; and generating a pore pressure log indicative of the difference between the overburden stress and the vertical effective stress.

  16. A one-dimensional analysis of sol-gel film-coating drying: Pore evolution, network shrinkage and stress development

    SciTech Connect

    Chen, K.S.; Schunk, P.R.

    1998-02-01

    Highly porous sol-gel films have potential applications as electrical and thermal insulators, catalyst supports, sensors, and membranes for gas separations. Pore dimensions in these sol-gel films are usually small e.g., on the order of tens of nanometers or less. Their successful fabrications, however, greatly depend on the fundamental understanding of mechanisms that underlie the phenomena of pore evolution, network shrinkage, and stress development since the final microstructure of a solid gel film is strongly affected by composition of its starting sol and its processing conditions. This report documents a simplified one-dimensional analysis of drying a solidifying sol-gel thin film coating supported by an impermeable solid substrate. Portions of this work were presented at the 1994 Annual Joint Meeting of the New Mexico Section of the American Ceramic Society and Materials Research Society in Albuquerque. The authors considered the solid/liquid two phase coexistent regime during the drying solidifying process in which solvent is removed continuously via evaporation, the solid phase grows significantly in mechanical strength, and pore space shrinks appreciably. From overall and differential mass balances and a force balance at equilibrium, coupled with empirical correlations of solid phase modulus and permeability to strain or deformation, the authors followed the evolution of pore space, solid phase elastic stress, and liquid phase hydrodynamic pressure; they also determined their respective values at equilibrium. By assuming microscopic pore shape models, they estimated and compared the predicted mean pore radii. Their simplified one-dimensional analysis shows that the final mean pore radius is controlled by four parameters: pore-liquid surface tension, solid phase modulus, mean pore radius, and porosity at the initial stress-free state. The one-dimensional model can be employed to guide process design and optimization in sol-gel film fabrications.

  17. 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

  18. Mechanics of membrane fusion/pore formation.

    PubMed

    Fuhrmans, Marc; Marelli, Giovanni; Smirnova, Yuliya G; Müller, Marcus

    2015-01-01

    Lipid bilayers play a fundamental role in many biological processes, and a considerable effort has been invested in understanding their behavior and the mechanism of topological changes like fusion and pore formation. Due to the time- and length-scale on which these processes occur, computational methods have proven to be an especially useful tool in their study. With their help, a number of interesting findings about the shape of fusion intermediates could be obtained, and novel hypotheses about the mechanism of topological changes and the involvement of peptides therein were suggested. In this work, we try to present a summary of these developments together with some hitherto unpublished results, featuring, among others, the shape of stalks and fusion pores, possible modes of action of the influenza HA fusion peptide and the SNARE protein complex, the mechanism of supported lipid bilayer formation by vesicle spreading, and the free energy and transition pathway of the fusion process.

  19. Mineral dissolution kinetics at the pore scale

    SciTech Connect

    Li, L.; Steefel, C.I.; Yang, L.

    2007-05-24

    Mineral dissolution rates in the field have been reported to be orders of magnitude slower than those measured in the laboratory, an unresolved discrepancy that severely limits our ability to develop scientifically defensible predictive or even interpretive models for many geochemical processes in the earth and environmental sciences. One suggestion links this discrepancy to the role of physical and chemical heterogeneities typically found in subsurface soils and aquifers in producing scale-dependent rates where concentration gradients develop. In this paper, we examine the possibility that scale-dependent mineral dissolution rates can develop even at the single pore and fracture scale, the smallest and most fundamental building block of porous media. To do so, we develop two models to analyze mineral dissolution kinetics at the single pore scale: (1) a Poiseuille Flow model that applies laboratory-measured dissolution kinetics at the pore or fracture wall and couples this to a rigorous treatment of both advective and diffusive transport, and (2) a Well-Mixed Reactor model that assumes complete mixing within the pore, while maintaining the same reactive surface area, average flow rate, and geometry as the Poiseuille Flow model. For a fracture, a 1D Plug Flow Reactor model is considered in addition to quantify the effects of longitudinal versus transverse mixing. The comparison of averaged dissolution rates under various conditions of flow, pore size, and fracture length from the three models is used as a means to quantify the extent to which concentration gradients at the single pore and fracture scale can develop and render rates scale-dependent. Three important minerals that dissolve at widely different rates, calcite, plagioclase, and iron hydroxide, are considered. The modeling indicates that rate discrepancies arise primarily where concentration gradients develop due to comparable rates of reaction and advective transport, and incomplete mixing via molecular

  20. Statistical scaling of geometric characteristics in stochastically generated pore microstructures

    SciTech Connect

    Hyman, Jeffrey D.; Guadagnini, Alberto; Winter, C. Larrabee

    2015-05-21

    In this study, we analyze the statistical scaling of structural attributes of virtual porous microstructures that are stochastically generated by thresholding Gaussian random fields. Characterization of the extent at which randomly generated pore spaces can be considered as representative of a particular rock sample depends on the metrics employed to compare the virtual sample against its physical counterpart. Typically, comparisons against features and/patterns of geometric observables, e.g., porosity and specific surface area, flow-related macroscopic parameters, e.g., permeability, or autocorrelation functions are used to assess the representativeness of a virtual sample, and thereby the quality of the generation method. Here, we rely on manifestations of statistical scaling of geometric observables which were recently observed in real millimeter scale rock samples [13] as additional relevant metrics by which to characterize a virtual sample. We explore the statistical scaling of two geometric observables, namely porosity (Φ) and specific surface area (SSA), of porous microstructures generated using the method of Smolarkiewicz and Winter [42] and Hyman and Winter [22]. Our results suggest that the method can produce virtual pore space samples displaying the symptoms of statistical scaling observed in real rock samples. Order q sample structure functions (statistical moments of absolute increments) of Φ and SSA scale as a power of the separation distance (lag) over a range of lags, and extended self-similarity (linear relationship between log structure functions of successive orders) appears to be an intrinsic property of the generated media. The width of the range of lags where power-law scaling is observed and the Hurst coefficient associated with the variables we consider can be controlled by the generation parameters of the method.

  1. Statistical scaling of geometric characteristics in stochastically generated pore microstructures

    DOE PAGES

    Hyman, Jeffrey D.; Guadagnini, Alberto; Winter, C. Larrabee

    2015-05-21

    In this study, we analyze the statistical scaling of structural attributes of virtual porous microstructures that are stochastically generated by thresholding Gaussian random fields. Characterization of the extent at which randomly generated pore spaces can be considered as representative of a particular rock sample depends on the metrics employed to compare the virtual sample against its physical counterpart. Typically, comparisons against features and/patterns of geometric observables, e.g., porosity and specific surface area, flow-related macroscopic parameters, e.g., permeability, or autocorrelation functions are used to assess the representativeness of a virtual sample, and thereby the quality of the generation method. Here, wemore » rely on manifestations of statistical scaling of geometric observables which were recently observed in real millimeter scale rock samples [13] as additional relevant metrics by which to characterize a virtual sample. We explore the statistical scaling of two geometric observables, namely porosity (Φ) and specific surface area (SSA), of porous microstructures generated using the method of Smolarkiewicz and Winter [42] and Hyman and Winter [22]. Our results suggest that the method can produce virtual pore space samples displaying the symptoms of statistical scaling observed in real rock samples. Order q sample structure functions (statistical moments of absolute increments) of Φ and SSA scale as a power of the separation distance (lag) over a range of lags, and extended self-similarity (linear relationship between log structure functions of successive orders) appears to be an intrinsic property of the generated media. The width of the range of lags where power-law scaling is observed and the Hurst coefficient associated with the variables we consider can be controlled by the generation parameters of the method.« less

  2. Probing pores using elementary quantum mechanics.

    PubMed

    Ryu, S

    2001-01-01

    The relaxation of polarized spins in a porous medium has been utilized as a probe of its structure. We note that the governing diffusion problem has a close parallel to that of a particle in a box, an elementary Quantum mechanics toy model. Following the spirits of "free electron" model, we use generic properties of the eigen spectrum to understand features common to a wide variety of pore geometry, consistent with large scale numerical simulations and experimental data.

  3. Further characterization of Closed Pore Insulation (CPI)

    NASA Technical Reports Server (NTRS)

    Russak, M.; Feldman, C.

    1973-01-01

    The thermophysical and mechanical properties of closed pore insulation (CPI) were measured after exposure to 25 simulated reentry thermal cycles. In addition, mechanical properties were obtained at elevated temperatures before and after cycling. The properties of CPI were not compromised by the cycling. High temperature creep studies were done on three CPI compositions (4, 8, and 12 Wt% CoO additive). CPI-4 had the best creep resistance at temperatures up to 1363 K.

  4. What is the mitochondrial permeability transition pore?

    PubMed

    Halestrap, Andrew P

    2009-06-01

    Under conditions of mitochondrial calcium overload, especially when accompanied by oxidative stress, elevated phosphate concentrations and adenine nucleotide depletion, a non-specific pore, the mitochondrial permeability transition pore (MPTP), opens in the inner mitochondrial membrane. MPTP opening enables free passage into the mitochondria of molecules of <1.5 kDa including protons. The resulting uncoupling of oxidative phosphorylation leads to ATP depletion and necrotic cell death and it is now widely recognised that MPTP opening is a major cause of reperfusion injury and an effective target for cardioprotection. The properties of the MPTP are well defined, but despite extensive research in many laboratories, its exact molecular identity remains uncertain. Knockout studies have confirmed a role for cyclophilin-D (CyP-D), probably mediated by its peptidyl-prolyl cis-trans isomerase activity facilitating a conformational change of an inner membrane protein. However, the identity of the membrane component(s) remains controversial. Knockout studies have eliminated an essential role for either the voltage dependent anion channel (VDAC) or the adenine nucleotide translocase (ANT), although a regulatory role for the ANT was confirmed. Our own studies implicate the mitochondrial phosphate carrier (PiC) in MPTP formation and are consistent with a calcium-triggered conformational change of the PiC, facilitated by CyP-D, inducing pore opening. We propose that this is enhanced by an association of the PiC with the "c" conformation of the ANT. Agents that modulate pore opening may act on either or both the PiC and the ANT. However, knockdown and reconstitution studies are awaited to confirm or refute this model.

  5. Integration of Petrophysical Methods and 3D Printing Technology to Replicate Reservoir Pore Systems

    NASA Astrophysics Data System (ADS)

    Ishutov, S.; Hasiuk, F.; Gray, J.; Harding, C.

    2014-12-01

    Pore-scale imaging and modeling are becoming routine geoscience techniques of reservoir analysis and simulation in oil and gas industry. Three-dimensional printing may facilitate the transformation of pore-space imagery into rock models, which can be compared to traditional laboratory methods and literature data. Although current methodologies for rapid rock modeling and printing obscure many details of grain geometry, computed tomography data is one route to refine pore networks and experimentally test hypotheses related to rock properties, such as porosity and permeability. This study uses three-dimensional printing as a novel way of interacting with x-ray computed tomography data from reservoir core plugs based on digital modeling of pore systems in coarse-grained sandstones and limestones. The advantages of using artificial rocks as a proxy are to better understand the contributions of pore system characteristics at various scales to petrophysical properties in oil and gas reservoirs. Pore radii of reservoir sandstones used in this study range from 1 to 100s of microns, whereas the pore radii for limestones vary from 0.01 to 10s of microns. The resolution of computed tomography imaging is ~10 microns; the resolution of 3D digital printing used in the study varies from 2.5 to 300 microns. For this technology to be useful, loss of pore network information must be minimized in the course of data acquisition, modeling, and production as well as verified against core-scale measurements. The ultimate goal of this study is to develop a reservoir rock "photocopier" that couples 3D scanning and modeling with 3D printing to reproduce a) petrophyscially accurate copies of reservoir pore systems and b) digitally modified pore systems for testing hypotheses about reservoir flow. By allowing us to build porous media with known properties (porosity, permeability, surface area), technology will also advance our understanding of the tools used to measure these quantities (e

  6. Identification and isolation of closed pore in porous rock using digital rock physics approach

    NASA Astrophysics Data System (ADS)

    Latief, Fourier Dzar Eljabbar

    2015-09-01

    The presence of closed pore in porous rock provide various effect with regard to its structural, elastic and flow properties. Physical based approach to measure porosity such as mercury porosimetry injection is unable to locate closed pore inside porous rock even though it is still possible to quantify the closed porosity. Digital data of porous rock in the form of three dimensional image can now be obtained by means of several methods such as micro-CT scan. Using the digital data, closed pore can be identified and isolated using digital rock physics approach. We first construct a synthetic three dimensional porous sample which consist of two simple side-to-side connected pore (cylinder and box shaped) and two spherical isolated pore which has closed porosity of 1.41 %. The digital image analysis which implemented in software CTAn (Bruker Micro-CT) still produce error of 0.04% which is very low. However, analysis using Lattice Boltzmann Method based simulation of fluid flow provide exact match to the closed porosity of the synthetic sample. Nevertheless, there are two disadvantages of this method, i.e., the simulation could take hours compared to the digital image analysis which only took several minutes and the limitation of numerical definition of zero velocity. Thus we apply both methods in order to overcome the drawbacks of each methods to analyze the digital sample of Fontainebleau sandstone. Using CTAn, we obtained the closed porosity of 0.02891845 % and using the LBM based fluid flow simulation of 0.028948346 %. The closed pore can then be isolated to further calculate the surface area. The result also confirmed that pore space of Fontainebleau sandstone is well connected.

  7. Nuclear pore complex ion channels (review).

    PubMed

    Bustamante, J O; Liepins, A; Hanover, J A

    1994-01-01

    It is currently thought that nuclear pore complexes (NPCs) primarily govern nucleocytoplasmic interactions via selective recognition and active transport of macromolecules. However, in various nuclear preparations, patch-clamp and fluorescence, luminiscence and ion microscopy support classical microelectrode measurements indicating that monoatomic ion flow across the nuclear envelope (NE) is strictly regulated. Gating of large conductance nuclear envelope ion channels (NICs) somewhat resembles that of gap junctional channels. In other respects, NICs are distinct in that they require cytosolic factors, are blocked by wheat germ agglutinin and are blocked and/or modified by antibodies to epitopes of NPC glycoproteins. Therefore, NIC activity, recorded as electrical current/conductance is likely to be intrinsic to NPCs. This observation suggests a potential use for the patch-clamp technique in establishing the mechanisms underlying nuclear pore gating in response to cytosolic and nucleosolic factors such as transcription and growth factors, oncogene and proto-oncogene products and receptors for retinoids, steroids and thyroid hormone. NIC activity may also be useful in evaluating the mechanisms of nuclear import of foreign nucleic acid material such as that contained in virons and viroids. Finally, in consideration to the electrophysiological data accumulated so far, the study of nuclear pore ion channel activity may help our understanding of other important issues such as cell suicide, programmed cell death or apoptosis.

  8. INVESTIGATIONS INTO BIOFOULING PHENOMENA IN FINE PORE AERATION DEVICES

    EPA Science Inventory

    Microbiologically-based procedures were used to describe biofouling phenomena on fine pore aeration devices and to determine whether biofilm characteristics could be related to diffuser process performance parameters. Fine pore diffusers were obtained from five municipal wastewa...

  9. Dilation of fusion pores by crowding of SNARE proteins.

    PubMed

    Wu, Zhenyong; Bello, Oscar D; Thiyagarajan, Sathish; Auclair, Sarah Marie; Vennekate, Wensi; Krishnakumar, Shyam S; O'Shaughnessy, Ben; Karatekin, Erdem

    2017-03-27

    Hormones and neurotransmitters are released through fluctuating exocytotic fusion pores that can flicker open and shut multiple times. Cargo release and vesicle recycling depend on the fate of the pore, which may reseal or dilate irreversibly. Pore nucleation requires zippering between vesicle-associated v- and target membrane t-SNAREs, but the mechanisms governing the subsequent pore dilation are not understood. Here, we probed dilation of single fusion pores using v-SNARE-reconstituted ~23 nm diameter discoidal nanolipoprotein particles (vNLPs) as fusion partners with cells ectopically expressing cognate, 'flipped' t-SNAREs. Pore nucleation required a minimum of 2, and reached a maximum above ~4 copies per face, but the probability of pore dilation was far from saturating at 15 copies, the NLP capacity. Our experimental and computational results suggest SNARE availability may be pivotal in determining whether neurotransmitters or hormones are released through a transient (kiss & run) or an irreversibly dilating pore (full fusion).

  10. Assembly of Bak homodimers into higher order homooligomers in the mitochondrial apoptotic pore

    PubMed Central

    Mandal, Tirtha; Shin, Seungjin; Aluvila, Sreevidya; Chen, Hui-Chen; Grieve, Carter; Choe, Jun-Yong; Cheng, Emily H.; Hustedt, Eric J.; Oh, Kyoung Joon

    2016-01-01

    In mitochondrial apoptosis, Bak is activated by death signals to form pores of unknown structure on the mitochondrial outer membrane via homooligomerization. Cytochrome c and other apoptotic factors are released from the intermembrane space through these pores, initiating downstream apoptosis events. Using chemical crosslinking and double electron electron resonance (DEER)-derived distance measurements between specific structural elements in Bak, here we clarify how the Bak pore is assembled. We propose that previously described BH3-in-groove homodimers (BGH) are juxtaposed via the ‘α3/α5’ interface, in which the C-termini of helices α3 and α5 are in close proximity between two neighboring Bak homodimers. This interface is observed concomitantly with the well-known ‘α6:α6’ interface. We also mapped the contacts between Bak homodimers and the lipid bilayer based on EPR spectroscopy topology studies. Our results suggest a model for the lipidic Bak pore, whereby the mitochondrial targeting C-terminal helix does not change topology to accommodate the lining of the pore lumen by BGH. PMID:27488021

  11. Effect of pore size on the performance of immobilised enzymes.

    PubMed

    Bayne, Lauren; Ulijn, Rein V; Halling, Peter J

    2013-12-07

    Porous materials are widely employed as supports in the immobilisation of enzymes. Traditionally macroporous materials with pore diameters >50 nm were believed to be the most suitable support material, ensuring no spatial restrictions upon enzyme molecules entering such large pores. In recent years however, there has been growing emphasis in the use of mesoporous supports with pore diameters ranging between 2 and 50 nm. It is thought this smaller pore range may offer enhanced conformational stability to immobilised enzymes while not being so small as to restrict enzyme access. Despite their increasing popularity, many argue that mesoporous materials have not yet proven superior to traditional macroporous supports for enzyme immobilisation. Through the design and application of a unique confidence rating system we were able to accurately compare data and establish trends between pore characteristics and protein loading. By analysing published data (182 experiments in total) and extracting pore characteristics and protein loading values, we have described three categories of pore diameters in which correlations between pore characteristics and protein loading are noted. With pore diameters less than 10 nm we see a general decrease in protein loading as the enzymes find physical restrictions in accessing the high surface offered in this pore diameter range. At pore sizes greater than 100 nm, protein loading generally decreases due to a concomitant reduction in available surface area. In the pore range of 10-100 nm there it is expected to see a decrease in protein loading level with increasing pore diameter. In fact protein loading in this range remains largely constant, suggesting some degree of protein-protein interaction blocking pores and restricting access to the increasing surface area available at decreasing pore diameters. No trends were established between pore characteristics and retention of activity.

  12. Physical Pore Properties and Grain Interactions of SAX04 Sands

    DTIC Science & Technology

    2010-07-01

    serve as flow junctions and ac- count for void volume in these models, while pore throats serve as conduits between the pore bodies and provide...properties can be addressed and quantified using a network, similar to an electrical circuit, of interconnected pore bodies ( junctions ) and pore...Berger, M. J. Buckingham, N. P. Chotiros, P. H. Dahl, N. T. Dewitt, P. Fleischer, R. Flood, C. F. Greenlaw. D. V. Holliday , M. H. Hulbert. M. P. Hutnak

  13. Salt Templating with Pore Padding: Hierarchical Pore Tailoring towards Functionalised Porous Carbons.

    PubMed

    Kumar, K Vasanth; Gadipelli, Srinivas; Preuss, Kathrin; Porwal, Harshit; Zhao, Tingting; Guo, Zheng Xiao; Titirici, Maria-Magdalena

    2017-01-10

    We propose a new synthetic route towards nanoporous functional carbon materials based on salt templating with pore-padding approach (STPP). STPP relies on the use of a pore-padding agent that undergoes an initial polymerisation/ condensation process prior to the formation of a solid carbon framework. The pore-padding agent allows tailoring hierarchically the pore-size distribution and controlling the amount of heteroatom (nitrogen in this case) functionalities as well as the type of nitrogen (graphitic, pyridinic, oxides of nitrogen) incorporated within the carbon framework in a single-step-process. Our newly developed STPP method offers a unique pathway and new design principle to create simultaneously high surface area, microporosity, functionality and pore hierarchy. The functional carbon materials produced by STPP showed a remarkable CO2 /N2 selectivity. At 273 K, a carbon with only micropores offered an exceptionally high CO2 adsorption capacity whereas a carbon with only mesopores showed promising CO2 -philicity with high CO2 /N2 selectivity in the range of 46-60 %, making them excellent candidates for CO2 capture from flue gas or for CO2 storage.

  14. Pore network and pore scale modeling of reactive transport in porous media

    NASA Astrophysics Data System (ADS)

    Adler, P. M.; Vu, T. M.; Varloteaux, C.; Bekri, S.

    2012-12-01

    The study of the evolution of a porous medium where a reactive fluid flows is conditioned by the accurate determination of three macroscopic parameters governing the solute displacement, namely the solute velocity, dispersion and mean reaction rate. Of course, a possible application of such studies is CO2 sequestration. This presentation proposes to approach the determination of these parameters by two different ways and to compare them; both are on the pore scale. In the first one called PNM (for pore-network model), a pore-network is extracted from micro tomography images of a real porous medium. This network is composed of spherical pores joined by circular tubes; it is used to calculate transport macroscopic parameters and porosity-permeability evolution during the reactive transport flow as functions of dimensionless numbers representing the reaction and flow rate regimes. The flow is calculated by using Kirchhoff laws. Transport is determined in the asymptotic regime where the solute concentration undergoes an exponential evolution with time. In the second approach called PSM (for pore scale model), the pore-network model is used as a three dimensional medium which is discretized by the Level Set Method. The Stokes equations are solved in order to determine the local flow field and the corresponding permeability. The solute concentration is obtained by solving the local convection-diffusion equation in the 3D pore-network; numerical dispersion is reduced by a Flux Limiting Scheme. Two different geometries of porous media are addressed by both numerical codes. The first pore-network geometry is used to validate the PNM assumptions, whereas the second pore-network is defined for a better understanding of the dominant solute distribution. One of the main results obtained with the first pore-network is the dependence of the concentration profile on the Péclet number Pe in the pore-bodies. When this number increases, one has to switch from an assumption of

  15. Droplet fragmentation: 3D imaging of a previously unidentified pore-scale process during multiphase flow in porous media

    PubMed Central

    Pak, Tannaz; Butler, Ian B.; Geiger, Sebastian; van Dijke, Marinus I. J.; Sorbie, Ken S.

    2015-01-01

    Using X-ray computed microtomography, we have visualized and quantified the in situ structure of a trapped nonwetting phase (oil) in a highly heterogeneous carbonate rock after injecting a wetting phase (brine) at low and high capillary numbers. We imaged the process of capillary desaturation in 3D and demonstrated its impacts on the trapped nonwetting phase cluster size distribution. We have identified a previously unidentified pore-scale event during capillary desaturation. This pore-scale event, described as droplet fragmentation of the nonwetting phase, occurs in larger pores. It increases volumetric production of the nonwetting phase after capillary trapping and enlarges the fluid−fluid interface, which can enhance mass transfer between the phases. Droplet fragmentation therefore has implications for a range of multiphase flow processes in natural and engineered porous media with complex heterogeneous pore spaces. PMID:25646491

  16. Energy conversion device with support member having pore channels

    DOEpatents

    Routkevitch, Dmitri [Longmont, CO; Wind, Rikard A [Johnstown, CO

    2014-01-07

    Energy devices such as energy conversion devices and energy storage devices and methods for the manufacture of such devices. The devices include a support member having an array of pore channels having a small average pore channel diameter and having a pore channel length. Material layers that may include energy conversion materials and conductive materials are coaxially disposed within the pore channels to form material rods having a relatively small cross-section and a relatively long length. By varying the structure of the materials in the pore channels, various energy devices can be fabricated, such as photovoltaic (PV) devices, radiation detectors, capacitors, batteries and the like.

  17. Displacement of soil pore water by trichloroethylene

    USGS Publications Warehouse

    Wershaw, R. L.; Aiken, G.R.; Imbrigiotta, T.E.; Goldberg, M.C.

    1994-01-01

    Dense nonaqueous phase liquids (DNAPLS) are important pollutants because of their widespread use as chemical and industrial solvents. An example of the pollution caused by the discharge of DNAPLs is found at the Picatinny Arsenal, New Jersey, where trichloroethylene (TCE) has been discharged directly into the unsaturated zone. This discharge has resulted in the formation of a plume of TCE-contaminated water in the aquifer downgradient of the discharge. A zone of dark-colored groundwater containing a high dissolved organic C content has been found near the point of discharge of the TCE. The colored-water plume extends from the point of discharge at least 30 m (100 feet) downgradient. Fulvic acids isolated from the colored-waters plume, from water from a background well that has not been affected by the discharge of chlorinated solvents, and from soil pore water collected in a lysimeter installed at an uncontaminated site upgradient of the study area have been compared. Nuclear magnetic resonance spectra of the fulvic acids from the colored waters and from the lysimeter are very similar, but are markedly different from the nuclear magnetic resonance spectrum of the fulvic acid from the background well. The three-dimensional fluorescence spectrum and the DOC fractionation profile of the colored groundwater and the soil pore water are very similar to each other, but quite different from those of the background water. It is proposed from these observations that this colored water is soil pore water that has been displaced by a separate DNAPL liquid phase downward to the saturated zone.

  18. Displacement of soil pore water by trichloroethylene

    SciTech Connect

    Wershaw, R.L.; Aiken, G.R.; Imbrigiotta, T.E.

    1994-07-01

    Dense nonaqueous phase liquids (DNAPLS) are important pollutants because of their widespread use as chemical and industrial solvents. An example of the pollution caused by the discharge of DNAPLs is found at the Picatinny Arsenal, New Jersey, where trichloroethylene (TCE) has been discharged directly into the unsaturated zone. This discharge has resulted in the formation of a plume of TCE-contaminated water in the aquifer downgradient of the discharge. A zone of dark-colored groundwater containing a high dissolved organic C content has been found near the point of discharge of the TCE. The colored-water plume extends from the point of discharge at least 30 m (100 feet) downgradient. Fulvic acids isolated from the colored-waters plume, from water from a background well that has not been affected by the discharge of chlorinated solvents, and from soil pore water collected in a lysimeter installed at an uncontaminated site upgradient of the study area have been compared. Nuclear magnetic resonance spectra of the fulvic acids from the colored waters and from the lysimeter am very similar, but are markedly different from the nuclear magnetic resonance spectrum of the fulvic acid from the background well. The three-dimensional fluorescence spectrum and the DOC fractionation profile of the colored groundwater and the soil pore water are very similar to each other, but quite different from those of the background water. It is proposed from these observations that this colored water is soil pore water that has been displaced by a separate DNAPL liquid phase downward to the saturated zone. 15 refs., 6 figs., 4 tabs.

  19. Characterization of Connectivity between Fractures and Nano-pores in Shale Using Gas Adsorption Analysis

    NASA Astrophysics Data System (ADS)

    Jiang, H.; Daigle, H.; Hayman, N. W.

    2015-12-01

    Most pores hosting hydrocarbon in mudrocks are at the nanometer to tens of nanometer scale. However, observational evidence shows that natural and induced fractures which govern the permeability of mudrocks appear to be spaced at centimeter scale or greater. The mismatch in scales raises the question of how the hydrocarbons in the nanopores can gain access to the induced hydraulic fracture systems. To answer the question, we experimentally induced fractures on core-scale samples, and characterized microstructure around the stimulated fracture networks and in the surrounding, unfractured rock matrix. Confined compressive strength tests were performed on preserved core plugs from the Eagle Ford shale and a siliceous, oil-bearing mudrock from the northern Rocky Mountains. Dried, ground specimens were collected from before-test (intact) and after-test (failed) samples. Their pore structure was analyzed by N2/CO2 gas adsorption, which together can measure pore diameters between 0.35 and 300 nm. Adsorption data shows a Type IV N2 isotherm and a Type I CO2 isotherm. The hysteresis loop in the N2 adsorption curve indicates the presence of slit-shaped pores. Failed siliceous samples exhibit higher overall N2 and CO2 adsorbed gas amount compared with the intact samples, indicating a wide range increase of nanoporosity. Eagle Ford samples, however, show no significant change in adsorbed gas amount. We determined pore size distributions (PSDs) using density functional theory (DFT). The N2 PSDs of the siliceous samples appear to be bimodal, with a peak around 1 nm pore size, while the N2 PSDs of the Eagle Ford samples is unimodal. Comparison of intact and failed samples reveals no significant change in pore volume for Eagle Ford samples. The siliceous samples, in contrast, increase their nanopore volume (1-100 nm pore diameter) after fracturing. The increased nanoporosity may result from microcracks that develop in the matrix surrounding the main fractures that connect nano

  20. Extreme accumulation of nucleotides in simulated hydrothermal pore systems

    PubMed Central

    Baaske, Philipp; Weinert, Franz M.; Duhr, Stefan; Lemke, Kono H.; Russell, Michael J.; Braun, Dieter

    2007-01-01

    We simulate molecular transport in elongated hydrothermal pore systems influenced by a thermal gradient. We find extreme accumulation of molecules in a wide variety of plugged pores. The mechanism is able to provide highly concentrated single nucleotides, suitable for operations of an RNA world at the origin of life. It is driven solely by the thermal gradient across a pore. On the one hand, the fluid is shuttled by thermal convection along the pore, whereas on the other hand, the molecules drift across the pore, driven by thermodiffusion. As a result, millimeter-sized pores accumulate even single nucleotides more than 108-fold into micrometer-sized regions. The enhanced concentration of molecules is found in the bulk water near the closed bottom end of the pore. Because the accumulation depends exponentially on the pore length and temperature difference, it is considerably robust with respect to changes in the cleft geometry and the molecular dimensions. Whereas thin pores can concentrate only long polynucleotides, thicker pores accumulate short and long polynucleotides equally well and allow various molecular compositions. This setting also provides a temperature oscillation, shown previously to exponentially replicate DNA in the protein-assisted PCR. Our results indicate that, for life to evolve, complicated active membrane transport is not required for the initial steps. We find that interlinked mineral pores in a thermal gradient provide a compelling high-concentration starting point for the molecular evolution of life. PMID:17494767

  1. Catalytic reforming catalyst with modified pore size distribution

    SciTech Connect

    Unmuth, E.E.; Fleming, B.A.

    1987-10-27

    In a naphtha reforming catalyst having at least one catalytic metal deposited on a porous solid catalyst support, an improvement is described which comprises the catalyst having the following in combination: (A) a surface area above about 250M/sup 2//gram of catalyst; (B) A pore volume above about 0.4 cc/gram of catalyst in pores having diameters of from about 30 angstroms to about 38,000 angstroms; and (C) A pore volume distribution wherein about 70 percent or less of the pore volume is in pores having diameters of from about 30 angstroms to about 400 angstroms, and 30 percent or more of the pore volume is in pores having diameters of from about 400 angstroms to about 38,000 angstroms.

  2. Flux theory for Poisson distributed pores with Gaussian permeability.

    PubMed

    Salinas, Dino G

    2016-01-01

    The mean of the solute flux through membrane pores depends on the random distribution and permeability of the pores. Mathematical models including such randomness factors make it possible to obtain statistical parameters for pore characterization. Here, assuming that pores follow a Poisson distribution in the lipid phase and that their permeabilities follow a Gaussian distribution, a mathematical model for solute dynamics is obtained by applying a general result from a previous work regarding any number of different kinds of randomly distributed pores. The new proposed theory is studied using experimental parameters obtained elsewhere, and a method for finding the mean single pore flux rate from liposome flux assays is suggested. This method is useful for pores without requiring studies by patch-clamp in single cells or single-channel recordings. However, it does not apply in the case of ion-selective channels, in which a more complex flux law combining the concentration and electrical gradient is required.

  3. Size of diffusion pore of Alcaligenes faecalis.

    PubMed Central

    Ishii, J; Nakae, T

    1988-01-01

    The diffusion pore of the outer membrane of Alcaligenes faecalis was shown to be substantially smaller than the Escherichia coli porin pore. In experiments with intact cells, pentoses and hexoses penetrated into the NaCl-expanded periplasm, whereas saccharides of Mr greater than 342 did not. Cells treated with 0.5 M saccharides of Mr greater than 342 weighed 33 to 38% less than cells treated with isotonic solution, suggesting that these saccharides do not permeate through the outer membrane. The diffusion rates of various solutes through the liposome membranes reconstituted from the Mr-43,000 outer membrane protein showed the following characteristics. (i) The relative diffusion rates of pentoses, hexoses, and methylhexoses appeared to be about 1.0, 0.6, and negligibly small, respectively. (ii) The diffusion rate of glucose appeared to be about 1/10th that with the E. coli B porin. (iii) The diffusion rate of gluconic acid was five to seven times higher than that of glucose. (iv) The diffusion rates of beta-lactam antibiotics appeared to be 40 to less than 10% of those with the E. coli B porin. Images PMID:2835003

  4. Designing biomimetic pores based on carbon nanotubes

    PubMed Central

    García-Fandiño, Rebeca; Sansom, Mark S. P.

    2012-01-01

    Biomimetic nanopores based on membrane-spanning single-walled carbon nanotubes have been designed to include selectivity filters based on combinations of anionic and cationic groups mimicking those present in bacterial porins and in voltage-gated sodium and calcium channels. The ion permeation and selectivity properties of these nanopores when embedded in a phospholipid bilayer have been explored by molecular dynamics simulations and free energy profile calculations. The interactions of the nanopores with sodium, potassium, calcium, and chloride ions have been explored as a function of the number of anionic and cationic groups within the selectivity filter. Unbiased molecular dynamics simulations show that the overall selectivity is largely determined by the net charge of the filter. Analysis of distribution functions reveals considerable structuring of the distribution of ions and water within the nanopores. The distributions of ions along the pore axis reveal local selectivity for cations around filter, even in those nanopores (C0) where the net filter charge is zero. Single ion free energy profiles also reveal clear evidence for cation selectivity, even in the C0 nanopores. Detailed analysis of the interactions of the C0 nanopore with Ca2+ ions reveals that local interactions with the anionic (carboxylate) groups of the selectivity filter lead to (partial) replacement of solvating water as the ion passes through the pore. These studies suggest that a computational biomimetic approach can be used to evaluate our understanding of the design principles of nanopores and channels. PMID:22509000

  5. High-pressure replica technique for in vitro imaging of pore morphologies in teeth.

    PubMed

    Uchtmann, H; Wilkie, D

    1997-11-01

    The presence of a natural pore morphology is an essential factor in chemical and mechanical stability of teeth. Common histological methods give only an insufficient picture of the three-dimensional pore distribution in sound or carious teeth. This paper describes a new technique to obtain complete images of the pore structure in teeth or other biological hard tissues. Whole extracted human teeth from orthodontic therapy are mechanically cleaned and organic remnants removed chemically. After being (partly) dried, the teeth are penetrated by a freshly prepared and colored (rhodamine B dye) two-component epoxy resin. The resin is pressed into the pores and cavities of the teeth with pressures of up to 2000 bar in a high-pressure vessel by means of a manually driven piston screw pump for pressure generation. The resin fills all hollow spaces of the tooth down to sizes below 0.1 micron. The pulp and the root canals are cast in massive forms of the hardened epoxy resin, giving an exact replica of the natural structure. The penetrated samples in the form of whole, intact teeth are investigated microscopically so that the pore morphology of the tooth surface, including carious defects, can be examined. The structure of the pores extending into the interior of the tooth can be made visible by dissolution of the hard tissue--for example, in acid solutions. Micro-cavities filled with the resin are observed in thin, ground, and polished cross- and longitudinal sections cut from the teeth. The colored resin induces a high contrast to the dental apatite material. In fluorescence microscopy, only the resin structures are visible.

  6. Computational modeling of electrokinetic transport in random networks of micro-pores and nano-pores

    NASA Astrophysics Data System (ADS)

    Alizadeh, Shima; Mani, Ali

    2014-11-01

    A reduced order model has been developed to study the nonlinear electrokinetic behaviors emerging in the transport of ionic species through micro-scale and nano-scale porous media. In this approach a porous structure is modeled as a network of long and thin pores. By assuming transport equilibrium in the thin dimensions for each pore, a 1D transport equation is developed in the longitudinal direction covering a wide range of conditions including extreme limits of thick and thin electric double layers. This 1D model includes transport via diffusion, electromigration and wide range of advection mechanisms including pressure driven flow, electroosmosis, and diffusion osmosis. The area-averaged equations governing the axial transport from different pores are coupled at the pore intersections using the proper conservation laws. Moreover, an asymptotic treatment has been included in order to remove singularities in the limit of small concentration. The proposed method provides an efficient framework for insightful simulations of porous electrokinetic systems with applications in water desalination and energy storage. PhD student in Mechanical Engineering, Stanford University. She received her Master's degree in Mechanical Engineering from Stanford at 2013. Her research interests include CFD, high performance computing, and optimization.

  7. From the pore scale to the core scale: How to model the spatial interactions in soils?

    NASA Astrophysics Data System (ADS)

    Garnier, Patricia; Pot, Valerie; Monga, Oivier; Chenu, Claire; Vieuble-Gonod, Laurent; Vogel, Laure; Nunan, Naoise; Otten, Wilfried; Baveye, Philippe

    2015-04-01

    Recently, innovative modeling tools have been developed to describe the physico-chemical processes occurring in soil pores at scales directly relevant to microorganisms. Modelling efforts have attempted to understand how microbial processes such as decomposition or competition among species are affected by diffusion in 2-D or 3-D environments. Most of these models use a virtual representative pore network that can have the same features as soil pores with regular lattice grid. The most recent and innovative of these models use real images of soil structure from binarized 3D images. These models are able to simulate microbial degradation although microorganisms and organic matter are placed at different locations in the pore space. Then, the encounter of nutrients and microorganisms is achieved through the implementation of the diffusion process of the soluble substrates in the connected water-filled space. The high computational demand of this type of approach restricts its applicability to small-scale systems, typically in the order of micrometers or millimeters. The numerical techniques used to solve the equations include the lattice Boltzmann method, algorithmic methods and finite element methods. Most of these models have not yet been tested with experimental data because of the difficulties of investigating such small scales. On the other hand, many experimental results developed at the core scale have showed the importance of soil microbial habitat and especially how physical characteristics (pore sizes, connectivity) control the decomposition of organic substrates via their accessibility by microorganisms. The general question we have now to answer is whether information on the spatial heterogeneity of soils at the microscale can be used to predict the processes observed at the macroscale in soils

  8. Pore detection in Computed Tomography (CT) soil 3D images using singularity map analysis

    NASA Astrophysics Data System (ADS)

    Sotoca, Juan J. Martin; Tarquis, Ana M.; Saa Requejo, Antonio; Grau, Juan B.

    2016-04-01

    X-ray Computed Tomography (CT) images have significantly helped the study of the internal soil structure. This technique has two main advantages: 1) it is a non-invasive technique, i.e., it doesńt modify the internal soil structure, and 2) it provides a good resolution. The major disadvantage is that these images are sometimes low-contrast in the solid/pore interface. One of the main problems in analyzing soil structure through CT images is to segment them in solid/pore space. To do so, we have different segmentation techniques at our disposal that are mainly based on thresholding methods in which global or local thresholds are calculated to separate pore space from solid space. The aim of this presentation is to develop the fractal approach to soil structure using "singularity maps" and the "Concentration-Area (CA) method". We will establish an analogy between mineralization processes in ore deposits and morphogenesis processes in soils. Resulting from this analogy a new 3D segmentation method is proposed, the "3D Singularity-CA" method. A comparison with traditional 3D segmentation methods will be performed to show the main differences among them.

  9. High Transmembrane Voltage Raised by Close Contact Initiates Fusion Pore.

    PubMed

    Bu, Bing; Tian, Zhiqi; Li, Dechang; Ji, Baohua

    2016-01-01

    Membrane fusion lies at the heart of neuronal communication but the detailed mechanism of a critical step, fusion pore initiation, remains poorly understood. Here, through atomistic molecular dynamics simulations, a transient pore formation induced by a close contact of two apposed bilayers is firstly reported. Such a close contact gives rise to a high local transmembrane voltage that induces the transient pore formation. Through simulations on two apposed bilayers fixed at a series of given distances, the process in which two bilayers approaching to each other under the pulling force from fusion proteins for membrane fusion was mimicked. Of note, this close contact induced fusion pore formation is contrasted with previous reported electroporation under ad hoc applied external electric field or ionic charge in-balance. We show that the transmembrane voltage increases with the decrease of the distance between the bilayers. Below a critical distance, depending on the lipid composition, the local transmembrane voltage can be sufficiently high to induce the transient pores. The size of these pores is approximately 1~2 nm in diameter, which is large enough to allow passing of neurotransmitters. A resealing of the membrane pores resulting from the neutralization of the transmembrane voltage by ions through the pores was then observed. We also found that the membrane tension can either prolong the lifetime of transient pores or cause them to dilate for full collapse. This result provides a possible mechanism for fusion pore formation and regulation of pathway of fusion process.

  10. High Transmembrane Voltage Raised by Close Contact Initiates Fusion Pore

    PubMed Central

    Bu, Bing; Tian, Zhiqi; Li, Dechang; Ji, Baohua

    2016-01-01

    Membrane fusion lies at the heart of neuronal communication but the detailed mechanism of a critical step, fusion pore initiation, remains poorly understood. Here, through atomistic molecular dynamics simulations, a transient pore formation induced by a close contact of two apposed bilayers is firstly reported. Such a close contact gives rise to a high local transmembrane voltage that induces the transient pore formation. Through simulations on two apposed bilayers fixed at a series of given distances, the process in which two bilayers approaching to each other under the pulling force from fusion proteins for membrane fusion was mimicked. Of note, this close contact induced fusion pore formation is contrasted with previous reported electroporation under ad hoc applied external electric field or ionic charge in-balance. We show that the transmembrane voltage increases with the decrease of the distance between the bilayers. Below a critical distance, depending on the lipid composition, the local transmembrane voltage can be sufficiently high to induce the transient pores. The size of these pores is approximately 1~2 nm in diameter, which is large enough to allow passing of neurotransmitters. A resealing of the membrane pores resulting from the neutralization of the transmembrane voltage by ions through the pores was then observed. We also found that the membrane tension can either prolong the lifetime of transient pores or cause them to dilate for full collapse. This result provides a possible mechanism for fusion pore formation and regulation of pathway of fusion process. PMID:28018169

  11. Decreasing transmembrane segment length greatly decreases perfringolysin O pore size

    SciTech Connect

    Lin, Qingqing; Li, Huilin; Wang, Tong; London, Erwin

    2015-04-08

    Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakage assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.

  12. Decreasing transmembrane segment length greatly decreases perfringolysin O pore size

    DOE PAGES

    Lin, Qingqing; Li, Huilin; Wang, Tong; ...

    2015-04-08

    Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakagemore » assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.« less

  13. A Stereolithography Pore-Throat Model

    NASA Astrophysics Data System (ADS)

    Crandall, D.; Ahmadi, G.; Ferer, M.; Smith, D. H.

    2007-12-01

    A new experimental, heterogeneous pore-throat model has been designed and fabricated using stereolithography (SL). In SL production, a laser cures a thin layer of photo-sensitive resin on the surface of a vat of liquid resin; a moveable platform then submerges the cured layer and a new layer is cured on top of the previous one, creating a physical model from a computer generated model. This layered fabrication of a computer generated model has enabled the production of an experimental porous medium with improved fluid resistance properties, as compared to previously studied, constant-height etched cells. A uniform distribution of throat widths was randomly placed throughout the pore-throat matrix and the throat height of each throat was assigned to increase the range of viscous and capillary resistances within the physical model. This variation in both throat height and width generated a porous medium with fairly low porosity (43%), permeability (~400 D), and wide range of geometric resistance properties. Experimental, two-phase immiscible drainage studies in the porous flowcell were performed. Analysis of the captured images was performed with open-source image processing software. These analysis techniques utilized the capability of both ImageJ and the Gnu Image Manipulation Program to be customized with ancillary codes. This enabled batch procedures to be created that converted the original grey-scale bitmaps to binary data sets, which were then analyzed with in-house codes. The fractal dimension, Df, (measured with box-counting) and percent saturation of these experiments were calculated and shown to compare favorably to fractal predictions and previous flowcell studies. Additionally, using the computer generated pore-throat geometry, a computational fluid dynamics model of two- phase flow through the porous medium was created. This model was created using FLUENT code and the Volume of Fluid method. The percent saturation of the less-viscous invading fluid

  14. Furthering Chemical and Geophysical Computations: Analysis of SACROC SEM and CT images to obtain pore percentage, size, and connectivity data

    NASA Astrophysics Data System (ADS)

    Mur, A. J.; Purcell, C. C.; Harbert, W. P.; Soong, Y.; Kutchko, B. G.; Kennedy, S.; McIntryre, D.

    2009-12-01

    The National Energy Technology Laboratory of the United States Department of Energy, in collaboration with the Bureau of Economic Geology in Austin, Texas has been involved in an extensive study of the many aspects involved in the injection of CO2 into the 2042 meter deep Permian reef structure at the SACROC field. Subsamples of reef limestone cores used for seismic velocity measurements were obtained. XRD determined the sample to be ~99% Calcite and ~1% Dolomite with a small amount of impurities. Preliminary petrographic slides revealed a vuggy porosity. We acquired CT scans of a SACROC limestone core at the Morgantown NETL site. We also acquired a high pixel resolution (112 MB) SEM secondary electron image of the reef limestone at RJ Lee Group. By using ArcMap , we created a tool that groups grayscale ranges into three categories, cleans boundaries between groups, and produces a polygon map of the macropores, micropores, and matrix. The darkest areas in the SEM image were cavern-like pores and were thus called macropores. Micropores, the brightest regions, are textured micrite faces that create many, small pore spaces. Using ImageJ, the CT and Arc pore maps were analyzed to reveal pore shape statistics. Average pore perimeter, average pore area, and pore connectivity is essential for chemistry experiments that will emulate time exposure of CO2 to limestone. Further, ImageJ allows us to obtain pore orientation information. This is important in understanding the anisotropic conditions that may or may not affect seismic data. The image is 10240x11264 pixels which correspond to ~ 8890.00x9780.00 micrometers. Micro- and macropores combined, there were 613744 pores mapped. Differing statistical methods revealed differing results. For example, the average pore perimeter was ~28 microns while the average pore area was <1 square micron. This inconsistency is due to pores sharing boundaries, being contained by one another, or being lighter colored crystals. We used two

  15. Silicon pore optics development for ATHENA

    NASA Astrophysics Data System (ADS)

    Collon, Maximilien J.; Vacanti, Giuseppe; Günther, Ramses; Yanson, Alex; Barrière, Nicolas; Landgraf, Boris; Vervest, Mark; Chatbi, Abdelhakim; Beijersbergen, Marco W.; Bavdaz, Marcos; Wille, Eric; Haneveld, Jeroen; Koelewijn, Arenda; Leenstra, Anne; Wijnperle, Maurice; van Baren, Coen; Müller, Peter; Krumrey, Michael; Burwitz, Vadim; Pareschi, Giovanni; Conconi, Paolo; Christensen, Finn E.

    2015-09-01

    The ATHENA mission, a European large (L) class X-ray observatory to be launched in 2028, will essentially consist of an X-ray lens and two focal plane instruments. The lens, based on a Wolter-I type double reflection grazing incidence angle design, will be very large (~ 3 m in diameter) to meet the science requirements of large effective area (1-2 m2 at a few keV) at a focal length of 12 m. To meet the high angular resolution (5 arc seconds) requirement the X-ray lens will also need to be very accurate. Silicon Pore Optics (SPO) technology has been invented to enable building such a lens and thus enabling the ATHENA mission. We will report in this paper on the latest status of the development, including details of X-ray test campaigns.

  16. Pore size matters for potassium channel conductance.

    PubMed

    Naranjo, David; Moldenhauer, Hans; Pincuntureo, Matías; Díaz-Franulic, Ignacio

    2016-10-01

    Ion channels are membrane proteins that mediate efficient ion transport across the hydrophobic core of cell membranes, an unlikely process in their absence. K(+) channels discriminate K(+) over cations with similar radii with extraordinary selectivity and display a wide diversity of ion transport rates, covering differences of two orders of magnitude in unitary conductance. The pore domains of large- and small-conductance K(+) channels share a general architectural design comprising a conserved narrow selectivity filter, which forms intimate interactions with permeant ions, flanked by two wider vestibules toward the internal and external openings. In large-conductance K(+) channels, the inner vestibule is wide, whereas in small-conductance channels it is narrow. Here we raise the idea that the physical dimensions of the hydrophobic internal vestibule limit ion transport in K(+) channels, accounting for their diversity in unitary conductance.

  17. Distributed Pore Chemistry in Porous Organic Polymers

    NASA Technical Reports Server (NTRS)

    Koontz, Steven L. (Inventor)

    1998-01-01

    A method for making a biocompatible polymer article using a uniform atomic oxygen treatment is disclosed. The sub-strate may be subsequently optionally grated with a compatibilizing compound. Compatibilizing compounds may include proteins, phosphorylcholine groups, platelet adhesion preventing polymers, albumin adhesion promoters, and the like. The compatibilized substrate may also have a living cell layer adhered thereto. The atomic oxygen is preferably produced by a flowing afterglow microwave discharge, wherein the substrate resides in a sidearm out of the plasma. Also, methods for culturing cells for various purposes using the various membranes are disclosed as well. Also disclosed are porous organic polymers having a distributed pore chemistry (DPC) comprising hydrophilic and hydrophobic region, and a method for making the DPC by exposing the polymer to atomic oxygen wherein the rate of hydrophilization is greater than the rate of mass loss.

  18. Distributed Pore Chemistry in Porous Organic Polymers

    NASA Technical Reports Server (NTRS)

    Koontz, Steven L. (Inventor)

    1999-01-01

    A method for making a biocompatible polymer article using a uniform atomic oxygen treatment is disclosed. The substrate may be subsequently optionally grated with a compatibilizing compound. Compatibilizing compounds may include proteins, phosphorylcholine groups, platelet adhesion preventing polymers, albumin adhesion promoters, and the like. The compatibilized substrate may also have a living cell layer adhered thereto. The atomic oxygen is preferably produced by a flowing afterglow microwave discharge. wherein the substrate resides in a sidearm out of the plasma. Also, methods for culturing cells for various purposes using the various membranes are disclosed as well. Also disclosed are porous organic polymers having a distributed pore chemistry (DPC) comprising hydrophilic and hydrophobic regions. and a method for making the DPC by exposing the polymer to atomic oxygen wherein the rate of hydrophilization is greater than the rate of mass loss.

  19. Silicon pore optics for the ATHENA telescope

    NASA Astrophysics Data System (ADS)

    Collon, Maximilien J.; Vacanti, Giuseppe; Günther, Ramses; Yanson, Alex; Barriere, Nicolas; Landgraf, Boris; Vervest, Mark; Chatbi, Abdelhakim; van der Hoeven, Roy; Beijersbergen, Marco W.; Bavdaz, Marcos; Wille, Eric; Shortt, Brian; Haneveld, Jeroen; Koelewijn, Arenda; van Baren, Coen; Eigenraam, Alexander; Müller, Peter; Krumrey, Michael; Burwitz, Vadim; Pareschi, Giovanni; Conconi, Paolo; Massahi, Sonny; Christensen, Finn E.; Valsecchi, Giuseppe

    2016-07-01

    Silicon Pore Optics is a high-energy optics technology, invented to enable the next generation of high-resolution, large area X-ray telescopes such as the ATHENA observatory, a European large (L) class mission with a launch date of 2028. The technology development is carried out by a consortium of industrial and academic partners and focuses on building an optics with a focal length of 12 m that shall achieve an angular resolution better than 5". So far we have built optics with a focal length of 50 m and 20 m. This paper presents details of the work carried out to build silicon stacks for a 12 m optics and to integrate them into mirror modules. It will also present results of x-ray tests taking place at PTB's XPBF with synchrotron radiation and the PANTER test facility.

  20. Sumoylation and transcription regulation at nuclear pores.

    PubMed

    Texari, Lorane; Stutz, Françoise

    2015-03-01

    Increasing evidence indicates that besides promoters, enhancers, and epigenetic modifications, nuclear organization is another parameter contributing to optimal control of gene expression. Although differences between species exist, the influence of gene positioning on expression seems to be a conserved feature from yeast to Drosophila and mammals. The nuclear periphery is one of the nuclear compartments implicated in gene regulation. It consists of the nuclear envelope (NE) and the nuclear pore complexes (NPC), which have distinct roles in the control of gene expression. The NPC has recently been shown to tether proteins involved in the sumoylation pathway. Here, we will focus on the importance of gene positioning and NPC-linked sumoylation/desumoylation in transcription regulation. We will mainly discuss observations made in the yeast Saccharomyces cerevisiae model system and highlight potential parallels in metazoan species.

  1. Mitochondrial permeability transition pore and calcium handling.

    PubMed

    Wong, Renee; Steenbergen, Charles; Murphy, Elizabeth

    2012-01-01

    Opening of a large conductance channel in the inner mitochondrial membrane, known as the mitochondrial permeability transition (MPT) pore, has been shown to be a primary mediator of cell death in the heart subjected to ischemia-reperfusion injury. Inhibitors of the MPT have been shown to reduce cardiac ischemia-reperfusion injury. Furthermore, most cardioprotective strategies appear to reduce ischemic cell death either by reducing the triggers for the opening of the MPT, such as reducing calcium overload or reactive oxygen species, or by more direct inhibition of the MPT. This chapter focuses on key issues in the study of the MPT and provides some methods for measuring MPT opening in isolated mitochondria.

  2. Pore size matters for potassium channel conductance

    PubMed Central

    Moldenhauer, Hans; Pincuntureo, Matías

    2016-01-01

    Ion channels are membrane proteins that mediate efficient ion transport across the hydrophobic core of cell membranes, an unlikely process in their absence. K+ channels discriminate K+ over cations with similar radii with extraordinary selectivity and display a wide diversity of ion transport rates, covering differences of two orders of magnitude in unitary conductance. The pore domains of large- and small-conductance K+ channels share a general architectural design comprising a conserved narrow selectivity filter, which forms intimate interactions with permeant ions, flanked by two wider vestibules toward the internal and external openings. In large-conductance K+ channels, the inner vestibule is wide, whereas in small-conductance channels it is narrow. Here we raise the idea that the physical dimensions of the hydrophobic internal vestibule limit ion transport in K+ channels, accounting for their diversity in unitary conductance. PMID:27619418

  3. Freeze-cast alumina pore networks: Effects of freezing conditions and dispersion medium

    SciTech Connect

    Miller, S. M.; Xiao, X.; Faber, K. T.

    2015-11-01

    Alumina ceramics were freeze-cast from water- and camphene-based slurries under varying freezing conditions and examined using X-ray computed tomography (XCT). Pore network characteristics, i.e., porosity, pore size, geometric surface area, and tortuosity, were measured from XCT reconstructions and the data were used to develop a model to predict feature size from processing conditions. Classical solidification theory was used to examine relationships between pore size, temperature gradients, and freezing front velocity. Freezing front velocity was subsequently predicted from casting conditions via the two-phase Stefan problem. Resulting models for water-based samples agreed with solidification-based theories predicting lamellar spacing of binary eutectic alloys, and models for camphene-based samples concurred with those for dendritic growth. Relationships between freezing conditions and geometric surface area were also modeled by considering the inverse relationship between pore size and surface area. Tortuosity was determined to be dependent primarily on the type of dispersion medium. (C) 2015 Elsevier Ltd. All rights reserved.

  4. X-ray microtomography shows pore structure and tortuosity in alkali-activated binders

    SciTech Connect

    Provis, John L.; Myers, Rupert J.; White, Claire E.; Rose, Volker; Deventer, Jannie S.J. van

    2012-06-15

    Durability of alkali-activated binders is of vital importance in their commercial application, and depends strongly on microstructure and pore network characteristics. X-ray microtomography ({mu}CT) offers, for the first time, direct insight into microstructural and pore structure characteristics in three dimensions. Here, {mu}CT is performed on a set of sodium metasilicate-activated fly ash/slag blends, using a synchrotron beamline instrument. Segmentation of the samples into pore and solid regions is then conducted, and pore tortuosity is calculated by a random walker method. Segmented porosity and diffusion tortuosity are correlated, and vary as a function of slag content (slag addition reduces porosity and increases tortuosity), and sample age (extended curing gives lower porosity and higher tortuosity). This is particularly notable for samples with {>=} 50% slag content, where a space-filling calcium (alumino)silicate hydrate gel provides porosity reductions which are not observed for the sodium aluminosilicate ('geopolymer') gels which do not chemically bind water of hydration.

  5. Effects of a nearshore wastewater discharge: Water column and sediment pore water toxicity

    SciTech Connect

    Krause, P.R.; Carr, R.S.

    1995-12-31

    The relationship between water column and sediment pore water toxicity was investigated near a municipal-industrial wastewater discharge in southern Texas. Toxicity associated with effluent distributions in the water column are known to vary in both time and space. Toxicity of sediment, however, is often more stable over time. Sediment can serve as a long-term integrator of toxicity in areas subject to chronic exposure of effluents. This study addressed the relationship between water column toxicity and that found in the sediments on both spatial and temporal scales. Four 2 Km transacts were established around a nearshore wastewater outfall. Eight stations along each transact were sampled for both surface waters and sediment pore water toxicity. Toxicity was determined using a modified sea urchin fertilization test. Surface waters were sampled and tested for eight consecutive months, while sediment pore waters were sampled on three occasions over the length of this study. Results have shown that toxicity in receiving waters was a good indicator to trace movements of the highly variable effluent plume. The distribution of effluent in the water column, and hence water column toxicity, was primarily driven by local wind conditions. Toxicity in sediment porewater was, much less variable and more evenly distributed over the study site. Sediment pore water toxicity was also a good predictor of the distribution of benthic infaunal invertebrates over much of the study site.

  6. Fabrication of Al-Cu alloy with elongated pores by continuous casting technique

    NASA Astrophysics Data System (ADS)

    Suzuki, S.; Kim, T.-B.; Nakajima, H.

    2009-05-01

    A1-4.5wt%Cu was unidirectionally solidified by continuous casting technique under hydrogen pressure of 0.1MPa at the transference velocities ranging from 1 to 50 mmmidmin-1. The fabricated slabs have microstructures of columnar α-dendrite and eutectic, which are typical for hypo-eutectic Al-Cu alloys. Elongated pores are observed in the eutectic region surrounded by several columnar α-dendrites. The shapes of the pores are affected by that of the surrounding α-dendrites. The average pores diameter is several ten μm smaller than the average dendrite arm spacing, which decreases with increasing solidification rate. Therefore, the pore diameter varies from about 200 μm to 30 μm with increasing transference velocity from 1 to 50 mmmidmin-1. The porosity of the fabricated samples is in the range between 2 ~ 6 %. There is not significant dependence of the porosity on the transference velocity in the range of the present study. The porosity is similar to the reported value of Al-Si, where the area fraction of eutectic region is smaller than that of α-dendrite.

  7. Pore diameter effects on phase behavior of a gas condensate in graphitic one-and two-dimensional nanopores.

    PubMed

    Welch, William R W; Piri, Mohammad

    2016-01-01

    Molecular dynamics (MD) simulations were performed on a hydrocarbon mixture representing a typical gas condensate composed mostly of methane and other small molecules with small fractions of heavier hydrocarbons, representative of mixtures found in tight shale reservoirs. The fluid was examined both in bulk and confined to graphitic nano-scale slits and pores. Numerous widths and diameters of slits and pores respectively were examined under variable pressures at 300 K in order to find conditions in which the fluid at the center of the apertures would not be affected by capillary condensation due to the oil-wet walls. For the bulk fluid, retrograde phase behavior was verified by liquid volumes obtained from Voronoi tessellations. In cases of both one and two-dimensional confinement, for the smallest apertures, heavy molecules aggregated inside the pore space and compression of the gas outside the solid structure lead to decreases in density of the confined fluid. Normal density/pressure relationships were observed for slits having gaps of above 3 nm and pores having diameters above 6 nm. At 70 bar, the minimum gap width at which the fluid could pass through the center of slits without condensation effects was predicted to be 6 nm and the corresponding diameter in pores was predicted to be 8 nm. The models suggest that in nanoscale networks involving pores smaller than these limiting dimensions, capillary condensation should significantly impede transmission of natural gases with similar composition.

  8. Effect of Pore Structure Regulation on the Properties of Porous TiNbZr Shape Memory Alloys for Biomedical Application

    NASA Astrophysics Data System (ADS)

    Lai, Ming; Gao, Yan; Yuan, Bin; Zhu, Min

    2015-01-01

    Recently, porous Ti-Nb-based shape memory alloys have been considered as promising implants for biomedical application, because of their non-toxic elements, low elastic modulus, and stable superelasticity. However, the inverse relationship between pore characteristics and superelasticity of porous SMAs will strongly affect their clinical application. Until now, there have been few works specifically focusing on the effect of pore structure on the mechanical properties and superelasticity of porous Ti-Nb-based SMAs. In this study, the pore structure, including porosity and pore size, of porous Ti-22Nb-6Zr alloys was successfully regulated by adjusting the amount and size of space-holder particles. XRD and SEM investigation showed that all these porous alloys had homogeneous composition. Compression tests indicated that porosity played an important role in the mechanical properties and superelasticity of these porous alloys. Those alloys with porosity in the range of 38.5%-49.7% exhibited mechanical properties approaching to cortical bones, with elastic modulus, compressive strength, and recoverable strain in the range of 7.2-11.4 GPa, 188-422 MPa, and 2.4%-2.6%, respectively. Under the same porosity, the alloys with larger pores exhibited lower elastic modulus, while the alloys with smaller pores presented higher compressive strength.

  9. Application of real rock pore-threat statistics to a regular pore network model

    SciTech Connect

    Rakibul, M.; Sarker, H.; McIntyre, D.; Ferer, M.; Siddiqui, S.; Bromhal. G.

    2011-01-01

    This work reports the application of real rock statistical data to a previously developed regular pore network model in an attempt to produce an accurate simulation tool with low computational overhead. A core plug from the St. Peter Sandstone formation in Indiana was scanned with a high resolution micro CT scanner. The pore-throat statistics of the three-dimensional reconstructed rock were extracted and the distribution of the pore-throat sizes was applied to the regular pore network model. In order to keep the equivalent model regular, only the throat area or the throat radius was varied. Ten realizations of randomly distributed throat sizes were generated to simulate the drainage process and relative permeability was calculated and compared with the experimentally determined values of the original rock sample. The numerical and experimental procedures are explained in detail and the performance of the model in relation to the experimental data is discussed and analyzed. Petrophysical properties such as relative permeability are important in many applied fields such as production of petroleum fluids, enhanced oil recovery, carbon dioxide sequestration, ground water flow, etc. Relative permeability data are used for a wide range of conventional reservoir engineering calculations and in numerical reservoir simulation. Two-phase oil water relative permeability data are generated on the same core plug from both pore network model and experimental procedure. The shape and size of the relative permeability curves were compared and analyzed and good match has been observed for wetting phase relative permeability but for non-wetting phase, simulation results were found to be deviated from the experimental ones. Efforts to determine petrophysical properties of rocks using numerical techniques are to eliminate the necessity of regular core analysis, which can be time consuming and expensive. So a numerical technique is expected to be fast and to produce reliable results

  10. Application of real rock pore-throat statistics to a regular pore network model

    SciTech Connect

    Sarker, M.R.; McIntyre, D.; Ferer, M.; Siddigui, S.; Bromhal. G.

    2011-01-01

    This work reports the application of real rock statistical data to a previously developed regular pore network model in an attempt to produce an accurate simulation tool with low computational overhead. A core plug from the St. Peter Sandstone formation in Indiana was scanned with a high resolution micro CT scanner. The pore-throat statistics of the three-dimensional reconstructed rock were extracted and the distribution of the pore-throat sizes was applied to the regular pore network model. In order to keep the equivalent model regular, only the throat area or the throat radius was varied. Ten realizations of randomly distributed throat sizes were generated to simulate the drainage process and relative permeability was calculated and compared with the experimentally determined values of the original rock sample. The numerical and experimental procedures are explained in detail and the performance of the model in relation to the experimental data is discussed and analyzed. Petrophysical properties such as relative permeability are important in many applied fields such as production of petroleum fluids, enhanced oil recovery, carbon dioxide sequestration, ground water flow, etc. Relative permeability data are used for a wide range of conventional reservoir engineering calculations and in numerical reservoir simulation. Two-phase oil water relative permeability data are generated on the same core plug from both pore network model and experimental procedure. The shape and size of the relative permeability curves were compared and analyzed and good match has been observed for wetting phase relative permeability but for non-wetting phase, simulation results were found to be deviated from the experimental ones. Efforts to determine petrophysical properties of rocks using numerical techniques are to eliminate the necessity of regular core analysis, which can be time consuming and expensive. So a numerical technique is expected to be fast and to produce reliable results

  11. Movement of ions through fixed pores in the neural membrane.

    PubMed Central

    Wooldridge, D E

    1984-01-01

    A simple configuration is first proposed for the pores used by sodium and potassium ions in moving through the neural membrane. The voltage dependence of the ion current through a system of such pores is then derived from diffusion theory and shown not to agree well with experimental observation. Good agreement is obtained, however, when the end segments of the pores are modified to include constrictions and ion-specific trapping centers. PMID:6089215

  12. Tension-induced pore formation and leakage in adhering vesicles

    NASA Astrophysics Data System (ADS)

    Lenz, P.; Johnson, J. M.; Chan, Y.-H. M.; Boxer, S. G.

    2006-08-01

    The influence of inclusion-induced tension on pore formation is studied theoretically and experimentally. It is shown that fluorescently labeled lipids can enhance pore formation and induce leakage of adhering vesicles. These effects are more pronounced for smaller vesicles. The theoretical predictions are confirmed by experimental two-color fluorescent data. Finally, the influence of the pore formation dynamics on rupture processes of vesicles is analyzed yielding a new picture of the transition to bilayer disks.

  13. Preparation of mesoporous cadmium sulfide nanoparticles with moderate pore size

    SciTech Connect

    Han Zhaohui Zhu, Huaiyong; Shi, Jeffrey; Parkinson, Gordon; Lu, G.Q.

    2007-03-15

    The preparation of cadmium sulfide nanoparticles that have a moderate pore size is reported. This preparation method involves a hydrothermal process that produces a precursor mixture and a following acid treatment of the precursor to get the porous material. The majority of the particles have a pore size close to 20nm, which complements and fills in the gap between the existing cadmium sulfide materials, which usually have a pore size either less than 10nm or are well above 100nm.

  14. Hydration State and Aqueous Phase Connectivity Shape Microbial Dispersal Rates in Unsaturated Angular Pore Networks

    NASA Astrophysics Data System (ADS)

    Or, D.; Ebrahimi, A.

    2014-12-01

    The limited dispersal of self-propelled microorganisms and constrained nutrient transport in unsaturated soils are considered key factors in the promotion and maintenance of soil microbial diversity. Despite the importance of microbial dispersal to biogeochemical and ecological functioning of soil, little is known about how pore spaces and hydration conditions affect dispersal ranges and rates of motile bacteria. To address these questions quantitatively, we developed a novel 3-D pore network model (PNM) composed of triangular bonds connected to cubic (volumeless) bonds to mimic the salient geometrical and physical properties of natural pore spaces. Within this abstracted physical domain we employed individual based models for motile microorganisms that are capable of motion, nutrient consumption, growth and cell division. We focused on dispersal rates through the network as a function of hydration conditions through its impact on aqueous phase fragmentation that suppress nutrient diffusion (hence growth rates) and dispersal rates in good agreement with limited experimental data. Chemotactically-biased mean travel rates of microbial cells across the saturated PNM was ~3 mm/hr and decreased exponentially to 0.45 mm/hr for matric potential of (at dispersal practically ceases and cells are pinned by capillary forces). Individual-based results were upscaled to describe population scale dispersal rates, and PNM predictions considering different microbial cell sizes were in good agreement with experimental results for unsaturated soils. The role of convection for most unsaturated conditions was negligible relative to self-motility highlighting the need to constrain continuum models with respect to cell size and motility to imporve predictions of transport of motile microorganisms. The modeling platform confirms universal predictions based on percolation theory for the onset of aqueous phase fragmentation that limit dispersal and provide niches essential for species

  15. Ultrafast laser fabrication of submicrometer pores in borosilicate glass.

    PubMed

    An, Ran; Uram, Jeffrey D; Yusko, Erik C; Ke, Kevin; Mayer, Michael; Hunt, Alan J

    2008-05-15

    We demonstrate rapid fabrication of submicrometer-diameter pores in borosilicate glass using femtosecond laser machining and subsequent wet-etch techniques. This approach allows direct and repeatable fabrication of high-quality pores with diameters of 400-800 nm. Such small pores coupled with the desirable electrical and chemical properties of glass enable sensitive resistive-pulse analysis to determine the size and concentration of macromolecules and nanoparticles. Plasma-enhanced chemical vapor deposition allows further reduction of pore diameters to below 300 nm.

  16. Extraction of pores from microtomographic reconstructions of intact soil aggregates

    SciTech Connect

    Albee, P. B.; Stockman, G. C.; Smucker, A. J. M.

    2000-02-29

    Segmentation of features is often a necessary step in the analysis of volumetric data. The authors have developed a simple technique for extracting voids from irregular volumetric data sets. In this work they look at extracting pores from soil aggregates. First, they identify a threshold that gives good separability of the object from the background. They then segment the object, and perform connected components analysis on the pores within the object. Using their technique pores that break the surface can be segmented along with pores completely contained in the initially segmented object.

  17. Pore-size-distribution of cationic polyacrylamide hydrogels. Progress report

    SciTech Connect

    Kremer, M.; Prausnitz, J.M.

    1992-06-01

    The pore size distribution of a AAm/MAPTAC (acrylamide copolymerized with (3-methacrylamidopropyl)trimethylammonium chloride) hydrogel was investigated using Kuga`s mixed-solute-exclusion method, taking into account the wall effect. A Brownian-motion model is also used. Results show the feasibility of determining pore-size distribution of porous materials using the mixed-solute-exclusion method in conjunction with solution of the Fredholm equation; good agreement was obtained with experiment, even for bimodal pore structures. However, different pore size distributions were calculated for the two different probe-solutes (Dextran and poly(ethylene glycol/oxide)). Future work is outlined. 32 figs, 25 refs.

  18. Pore-size-distribution of cationic polyacrylamide hydrogels

    SciTech Connect

    Kremer, M.; Prausnitz, J.M.

    1992-06-01

    The pore size distribution of a AAm/MAPTAC (acrylamide copolymerized with (3-methacrylamidopropyl)trimethylammonium chloride) hydrogel was investigated using Kuga's mixed-solute-exclusion method, taking into account the wall effect. A Brownian-motion model is also used. Results show the feasibility of determining pore-size distribution of porous materials using the mixed-solute-exclusion method in conjunction with solution of the Fredholm equation; good agreement was obtained with experiment, even for bimodal pore structures. However, different pore size distributions were calculated for the two different probe-solutes (Dextran and poly(ethylene glycol/oxide)). Future work is outlined. 32 figs, 25 refs.

  19. Extending membrane pore lifetime with AC fields: A modeling study

    NASA Astrophysics Data System (ADS)

    Garner, Allen L.; Bogdan Neculaes, V.

    2012-07-01

    AC (sinusoidal) fields with frequencies from kilohertz to gigahertz have been used for gene delivery. To understand the impact of AC fields on electroporation dynamics, we couple a nondimensionalized Smoluchowski equation to an exact representation of the cell membrane voltage obtained solving the Laplace equation. The slope of the pore energy function, dφ/dr, with respect to pore radius is critical in predicting pore dynamics in AC fields because it can vary from positive, inducing pore shrinkage, to negative, driving pore growth. Specifically, the net sign of the integral of dφ/dr over time determines whether the average pore size grows (negative), shrinks (positive), or oscillates (zero) indefinitely about a steady-state radius, rss. A simple analytic relationship predicting the amplitude of the membrane voltage necessary for this behavior agrees well with simulation for frequencies from 500 kHz to 5 MHz for rss < 10 nm. For larger pore size (rss > 10 nm), dφ/dr oscillates about a negative value, suggesting that a net creation of pores may be necessary to maintain a constant pore size. In both scenarios, the magnitude of rss depends only upon the amplitude of the membrane voltage and not directly upon the applied field frequency other than the relationship between the amplitudes of the applied field and membrane voltage.

  20. Single-Pore Membranes Gated by Microelectromagnetic Traps

    SciTech Connect

    Basore, Joseph; Baker, Lane; Lavrik, Nickolay V

    2010-01-01

    Gating of a single pore with a microelectromagnetic trap consisting of a single-turn gold wire microfabricated on a silicon membrane is described. A single micrometer-sized pore in the center of the microcoil conducts ionic current under the application of an applied transmembrane potential. When energized, the microelectromagnetic trap attracts a droplet of magnetic fluid, bringing the fluid to rest in the center of the trap, blocking the transport of ions through the pore, turning it 'off'. Reversal of the current flow through the trap moves the droplet to the periphery of the trap, turning the pore 'on'.

  1. Pore morphologies of root induced biopores from single pore to network scale investigated by XRCT

    NASA Astrophysics Data System (ADS)

    Peth, Stephan; Wittig, Marlen C.; Uteau Puschmann, Daniel; Pagenkemper, Sebastian; Haas, Christoph; Holthusen, Dörthe; Horn, Rainer

    2015-04-01

    Biopores are assumed to be an important factor for nutrient acquisition by providing biologically highly active soil-root interfaces to re-colonizing roots and controlling oxygen and water flows at the pedon scale and within the rhizosphere through the formation of branching channel networks which potentially enhance microbial turnover processes. Characteristic differences in pore morphologies are to be expected depending on the genesis of biopores which, for example, can be earthworm-induced or root-induced or subsequently modified by one of the two. Our understanding of biophysical interactions between plants and soil can be significantly improved by quantifying 3D biopore architectures across scales ranging from single biopores to pedon scale pore networks and linking pore morphologies to microscale measurements of transport processes (e.g. oxygen diffusion). While a few studies in the past have investigated biopore networks on a larger scale yet little is known on the micro-morphology of root-induces biopores and their associated rhizosphere. Also little data is available on lateral transport of oxygen through the rhizosphere which will strongly influence microbial turnover processes and consequently control the release and uptake of nutrients. This paper highlights results gathered within a research unit on nutrient acquisition from the subsoil. Here we focus on X-ray microtomography (XRCT) studies ranging from large soil columns (70 cm length and 20 cm diameter) to individual biopores and its surrounding rhizosphere. Samples were collected from sites with different preceding crops (fescue, chicory, alfalfa) and various cropping durations (1-3 years). We will present an approach for quantitative image analysis combined with micro-sensor measurements of oxygen diffusion and spatial gradients of O2 partial pressures to relate pore structure with transport functions. Implications of various biopore architectures for the accessibility of nutrient resources in

  2. Mineral Dissolution Rates at the Pore Scale: Scaling Effects

    NASA Astrophysics Data System (ADS)

    Li, L.; Steefel, C. I.; Yang, L.

    2006-12-01

    Mineral dissolution reactions play an important role in various physical, chemical and biological processes in nature. Although rates of these reactions have been extensively studied in laboratories, they have been found to be orders of magnitude faster than those measured in the natural systems. This work examines some of the mechanisms that can produce such a discrepancy at the pore scale, while quantifying the conditions under which the discrepancy becomes significant. This work used the reactive transport model CrunchFlow to examine the dissolution rates of three minerals, calcite, labradorite, and iron hydroxide, in a single pore. Pores were assumed to be cylindrical, with axisymmetric flow given by the analytical solution for Poiseuille flow in a cylinder. Mineral dissolution occurs only at the pore wall, with the reactive surface area of the dissolving phase specified geometrically. The average dissolution rates in the pore (R_D) for various flow velocities is determined by the flux-weighted change in concentration over the length of the pore and is compared to the rates that assume complete mixing (R_M). The differences in rates between the two models, quantified by the ratio of R_D over R_M, provide a measure of the scaling effect. The modeling results were validated by a microfluidic reactive flow experiment using a cylindrical pore in calcite. Modeling results show that the scaling effect arises due to the development of large concentration gradients caused by incomplete mixing within a pore when transport and reaction rates are comparable. The magnitude of the scaling effect depends on the reaction kinetics, flow velocity, and pore size. For labradorite and iron hydroxide, the scaling effect is negligible under all conditions due to their slow dissolution rates, thus limiting the development of any intra-pore concentration gradients. For calcite dissolution at low (smaller than 0.1 cm/s) and high (larger than 1000 cm/s) flow velocities the scaling

  3. Effects of supersaturation on pore shape in solid

    NASA Astrophysics Data System (ADS)

    Wei, P. S.; Hsiao, S. Y.

    2017-02-01

    The shape of a pore resulting from a bubble entrapped by a solidification front with different supersaturation ratios is predicted in this work. Supersaturation ratio, representing the ratio between solute concentration and saturation solute concentration, determines nucleation of a bubble and development of the pore shape in the early stage. Pore formation and its shape in solid influence contemporary issues of biology, engineering, foods, geophysics and climate change, etc. This work extends and combines previous models accounting for realistic mass and momentum transport, and physico-chemical equilibrium of solute gas across the bubble cap to self-consistently determine shape of the bubble cap beyond the solidification front and the pore shape in solid. The study also deal with that pore formation can be resulted from three different mechanisms, depending on the directions and magnitude of solute gas transport across the bubble cap. Case 1 is subject to solute transport from the pore across the cap into the surrounding liquid in the early stage. Cases 2a and 2b indicate opposite direction of solute transport. In contrast to Case 2b, the effect of solute transport on solute gas pressure in the pore in Case 2a is stronger than that of pore volume expansionin the last stage. The results find that an increase in supersaturation ratio decreases pore radius and time for bubble entrapment in Case 1. The bubble cannot be entrapped in Case 2. The predicted pore shape in solid agrees with experimental data. Understanding, prediction and control of the growth of the pore shape have therefore been obtained.

  4. Characterisation of the passive permeability barrier of nuclear pore complexes

    PubMed Central

    Mohr, Dagmar; Frey, Steffen; Fischer, Torsten; Güttler, Thomas; Görlich, Dirk

    2009-01-01

    Nuclear pore complexes (NPCs) restrict uncontrolled nucleocytoplasmic fluxes of inert macromolecules but permit facilitated translocation of nuclear transport receptors and their cargo complexes. We probed the passive barrier of NPCs and observed sieve-like properties with a dominating mesh or channel radius of 2.6 nm, which is narrower than proposed earlier. A small fraction of diffusion channels has a wider opening, explaining the very slow passage of larger molecules. The observed dominant passive diameter approximates the distance of adjacent hydrophobic clusters of FG repeats, supporting the model that the barrier is made of FG repeat domains cross-linked with a spacing of an FG repeat unit length. Wheat germ agglutinin and the dominant-negative importin β45-462 fragment were previously regarded as selective inhibitors of facilitated NPC passage. We now observed that they do not distinguish between the passive and the facilitated mode. Instead, their inhibitory effect correlates with the size of the NPC-passing molecule. They have little effect on small species, inhibit the passage of green fluorescent protein-sized objects >10-fold and virtually block the translocation of larger ones. This suggests that passive and facilitated NPC passage proceed through one and the same permeability barrier. PMID:19680228

  5. Pore and Continuum Scale Study of the Effect of Subgrid Transport Heterogeneity on Redox Reaction Rates

    SciTech Connect

    Liu, Yuanyuan; Liu, Chongxuan; Zhang, Changyong; Yang, Xiaofan; Zachara, John M.

    2015-08-01

    A micromodel system with a pore structure for heterogeneous flow and transport was used to investigate the effect of subgrid transport heterogeneity on redox reaction rates. Hematite reductive dissolution by injecting a reduced form of flavin mononucleotide (FMNH2) at variable flow rates was used as an example to probe the variations of redox reaction rates in different subgrid transport domains. Experiments, pore-scale simulations, and macroscopic modeling were performed to measure and simulate in-situ hematite reduction and to evaluate the scaling behavior of the redox reaction rates from the pore to macroscopic scales. The results indicated that the measured pore-scale rates of hematite reduction were consistent with the predictions from a pore scale reactive transport model. A general trend is that hematite reduction followed reductant transport pathways, starting from the advection-dominated pores toward the interior of diffusion-dominated domains. Two types of diffusion domains were considered in the micromodel: a micropore diffusion domain, which locates inside solid grains or aggregates where reactant transport is limited by diffusion; and a macropore diffusion domain, which locates at wedged, dead-end pore spaces created by the grain-grain contacts. The rate of hematite reduction in the advection-dominated domain was faster than those in the diffusion-controlled domains, and the rate in the macropore diffusion domain was faster than that in the micropore domain. The reduction rates in the advection and macropore diffusion domains increased with increasing flow rate, but were affected by different mechanisms. The rate increase in the advection domain was controlled by the mass action effect as a faster flow supplied more reactants, and the rate increase in the macropore domain was more affected by the rate of mass exchange with the advection domain, which increased with increasing flow rate. The hematite reduction rate in the micropore domain was, however

  6. Physiologic upper limits of pore size of different blood capillary types and another perspective on the dual pore theory of microvascular permeability

    PubMed Central

    2010-01-01

    continuity or lack thereof. Non-sinusoidal blood capillaries were further sub-classified as non-fenestrated or fenestrated based on the absence or presence of endothelial cells with fenestrations. The sinusoidal blood capillaries of the liver, myeloid (red) bone marrow, and spleen were sub-classified as reticuloendothelial or non-reticuloendothelial based on the phago-endocytic capacity of the endothelial cells. Results The physiologic upper limit of pore size for transvascular flow across capillary walls of non-sinusoidal non-fenestrated blood capillaries is less than 1 nm for those with interendothelial cell clefts lined with zona occludens junctions (i.e. brain and spinal cord), and approximately 5 nm for those with clefts lined with macula occludens junctions (i.e. skeletal muscle). The physiologic upper limit of pore size for transvascular flow across the capillary walls of non-sinusoidal fenestrated blood capillaries with diaphragmed fenestrae ranges between 6 and 12 nm (i.e. exocrine and endocrine glands); whereas, the physiologic upper limit of pore size for transvascular flow across the capillary walls of non-sinusoidal fenestrated capillaries with open 'non-diaphragmed' fenestrae is approximately 15 nm (kidney glomerulus). In the case of the sinusoidal reticuloendothelial blood capillaries of myeloid bone marrow, the transvascular transport of non-endogenous macromolecules larger than 5 nm into the bone marrow interstitial space takes place via reticuloendothelial cell-mediated phago-endocytosis and transvascular release, which is the case for systemic bone marrow imaging agents as large as 60 nm in diameter. Conclusions The physiologic upper limit of pore size in the capillary walls of most non-sinusoidal blood capillaries to the transcapillary passage of lipid-insoluble endogenous and non-endogenous macromolecules ranges between 5 and 12 nm. Therefore, macromolecules larger than the physiologic upper limits of pore size in the non-sinusoidal blood capillary types

  7. Freezing of charged colloids in slit pores.

    PubMed

    Grandner, Stefan; Klapp, Sabine H L

    2008-12-28

    Using Monte Carlo simulations in the grand canonical and isobaric ensembles we investigate freezing phenomena in a charged colloidal suspension confined to narrow slit pores. Our model involves only the macroions which interact via a Derjaguin-Landau-Verwey-Overbeek (DLVO) potential supplemented by a soft-sphere potential. We focus on DLVO parameters typical for moderately charged silica particles (with charges Z approximately 35) in solvents of low ionic strengths. The corresponding DLVO interactions are too weak to drive a (bulk) freezing transition. Nevertheless, for sufficiently small surface separations L(z) the confined systems display not only layering but also significant in-plane crystalline order at chemical potentials where the bulk system is a globally stable fluid (capillary freezing). At confinement conditions related to two-layer systems the observed in-plane structures are consistent with those detected in ground state calculations for perfect Yukawa bilayers [R. Messina and H. Lowen, Phys. Rev. Lett. 91, 146101 (2003)]. Here we additionally observe (at fixed L(z)) a compression-induced first-order phase transition from a two-layer to a three-layer system with different in-plane structure, in agreement with previous findings for pure hard spheres.

  8. Gating of two pore domain potassium channels.

    PubMed

    Mathie, Alistair; Al-Moubarak, Ehab; Veale, Emma L

    2010-09-01

    Two-pore-domain potassium (K2P) channels are responsible for background leak currents which regulate the membrane potential and excitability of many cell types. Their activity is modulated by a variety of chemical and physical stimuli which act to increase or decrease the open probability of individual K2P channels. Crystallographic data and homology modelling suggest that all K(+) channels possess a highly conserved structure for ion selectivity and gating mechanisms. Like other K(+) channels, K2P channels are thought to have two primary conserved gating mechanisms: an inactivation (or C-type) gate at the selectivity filter close to the extracellular side of the channel and an activation gate at the intracellular entrance to the channel involving key, identified, hinge glycine residues. Zinc and hydrogen ions regulate Drosophila KCNK0 and mammalian TASK channels, respectively, by interacting with the inactivation gate of these channels. In contrast, the voltage dependence of TASK3 channels is mediated through its activation gate. For KCNK0 it has been shown that the gates display positive cooperativity. It is of much interest to determine whether other K2P regulatory compounds interact with either the activation gate or the inactivation gate to alter channel activity or, indeed, whether additional regulatory gating pathways exist.

  9. Gating of two pore domain potassium channels

    PubMed Central

    Mathie, Alistair; Al-Moubarak, Ehab; Veale, Emma L

    2010-01-01

    Two-pore-domain potassium (K2P) channels are responsible for background leak currents which regulate the membrane potential and excitability of many cell types. Their activity is modulated by a variety of chemical and physical stimuli which act to increase or decrease the open probability of individual K2P channels. Crystallographic data and homology modelling suggest that all K+ channels possess a highly conserved structure for ion selectivity and gating mechanisms. Like other K+ channels, K2P channels are thought to have two primary conserved gating mechanisms: an inactivation (or C-type) gate at the selectivity filter close to the extracellular side of the channel and an activation gate at the intracellular entrance to the channel involving key, identified, hinge glycine residues. Zinc and hydrogen ions regulate Drosophila KCNK0 and mammalian TASK channels, respectively, by interacting with the inactivation gate of these channels. In contrast, the voltage dependence of TASK3 channels is mediated through its activation gate. For KCNK0 it has been shown that the gates display positive cooperativity. It is of much interest to determine whether other K2P regulatory compounds interact with either the activation gate or the inactivation gate to alter channel activity or, indeed, whether additional regulatory gating pathways exist. PMID:20566661

  10. Porous Boron Nitride with Tunable Pore Size.

    PubMed

    Dai, Jun; Wu, Xiaojun; Yang, Jinlong; Zeng, Xiao Cheng

    2014-01-16

    On the basis of a global structural search and first-principles calculations, we predict two types of porous boron-nitride (BN) networks that can be built up with zigzag BN nanoribbons (BNNRs). The BNNRs are either directly connected with puckered B (N) atoms at the edge (type I) or connected with sp(3)-bonded BN chains (type II). Besides mechanical stability, these materials are predicted to be thermally stable at 1000 K. The porous BN materials entail large surface areas, ranging from 2800 to 4800 m(2)/g. In particular, type-II BN material with relatively large pores is highly favorable for hydrogen storage because the computed hydrogen adsorption energy (-0.18 eV) is very close to the optimal adsorption energy (-0.15 eV) suggested for reversible hydrogen storage at room temperature. Moreover, the type-II materials are semiconductors with width-dependent direct bandgaps, rendering the type-II BN materials promising not only for hydrogen storage but also for optoelectronic and photonic applications.

  11. Pore formation in lipid membranes by alamethicin.

    PubMed Central

    Fringeli, U P; Fringeli, M

    1979-01-01

    The conformation of the linear peptide antibiotic alamethicin in dipalmitoyl phosphatidylcholine multilayers was investigated in the absence of an electric field by means of infrared attenuated total reflection spectroscopy. Alamethicin was found to be incorporated into the lipid membrane not only in the dry state but also in an aqueous environment. Its molecular conformation, however, changed from a helix when dry to an extended chain when aqueous. The extended chain aggregated to di- and multimers spanning the lipid bilayer. The equilibrium concentration of alamethicin in the surrounding water was 90 nM, which is in the range of concentrations used in black film experiments. The corresponding molar ratio of lipid to peptide was 80:1. Concerning the molecular mechanism of electric field-induced pore formation, one has to conclude that the dipole model proposed by several authors is very unlikely because it is based on the assumption that the major part of alamethicin is adsorbed on the membrane surface, from which small amounts flip into the membrane under the influence of an electric field. An alternative mechanism is proposed, based on a field-induced conformational change of the peptide from the extended state to a helix. This transition is favored by the resulting dipole moment of the alamethicin helix. PMID:291045

  12. Evaluating transport in irregular pore networks

    NASA Astrophysics Data System (ADS)

    Klimenko, Dimitri A.; Hooman, Kamel; Klimenko, Alexander Y.

    2012-07-01

    A general approach for investigating transport phenomena in porous media is presented. This approach has the capacity to represent various kinds of irregularity in porous media without the need for excessive detail or computational effort. The overall method combines a generalized effective medium approximation (EMA) with a macroscopic continuum model in order to derive a transport equation with explicit analytical expressions for the transport coefficients. The proposed form of the EMA is an anisotropic and heterogeneous extension of Kirkpatrick's EMA [Rev. Mod. Phys.RMPHAT0034-686110.1103/RevModPhys.45.574 45, 574 (1973)] which allows the overall model to account for microscopic alterations in connectivity (with the locations of the pores and the orientation and length of the throat) as well as macroscopic variations in transport properties. A comparison to numerical results for randomly generated networks with different properties is given, indicating the potential for this methodology to handle cases that would pose significant difficulties to many other analytical models.

  13. Mutant Huntingtin Disrupts the Nuclear Pore Complex.

    PubMed

    Grima, Jonathan C; Daigle, J Gavin; Arbez, Nicolas; Cunningham, Kathleen C; Zhang, Ke; Ochaba, Joseph; Geater, Charlene; Morozko, Eva; Stocksdale, Jennifer; Glatzer, Jenna C; Pham, Jacqueline T; Ahmed, Ishrat; Peng, Qi; Wadhwa, Harsh; Pletnikova, Olga; Troncoso, Juan C; Duan, Wenzhen; Snyder, Solomon H; Ranum, Laura P W; Thompson, Leslie M; Lloyd, Thomas E; Ross, Christopher A; Rothstein, Jeffrey D

    2017-04-05

    Huntington's disease (HD) is caused by an expanded CAG repeat in the Huntingtin (HTT) gene. The mechanism(s) by which mutant HTT (mHTT) causes disease is unclear. Nucleocytoplasmic transport, the trafficking of macromolecules between the nucleus and cytoplasm, is tightly regulated by nuclear pore complexes (NPCs) made up of nucleoporins (NUPs). Previous studies offered clues that mHTT may disrupt nucleocytoplasmic transport and a mutation of an NUP can cause HD-like pathology. Therefore, we evaluated the NPC and nucleocytoplasmic transport in multiple models of HD, including mouse and fly models, neurons transfected with mHTT, HD iPSC-derived neurons, and human HD brain regions. These studies revealed severe mislocalization and aggregation of NUPs and defective nucleocytoplasmic transport. HD repeat-associated non-ATG (RAN) translation proteins also disrupted nucleocytoplasmic transport. Additionally, overexpression of NUPs and treatment with drugs that prevent aberrant NUP biology also mitigated this transport defect and neurotoxicity, providing future novel therapy targets.

  14. FINE PORE DIFFUSER FOULING: THE LOS ANGELES STUDIES

    EPA Science Inventory

    This report describes five fine pore diffuser evaluations conducted at three different wastewater treatment plants located in the greater Los Angeles area. The overall goal of the study was to evaluate the performance of fine pore diffusers using selected cleaning methods for ex...

  15. Reforming naphtha with boron-containing large-pore zeolites

    SciTech Connect

    Zones, S.I.; Holtermann, D.L.; Rainis, A.

    1992-05-19

    This patent describes a catalytic reforming process. It comprises contacting a hydrocarbonaceous feedstream under catalytic reforming conditions with a composition comprising larger-pore borosilicate zeolites having a pore size greater than 6 and less than 8 angstroms containing less that 1000 parts per million aluminum.

  16. MEASUREMENT AND CONTROL OF FOULING IN FINE PORE DIFFUSER SYSTEMS

    EPA Science Inventory

    The purpose of the study was two-fold: First, to define the efficiency of various methods of cleaning fine pore diffusers and, second, to develop a methodology that could be used to evaluate the efficiency of the cleaning techniques. Dirty fine pore domes from the North Texas Mu...

  17. Reversible Self-Actuated Thermo-Responsive Pore Membrane

    PubMed Central

    Park, Younggeun; Gutierrez, Maria Paz; Lee, Luke P.

    2016-01-01

    Smart membranes, which can selectively control the transfer of light, air, humidity and temperature, are important to achieve indoor climate regulation. Even though reversible self-actuation of smart membranes is desirable in large-scale, reversible self-regulation remains challenging. Specifically, reversible 100% opening/closing of pore actuation showing accurate responsiveness, reproducibility and structural flexibility, including uniform structure assembly, is currently very difficult. Here, we report a reversible, thermo-responsive self-activated pore membrane that achieves opening and closing of pores. The reversible, self-actuated thermo-responsive pore membrane was fabricated with hybrid materials of poly (N-isopropylacrylamide), (PNIPAM) within polytetrafluoroethylene (PTFE) to form a multi-dimensional pore array. Using Multiphysics simulation of heat transfer and structural mechanics based on finite element analysis, we demonstrated that pore opening and closing dynamics can be self-activated at environmentally relevant temperatures. Temperature cycle characterizations of the pore structure revealed 100% opening ratio at T = 40 °C and 0% opening ratio at T = 20 °C. The flexibility of the membrane showed an accurate temperature-responsive function at a maximum bending angle of 45°. Addressing the importance of self-regulation, this reversible self-actuated thermo-responsive pore membrane will advance the development of future large-scale smart membranes needed for sustainable indoor climate control. PMID:27991563

  18. Reversible Self-Actuated Thermo-Responsive Pore Membrane

    NASA Astrophysics Data System (ADS)

    Park, Younggeun; Gutierrez, Maria Paz; Lee, Luke P.

    2016-12-01

    Smart membranes, which can selectively control the transfer of light, air, humidity and temperature, are important to achieve indoor climate regulation. Even though reversible self-actuation of smart membranes is desirable in large-scale, reversible self-regulation remains challenging. Specifically, reversible 100% opening/closing of pore actuation showing accurate responsiveness, reproducibility and structural flexibility, including uniform structure assembly, is currently very difficult. Here, we report a reversible, thermo-responsive self-activated pore membrane that achieves opening and closing of pores. The reversible, self-actuated thermo-responsive pore membrane was fabricated with hybrid materials of poly (N-isopropylacrylamide), (PNIPAM) within polytetrafluoroethylene (PTFE) to form a multi-dimensional pore array. Using Multiphysics simulation of heat transfer and structural mechanics based on finite element analysis, we demonstrated that pore opening and closing dynamics can be self-activated at environmentally relevant temperatures. Temperature cycle characterizations of the pore structure revealed 100% opening ratio at T = 40 °C and 0% opening ratio at T = 20 °C. The flexibility of the membrane showed an accurate temperature-responsive function at a maximum bending angle of 45°. Addressing the importance of self-regulation, this reversible self-actuated thermo-responsive pore membrane will advance the development of future large-scale smart membranes needed for sustainable indoor climate control.

  19. Fractal geometry impact on nuclear relaxation in irregular pores.

    PubMed

    Sapoval, B; Russ, S; Petit, D; Korb, J P

    1996-01-01

    We apply a fractal description of pore surface irregularity to study the nuclear relaxation of a confined liquid. From the introduction of a length characteristic of diffusive and surface relaxing properties we describe three different relaxation regimes. These regimes show that the nuclear relaxation can be drastically modified by pore surface irregularity.

  20. DNA translocation through protein and synthetic nano pores

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Aniket

    2007-03-01

    DNA translocation through narrow protein channels is recognized as an important process in biology. Recently it has attracted lot of attention in the biophysical community following several experiments on DNA translocation through protein nano-pores, and more recently, through synthetic silicon nano-pores. A fundamental understanding is needed for various biological processes, e.g., entry and exit of a DNA in and out of a cell, efficient separation methods for macromolecules, and, possibly fast DNA sequencing. In this talk I will be presenting results for the DNA translocation using a coarse-grained model for an idealized DNA as well as the pore. I will consider several scenarios for the DNA translocation. First, I will show scaling of translocation time of a homopolymer as it escapes from the trans side to the cis side of an idealized thin membrane. Then I will consider DNA dynamics subject to a driving force inside the pore. Next, I will consider heteropolymer threading through a nano-pore. Specifically we will consider both highly ordered and completely random sequences of the chain and relate specific sequences to the distribution of the translocation time and the residence time inside the pore. These studies also will include effects due to different environment on either side of the pore, specific DNA-pore interactions located at selective sites, etc.. I will discuss relevance of these simulation results to recent experiments and theoretical models. A. Milchev, K. Binder, and Aniket Bhattacharya, J. Chem. Phys. 121, 6042 (2004).

  1. Reversible Self-Actuated Thermo-Responsive Pore Membrane.

    PubMed

    Park, Younggeun; Gutierrez, Maria Paz; Lee, Luke P

    2016-12-19

    Smart membranes, which can selectively control the transfer of light, air, humidity and temperature, are important to achieve indoor climate regulation. Even though reversible self-actuation of smart membranes is desirable in large-scale, reversible self-regulation remains challenging. Specifically, reversible 100% opening/closing of pore actuation showing accurate responsiveness, reproducibility and structural flexibility, including uniform structure assembly, is currently very difficult. Here, we report a reversible, thermo-responsive self-activated pore membrane that achieves opening and closing of pores. The reversible, self-actuated thermo-responsive pore membrane was fabricated with hybrid materials of poly (N-isopropylacrylamide), (PNIPAM) within polytetrafluoroethylene (PTFE) to form a multi-dimensional pore array. Using Multiphysics simulation of heat transfer and structural mechanics based on finite element analysis, we demonstrated that pore opening and closing dynamics can be self-activated at environmentally relevant temperatures. Temperature cycle characterizations of the pore structure revealed 100% opening ratio at T = 40 °C and 0% opening ratio at T = 20 °C. The flexibility of the membrane showed an accurate temperature-responsive function at a maximum bending angle of 45°. Addressing the importance of self-regulation, this reversible self-actuated thermo-responsive pore membrane will advance the development of future large-scale smart membranes needed for sustainable indoor climate control.

  2. Single hepatitis-B virus core capsid binding to individual nuclear pore complexes in Hela cells.

    PubMed

    Lill, Yoriko; Lill, Markus A; Fahrenkrog, Birthe; Schwarz-Herion, Kyrill; Paulillo, Sara; Aebi, Ueli; Hecht, Bert

    2006-10-15

    We investigate the interaction of hepatitis B virus capsids lacking a nuclear localization signal with nuclear pore complexes (NPCs) in permeabilized HeLa cells. Confocal and wide-field optical images of the nuclear envelope show well-spaced individual NPCs. Specific interactions of capsids with single NPCs are characterized by extended residence times of capsids in the focal volume which are characterized by fluorescence correlation spectroscopy. In addition, single-capsid-tracking experiments using fast wide-field fluorescence microscopy at 50 frames/s allow us to directly observe specific binding via a dual-color colocalization of capsids and NPCs. We find that binding occurs with high probability on the nuclear-pore ring moiety, at 44 +/- 9 nm radial distance from the central axis.

  3. Virus-sized colloid transport in a single pore: model development and sensitivity analysis.

    PubMed

    Seetha, N; Mohan Kumar, M S; Majid Hassanizadeh, S; Raoof, Amir

    2014-08-01

    A mathematical model is developed to simulate the transport and deposition of virus-sized colloids in a cylindrical pore throat considering various processes such as advection, diffusion, colloid-collector surface interactions and hydrodynamic wall effects. The pore space is divided into three different regions, namely, bulk, diffusion and potential regions, based on the dominant processes acting in each of these regions. In the bulk region, colloid transport is governed by advection and diffusion whereas in the diffusion region, colloid mobility due to diffusion is retarded by hydrodynamic wall effects. Colloid-collector interaction forces dominate the transport in the potential region where colloid deposition occurs. The governing equations are non-dimensionalized and solved numerically. A sensitivity analysis indicates that the virus-sized colloid transport and deposition is significantly affected by various pore-scale parameters such as the surface potentials on colloid and collector, ionic strength of the solution, flow velocity, pore size and colloid size. The adsorbed concentration and hence, the favorability of the surface for adsorption increases with: (i) decreasing magnitude and ratio of surface potentials on colloid and collector, (ii) increasing ionic strength and (iii) increasing pore radius. The adsorbed concentration increases with increasing Pe, reaching a maximum value at Pe=0.1 and then decreases thereafter. Also, the colloid size significantly affects particle deposition with the adsorbed concentration increasing with increasing particle radius, reaching a maximum value at a particle radius of 100nm and then decreasing with increasing radius. System hydrodynamics is found to have a greater effect on larger particles than on smaller ones. The secondary minimum contribution to particle deposition has been found to increase as the favorability of the surface for adsorption decreases. The sensitivity of the model to a given parameter will be high if

  4. Effect of pore pressure on damage accumulation in salt

    SciTech Connect

    PFEIFLE,T.W.; HURTADO,L. DIANE

    2000-06-12

    Laboratory data acquired from two multistage, triaxial compression creep experiments are presented for bedded salt. The experiments were conducted to study the effect of pore pressure changes on the accumulation of damage (dilatant volumetric strain). The first experiment comprised five constant total stress tests in which the internal pore pressure was incremented during successive stages, while the externally applied axial and radial stresses were maintained constant. The second experiment comprised three constant effective stress tests in which the pore pressure and the externally applied axial and radial stresses were increased in equal increments in successive stages. Volumetric strain rates were determined both before and after the pore pressure changes were made in all tests. The data suggest pore pressure changes made during the constant total stress tests have a greater effect on salt dilation than do changes made during the constant effective stress tests.

  5. Optimal conditions for opening of membrane pore by amphiphilic peptides

    NASA Astrophysics Data System (ADS)

    Kabelka, Ivo; Vácha, Robert

    2015-12-01

    Amphiphilic peptides can interact with biological membranes and severely affect their barrier and signaling functions. These peptides, including antimicrobial peptides, can self-assemble into transmembrane pores that cause cell death. Despite their medical importance, the conditions required for pore formation remain elusive. Monte Carlo simulations with coarse-grained models enabled us to calculate the free energies of pore opening under various conditions. In agreement with oriented circular dichroism experiments, a high peptide-to-lipid ratio was found to be necessary for spontaneous pore assembly. The peptide length has a non-monotonic impact on pore formation, and the optimal length matches with the membrane thickness. Furthermore, the hydrophobicity of the peptide ends and the mutual positions of peptides on the membrane play a role.

  6. Open-closed switching of synthetic tubular pores

    NASA Astrophysics Data System (ADS)

    Kim, Yongju; Kang, Jiheong; Shen, Bowen; Wang, Yanqiu; He, Ying; Lee, Myongsoo

    2015-10-01

    While encouraging progress has been made on switchable nanopores to mimic biological channels and pores, it remains a great challenge to realize long tubular pores with a dynamic open-closed motion. Here we report μm-long, dynamic tubular pores that undergo rapid switching between open and closed states in response to a thermal signal in water. The tubular walls consist of laterally associated primary fibrils stacked from disc-shaped molecules in which the discs readily tilt by means of thermally regulated dehydration of the oligoether chains placed on the wall surfaces. Notably, this pore switching mediates a controlled water-pumping catalytic action for the dehydrative cyclization of adenosine monophosphate to produce metabolically active cyclic adenosine monophosphate. We believe that our work may allow the creation of a variety of dynamic pore structures with complex functions arising from open-closed motion.

  7. Open–closed switching of synthetic tubular pores

    PubMed Central

    Kim, Yongju; Kang, Jiheong; Shen, Bowen; Wang, Yanqiu; He, Ying; Lee, Myongsoo

    2015-01-01

    While encouraging progress has been made on switchable nanopores to mimic biological channels and pores, it remains a great challenge to realize long tubular pores with a dynamic open–closed motion. Here we report μm-long, dynamic tubular pores that undergo rapid switching between open and closed states in response to a thermal signal in water. The tubular walls consist of laterally associated primary fibrils stacked from disc-shaped molecules in which the discs readily tilt by means of thermally regulated dehydration of the oligoether chains placed on the wall surfaces. Notably, this pore switching mediates a controlled water-pumping catalytic action for the dehydrative cyclization of adenosine monophosphate to produce metabolically active cyclic adenosine monophosphate. We believe that our work may allow the creation of a variety of dynamic pore structures with complex functions arising from open–closed motion. PMID:26456695

  8. Voltage Dependent Charge Storage Modes and Capacity in Subnanometer Pores

    SciTech Connect

    Qiao, Rui; Meunier, V.; Huang, Jingsong; Wu, Peng; Sumpter, Bobby G

    2012-01-01

    Using molecular dynamics simulations, we show that charge storage in subnanometer pores follows a distinct voltage-dependent behavior. Specifically, at lower voltages, charge storage is achieved by swapping co-ions in the pore with counterions in the bulk electrolyte. As voltage increases, further charge storage is due mainly to the removal of co-ions from the pore, leading to a capacitance increase. The capacitance eventually reaches a maximum when all co-ions are expelled from the pore. At even higher electrode voltages, additional charge storage is realized by counterion insertion into the pore, accompanied by a reduction of capacitance. The molecular mechanisms of these observations are elucidated and provide useful insight for optimizing energy storage based on supercapacitors.

  9. Electroosmotic flow rectification in pyramidal-pore mica membranes.

    PubMed

    Jin, Pu; Mukaibo, Hitomi; Horne, Lloyd P; Bishop, Gregory W; Martin, Charles R

    2010-02-24

    We demonstrate here a new electrokinetic phenomenon, Electroosmotic flow (EOF) rectification, in synthetic membranes containing asymmetric pores. Mica membranes with pyramidally shaped pores prepared by the track-etch method were used. EOF was driven through these membranes by using an electrode in solutions on either side to pass a constant ionic current through the pores. The velocity of EOF depends on the polarity of the current. A high EOF velocity is obtained when the polarity is such that EOF is driven from the larger base opening to the smaller tip opening of the pore. A smaller EOF velocity is obtained when the polarity is reversed such that EOF goes from tip to base. We show that this rectified EOF phenomenon is the result of ion current-rectification observed in such asymmetric-pore membranes.

  10. Electroosmotic Flow Rectification in Pyramidal-Pore Mica Membranes

    SciTech Connect

    Jin, P.; Mukaibo, H.; Horne, L.; Bishop, G.; Martin, C. R.

    2010-02-01

    We demonstrate here a new electrokinetic phenomenon, Electroosmotic flow (EOF) rectification, in synthetic membranes containing asymmetric pores. Mica membranes with pyramidally shaped pores prepared by the track-etch method were used. EOF was driven through these membranes by using an electrode in solutions on either side to pass a constant ionic current through the pores. The velocity of EOF depends on the polarity of the current. A high EOF velocity is obtained when the polarity is such that EOF is driven from the larger base opening to the smaller tip opening of the pore. A smaller EOF velocity is obtained when the polarity is reversed such that EOF goes from tip to base. We show that this rectified EOF phenomenon is the result of ion current-rectification observed in such asymmetric-pore membranes.

  11. Pore architecture of nanoporous gold and titania by hydrogen thermoporometry

    NASA Astrophysics Data System (ADS)

    Johnston, L. T.; Biener, M. M.; Ye, J. C.; Baumann, T. F.; Kucheyev, S. O.

    2015-07-01

    Nanoporous gold (NPG) and materials derived from it by templating have complex pore architecture that determines their technologically relevant physical properties. Here, we apply high-resolution hydrogen thermoporometry to study the pore structure of NPG and NPG-derived titania nanofoam (TNF). Results reveal complex multimodal pore size distributions for NPG and TNF. The freezing-melting hysteresis is pronounced, with freezing and melting scans having entirely different shapes. Experiments involving partial freeze-melt cycles reveal the lack of direct correlation between individual freezing and melting peaks, pointing to phenomena that are beyond the Gibbs-Thomson formalism. The depression of the average freezing temperature scales linearly with the ratio of the internal surface area (measured by gas sorption) and the total pore volume derived from the density of monoliths. Thermoporometry yields total pore volumes in good agreement with those derived from monolith densities for both NPG and TNF.

  12. Influence of Pore Structure on Compressive Strength of Cement Mortar

    PubMed Central

    Zhao, Haitao; Xiao, Qi; Huang, Donghui

    2014-01-01

    This paper describes an experimental investigation into the pore structure of cement mortar using mercury porosimeter. Ordinary Portland cement, manufactured sand, and natural sand were used. The porosity of the manufactured sand mortar is higher than that of natural sand at the same mix proportion; on the contrary, the probable pore size and threshold radius of manufactured sand mortar are finer. Besides, the probable pore size and threshold radius increased with increasing water to cement ratio and sand to cement ratio. In addition, the existing models of pore size distribution of cement-based materials have been reviewed and compared with test results in this paper. Finally, the extended Bhattacharjee model was built to examine the relationship between compressive strength and pore structure. PMID:24757414

  13. Pore size engineering applied to starved electrochemical cells and batteries

    NASA Technical Reports Server (NTRS)

    Abbey, K. M.; Thaller, L. H.

    1982-01-01

    To maximize performance in starved, multiplate cells, the cell design should rely on techniques which widen the volume tolerance characteristics. These involve engineering capillary pressure differences between the components of an electrochemical cell and using these forces to promote redistribution of electrolyte to the desired optimum values. This can be implemented in practice by prescribing pore size distributions for porous back-up plates, reservoirs, and electrodes. In addition, electrolyte volume management can be controlled by incorporating different pore size distributions into the separator. In a nickel/hydrogen cell, the separator must contain pores similar in size to the small pores of both the nickel and hydrogen electrodes in order to maintain an optimum conductive path for the electrolyte. The pore size distributions of all components should overlap in such a way as to prevent drying of the separator and/or flooding of the hydrogen electrode.

  14. Role of pore-forming toxins in neonatal sepsis.

    PubMed

    Sonnen, Andreas F-P; Henneke, Philipp

    2013-01-01

    Protein toxins are important virulence factors contributing to neonatal sepsis. The major pathogens of neonatal sepsis, group B Streptococci, Escherichia coli, Listeria monocytogenes, and Staphylococcus aureus, secrete toxins of different molecular nature, which are key for defining the disease. Amongst these toxins are pore-forming exotoxins that are expressed as soluble monomers prior to engagement of the target cell membrane with subsequent formation of an aqueous membrane pore. Membrane pore formation is not only a means for immediate lysis of the targeted cell but also a general mechanism that contributes to penetration of epithelial barriers and evasion of the immune system, thus creating survival niches for the pathogens. Pore-forming toxins, however, can also contribute to the induction of inflammation and hence to the manifestation of sepsis. Clearly, pore-forming toxins are not the sole factors that drive sepsis progression, but they often act in concert with other bacterial effectors, especially in the initial stages of neonatal sepsis manifestation.

  15. Biophysics, pathophysiology, and pharmacology of ion channel gating pores

    PubMed Central

    Moreau, Adrien; Gosselin-Badaroudine, Pascal; Chahine, Mohamed

    2014-01-01

    Voltage sensor domains (VSDs) are a feature of voltage gated ion channels (VGICs) and voltage sensitive proteins. They are composed of four transmembrane (TM) segments (S1–S4). Currents leaking through VSDs are called omega or gating pore currents. Gating pores are caused by mutations of the highly conserved positively charged amino acids in the S4 segment that disrupt interactions between the S4 segment and the gating charge transfer center (GCTC). The GCTC separates the intracellular and extracellular water crevices. The disruption of S4–GCTC interactions allows these crevices to communicate and create a fast activating and non-inactivating alternative cation-selective permeation pathway of low conductance, or a gating pore. Gating pore currents have recently been shown to cause periodic paralysis phenotypes. There is also increasing evidence that gating pores are linked to several other familial diseases. For example, gating pores in Nav1.5 and Kv7.2 channels may underlie mixed arrhythmias associated with dilated cardiomyopathy (DCM) phenotypes and peripheral nerve hyperexcitability (PNH), respectively. There is little evidence for the existence of gating pore blockers. Moreover, it is known that a number of toxins bind to the VSD of a specific domain of Na+ channels. These toxins may thus modulate gating pore currents. This focus on the VSD motif opens up a new area of research centered on developing molecules to treat a number of cell excitability disorders such as epilepsy, cardiac arrhythmias, and pain. The purpose of the present review is to summarize existing knowledge of the pathophysiology, biophysics, and pharmacology of gating pore currents and to serve as a guide for future studies aimed at improving our understanding of gating pores and their pathophysiological roles. PMID:24772081

  16. An undulation theory for condensation in open end slit pores: critical hysteresis temperature & critical hysteresis pore size.

    PubMed

    Fan, Chunyan; Zeng, Yonghong; Do, D D; Nicholson, D

    2014-06-28

    A new theory of condensation in an open end slit pore, based on the concept of temperature dependent undulation, at the interface separating the adsorbed phase and the gas-like region, is presented. The theory, describes, for the first time, the microscopic origin of the critical hysteresis temperature and the critical hysteresis pore size, properties which are not accessible to any classical theories.

  17. Pore Scale Dynamics of Microemulsion Formation.

    PubMed

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

    2016-07-19

    consequences on the pore scale mixing behavior and resulting microemulsion properties.

  18. Numerical Modelling of the IP-Effect at the Pore Scale

    NASA Astrophysics Data System (ADS)

    Blaschek, R.; Hoerdt, A.

    2008-12-01

    Attempts have been made to estimate hydraulic conductivity using induced polarization (IP). However, until now no correlation has been found that is applicable to more than just a few special cases. Empirical relationships and equivalent circuits often neglect the description of the real processes in the pore space. Two man theories exist to explain the IP-effect. One is based on processes within the electrical double layer (EDL) along the boundary between grain surface and pore fluid. An external voltage leads to a charge buildup caused by the excess of ions that are moving at different speeds along the EDL, and the grain size controls the relaxation time. In another approach the charge buildup is caused by pore spaces of varying thickness where narrow passages act as ion-selective membranes. Here, theory suggests that the length of the pore-throat is controlling the relaxation time. The numerical simulation of the processes is a new promising approach to obtain a deeper understanding of the behaviour of the ions. Our modelling is based on a work of the late 1950s that estimates the maximum frequency effect for a 1D pore space with two alternating media. The equations of motion for the ions are solved in a coupled system with cation concentration, anion concentration and electrical potential as free parameters. We solve the numerical problem with a commercial software based on finite elements. The solution is possible for flexible geometries and materials and allows calculation of full magnitude and phase spectra. This constitutes a considerable extension compared to the original work where only ac- and dc-limits could be estimated. Our results show a significant dependence between ion mobility and relaxation time, as well as between mobility contrast and maximum phase shift, and we are able to derive relationships between relaxation time and length scale. The spectra display behaviour similar to that observed with some laboratory data, with a distinct phase

  19. Pore size and pore throat types in a heterogeneous dolostone reservoir, Devonian Grosmont formation, western Canada sedimentary basin

    SciTech Connect

    Luo, P.; Machel, H. G.

    1995-11-01

    The Devonian Grosmont Formation in northeastern Alberta, Canada, is a giant heavy-oil reservoir. The main reservoir rocks are dolomitized and karstified platform and ramp carbonates, and the best reservoir facies occur in the upper Grosmont (UGM) units 3 and 2. In these units, reservoir properties are highly heterogeneous. Hand specimen, thin section, UV, and SEM petrography, as well as grading scales, mercury capillary pressure curve analysis, and statistics, have been used to characterize reservoir heterogeneity. Our investigation led to a new pore size classification for carbonate reservoirs; this new classification has four pore sizes: microporosity (pore diameters <1 {mu}m), mesoporosity (pore diameters 1-1000 {mu}m), macroporosity (pore diameters 1-256 mm), and megaporosity (pore diameters >256 mm). A combination of microscopic observations and capillary pressure curve characteristics led to the recognition of four pore throat texture types on the microporosity scale, and to five types on the mesoporosity scale. Microporosity pore types include (1) intracrystal dissolution porosity, (2) pervasive intercrystal and intracrystal dissolution porosity, (3) intergranular and/or intercrystal porosity in grainstones, and (4) primary or solution microporosity in mud matrix (only in limestones). Mesoporosity pore types include (1) intercrystal porosity, (2) solution-enhanced intercrystal porosity, (3) oversized porosity, (4) intragranular solution porosity, and (5) intergranular solution porosity. Some of these types are homogeneous (e.g., non-fabric selective dissolution porosity and intercrystal primary porosity), whereas others are heterogeneous. Generally, hydrocarbon recovery efficiency is good in the homogeneous pore throat types, but poor in the heterogeneous types.

  20. Nuclear Pore-Like Structures in a Compartmentalized Bacterium

    PubMed Central

    Sagulenko, Evgeny; Green, Kathryn; Yee, Benjamin; Morgan, Garry; Leis, Andrew; Lee, Kuo-Chang; Butler, Margaret K.; Chia, Nicholas; Pham, Uyen Thi Phuong; Lindgreen, Stinus; Catchpole, Ryan; Poole, Anthony M.; Fuerst, John A.

    2017-01-01

    Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence. PMID:28146565

  1. Clostridial pore-forming toxins: powerful virulence factors.

    PubMed

    Popoff, Michel R

    2014-12-01

    Pore formation is a common mechanism of action for many bacterial toxins. More than one third of clostridial toxins are pore-forming toxins (PFTs) belonging to the β-PFT class. They are secreted as soluble monomers rich in β-strands, which recognize a specific receptor on target cells and assemble in oligomers. Then, they undergo a conformational change leading to the formation of a β-barrel, which inserts into the lipid bilayer forming functional pore. According to their structure, clostridial β-PFTs are divided into several families. Clostridial cholesterol-dependent cytolysins form large pores, which disrupt the plasma membrane integrity. They are potent virulence factors mainly involved in myonecrosis. Clostridial heptameric β-PFTs (aerolysin family and staphylococcal α-hemolysin family) induce small pores which trigger signaling cascades leading to different cell responses according to the cell types and toxins. They are mainly responsible for intestinal diseases, like necrotic enteritis, or systemic diseases/toxic shock from intestinal origin. Clostridial intracellularly active toxins exploit pore formation through the endosomal membrane to translocate the enzymatic component or domain into the cytosol. Single chain protein toxins, like botulinum and tetanus neurotoxins, use hydrophobic α-helices to form pores, whereas clostridial binary toxins encompass binding components, which are structurally and functionally related to β-PFTs, but which have acquired the specific activity to internalize their corresponding enzymatic components. Structural analysis suggests that β-PFTs and binding components share a common evolutionary origin.

  2. Lipid flow through fusion pores connecting membranes of different tensions.

    PubMed

    Chizmadzhev, Y A; Kumenko, D A; Kuzmin, P I; Chernomordik, L V; Zimmerberg, J; Cohen, F S

    1999-06-01

    When two membranes fuse, their components mix; this is usually described as a purely diffusional process. However, if the membranes are under different tensions, the material will spread predominantly by convection. We use standard fluid mechanics to rigorously calculate the steady-state convective flux of lipids. A fusion pore is modeled as a toroid shape, connecting two planar membranes. Each of the membrane monolayers is considered separately as incompressible viscous media with the same shear viscosity, etas. The two monolayers interact by sliding past each other, described by an intermonolayer viscosity, etar. Combining a continuity equation with an equation that balances the work provided by the tension difference, Deltasigma, against the energy dissipated by flow in the viscous membrane, yields expressions for lipid velocity, upsilon, and area of lipid flux, Phi. These expressions for upsilon and Phi depend on Deltasigma, etas, etar, and geometrical aspects of a toroidal pore, but the general features of the theory hold for any fusion pore that has a roughly hourglass shape. These expressions are readily applicable to data from any experiments that monitor movement of lipid dye between fused membranes under different tensions. Lipid velocity increases nonlinearly from a small value for small pore radii, rp, to a saturating value at large rp. As a result of velocity saturation, the flux increases linearly with pore radius for large pores. The calculated lipid flux is in agreement with available experimental data for both large and transient fusion pores.

  3. Lipid flow through fusion pores connecting membranes of different tensions.

    PubMed Central

    Chizmadzhev, Y A; Kumenko, D A; Kuzmin, P I; Chernomordik, L V; Zimmerberg, J; Cohen, F S

    1999-01-01

    When two membranes fuse, their components mix; this is usually described as a purely diffusional process. However, if the membranes are under different tensions, the material will spread predominantly by convection. We use standard fluid mechanics to rigorously calculate the steady-state convective flux of lipids. A fusion pore is modeled as a toroid shape, connecting two planar membranes. Each of the membrane monolayers is considered separately as incompressible viscous media with the same shear viscosity, etas. The two monolayers interact by sliding past each other, described by an intermonolayer viscosity, etar. Combining a continuity equation with an equation that balances the work provided by the tension difference, Deltasigma, against the energy dissipated by flow in the viscous membrane, yields expressions for lipid velocity, upsilon, and area of lipid flux, Phi. These expressions for upsilon and Phi depend on Deltasigma, etas, etar, and geometrical aspects of a toroidal pore, but the general features of the theory hold for any fusion pore that has a roughly hourglass shape. These expressions are readily applicable to data from any experiments that monitor movement of lipid dye between fused membranes under different tensions. Lipid velocity increases nonlinearly from a small value for small pore radii, rp, to a saturating value at large rp. As a result of velocity saturation, the flux increases linearly with pore radius for large pores. The calculated lipid flux is in agreement with available experimental data for both large and transient fusion pores. PMID:10354423

  4. Cation and anion transport through hydrophilic pores in lipid bilayers

    NASA Astrophysics Data System (ADS)

    Kandasamy, Senthil K.; Larson, Ronald G.

    2006-08-01

    To understand the origin of transmembrane potentials, formation of transient pores, and the movement of anions and cations across lipid membranes, we have performed systematic atomistic molecular dynamics simulations of palmitoyl-oleoyl-phosphatidylcholine (POPC) lipids. A double bilayer setup was employed and different transmembrane potentials were generated by varying the anion (Cl-) and cation (Na+) concentrations in the two water compartments. A transmembrane potential of ˜350mV was thereby generated per bilayer for a unit charge imbalance. For transmembrane potential differences of up to ˜1.4V, the bilayers were stable, over the time scale of the simulations (10-50ns). At larger imposed potential differences, one of the two bilayers breaks down through formation of a water pore, leading to both anion and cation translocations through the pore. The anions typically have a short residence time inside the pore, while the cations show a wider range of residence times depending on whether they bind to a lipid molecule or not. Over the time scale of the simulations, we do not observe the discharge of the entire potential difference, nor do we observe pore closing, although we observe that the size of the pore decreases as more ions translocate. We also observed a rare lipid flip-flop, in which a lipid molecule translocated from one bilayer leaflet to the opposite leaflet, assisted by the water pore.

  5. Impedance nanopore biosensor: influence of pore dimensions on biosensing performance.

    PubMed

    Kant, Krishna; Yu, Jingxian; Priest, Craig; Shapter, Joe G; Losic, Dusan

    2014-03-07

    Knowledge about electrochemical and electrical properties of nanopore structures and the influence of pore dimensions on these properties is important for the development of nanopore biosensing devices. The aim of this study was to explore the influence of nanopore dimensions (diameter and length) on biosensing performance using non-faradic electrochemical impedance spectroscopy (EIS). Nanoporous alumina membranes (NPAMs) prepared by self-ordered electrochemical anodization of aluminium were used as model nanopore sensing platforms. NPAMs with different pore diameters (25-65 nm) and lengths (4-18 μm) were prepared and the internal pore surface chemistry was modified by covalently attaching streptavidin and biotin. The performance of this antibody nanopore biosensing platform was evaluated using various concentrations of biotin as a model analyte. EIS measurements of pore resistivity and conductivity were carried out for pores with different diameters and lengths. The results showed that smaller pore dimensions of 25 nm and pore lengths up to 10 μm provide better biosensing performance.

  6. EFFECT OF PORE SIZE ON TRAPPING ZINC VAPORS

    SciTech Connect

    Korinko, P.

    2010-12-17

    A series of experiments were conducted to determine the effect of pore size on pumping efficiency and zinc vapor trapping efficiency. A simple pumping efficiency test was conducted for all five pore diameters where it was observed that evacuation times were adversely affected by reducing the pore size below 5 {micro}m. Common test conditions for the zinc trapping efficiency experiments were used. These conditions resulted in some variability, to ascribe different efficiencies to the filter media. However, the data suggest that there is no significant difference in trapping efficiency for filter media with pores from 0.2 to 20 {micro}m with a thickness of 0.065-inch. Consequently, the 20 {micro}m pore filter media that is currently used at SRS is a suitable filter material for to utilize for future extractions. There is evidence that smaller pore filter will adversely affect the pumping times for the TEF and little evidence to suggest that a smaller pore diameters have significant impact on the trapping efficiency.

  7. Pore geometry as a control on rock strength

    NASA Astrophysics Data System (ADS)

    Bubeck, A.; Walker, R. J.; Healy, D.; Dobbs, M.; Holwell, D. A.

    2017-01-01

    The strength of rocks in the subsurface is critically important across the geosciences, with implications for fluid flow, mineralisation, seismicity, and the deep biosphere. Most studies of porous rock strength consider the scalar quantity of porosity, in which strength shows a broadly inverse relationship with total porosity, but pore shape is not explicitly defined. Here we use a combination of uniaxial compressive strength measurements of isotropic and anisotropic porous lava samples, and numerical modelling to consider the influence of pore shape on rock strength. Micro computed tomography (CT) shows that pores range from sub-spherical to elongate and flat ellipsoids. Samples that contain flat pores are weaker if compression is applied parallel to the short axis (i.e. across the minimum curvature), compared to compression applied parallel to the long axis (i.e. across the maximum curvature). Numerical models for elliptical pores show that compression applied across the minimum curvature results in relatively broad amplification of stress, compared to compression applied across the maximum curvature. Certain pore shapes may be relatively stable and remain open in the upper crust under a given remote stress field, while others are inherently weak. Quantifying the shape, orientations, and statistical distributions of pores is therefore a critical step in strength testing of rocks.

  8. A pore network model for adsorption in porous media

    SciTech Connect

    Satik, Cengiz; Yortsos, Yanis C.

    1995-01-26

    Using a pore network model to represent porous media we investigate adsorption-desorption processes over the entire range of the relative pressure, highlighting in particular capillary condensation. The model incorporates recent advances from density functional theory for adsorption-desorption in narrow pores (of order as low as 1 nm), which improve upon the traditional multi-layer adsorption and Kelvin's equation for phase change and provide for the dependence of the critical pore size on temperature. The limited accessibility of the pore network gives rise to hysteresis in the adsorption-desorption cycle. This is due to the blocking of larger pores, where adsorbed liquid is allowed to but cannot desorb, by smaller pores containing liquid that may not desorb. By allowing for the existence of supercritical liquid in pores in the nm range, it is found that the hysteresis area increases with an increase in temperature, in agreement with experiments of water adsorption-desorption in rock samples from The Geysers. It is also found that the hysteresis increases if the porous medium is represented as a fractured (dual porosity) system. The paper finds applications to general adsorption-desorption problems but it is illustrated here for geothermal applications in The Geysers.

  9. Connecting Wastewater Injection and Seismicity through Pore Pressure

    NASA Astrophysics Data System (ADS)

    Ge, S.; Weingarten, M.; Person, M. A.; Bekins, B. A.

    2014-12-01

    Increased seismicity in recent years in some geologically quiescent regions in the US has been linked to wastewater injection associated with oil and gas production. While seismicity in some cases appears to be well correlated with injection activities, in many other injection locations no seismicity has been reported. How pore pressures generated from injection propagate spatially and evolve temporally is likely a key control in inducing earthquakes, providing a physical linkage between injection activity and seismicity occurrence. Yet, the linkage remains controversial and inconclusive, in spite of the basic physics of pore pressure propagation being well established. This study aims at better understanding the physical processes of pore pressure propagation around injection sites and identifying factors that are most likely contributors to induced seismicity. Numerical modeling suggests that pore pressure increases in the Jones seismicity swarm northeast of Oklahoma City were primarily from several high rate injection wells. Preliminary analysis on injection and seismicity data from Greeley, Colorado also points to a potential pore pressure link between high injection rates and seismicity. Modeling of pore pressures in the Lake County, Ohio, illustrates that permeable faults in the crystalline basement could facilitate pore pressure propagation from injection in the basal aquifer and host earthquakes, which could explain the earthquakes that occurred in the mid-1980s. In many of the above examples, wastewater injection in basal aquifers promoted downward propagation of pore pressures into the crystalline basement. In connecting injection and seismicity through pore pressure propagation, high rate injection wells and permeable basement faults are merging as important players contributing to induced seismicity. It is the intention of this study that findings like these would provide a scientific basis to inform future regulations and policies on wastewater

  10. Role of tentacles and protein loading on pore accessibility and mass transfer in cation exchange materials for proteins.

    PubMed

    Thomas, Helen; Coquebert de Neuville, Bertrand; Storti, Giuseppe; Morbidelli, Massimo; Joehnck, Matthias; Schulte, Michael

    2013-04-12

    In protein chromatography, the size of the protein determines which fraction of pores it can access within a resin and at which rate of diffusion. Moreover, in the presence of grafted polymers like in advanced materials, adsorbed proteins and electrolytes complicate the interaction pore-protein. In this study, we evaluated in a comparative way the behavior of Fractogel EMD SO3 (M) and (S), "tentacle"-type, strong cation exchangers, as well as a reference material without tentacles, all of which are commonly used for protein purification. ISEC experiments were carried out with a set of Dextran tracers of largely different molecular size covering the typical range of protein sizes. Experimental values of porosity (internal and external to the particles) as well as of pore diffusion coefficients have been measured at different NaCl concentrations and under protein loading. These results provide useful insights into the complex interplay among mentioned factors: first, the presence of tentacles induces size exclusion selectivity in the materials; second, the salt induces conformational changes of the tentacles, leading to porosities larger than expected in tentacle materials; third, protein adsorption mainly leads to a reduction of porosity due to pore space occupied by the protein and to a decrease of pore diffusion coefficient.

  11. Driven DNA Transport into an Asymmetric Nanometer-Scale Pore

    NASA Astrophysics Data System (ADS)

    Henrickson, Sarah E.; Misakian, Martin; Robertson, Baldwin; Kasianowicz, John J.

    2000-10-01

    To understand the mechanism by which individual DNA molecules enter nanometer-scale pores, we studied the concentration and voltage dependence of polynucleotide-induced ionic-current blockades of a single α-hemolysin ion channel. We find that the blockade frequency is proportional to the polymer concentration, that it increases exponentially with the applied potential, and that DNA enters the pore more readily through the entrance that has the larger vestibule. We also measure the minimum value of the electrical potential that confines a modified polymer inside the pore against random diffusion and repulsive forces.

  12. 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.

  13. 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.

  14. Crystalline mesoporous zirconia catalysts having stable tetragonal pore wall structure

    DOEpatents

    Sachtler, Wolfgang M. H.; Huang, Yin-Yan

    1998-01-01

    Methods for the preparation of new sulfated mesoporous zirconia materials/catalysts with crystalline pore walls of predominantly tetragonal crystal structure, characterized by nitrogen physisorption measurement, X-ray diffraction, transmission electron microscopy and catalytic tests using n-butane isomerization to iso-butane and alkylation of 1-naphthol with 4-tert-butylstyrene as probe reactions. Sulfate deposition is preferred for the transformation of a mesoporous precursor with amorphous pore walls into a material with crystalline pore walls maintaining the mesoporous characteristics.

  15. Crystalline mesoporous zirconia catalysts having stable tetragonal pore wall structure

    DOEpatents

    Sachtler, W.M.H.; Huang, Y.Y.

    1998-07-28

    Methods are disclosed for the preparation of new sulfated mesoporous zirconia materials/catalysts with crystalline pore walls of predominantly tetragonal crystal structure, characterized by nitrogen physical sorption measurement, X-ray diffraction, transmission electron microscopy and catalytic tests using n-butane isomerization to iso-butane and alkylation of 1-naphthol with 4-tert-butylstyrene as probe reactions. Sulfate deposition is preferred for the transformation of a mesoporous precursor with amorphous pore walls into a material with crystalline pore walls maintaining the mesoporous characteristics. 17 figs.

  16. Simple model of capillary condensation in cylindrical pores.

    PubMed

    Szybisz, Leszek; Urrutia, Ignacio

    2002-11-01

    A simple model based on an approximation of the dropletlike model is formulated for studying adsorption of fluids into cylindrical pores. This model yields a nearly universal description of capillary condensation transitions for noble gases confined by alkali metals. The system's thermodynamical behavior is predicted from the values of two dimensionless parameters: D* (the reduced asymptotic strength of the fluid-adsorber interaction, a function of temperature) and R* (the reduced radius of the pore). The phenomenon of hysteresis inherently related to capillary condensation is discussed. The connection to a previously proposed universality for cylindrical pores is also established.

  17. Simple model of capillary condensation in cylindrical pores

    NASA Astrophysics Data System (ADS)

    Szybisz, Leszek; Urrutia, Ignacio

    2002-11-01

    A simple model based on an approximation of the dropletlike model is formulated for studying adsorption of fluids into cylindrical pores. This model yields a nearly universal description of capillary condensation transitions for noble gases confined by alkali metals. The system's thermodynamical behavior is predicted from the values of two dimensionless parameters: D* (the reduced asymptotic strength of the fluid-adsorber interaction, a function of temperature) and R* (the reduced radius of the pore). The phenomenon of hysteresis inherently related to capillary condensation is discussed. The connection to a previously proposed universality for cylindrical pores is also established.

  18. Structure, dynamics and function of nuclear pore complexes

    PubMed Central

    D’Angelo, M. A.; Hetzer, M. W.

    2009-01-01

    Nuclear pore complexes are large aqueous channels that penetrate the nuclear envelope, connecting the nuclear interior with the cytoplasm. Until recently, these macromolecular complexes were viewed as static structures whose only function was to control the molecular trafficking between the two compartments. It has now become evident that this simplistic scenario is inaccurate and that nuclear pore complexes are highly dynamic multiprotein assemblies involved in diverse cellular processes ranging from the organization of the cytoskeleton to gene expression. In this review, we will discuss the most recent developments in the nuclear pore complex field, focusing in the assembly, disassembly, maintenance and function of this macromolecular structure. PMID:18786826

  19. Observations of the Dynamic Connectivity of the Non-Wetting Phase During Steady State Flow at the Pore Scale Using 3D X-ray Microtomography

    NASA Astrophysics Data System (ADS)

    Reynolds, C. A.; Menke, H. P.; Blunt, M. J.; Krevor, S. C.

    2015-12-01

    We observe a new type of non-wetting phase flow using time-resolved pore scale imaging. The traditional conceptual model of drainage involves a non-wetting phase invading a porous medium saturated with a wetting phase as either a fixed, connected flow path through the centres of pores or as discrete ganglia which move individually through the pore space, depending on the capillary number. We observe a new type of flow behaviour at low capillary number in which the flow of the non-wetting phase occurs through networks of persistent ganglia that occupy the large pores but continuously rearrange their connectivity (Figure 1). Disconnections and reconnections occur randomly to provide short-lived pseudo-steady state flow paths between pores. This process is distinctly different to the notion of flowing ganglia which coalesce and break-up. The size distribution of ganglia is dependent on capillary number. Experiments were performed by co-injecting N2and 25 wt% KI brine into a Bentheimer sandstone core (4mm diameter, 35mm length) at 50°C and 10 MPa. Drainage was performed at three flow rates (0.04, 0.3 and 1 ml/min) at a constant fractional flow of 0.5 and the variation in ganglia populations and connectivity observed. We obtained images of the pore space during steady state flow with a time resolution of 43 s over 1-2 hours. Experiments were performed at the Diamond Light Source synchrotron. Figure 1. The position of N2 in the pore space during steady state flow is summed over 40 time steps. White indicates that N2 occupies the space over >38 time steps and red <5 time steps.

  20. Effect of sub-pore scale morphology of biological deposits on porous media flow properties

    NASA Astrophysics Data System (ADS)

    Ghezzehei, T. A.

    2012-12-01

    Biological deposits often influence fluid flow by altering the pore space morphology and related hydrologic properties such as porosity, water retention characteristics, and permeability. In most coupled-processes models changes in porosity are inferred from biological process models using mass-balance. The corresponding evolution of permeability is estimated using (semi-) empirical porosity-permeability functions such as the Kozeny-Carman equation or power-law functions. These equations typically do not account for the heterogeneous spatial distribution and morphological irregularities of the deposits. As a result, predictions of permeability evolution are generally unsatisfactory. In this presentation, we demonstrate the significance of pore-scale deposit distribution on porosity-permeability relations using high resolution simulations of fluid flow through a single pore interspersed with deposits of varying morphologies. Based on these simulations, we present a modification to the Kozeny-Carman model that accounts for the shape of the deposits. Limited comparison with published experimental data suggests the plausibility of the proposed conceptual model.

  1. Nanometer-scale imaging and pore-scale fluid flow modeling inchalk

    SciTech Connect

    Tomutsa, Liviu; Silin, Dmitriy; Radmilovich, Velimir

    2005-08-23

    For many rocks of high economic interest such as chalk,diatomite, tight gas sands or coal, nanometer scale resolution is neededto resolve the 3D-pore structure, which controls the flow and trapping offluids in the rocks. Such resolutions cannot be achieved with existingtomographic technologies. A new 3D imaging method, based on serialsectioning and using the Focused Ion Beam (FIB) technology has beendeveloped. FIB allows for the milling of layers as thin as 10 nanometersby using accelerated Ga+ ions to sputter atoms from the sample surface.After each milling step, as a new surface is exposed, a 2D image of thissurface is generated. Next, the 2D images are stacked to reconstruct the3D pore or grain structure. Resolutions as high as 10 nm are achievableusing this technique. A new image processing method uses directmorphological analysis of the pore space to characterize thepetrophysical properties of diverse formations. In addition to estimationof the petrophysical properties (porosity, permeability, relativepermeability and capillary pressures), the method is used for simulationof fluid displacement processes, such as those encountered in variousimproved oil recovery (IOR) approaches. Computed with the new methodcapillary pressure curves are in good agreement with laboratory data. Themethod has also been applied for visualization of the fluid distributionat various saturations from the new FIB data.

  2. High resolution masks for ion milling pores through substrates of biological interest

    NASA Technical Reports Server (NTRS)

    Donovan, S. S.

    1978-01-01

    The feasibility was investigated of electrochemically oxidizing vapor deposited aluminum coatings to produce porous aluminum oxide coatings with submicron pore diameters and with straight channels normal to the substrate surface. Porous aluminum oxide coatings were produced from vapor deposited aluminum coatings on thin stainless steel (304), copper, Teflon (FEP) and Kapton substrates and also on pure aluminum substrates. Scanning electron microscope examination indicated that porous oxide coatings can be produced with straight channels, appropriate pore diameters and none or minimal intervening residual aluminum. The oxide coatings on the copper and Kapton substrates had the straightest channels and in general were superior to those fabricated on the other substrate materials. For oxide coatings fabricated at 600 V and 300 V, pore diameters were 0.4-0.6, and 0.3 micron with center-to-center spacing of 0.7-0.8, and 0.4 micron, respectively. Estimated direct labor and materials costs to prepare an oxide mask is anticipated to be about $4-$6 per square foot.

  3. Pore Water Extraction Test Near 241-SX Tank Farm at the Hanford Site, Washington, USA

    SciTech Connect

    Eberlein, Susan J.; Parker, Danny L.; Tabor, Cynthia L.; Holm, Melissa J.

    2013-11-11

    A proof-of-principle test is underway near the Hanford Site 241-SX Tank Farm. The test will evaluate a potential remediation technology that will use tank farm-deployable equipment to remove contaminated pore water from vadose zone soils. The test system was designed and built to address the constraints of working within a tank farm. Due to radioactive soil contamination and limitations in drilling near tanks, small-diameter direct push drilling techniques applicable to tank farms are being utilized for well placement. To address space and weight limitations in working around tanks and obstacles within tank farms, the above ground portions of the test system have been constructed to allow deployment flexibility. The test system utilizes low vacuum over a sealed well screen to establish flow into an extraction well. Extracted pore water is collected in a well sump,and then pumped to the surface using a small-diameter bladder pump.If pore water extraction using this system can be successfully demonstrated, it may be possible to target local contamination in the vadose zone around underground storage tanks. It is anticipated that the results of this proof-of-principle test will support future decision making regarding interim and final actions for soil contamination within the tank farms.

  4. Discontinuous pore fluid distribution under microgravity--KC-135 flight investigations

    NASA Technical Reports Server (NTRS)

    Reddi, Lakshmi N.; Xiao, Ming; Steinberg, Susan L.

    2005-01-01

    Designing a reliable plant growth system for crop production in space requires the understanding of pore fluid distribution in porous media under microgravity. The objective of this experimental investigation, which was conducted aboard NASA KC-135 reduced gravity flight, is to study possible particle separation and the distribution of discontinuous wetting fluid in porous media under microgravity. KC-135 aircraft provided gravity conditions of 1, 1.8, and 10(-2) g. Glass beads of a known size distribution were used as porous media; and Hexadecane, a petroleum compound immiscible with and lighter than water, was used as wetting fluid at residual saturation. Nitrogen freezer was used to solidify the discontinuous Hexadecane ganglia in glass beads to preserve the ganglia size changes during different gravity conditions, so that the blob-size distributions (BSDs) could be measured after flight. It was concluded from this study that microgravity has little effect on the size distribution of pore fluid blobs corresponding to residual saturation of wetting fluids in porous media. The blobs showed no noticeable breakup or coalescence during microgravity. However, based on the increase in bulk volume of samples due to particle separation under microgravity, groups of particles, within which pore fluid blobs were encapsulated, appeared to have rearranged themselves under microgravity.

  5. Characterization of the intragranular water regime within subsurface sediments: pore volume, surface area, and mass transfer limitations

    USGS Publications Warehouse

    Hay, Michael B.; Stoliker, Deborah L.; Davis, James A.; Zachara, John M.

    2011-01-01

    Although "intragranular" pore space within grain aggregates, grain fractures, and mineral surface coatings may contain a relatively small fraction of the total porosity within a porous medium, it often contains a significant fraction of the reactive surface area, and can thus strongly affect the transport of sorbing solutes. In this work, we demonstrate a batch experiment procedure using tritiated water as a high-resolution diffusive tracer to characterize the intragranular pore space. The method was tested using uranium-contaminated sediments from the vadose and capillary fringe zones beneath the former 300A process ponds at the Hanford site (Washington). Sediments were contacted with tracers in artificial groundwater, followed by a replacement of bulk solution with tracer-free groundwater and the monitoring of tracer release. From these data, intragranular pore volumes were calculated and mass transfer rates were quantified using a multirate first-order mass transfer model. Tritium-hydrogen exchange on surface hydroxyls was accounted for by conducting additional tracer experiments on sediment that was vacuum dried after reaction. The complementary ("wet" and "dry") techniques allowed for the simultaneous determination of intragranular porosity and surface area using tritium. The Hanford 300A samples exhibited intragranular pore volumes of ~1% of the solid volume and intragranular surface areas of ~20%–35% of the total surface area. Analogous experiments using bromide ion as a tracer yielded very different results, suggesting very little penetration of bromide into the intragranular porosity.

  6. Characterization of the intragranular water regime within subsurface sediments: Pore volume, surface area, and mass transfer limitations

    USGS Publications Warehouse

    Hay, M.B.; Stoliker, D.L.; Davis, J.A.; Zachara, J.M.

    2011-01-01

    Although "intragranular" pore space within grain aggregates, grain fractures, and mineral surface coatings may contain a relatively small fraction of the total porosity within a porous medium, it often contains a significant fraction of the reactive surface area, and can thus strongly affect the transport of sorbing solutes. In this work, we demonstrate a batch experiment procedure using tritiated water as a high-resolution diffusive tracer to characterize the intragranular pore space. The method was tested using uranium-contaminated sediments from the vadose and capillary fringe zones beneath the former 300A process ponds at the Hanford site (Washington). Sediments were contacted with tracers in artificial groundwater, followed by a replacement of bulk solution with tracer-free groundwater and the monitoring of tracer release. From these data, intragranular pore volumes were calculated and mass transfer rates were quantified using a multirate first-order mass transfer model. Tritium-hydrogen exchange on surface hydroxyls was accounted for by conducting additional tracer experiments on sediment that was vacuum dried after reaction. The complementary ("wet" and "dry") techniques allowed for the simultaneous determination of intragranular porosity and surface area using tritium. The Hanford 300A samples exhibited intragranular pore volumes of ???1% of the solid volume and intragranular surface areas of ???20%-35% of the total surface area. Analogous experiments using bromide ion as a tracer yielded very different results, suggesting very little penetration of bromide into the intragranular porosity. Copyright 2011 by the American Geophysical Union.

  7. Hydrochromic conjugated polymers for human sweat pore mapping

    NASA Astrophysics Data System (ADS)

    Lee, Joosub; Pyo, Minkyeong; Lee, Sang-Hwa; Kim, Jaeyong; Ra, Moonsoo; Kim, Whoi-Yul; Park, Bum Jun; Lee, Chan Woo; Kim, Jong-Man

    2014-04-01

    Hydrochromic materials have been actively investigated in the context of humidity sensing and measuring water contents in organic solvents. Here we report a sensor system that undergoes a brilliant blue-to-red colour transition as well as ‘Turn-On’ fluorescence upon exposure to water. Introduction of a hygroscopic element into a supramolecularly assembled polydiacetylene results in a hydrochromic conjugated polymer that is rapidly responsive (<20 μs), spin-coatable and inkjet-compatible. Importantly, the hydrochromic sensor is found to be suitable for mapping human sweat pores. The exceedingly small quantities (sub-nanolitre) of water secreted from sweat pores are sufficient to promote an instantaneous colorimetric transition of the polymer. As a result, the sensor can be used to construct a precise map of active sweat pores on fingertips. The sensor technology, developed in this study, has the potential of serving as new method for fingerprint analysis and for the clinical diagnosis of malfunctioning sweat pores.

  8. 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.

  9. Applications of biological pores in nanomedicine, sensing, and nanoelectronics

    PubMed Central

    Majd, Sheereen; Yusko, Erik C; Billeh, Yazan N; Macrae, Michael X; Yang, Jerry; Mayer, Michael

    2011-01-01

    Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated – often regulated – functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics. PMID:20561776

  10. Nitrocellulose Templated Hierarchical Pore Structure in Mesoporous Thin Films

    SciTech Connect

    Li, Xiaohong S.; Fryxell, Glen E.; Wang, Chong M.; Young, James S.

    2006-01-01

    Over the last decade, a great deal of effort has been expended on the templated synthesis of nanoporous materials. Many different templates have been used to create this nanostructure (surfactants, polymers, latex spheres, etc.), but by far the most widely used has been micelles composed of surfactants. This is a versatile, and highly useful, synthetic method, capable of producing a wide variety of materials and structures. More recently, the synthesis of hierarchical pore structures (i.e. small pores leading to large pores) has been of great interest as a means of enhancing mass transport within these materials.[1] Such hierarchical pore structures have been made by combining surfactant templating methods with latex beads [2], by assembling as-synthesized MCM-41 particles around block co-polymer micelles, followed by crosslinking and calcination [3], by spray drying MCM-41 and MCM-48 agglomerates [4], and by using ''evaporation induced self-assembly'' [5-9].

  11. Role of the synaptobrevin C terminus in fusion pore formation

    PubMed Central

    Ngatchou, Annita N.; Kisler, Kassandra; Fang, Qinghua; Walter, Alexander M.; Zhao, Ying; Bruns, Dieter; Sørensen, Jakob B.; Lindau, Manfred

    2010-01-01

    Neurotransmitter release is mediated by the SNARE proteins synaptobrevin II (sybII, also known as VAMP2), syntaxin, and SNAP-25, generating a force transfer to the membranes and inducing fusion pore formation. However, the molecular mechanism by which this force leads to opening of a fusion pore remains elusive. Here we show that the ability of sybII to support exocytosis is inhibited by addition of one or two residues to the sybII C terminus depending on their energy of transfer from water to the membrane interface, following a Boltzmann distribution. These results suggest that following stimulation, the SNARE complex pulls the C terminus of sybII deeper into the vesicle membrane. We propose that this movement disrupts the vesicular membrane continuity leading to fusion pore formation. In contrast to current models, the experiments suggest that fusion pore formation begins with molecular rearrangements at the intravesicular membrane leaflet and not between the apposed cytoplasmic leaflets. PMID:20937897

  12. Hydrochromic conjugated polymers for human sweat pore mapping.

    PubMed

    Lee, Joosub; Pyo, Minkyeong; Lee, Sang-hwa; Kim, Jaeyong; Ra, Moonsoo; Kim, Whoi-Yul; Park, Bum Jun; Lee, Chan Woo; Kim, Jong-Man

    2014-04-29

    Hydrochromic materials have been actively investigated in the context of humidity sensing and measuring water contents in organic solvents. Here we report a sensor system that undergoes a brilliant blue-to-red colour transition as well as 'Turn-On' fluorescence upon exposure to water. Introduction of a hygroscopic element into a supramolecularly assembled polydiacetylene results in a hydrochromic conjugated polymer that is rapidly responsive (<20 μs), spin-coatable and inkjet-compatible. Importantly, the hydrochromic sensor is found to be suitable for mapping human sweat pores. The exceedingly small quantities (sub-nanolitre) of water secreted from sweat pores are sufficient to promote an instantaneous colorimetric transition of the polymer. As a result, the sensor can be used to construct a precise map of active sweat pores on fingertips. The sensor technology, developed in this study, has the potential of serving as new method for fingerprint analysis and for the clinical diagnosis of malfunctioning sweat pores.

  13. Exocytotic fusion pores are composed of both lipids and proteins

    PubMed Central

    Bao, Huan; Goldschen-Ohm, Marcel; Jeggle, Pia; Chanda, Baron; Edwardson, J Michael; Chapman, Edwin R

    2016-01-01

    During exocytosis, fusion pores form the first aqueous connection that allows escape of neurotransmitters and hormones from secretory vesicles. Although it is well established that SNARE proteins catalyze fusion, the structure and composition of fusion pores remain unknown. Here, we exploited the rigid framework and defined size of nanodiscs to interrogate the properties of reconstituted fusion pores, using the neurotransmitter glutamate as a content-mixing marker. Efficient Ca2+-stimulated bilayer fusion, and glutamate release, occurred with approximately two molecules of mouse synaptobrevin 2 reconstituted into ~6-nm nanodiscs. The transmembrane domains of SNARE proteins assumed distinct roles in lipid mixing versus content release and were exposed to polar solvent during fusion. Additionally, tryptophan substitutions at specific positions in these transmembrane domains decreased glutamate flux. Together, these findings indicate that the fusion pore is a hybrid structure composed of both lipids and proteins. PMID:26656855

  14. Molecular biology and biophysical properties of ion channel gating pores.

    PubMed

    Moreau, Adrien; Gosselin-Badaroudine, Pascal; Chahine, Mohamed

    2014-11-01

    The voltage sensitive domain (VSD) is a pivotal structure of voltage-gated ion channels (VGICs) and plays an essential role in the generation of electrochemical signals by neurons, striated muscle cells, and endocrine cells. The VSD is not unique to VGICs. Recent studies have shown that a VSD regulates a phosphatase. Similarly, Hv1, a voltage-sensitive protein that lacks an apparent pore domain, is a self-contained voltage sensor that operates as an H⁺ channel. VSDs are formed by four transmembrane helices (S1-S4). The S4 helix is positively charged due to the presence of arginine and lysine residues. It is surrounded by two water crevices that extend into the membrane from both the extracellular and intracellular milieus. A hydrophobic septum disrupts communication between these water crevices thus preventing the permeation of ions. The septum is maintained by interactions between the charged residues of the S4 segment and the gating charge transfer center. Mutating the charged residue of the S4 segment allows the water crevices to communicate and generate gating pore or omega pore. Gating pore currents have been reported to underlie several neuronal and striated muscle channelopathies. Depending on which charged residue on the S4 segment is mutated, gating pores are permeant either at depolarized or hyperpolarized voltages. Gating pores are cation selective and seem to converge toward Eisenmann's first or second selectivity sequences. Most gating pores are blocked by guanidine derivatives as well as trivalent and quadrivalent cations. Gating pores can be used to study the movement of the voltage sensor and could serve as targets for novel small therapeutic molecules.

  15. Using pore-scale imaging and modeling to provide new insights in multi-phase flow, transport and reaction phenomena in porous media (Invited)

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    Advances in X ray imaging techniques made it possible not only to accurately describe solid and fluid(s) distributions in the pore space but also to study dynamics of multi-phase flow and reactive transport in-situ. This has opened up a range of new opportunities to better understand fundamental physics at the pore scale by experiment, and test and validate theoretical models in order to develop predictive tools at the pore scale and use it for upscaling. Firstly, we illustrate this concept by describing a new methodology for predicting non-Fickian transport in millimeter-sized three-dimensional micro-CT images of a beadpack, a sandstone, and a carbonate, representing porous media with an increasing degree of pore-scale complexity. The key strategy is to retain the full information on flow and transport signature of a porous medium by using probability distribution functions (PDFs) of voxel velocities for flow, and both PDFs of particle displacements and PDFs of particle transit times between voxels for transport. For this purpose, direct-simulation flow and transport model is used to analyse the relationship between pore structure, velocity, and the dynamics of the evolving plume. The model predictions for PDFs of particle displacements obtained by the model are in excellent agreement with those measured on similar cores in nuclear magnetic resonance experiments. A key determinant for non-Fickian transport is the spread in velocity distribution in the pore space. Further, we present micro-CT imaging of capillary trapping of scCO2 at reservoir conditions in a range of carbonates and sandstones having different pore structure and demonstrate that substantial quantities of scCO2 can be trapped in the pore space. Higher residual scCO2 saturations are found in sandstones compared to carbonates. The trapped ganglia exhibit different distribution of size, related to the inherent structure of pore space. Pore structures with large, open pores that are well connected lead

  16. Critical behaviour of the Ising ferromagnet confined in quasi-cylindrical pores: a Monte Carlo study.

    PubMed

    Guisandez, Leandro E; Zarragoicoechea, Guillermo J; Albano, Ezequiel V

    2013-10-21

    The critical behaviour of the Ising ferromagnet confined in pores of radius R and length L is studied by means of Monte Carlo computer simulations. Quasi-cylindrical pores are obtained by replicating n-times a triangular lattice disc of radius R, where L = na and a is the spacing between consecutive replications. So, spins placed at the surface of the pores have less nearest-neighbours (NN) as compared to 8 NN for spins in the bulk. These "missing neighbour" effects undergone by surface spins cause a strong suppression of surface ordering, leading to an ordinary surface transition. Also, the effect propagates into the bulk for small tubes (R ≤ 12) and the effective critical temperature of the pores is shifted towards lower values than in the bulk case. By applying the standard finite-size scaling theory, subsequently supported by numerical data, we concluded that data collapse of relevant observables, e.g., magnetization (m), susceptibility, specific heat, etc., can only be observed by comparing simulation results obtained by keeping the aspect ratio C ≡ R∕L constant. Also, by extrapolating "effective" R-dependent critical temperatures to the thermodynamic limit (R → ∞, C fixed), we obtained T(C)(∞) = 6.208(4). As suggested by finite-size scaling arguments, the magnetization is measured at the critical point scales according to [|m|]Tc R(β/ν) is proportional to [R/L](1/2), where β and ν are the standard exponents for the order parameter and the correlation length, respectively. Furthermore, it is shown that close to criticality the axial correlation length decreases exponentially with the distance. That result is the signature of the formation of (randomly distributed) alternating domains of different magnetization, which can be directly observed by means of snapshot configurations, whose typical length (ξ) is given by the characteristic length of the exponential decay of correlations. Moreover, we show that at criticality ξ = 0.43(2)R.

  17. Distributed pore model for bio-molecule chromatography.

    PubMed

    Coquebert de Neuville, Bertrand; Tarafder, Abhijit; Morbidelli, Massimo

    2013-07-12

    One of the main peculiarities in protein chromatography is that the adsorbing proteins and the adsorbent pores have comparable sizes. This has the consequence that the pore accessibility depends not only on the solute size but also on the loading conditions of the adsorbent because protein adsorption significantly reduces the size of the pores. A model that accounts for the pore size distribution of the stationary phase and for the pore shrinkage due to protein adsorption has been developed to describe mass transport and adsorption in the porous particles. This model has been shown to be equivalent to the general rate model (GRM) in the case of processes under highly diluted conditions with little adsorption. This implies that the model parameters determination follows the same procedure as for the classical GRM. The new pore model has been applied and compared to the GRM for the simulation of lysozyme breakthrough experiments and for the prediction of 5% dynamic binding capacity values solely based on static capacity measurements.

  18. Melting transition of Lennard-Jones fluid in cylindrical pores.

    PubMed

    Das, Chandan K; Singh, Jayant K

    2014-05-28

    Three-stage pseudo-supercritical transformation path and multiple-histogram reweighting technique are employed for the determination of solid-liquid coexistence of the Lennard-Jones (12-6) fluid, in a structureless cylindrical pore of radius, R, ranging from 4 to 20 molecular diameters. The Gibbs free energy difference is evaluated using thermodynamic integration method by connecting solid and liquid phases under confinement via one or more intermediate states without any first order phase transition among them. The thermodynamic melting temperature, Tm, is found to oscillate for pore size, R < 8, which is in agreement with the behavior observed for the melting temperature in slit pores. However, Tm for almost all pore sizes is less than the bulk case, which is contrary to the behavior seen for the slit pore. The oscillation in Tm decays at around pore radius R = 8, and beyond that shift in the melting temperature with respect to the bulk case is in line with the prediction of the Gibbs-Thomson equation.

  19. Melting transition of Lennard-Jones fluid in cylindrical pores

    SciTech Connect

    Das, Chandan K.; Singh, Jayant K.

    2014-05-28

    Three-stage pseudo-supercritical transformation path and multiple-histogram reweighting technique are employed for the determination of solid-liquid coexistence of the Lennard-Jones (12-6) fluid, in a structureless cylindrical pore of radius, R, ranging from 4 to 20 molecular diameters. The Gibbs free energy difference is evaluated using thermodynamic integration method by connecting solid and liquid phases under confinement via one or more intermediate states without any first order phase transition among them. The thermodynamic melting temperature, T{sub m}, is found to oscillate for pore size, R < 8, which is in agreement with the behavior observed for the melting temperature in slit pores. However, T{sub m} for almost all pore sizes is less than the bulk case, which is contrary to the behavior seen for the slit pore. The oscillation in T{sub m} decays at around pore radius R = 8, and beyond that shift in the melting temperature with respect to the bulk case is in line with the prediction of the Gibbs-Thomson equation.

  20. 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.

  1. Anisotropic dynamics of dipolar liquids in narrow slit pores.

    PubMed

    Froltsov, Vladimir A; Klapp, Sabine H L

    2006-04-07

    We report molecular dynamics simulation results for Stockmayer fluids confined to narrow slitlike pores with structureless, nonconducting walls. The translational and rotational dynamics of the dipolar particles have been investigated by calculating autocorrelation functions, diffusion coefficients, and relaxation times for various pore widths (five or less particle diameters) and directions parallel and perpendicular to the walls. The dynamic properties of the confined systems are compared to bulk properties, where corresponding bulk and pore states at the same temperature and chemical potential are determined in parallel grand canonical Monte Carlo simulations. We find that the dynamic behavior inside the pore depends on the distance from the walls and can be strongly anisotropic even in globally isotropic systems. This concerns especially the particles in the surface layers close to the walls, where the single particle and collective dipolar relaxation resemble that of true two-dimensional dipolar fluids with different in-plane and out-of-plane relaxations. On the other hand, bulklike relaxation is observed in the pore center of sufficiently wide pores.

  2. Pore scale definition and computation from tomography data

    NASA Astrophysics Data System (ADS)

    Dupuy, P. M.; Austin, P.; Delaney, G. W.; Schwarz, M. P.

    2011-10-01

    During recent years characterisation capabilities of porous media have been transformed by advances in computation and visualisation technologies. It is now possible to obtain detailed topological and hydrodynamic information of porous media by combining tomographic and computational fluid dynamic studies. Despite the existence of these new capabilities, the characterisation process itself is based on the same antiquated experimental macroscopic concepts. We are interested in an up-scaling process where we can keep key information for every pore size present in the media in order to feed multi-scale transport models. Hydrometallurgical, environmental, food, pharmaceutical and chemical engineering are industries with process outcomes based on homogeneous and heterogeneous reactions and therefore sensitive to the reaction and transport processes happening at different pore scales. The present work addresses a key step in the information up-scaling process, i.e. a pore identification algorithm similar to alternating sequential filters. In a preliminary study, topological and hydrodynamic variables are correlated with the pore size. Micrometre and millimetre resolution tomographies are used to characterise the pore size distribution of a packed column and different rocks. Finally, we compute the inter-pore-scale redistribution function which is a measure of the heterogeneity of the media and magnitude needed in multi-scale modelling.

  3. Tailoring the pore size of hypercrosslinked polymer foams

    SciTech Connect

    Steckle, W.P. Jr.; Mitchell, M.A.; Apen, P.G.

    1996-12-31

    Organic analogues to inorganic zeolites would be a significant step forward in engineered porous materials and would provide advantages in range, selectivity, tailorability and processing. Rigid molecular foams or organic zeolites would not be crystalline materials and could be tailored over a broader range of pore sizes and volumes. A novel process for preparing hypercrosslinked polymeric foams has been developed via a Friedel-Crafts polycondensation reaction. A series of rigid hypercrosslinked foams have been prepared using simple rigid polyaromatic hydrocarbons including benzene, biphenyl, m-terphenyl, diphenylmethane, and polystyrene, with p-dichloroxylene (DCX) or divinylbenzene (DVB) as the crosslinking agent. Transparent gels are formed suggesting a very small pore size. After drying the foams are robust and rigid. Densities of the resulting foams can range from 0.15 g/cc to 0.75 g/cc. Nitrogen adsorption studies have shown that by judiciously selecting monomers and crosslinking agent along with the level of crosslinking and the cure time of the resulting gel, the pore size, pore size distribution, and the total surface area of the foam can be tailored. Surface areas range from 160 to 1,200 m{sup 2}/g with pore sizes ranging from 6{angstrom} to 2,000{angstrom}. Further evidence of the uniformity of the foams and their pore sizes has been confirmed by high resolution TEM.

  4. Atomic structure of anthrax protective antigen pore elucidates toxin translocation.

    PubMed

    Jiang, Jiansen; Pentelute, Bradley L; Collier, R John; Zhou, Z Hong

    2015-05-28

    Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (Φ)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed.

  5. Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases.

    PubMed

    Niether, Doreen; Afanasenkau, Dzmitry; Dhont, Jan K G; Wiegand, Simone

    2016-04-19

    Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007)Proc Natl Acad Sci USA104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of[Formula: see text]wt % that is typical for concentrations in shallow lakes on early Earth.

  6. Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases

    PubMed Central

    Niether, Doreen; Afanasenkau, Dzmitry; Dhont, Jan K. G.

    2016-01-01

    Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007) Proc Natl Acad Sci USA 104(22):9346−9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45–90 d, starting with an initial formamide weight fraction of 10−3 wt % that is typical for concentrations in shallow lakes on early Earth. PMID:27044100

  7. Mangrove pore water exchange across a latitudinal gradient

    NASA Astrophysics Data System (ADS)

    Tait, Douglas R.; Maher, Damien T.; Macklin, Paul A.; Santos, Isaac R.

    2016-04-01

    We combined observations of the natural tracer radon (222Rn) with hydrodynamic models across a broad latitudinal gradient covering several climate zones to estimate pore water exchange rates in mangroves. Pore water exchange ranged from 2.1 to 35.5 cm d-1 from temperate to tropical regions and averaged 16.3 ± 5.1 cm d-1. If upscaled to the global weighted mangrove area, pore water exchange in mangroves would recirculate the entire volume of water overlying the continental shelf in less than 153 years. Although pore water exchange (recirculated seawater) and river discharge represent different pathways for water entering the coastal ocean, the estimated global mangrove pore water exchange would be equal to approximately one third of annual global river discharge to the ocean (3.84 × 1013 m3 yr-1). Because biogeochemical processes in mangroves are largely dependent on pore water exchange, these large exchange rates have major implications for coastal nutrient, carbon, and greenhouse gas cycling in tropical marine systems.

  8. Multiscale pore-network representation of heterogeneous carbonate rocks

    NASA Astrophysics Data System (ADS)

    Pak, Tannaz; Butler, Ian B.; Geiger, Sebastian; van Dijke, Marinus I. J.; Jiang, Zeyun; Surmas, Rodrigo

    2016-07-01

    A multiscale network integration approach introduced by Jiang et al. (2013) is used to generate a representative pore-network for a carbonate rock with a pore size distribution across several orders of magnitude. We predict the macroscopic flow parameters of the rock utilising (i) 3-D images captured by X-ray computed microtomography and (ii) pore-network flow simulations. To capture the multiscale pore size distribution of the rock, we imaged four different rock samples at different resolutions and integrated the data to produce a pore-network model that combines information at several length-scales that cannot be recovered from a single tomographic image. A workflow for selection of the number and length-scale of the required input networks for the network integration process, as well as fine tuning the model parameters is presented. Mercury injection capillary-pressure data were used to evaluate independently the multiscale networks. We explore single-scale, two-scale, and three-scale network models and discuss their representativeness by comparing simulated capillary-pressure versus saturation curves with laboratory measurements. We demonstrate that for carbonate rocks with wide pore size distributions, it may be required to integrate networks extracted from two or three discrete tomographic data sets in order to simulate macroscopic flow parameters.

  9. 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

  10. Accurate relations between pore size and the pressure of capillary condensation and the evaporation of nitrogen in cylindrical pores.

    PubMed

    Morishige, Kunimitsu; Tateishi, Masayoshi

    2006-04-25

    To examine the theoretical and semiempirical relations between pore size and the pressure of capillary condensation or evaporation proposed so far, we constructed an accurate relation between the pore radius and the capillary condensation and evaporation pressure of nitrogen at 77 K for the cylindrical pores of the ordered mesoporous MCM-41 and SBA-15 silicas. Here, the pore size was determined from a comparison between the experimental and calculated X-ray diffraction patterns due to X-ray structural modeling recently developed. Among the many theoretical relations that differ from each other in the degree of theoretical improvements, a macroscopic thermodynamic approach based on Broekhoff-de Boer equations was found to be in fair agreement with the experimental relation obtained in the present study.

  11. Modeling of seismic field in porous medium:Simulation study of single pore and pore ensemble effects

    NASA Astrophysics Data System (ADS)

    Shatskaya, A. A.; Nemirovich-Danchenko, M. M.; Terre, D. A.

    2015-11-01

    The article considers the effect of porous media on elastic wave field. Based on numerical modeling, diffraction pattern of the wave propagating through a single pore in carbonates has been produced. Matrix properties (calcite and dolomite) and fluid (water) are modeled based on thin core section image. The qualitative comparison with the available computational data has been performed. Provided that ensemble of pores is involved, the effect of porous medium on seismic field has been studied. For comparison with experimental data the model of porous sintered aluminum Al-6061 has been considered. The processing of numerical modeling results made it possible to estimate average velocities in the model of porous aluminum and compare them with physical modeling data. The provided estimates have indicated qualitative (single pore) and quantitative (ensemble of pores) correlation of simulation and experiment results.

  12. Preparation of large-pore mesoporous nanocrystalline TiO2 thin films with tailored pore diameters.

    PubMed

    Liu, Kesong; Fu, Honggang; Shi, Keying; Xiao, Fengshou; Jing, Liqiang; Xin, Baifu

    2005-10-13

    A novel and facile synthesis route to large-pore mesoporous nanocrystalline anatase thin films with tunable pore diameters in narrow distribution of sizes ranging from 8.3 to 14 nm is reported, using triblock copolymer as the template and Ti(OBu(n))4 as the inorganic precursor. The obtained materials were characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, and nitrogen adsorption. A reasonable formation mechanism is also presented in this work.

  13. Neutrons measure phase behavior in pores at Angstrom size

    SciTech Connect

    Bardoel, Agatha A; Melnichenko, Yuri B

    2012-01-01

    Researchers have measured the phase behavior of green house gases in pores at the Angstrom-level, using small angle neutron scattering (SANS) at the Oak Ridge National Laboratory's High Flux Isotope Reactor. Yuri Melnichenko, an instrument scientist on the General Purpose Small Angle Neutron Scattering (GP SANS) Diffractometer at ORNL's High Flux Isotope Reactor, his postdoctoral associate Lilin He and collaborators Nidia Gallego and Cristian Contescu from the Material Sciences Division (ORNL) were engaged in the work. They were studying nanoporous carbons to assess their attractiveness as storage media for hydrogen, with a view to potential use for on-board hydrogen storage for transportation applications. Nanoporous carbons can also serve as electrode material for supercapacitors and batteries. The researchers successfully determined that the most efficiently condensing pore size in a carbon nanoporous material for hydrogen storage is less than one nanometer. In a paper recently published by the Journal of the American Chemical Society, the collaborators used small angle neutron scattering to study how hydrogen condenses in small pores at ambient temperature. They discovered that the surface-molecule interactions create internal pressures in pores that may exceed the external gas pressure by a factor of up to 50. 'This is an exciting result,' Melnichenko said, 'as you achieve extreme densification in pores 'for free', i.e. without spending any energy. These results can be used to guide the development of new carbon adsorbents tailored to maximize hydrogen storage capacities.' Another important factor that defines the adsorption capacity of sub-nanometer pores is their shape. In order to get accurate structural information and maximize sorption capacity, it is important that pores are small and of approximately uniform size. In collaboration with Drexel University's Yury Gogotsi who supplied the samples, Melnichenko and his collaborators used the GP SANS

  14. Unified method for the total pore volume and pore size distribution of hierarchical zeolites from argon adsorption and mercury intrusion.

    PubMed

    Kenvin, Jeffrey; Jagiello, Jacek; Mitchell, Sharon; Pérez-Ramírez, Javier

    2015-02-03

    A generalized approach to determine the complete distribution of macropores, mesopores, and micropores from argon adsorption and mercury porosimetry is developed and validated for advanced zeolite catalysts with hierarchically structured pore systems in powder and shaped forms. Rather than using a fragmented approach of simple overlays from individual techniques, a unified approach that utilizes a kernel constructed from model isotherms and model intrusion curves is used to calculate the complete pore size distribution and the total pore volume of the material. An added benefit of a single full-range pore size distribution is that the cumulative pore area and the area distribution are also obtained without the need for additional modeling. The resulting complete pore size distribution and the kernel accurately model both the adsorption isotherm and the mercury porosimetry. By bridging the data analysis of two primary characterization tools, this methodology fills an existing gap in the library of familiar methods for porosity assessment in the design of materials with multilevel porosity for novel technological applications.

  15. Pore-scale mechanisms of gas flow in tight sand reservoirs

    SciTech Connect

    Silin, D.; Kneafsey, T.J.; Ajo-Franklin, J.B.; Nico, P.

    2010-11-30

    Tight gas sands are unconventional hydrocarbon energy resource storing large volume of natural gas. Microscopy and 3D imaging of reservoir samples at different scales and resolutions provide insights into the coaredo not significantly smaller in size than conventional sandstones, the extremely dense grain packing makes the pore space tortuous, and the porosity is small. In some cases the inter-granular void space is presented by micron-scale slits, whose geometry requires imaging at submicron resolutions. Maximal Inscribed Spheres computations simulate different scenarios of capillary-equilibrium two-phase fluid displacement. For tight sands, the simulations predict an unusually low wetting fluid saturation threshold, at which the non-wetting phase becomes disconnected. Flow simulations in combination with Maximal Inscribed Spheres computations evaluate relative permeability curves. The computations show that at the threshold saturation, when the nonwetting fluid becomes disconnected, the flow of both fluids is practically blocked. The nonwetting phase is immobile due to the disconnectedness, while the permeability to the wetting phase remains essentially equal to zero due to the pore space geometry. This observation explains the Permeability Jail, which was defined earlier by others. The gas is trapped by capillarity, and the brine is immobile due to the dynamic effects. At the same time, in drainage, simulations predict that the mobility of at least one of the fluids is greater than zero at all saturations. A pore-scale model of gas condensate dropout predicts the rate to be proportional to the scalar product of the fluid velocity and pressure gradient. The narrowest constriction in the flow path is subject to the highest rate of condensation. The pore-scale model naturally upscales to the Panfilov's Darcy-scale model, which implies that the condensate dropout rate is proportional to the pressure gradient squared. Pressure gradient is the greatest near the matrix

  16. Characterizing 3-D flow velocity in evolving pore networks driven by CaCO3 precipitation and dissolution

    NASA Astrophysics Data System (ADS)

    Chojnicki, K. N.; Yoon, H.; Martinez, M. J.

    2015-12-01

    Understanding reactive flow in geomaterials is important for optimizing geologic carbon storage practices, such as using pore space efficiently. Flow paths can be complex in large degrees of geologic heterogeneities across scales. In addition, local heterogeneity can evolve as reactive transport processes alter the pore-scale morphology. For example, dissolved carbon dioxide may react with minerals in fractured rocks, confined aquifers, or faults, resulting in heterogeneous cementation (and/or dissolution) and evolving flow conditions. Both path and flow complexities are important and poorly characterized, making it difficult to determine their evolution with traditional 2-D transport models. Here we characterize the development of 3-D pore-scale flow with an evolving pore configuration due to calcium carbonate (CaCO3) precipitation and dissolution. A simple pattern of a microfluidic pore network is used initially and pore structures will become more complex due to precipitation and dissolution processes. At several stages of precipitation and dissolution, we directly visualize 3-D velocity vectors using micro particle image velocimetry and a laser scanning confocal microscope. Measured 3-D velocity vectors are then compared to 3-D simulated flow fields which will be used to simulate reactive transport. Our findings will highlight the importance of the 3-D flow dynamics and its impact on estimating reactive surface area over time. 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. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114.

  17. A functional protein pore with a "retro" transmembrane domain.

    PubMed Central

    Cheley, S.; Braha, O.; Lu, X.; Conlan, S.; Bayley, H.

    1999-01-01

    Extended retro (reversed) peptide sequences have not previously been accommodated within functional proteins. Here, we show that the entire transmembrane portion of the beta-barrel of the pore-forming protein alpha-hemolysin can be formed by retrosequences comprising a total of 175 amino acid residues, 25 contributed by the central sequence of each subunit of the heptameric pore. The properties of wild-type and retro heptamers in planar bilayers are similar. The single-channel conductance of the retro pore is 15% less than that of the wild-type heptamer and its current-voltage relationship denotes close to ohmic behavior, while the wild-type pore is weakly rectifying. Both wild-type and retro pores are very weakly anion selective. These results and the examination of molecular models suggest that beta-barrels may be especially accepting of retro sequences compared to other protein folds. Indeed, the ability to form a retro domain could be diagnostic of a beta-barrel, explaining, for example, the activity of the retro forms of many membrane-permeabilizing peptides. By contrast with the wild-type subunits, monomeric retro subunits undergo premature assembly in the absence of membranes, most likely because the altered central sequence fails to interact with the remainder of the subunit, thereby initiating assembly. Despite this difficulty, a technique was devised for obtaining heteromeric pores containing both wild-type and retro subunits. Most probably as a consequence of unfavorable interstrand side-chain interactions, the heteromeric pores are less stable than either the wild-type or retro homoheptamers, as judged by the presence of subconductance states in single-channel recordings. Knowledge about the extraordinary plasticity of the transmembrane beta-barrel of alpha-hemolysin will be very useful in the de novo design of functional membrane proteins based on the beta-barrel motif. PMID:10386875

  18. Extending electromagnetic methods to map coastal pore water salinities

    USGS Publications Warehouse

    Greenwood, Wm. J.; Kruse, S.; Swarzenski, P.

    2006-01-01

    The feasibility of mapping pore water salinity based on surface electromagnetic (EM) methods over land and shallow marine water is examined in a coastal wetland on Tampa Bay, Florida. Forward models predict that useful information on seabed conductivity can be obtained through <1.5 m of saline water, using floating EM-31 and EM-34 instruments from Geonics Ltd. The EM-31 functioned as predicted when compared against resistivity soundings and pore water samples and proved valuable for profiling in otherwise inaccessible terrain due to its relatively small size. Experiments with the EM-34 in marine water, however, did not reproduce the theoretical instrument response. The most effective technique for predicting pore water conductivities based on EM data entailed (1) computing formation factors from resistivity surveys and pore water samples at representative sites and (2) combining these formation factors with onshore and offshore EM-31 readings for broader spatial coverage. This method proved successful for imaging zones of elevated pore water conductivities/ salinities associated with mangrove forests, presumably caused by salt water exclusion by mangrove roots. These zones extend 5 to 10 m seaward from mangrove trunks fringing Tampa Bay. Modeling indicates that EM-31 measurements lack the resolution necessary to image the subtle pore water conductivity variations expected in association with diffuse submarine ground water discharge of fresher water in the marine water of Tampa Bay. The technique has potential for locating high-contrast zones and other pore water salinity anomalies in areas not accessible to conventional marine- or land-based resistivity arrays and hence may be useful for studies of coastal-wetland ecosystems. Copyright ?? 2005 National Ground Water Association.

  19. Long-pore Electrostatics in Inward-rectifier Potassium Channels

    PubMed Central

    Robertson, Janice L.; Palmer, Lawrence G.; Roux, Benoît

    2008-01-01

    Inward-rectifier potassium (Kir) channels differ from the canonical K+ channel structure in that they possess a long extended pore (∼85 Å) for ion conduction that reaches deeply into the cytoplasm. This unique structural feature is presumably involved in regulating functional properties specific to Kir channels, such as conductance, rectification block, and ligand-dependent gating. To elucidate the underpinnings of these functional roles, we examine the electrostatics of an ion along this extended pore. Homology models are constructed based on the open-state model of KirBac1.1 for four mammalian Kir channels: Kir1.1/ROMK, Kir2.1/IRK, Kir3.1/GIRK, and Kir6.2/KATP. By solving the Poisson-Boltzmann equation, the electrostatic free energy of a K+ ion is determined along each pore, revealing that mammalian Kir channels provide a favorable environment for cations and suggesting the existence of high-density regions in the cytoplasmic domain and cavity. The contribution from the reaction field (the self-energy arising from the dielectric polarization induced by the ion's charge in the complex geometry of the pore) is unfavorable inside the long pore. However, this is well compensated by the electrostatic interaction with the static field arising from the protein charges and shielded by the dielectric surrounding. Decomposition of the static field provides a list of residues that display remarkable correspondence with existing mutagenesis data identifying amino acids that affect conduction and rectification. Many of these residues demonstrate interactions with the ion over long distances, up to 40 Å, suggesting that mutations potentially affect ion or blocker energetics over the entire pore. These results provide a foundation for understanding ion interactions in Kir channels and extend to the study of ion permeation, block, and gating in long, cation-specific pores. PMID:19001143

  20. Pore-structure models of hydraulic conductivity for permeable pavement

    NASA Astrophysics Data System (ADS)

    Kuang, X.; Sansalone, J.; Ying, G.; Ranieri, V.

    2011-03-01

    SummaryPermeable pavement functions as a porous infrastructure interface allowing the infiltration and evaporation of rainfall-runoff while functioning as a relatively smooth load-bearing surface for vehicular transport. Hydraulic conductivity ( k) of permeable pavement is an important hydraulic property and is a function of the pore structure. This study examines k for a cementitious permeable pavement (CPP) through a series of pore-structure models. Measurements utilized include hydraulic head as well as total porosity, ( ϕ t), effective porosity ( ϕ e), tortuosity ( L e/ L) and pore size distribution (PSD) indices generated through X-ray tomography (XRT). XRT results indicate that the permeable pavement pore matrix is hetero-disperse, with high tortuosity and ϕ t ≠ ϕ e. Power law models of k- ϕ t and k- ϕ e relationships are developed for a CPP mix design. Results indicate that the Krüger, Fair-Hatch, Hazen, Slichter, Beyer and Terzaghi models based on simple pore-structure indices do not reproduce measured k values. The conventional Kozeny-Carman model (KCM), a more parameterized pore-structure model, did not reproduce measured k values. This study proposes a modified KCM utilizing ϕ e, specific surface area (SSA) pe and weighted tortuosity ( L e/ L) w. Results demonstrate that such permeable pavement pore-structure parameters with the modified KCM can predict k. The k results are combined with continuous simulation modeling using historical rainfall to provide nomographs examining permeable pavement as a low impact development (LID) infrastructure component.

  1. Reservoir Condition Pore-scale Imaging of Multiple Fluid Phases Using X-ray Microtomography

    PubMed Central

    Andrew, Matthew; Bijeljic, Branko; Blunt, Martin

    2015-01-01

    X-ray microtomography was used to image, at a resolution of 6.6 µm, the pore-scale arrangement of residual carbon dioxide ganglia in the pore-space of a carbonate rock at pressures and temperatures representative of typical formations used for CO2 storage. Chemical equilibrium between the CO2, brine and rock phases was maintained using a high pressure high temperature reactor, replicating conditions far away from the injection site. Fluid flow was controlled using high pressure high temperature syringe pumps. To maintain representative in-situ conditions within the micro-CT scanner a carbon fiber high pressure micro-CT coreholder was used. Diffusive CO2 exchange across the confining sleeve from the pore-space of the rock to the confining fluid was prevented by surrounding the core with a triple wrap of aluminum foil. Reconstructed brine contrast was modeled using a polychromatic x-ray source, and brine composition was chosen to maximize the three phase contrast between the two fluids and the rock. Flexible flow lines were used to reduce forces on the sample during image acquisition, potentially causing unwanted sample motion, a major shortcoming in previous techniques. An internal thermocouple, placed directly adjacent to the rock core, coupled with an external flexible heating wrap and a PID controller was used to maintain a constant temperature within the flow cell. Substantial amounts of CO2 were trapped, with a residual saturation of 0.203 ± 0.013, and the sizes of larger volume ganglia obey power law distributions, consistent with percolation theory. PMID:25741751

  2. Pore networks in continental and marine mudstones: Characteristics and controls on sealing behavior

    USGS Publications Warehouse

    Heath, J.E.; Dewers, T.A.; McPherson, B.J.O.L.; Petrusak, R.; Chidsey, T.C.; Rinehart, A.J.; Mozley, P.S.

    2011-01-01

    Mudstone pore networks are strong modifiers of sedimentary basin fluid dynamics and have a critical role in the distribution of hydrocarbons and containment of injected fluids. Using core samples from continental and marine mudstones, we investigate properties of pore types and networks from a variety of geologic environments, together with estimates of capillary beam- scanning electron microscopy, suggest seven dominant mudstone pore types distinguished by geometry and connectivity. A dominant planar pore type occurs in all investigated mudstones and generally has high coordination numbers (i.e., number of neighboring connected pores). Connected networks of pores of this type contribute to high mercury capillary pressures due to small pore throats at the junctions of connected pores and likely control most matrix transport in these mudstones. Other pore types are related to authigenic (e.g., replacement or pore-lining precipitation) clay minerals and pyrite nodules; pores in clay packets adjacent to larger, more competent clastic grains; pores in organic phases; and stylolitic and microfracture-related pores. Pores within regions of authigenic clay minerals often form small isolated networks (<3 ??m). Pores in stringers of organic phases occur as tubular pores or slit- and/or sheet-like pores. These form short, connected lengths in 3D reconstructions, but appear to form networks no larger than a few microns in size. Sealing efficiency of the studied mudstones increases with greater distal depositional environments and greater maximum depth of burial. ?? 2011 Geological Society of America.

  3. Pore-scale simulations of drainage in granular materials: Finite size effects and the representative elementary volume

    NASA Astrophysics Data System (ADS)

    Yuan, Chao; Chareyre, Bruno; Darve, Félix

    2016-09-01

    A pore-scale model is introduced for two-phase flow in dense packings of polydisperse spheres. The model is developed as a component of a more general hydromechanical coupling framework based on the discrete element method, which will be elaborated in future papers and will apply to various processes of interest in soil science, in geomechanics and in oil and gas production. Here the emphasis is on the generation of a network of pores mapping the void space between spherical grains, and the definition of local criteria governing the primary drainage process. The pore space is decomposed by Regular Triangulation, from which a set of pores connected by throats are identified. A local entry capillary pressure is evaluated for each throat, based on the balance of capillary pressure and surface tension at equilibrium. The model reflects the possible entrapment of disconnected patches of the receding wetting phase. It is validated by a comparison with drainage experiments. In the last part of the paper, a series of simulations are reported to illustrate size and boundary effects, key questions when studying small samples made of spherical particles be it in simulations or experiments. Repeated tests on samples of different sizes give evolution of water content which are not only scattered but also strongly biased for small sample sizes. More than 20,000 spheres are needed to reduce the bias on saturation below 0.02. Additional statistics are generated by subsampling a large sample of 64,000 spheres. They suggest that the minimal sampling volume for evaluating saturation is one hundred times greater that the sampling volume needed for measuring porosity with the same accuracy. This requirement in terms of sample size induces a need for efficient computer codes. The method described herein has a low algorithmic complexity in order to satisfy this requirement. It will be well suited to further developments toward coupled flow-deformation problems in which evolution of the

  4. Foil coverage of a crawl-space floor: measurements and modeling of radon entry.

    PubMed

    van der Spoel, W H; van der Graaf, E R; de Meijer, R J

    1998-05-01

    The mitigative impact of covering the floor of a crawl space with a membrane has been studied under well-defined and controlled conditions. The measurements have been done with a homogeneous column of dry sand covered with a sheet of polyethylene foil. An air-filled volume on top of the column simulates a crawl space. The experiments mainly concern long-term measurements of the crawl-space radon concentration in combination with steady-state diffusive and combined advective and diffusive transport through the sand column and crawl space. The experimental data are analyzed with both simplified mass-balance models for radon entry into the crawl space and with a two-dimensional numerical model based on a finite-difference approach. In all experiments the influence of atmospheric pressure variations is clearly present. For most experiments the agreement between calculations, which make use of independently measured transport parameters for both sand and foil, and measurements is within 10%. However, the discrepancy is larger for experiments with continuous advective transport from the crawl space to the sand. With undamaged foil, the calculations overestimate the measurements by 20%. Reversely, with an opening in the center of the foil, the calculations underestimate the measurements by 20-40%. The results show that under controlled conditions radon transport from a foil-covered sand column into a crawl-space can be described within 40% on basis of separately measured parameters.

  5. Final Report for Subcontract B541028, Pore-Scale Modeling to Support "Pore Connectivity" Research Work

    SciTech Connect

    Ewing, R P

    2009-02-25

    This report covers modeling aspects of a combined experimental and modeling task in support of the DOE Science and Technology Program (formerly OSTI) within the Office of Civilian Radioactive Waste Management (OCRWM). Research Objectives The research for this project dealt with diffusive retardation: solute moving through a fracture diffuses into and out of the rock matrix. This diffusive exchange retards overall solute movement, and retardation both dilutes waste being released, and allows additional decay. Diffusive retardation involves not only fracture conductivity and matrix diffusion, but also other issues and processes: contaminants may sorb to the rock matrix, fracture flow may be episodic, a given fracture may or may not flow depending on the volume of flow and the fracture's connection to the overall fracture network, the matrix imbibes water during flow episodes and dries between episodes, and so on. The objective of the project was to improve understanding of diffusive retardation of radionuclides due to fracture / matrix interactions. Results from combined experimental/modeling work were to (1) determine whether the current understanding and model representation of matrix diffusion is valid, (2) provide insights into the upscaling of laboratory-scale diffusion experiments, and (3) help in evaluating the impact on diffusive retardation of episodic fracture flow and pore connectivity in Yucca Mountain tuffs. Questions explored included the following: (1) What is the relationship between the diffusion coefficient measured at one scale, to that measured or observed at a different scale? In classical materials this relationship is trivial; in low-connectivity materials it is not. (2) Is the measured diffusivity insensitive to the shape of the sample? Again, in classical materials there should be no sample shape effect. (3) Does sorption affect diffusive exchange in low-connectivity media differently than in classical media? (4) What is the effect of matrix

  6. Idealized Shale Sorption Isotherm Measurements to Determine Pore Volume, Pore Size Distribution, and Surface Area

    NASA Astrophysics Data System (ADS)

    Holmes, R.; Wang, B.; Aljama, H.; Rupp, E.; Wilcox, J.

    2014-12-01

    One method for mitigating the impacts of anthropogenic CO2-related climate change is the sequestration of CO2 in depleted gas and oil reservoirs, including shale. The accurate characterization of the heterogeneous material properties of shale, including pore volume, surface area, pore size distributions (PSDs) and composition is needed to understand the interaction of CO2 with shale. Idealized powdered shale sorption isotherms were created by varying incremental amounts of four essential components by weight. The first two components, organic carbon and clay, have been shown to be the most important components for CO2 uptake in shales. Organic carbon was represented by kerogen isolated from a Silurian shale, and clay groups were represented by illite from the Green River shale formation. The rest of the idealized shale was composed of equal parts by weight of SiO2 to represent quartz and CaCO3 to represent carbonate components. Baltic, Eagle Ford, and Barnett shale sorption measurements were used to validate the idealized samples. The idealized and validation shale sorption isotherms were measured volumetrically using low pressure N2 (77K) and CO2 (273K) adsorbates on a Quantachrome Autosorb IQ2. Gravimetric isotherms were also produced for a subset of these samples using CO2 and CH4adsorbates under subsurface temperature and pressure conditions using a Rubotherm magnetic suspension balance. Preliminary analyses were inconclusive in validating the idealized samples. This could be a result of conflicting reports of total organic carbon (TOC) content in each sample, a problem stemming from the heterogeneity of the samples and different techniques used for measuring TOC content. The TOC content of the validation samples (Eagle Ford and Barnett) was measured by Rock-Eval pyrolysis at Weatherford Laboratories, while the TOC content in the Baltic validation samples was determined by LECO TOC. Development of a uniform process for measuring TOC in the validation samples is

  7. An investigation of pore collapse in asymmetric polysulfone membranes

    NASA Astrophysics Data System (ADS)

    Subrahmanyan, Sumitra

    2003-06-01

    Porous polysulfone membranes prepared by phase inversion can be tailored to suit filtration requirements by the choice of solvent and coagulant. In the current research polysulfone membranes were prepared by inverting a solution in N-methyl pyrrolidinone (NMP) in isopropanol to form uniform sized pores. Phase inversion resulted in the formation of an asymmetric membrane. The membranes have a characteristic "skin" which is supported by a highly porous substructure. Water-wet membranes experience capillary force during water evaporation. Since the modulus of the membranes is lower than the capillary force, the membrane walls shrink and thicken giving rise to a condensed structure. The "skin" regulates permeation through the membranes which is essential for filtration. A change in the pore structure of the skin alters the permeability. The current research investigates the influence of amine plasma treatments on the surface pore structure of polysulfone membranes. The permeation of a rhodamine dye through the plasma treated membranes and through non-plasma treated membranes is used to examine the influence of the plasma treatment. Furthermore, the influence of plasma treatment on the loss of water from the membranes leading to pore collapse is also explored. The study revealed that a plasma ablates the skin, increasing the permeation. An ammonia plasma treatment produced more etching, and hence increased permeation compared to permeation for an aniline plasma-treated membrane. A one-minute aniline plasma treatment only caused a moderate increase in permeation. Plasma treatments introduced significant surface modification by the introduction of new functionalities. However, permeation was not influenced by the surface modification. Water trapped in the pores is essential to maintain the pore structure of the membrane. The surface treatment dictates the pore size and therefore, the convection allowing water evaporation, leading to pore collapse. Heat treating also

  8. Pore-forming activity of clostridial binary toxins.

    PubMed

    Knapp, O; Benz, R; Popoff, M R

    2016-03-01

    Clostridial binary toxins (Clostridium perfringens Iota toxin, Clostridium difficile transferase, Clostridium spiroforme toxin, Clostridium botulinum C2 toxin) as Bacillus binary toxins, including Bacillus anthracis toxins consist of two independent proteins, one being the binding component which mediates the internalization into cell of the intracellularly active component. Clostridial binary toxins induce actin cytoskeleton disorganization through mono-ADP-ribosylation of globular actin and are responsible for enteric diseases. Clostridial and Bacillus binary toxins share structurally and functionally related binding components which recognize specific cell receptors, oligomerize, form pores in endocytic vesicle membrane, and mediate the transport of the enzymatic component into the cytosol. Binding components retain the global structure of pore-forming toxins (PFTs) from the cholesterol-dependent cytotoxin family such as perfringolysin. However, their pore-forming activity notably that of clostridial binding components is more related to that of heptameric PFT family including aerolysin and C. perfringens epsilon toxin. This review focuses upon pore-forming activity of clostridial binary toxins compared to other related PFTs. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.

  9. Pore network model of electrokinetic transport through charged porous media

    NASA Astrophysics Data System (ADS)

    Obliger, Amaël; Jardat, Marie; Coelho, Daniel; Bekri, Samir; Rotenberg, Benjamin

    2014-04-01

    We introduce a method for the numerical determination of the steady-state response of complex charged porous media to pressure, salt concentration, and electric potential gradients. The macroscopic fluxes of solvent, salt, and charge are computed within the framework of the Pore Network Model (PNM), which describes the pore structure of the samples as networks of pores connected to each other by channels. The PNM approach is used to capture the couplings between solvent and ionic flows which arise from the charge of the solid surfaces. For the microscopic transport coefficients on the channel scale, we take a simple analytical form obtained previously by solving the Poisson-Nernst-Planck and Stokes equations in a cylindrical channel. These transport coefficients are upscaled for a given network by imposing conservation laws for each pores, in the presence of macroscopic gradients across the sample. The complex pore structure of the material is captured by the distribution of channel diameters. We investigate the combined effects of this complex geometry, the surface charge, and the salt concentration on the macroscopic transport coefficients. The upscaled numerical model preserves the Onsager relations between the latter, as expected. The calculated macroscopic coefficients behave qualitatively as their microscopic counterparts, except for the permeability and the electro-osmotic coupling coefficient when the electrokinetic effects are strong. Quantitatively, the electrokinetic couplings increase the difference between the macroscopic coefficients and the corresponding ones for a single channel of average diameter.

  10. Regulation of soil organic C mineralisation at the pore scale.

    PubMed

    Ruamps, Léo S; Nunan, Naoise; Pouteau, Valérie; Leloup, Julie; Raynaud, Xavier; Roy, Virginie; Chenu, Claire

    2013-10-01

    Little is known about the factors that regulate C mineralisation at the soil pore scale or how these factors vary throughout the pore network. This study sought to understand how the decomposition of organic carbon varies within the soil pore network and to determine the relative importance of local environmental properties relative to biological properties as controlling factors. This was achieved by sterilising samples of soil and reinoculating them with axenic bacterial suspensions using the matric potential to target different locations in the pore network. Carbon mineralisation curves were described with two-compartment first-order models to distinguish CO2 derived from the labile organic carbon released during sterilisation from CO2 derived from organic C unaffected by sterilisation. The data indicated that the size of the labile pool of organic C, possibly of microbial origin, varied as a function of location in the pore network but that the organic carbon unaffected by sterilisation did not. The mineralisation rate of the labile C varied with the bacterial type inoculated, but the mineralisation rate of the organic C unaffected by sterilisation was insensitive to bacterial type. Taken together, the results suggest that microbial metabolism is a less significant regulator of soil organic carbon decomposition than are microbial habitat properties.

  11. Role of Pore-Forming Toxins in Neonatal Sepsis

    PubMed Central

    Sonnen, Andreas F.-P.

    2013-01-01

    Protein toxins are important virulence factors contributing to neonatal sepsis. The major pathogens of neonatal sepsis, group B Streptococci, Escherichia coli, Listeria monocytogenes, and Staphylococcus aureus, secrete toxins of different molecular nature, which are key for defining the disease. Amongst these toxins are pore-forming exotoxins that are expressed as soluble monomers prior to engagement of the target cell membrane with subsequent formation of an aqueous membrane pore. Membrane pore formation is not only a means for immediate lysis of the targeted cell but also a general mechanism that contributes to penetration of epithelial barriers and evasion of the immune system, thus creating survival niches for the pathogens. Pore-forming toxins, however, can also contribute to the induction of inflammation and hence to the manifestation of sepsis. Clearly, pore-forming toxins are not the sole factors that drive sepsis progression, but they often act in concert with other bacterial effectors, especially in the initial stages of neonatal sepsis manifestation. PMID:23710203

  12. Protein detection using tunable pores: resistive pulses and current rectification.

    PubMed

    Blundell, Emma L C J; Mayne, Laura J; Lickorish, Michael; Christie, Steven D R; Platt, Mark

    2016-12-12

    We present the first comparison between assays that use resistive pulses or rectification ratios on a tunable pore platform. We compare their ability to quantify the cancer biomarker Vascular Endothelial Growth Factor (VEGF). The first assay measures the electrophoretic mobility of aptamer modified nanoparticles as they traverse the pore. By controlling the aptamer loading on the particle surface, and measuring the speed of each translocation event we are able to observe a change in velocity as low as 18 pM. A second non-particle assay exploits the current rectification properties of conical pores. We report the first use of Layer-by-Layer (LbL) assembly of polyelectrolytes onto the surface of the polyurethane pore. The current rectification ratios demonstrate the presence of the polymers, producing pH and ionic strength-dependent currents. The LbL assembly allows the facile immobilisation of DNA aptamers onto the pore allowing a specific dose response to VEGF. Monitoring changes to the current rectification allows for a rapid detection of 5 pM VEGF. Each assay format offers advantages in their setup and ease of preparation but comparable sensitivities.

  13. Pore-throat sizes in sandstones, tight sandstones, and shales

    USGS Publications Warehouse

    Nelson, Philip H.

    2009-01-01

    Pore-throat sizes in silidclastic rocks form a continuum from the submillimeter to the nanometer scale. That continuum is documented in this article using previously published data on the pore and pore-throat sizes of conventional reservoir rocks, tight-gas sandstones, and shales. For measures of central tendency (mean, mode, median), pore-throat sizes (diameters) are generally greater than 2 μm in conventional reservoir rocks, range from about 2 to 0.03 μm in tight-gas sandstones, and range from 0.1 to 0.005 μm in shales. Hydrocarbon molecules, asphaltenes, ring structures, paraffins, and methane, form another continuum, ranging from 100 Å (0.01 μm for asphaltenes to 3.8 A (0.00038 μm) for methane. The pore-throat size continuum provides a useful perspective for considering (1) the emplacement of petroleum in consolidated siliciclastics and (2) fluid flow through fine-grained source rocks now being exploited as reservoirs.

  14. The effect of electrical conductivity on pore resistance and electroporation

    NASA Astrophysics Data System (ADS)

    Li, Jianbo; Lin, Hao

    2008-11-01

    Electroporation is an elegant means to gain access to the cytoplasm, and to deliver molecules into the cell while simultaneously maintaining viability and functionality. In this technique, an applied electric pulse transiently permeabilizes the cell membrane, through which biologically active agents such as DNA, RNA, and amino acids can enter the cell, and perform tasks such as gene and cancer therapy. Despite wide applications, current electroporation technologies fall short of desired efficiency and reliability, in part due to the lack of fundamental understanding and quantitative modeling tools. This work focuses on the modeling of cell membrane conductance due to the formation of aqueous conducting pores. An analytical expression is developed to determine effective pore resistance as a function of the membrane thickness, pore size, and intracellular and extracellular conductivities. The availability of this expression avoids empirical or ad hoc specification of the conductivity of the pore-filling solution which was adopted in previous works. Such pore resistance model is then incorporated into a whole-cell electroporation simulation to investigate the effect of conductivity ratio on membrane permeabilization. The results reveal that the degree of permeabilization strongly depends on the specific values of the extracellular and intracellular conductivities.

  15. Fabrication of polymeric scaffolds with a controlled distribution of pores.

    PubMed

    Capes, J S; Ando, H Y; Cameron, R E

    2005-12-01

    The design of tissue engineering scaffolds must take into account many factors including successful vascularisation and the growth of cells. Research has looked at refining scaffold architecture to promote more directed growth of tissues through well-defined anisotropy in the pore structure. In many cases it is also desirable to incorporate therapeutic ingredients, such as growth factors, into the scaffold so that their release occurs as the scaffold degrades. Therefore, scaffold fabrication techniques must be found to precisely control, not only the overall porosity of scaffolds, but also the pore size, shape and spatial distribution. This work describes the use of a regularly shaped porogen, sugar spheres, to manufacture polymeric scaffolds. Results show that pre-assembling the spheres created scaffolds with a constant porosity of 60%, but with varying pores sizes from 200-800 microm, leading to a variation in the surface area and likely degradation rate of the scaffolds. Employing different polymer impregnation techniques tailored the number of pores present with a diameter of less than 100 microm to suit different functions, and altering the packing structure of the sugar spheres created scaffolds with novel layered porosity. Replacing sugar spheres with sugar strands formed scaffolds with pores aligned in one direction.

  16. Pore fluid pressure, apparent friction, and Coulomb failure

    USGS Publications Warehouse

    Beeler, N.M.; Simpson, R.W.; Hickman, S.H.; Lockner, D.A.

    2000-01-01

    Many recent studies of stress-triggered seismicity rely on a fault failure model with a single free parameter, the apparent coefficient of friction, presumed to be a material constant with possible values 0 ≤ μ′ ≤ 1. These studies may present a misleading view of fault strength and the role of pore fluid pressure in earthquake failure. The parameter μ′ is intended to incorporate the effects of both friction and pore pressure, but is a material constant only if changes in pore fluid pressure induced by changes in stress are proportional to the normal stress change across the potential failure plane. Although specific models of fault zones permit such a relation, neither is it known that fault zones within the Earth behave this way, nor is this behavior expected in all cases. In contrast, for an isotropic homogeneous poroelastic model the pore pressure changes are proportional to changes in mean stress, μ′ is not a material constant, and −∞ ≤ μ′ ≤ +∞. Analysis of the change in Coulomb failure stress for tectonically loaded reverse and strike-slip faults shows considerable differences between these two pore pressure models, suggesting that such models might be distinguished from one another using observations of triggered seismicity (e.g., aftershocks). We conclude that using the constant apparent friction model exclusively in studies of Coulomb failure stress is unwise and could lead to significant errors in estimated stress change and seismic hazard.

  17. Tunable ultrathin membranes with nonvolatile pore shape memory.

    PubMed

    Kuroki, Hidenori; Islam, Crescent; Tokarev, Igor; Hu, Heng; Liu, Guojun; Minko, Sergiy

    2015-05-20

    The concept of a responsive nanoporous thin-film gel membranes whose pores could be tuned to a desired size by a specific "molecular signal" and whose pore geometry becomes "memorized" by the gel is reported. The ∼100 nm thick membranes were prepared by dip-coating from a solution mixture of a random copolymer comprising responsive and photo-cross-linkable units and monodisperse latex nanoparticles used as a sacrificial colloidal template. After stabilization of the films by photo-cross-linking the latex template was removed, yielding nanoporous structures with a narrow pore size distribution and a high porosity. The thin-film membranes could be transferred onto porous supports to serve as tunable size-selective barriers in various colloids separation applications. The pore dimensions and hence the membrane's colloidal-particle-size cutoff were reversibly regulated by swelling-shrinking of the polymer network with a specially selected low-molar-mass compound. The attained pore shape was "memorized" in aqueous media and "erased" by treatment in special solvents reverting the membrane to the original state.

  18. The role of pore geometry in single nanoparticle detection

    DOE PAGES

    Davenport, Matthew; Healy, Ken; Pevarnik, Matthew; ...

    2012-08-22

    In this study, we observe single nanoparticle translocation events via resistive pulse sensing using silicon nitride pores described by a range of lengths and diameters. Pores are prepared by focused ion beam milling in 50 nm-, 100 nm-, and 500 nm-thick silicon nitride membranes with diameters fabricated to accommodate spherical silica nanoparticles with sizes chosen to mimic that of virus particles. In this manner, we are able to characterize the role of pore geometry in three key components of the detection scheme, namely, event magnitude, event duration, and event frequency. We find that the electric field created by the appliedmore » voltage and the pore’s geometry is a critical factor. We develop approximations to describe this field, which are verified with computer simulations, and interactions between particles and this field. In so doing, we formulate what we believe to be the first approximation for the magnitude of ionic current blockage that explicitly addresses the invariance of access resistance of solid-state pores during particle translocation. These approximations also provide a suitable foundation for estimating the zeta potential of the particles and/or pore surface when studied in conjunction with event durations. We also verify that translocation achieved by electro-osmostic transport is an effective means of slowing translocation velocities of highly charged particles without compromising particle capture rate as compared to more traditional approaches based on electrophoretic transport.« less

  19. The role of pore geometry in single nanoparticle detection

    SciTech Connect

    Davenport, Matthew; Healy, Ken; Pevarnik, Matthew; Teslich, Nick; Cabrini, Stefano; Morrison, Alan P.; Siwy, Zuzanna S.; Letant, Sonia E.

    2012-08-22

    In this study, we observe single nanoparticle translocation events via resistive pulse sensing using silicon nitride pores described by a range of lengths and diameters. Pores are prepared by focused ion beam milling in 50 nm-, 100 nm-, and 500 nm-thick silicon nitride membranes with diameters fabricated to accommodate spherical silica nanoparticles with sizes chosen to mimic that of virus particles. In this manner, we are able to characterize the role of pore geometry in three key components of the detection scheme, namely, event magnitude, event duration, and event frequency. We find that the electric field created by the applied voltage and the pore’s geometry is a critical factor. We develop approximations to describe this field, which are verified with computer simulations, and interactions between particles and this field. In so doing, we formulate what we believe to be the first approximation for the magnitude of ionic current blockage that explicitly addresses the invariance of access resistance of solid-state pores during particle translocation. These approximations also provide a suitable foundation for estimating the zeta potential of the particles and/or pore surface when studied in conjunction with event durations. We also verify that translocation achieved by electro-osmostic transport is an effective means of slowing translocation velocities of highly charged particles without compromising particle capture rate as compared to more traditional approaches based on electrophoretic transport.

  20. Evidence for excess pore pressures in southwest Indian Ocean sediments

    SciTech Connect

    Abbott, D.; Menke, W.; Hobart, M.; Anderson, R.

    1981-03-10

    Brown clay cores from the Madagascar and Crozet basins show the following evidence of excess pore pressures: large amounts of flow-in, increasing average sedimentation rate with age, and nonlinear temperature gradients. Additionally, many hilltops in these basins have no visible sediment cover. The bare hilltops may result from periodic slumping caused by excess pore pressures. Calculated excess pore pressures which equal or exceed the overburden pressure were inferred from water fluxes predicted by nonlinear temperature gradients and laboratory permeability measurements by using Darcy's law. Since pore pressures which exceed the overburden pressure are unreasonable, we attribute this discrepancy to laboratory measures which underestimate the in situ permeability. The widespread presence of overpressured sediments in areas of irregular topography provides a process for resuspension of clay-sized particles. This mechanism does not require high current velocities for the erosion of clay and therefore can be applied to many areas where no strong currents are evident. Carbonate-rich sediments from the Madagascar Ridge, the Mozambique Ridge, and the Agulhas Plateau had almost no flow-in and occurred in areas where all topography was thickly draped with sediment, Since the age and tectonic location of the ridges and plateaus preclude water circulation in the basement, we attribute these differences between the brown clay and the carbonate-rich material to an absence of significant excess pore pressures in the plateau and ridge sediments.

  1. Pore-pressure sensitivities to dynamic strains: observations in active tectonic regions

    USGS Publications Warehouse

    Barbour, Andrew

    2015-01-01

    of the pore pressure response in fluid-saturated rock near active faults is controlled by shear strain accumulation associated with tectonic loading, which implies a strong feedback between fault strength and permeability: dynamic triggering susceptibilities may vary in space and also in time.

  2. A Natural Chimeric Pseudomonas Bacteriocin with Novel Pore-Forming Activity Parasitizes the Ferrichrome Transporter.

    PubMed

    Ghequire, Maarten G K; Kemland, Lieselore; Anoz-Carbonell, Ernesto; Buchanan, Susan K; De Mot, René

    2017-02-21

    Modular bacteriocins represent a major group of secreted protein toxins with a narrow spectrum of activity, involved in interference competition between Gram-negative bacteria. These antibacterial proteins include a domain for binding to the target cell and a toxin module at the carboxy terminus. Self-inhibition of producers is provided by coexpression of linked immunity genes that transiently inhibit the toxin's activity through formation of bacteriocin-immunity complexes or by insertion in the inner membrane, depending on the type of toxin module. We demonstrate strain-specific inhibitory activity for PmnH, a Pseudomonas bacteriocin with an unprecedented dual-toxin architecture, hosting both a colicin M domain, potentially interfering with peptidoglycan synthesis, and a novel colicin N-type domain, a pore-forming module distinct from the colicin Ia-type domain in Pseudomonas aeruginosa pyocin S5. A downstream-linked gene product confers PmnH immunity upon susceptible strains. This protein, ImnH, has a transmembrane topology similar to that of Pseudomonas colicin M-like and pore-forming immunity proteins, although homology with either of these is essentially absent. The enhanced killing activity of PmnH under iron-limited growth conditions reflects parasitism of the ferrichrome-type transporter for entry into target cells, a strategy shown here to be used as well by monodomain colicin M-like bacteriocins from pseudomonads. The integration of a second type of toxin module in a bacteriocin gene could offer a competitive advantage against bacteria displaying immunity against only one of both toxic activities.IMPORTANCE In their continuous struggle for ecological space, bacteria face a huge load of contenders, including phylogenetically related strains that compete for the same niche. One important group of secreted antibacterial proteins assisting in eliminating these rivals are modular bacteriocins of Gram-negative bacteria, comprising a domain for docking onto the

  3. Free energy landscape of rim-pore expansion in membrane fusion.

    PubMed

    Risselada, Herre Jelger; Smirnova, Yuliya; Grubmüller, Helmut

    2014-11-18

    The productive fusion pore in membrane fusion is generally thought to be toroidally shaped. Theoretical studies and recent experiments suggest that its formation, in some scenarios, may be preceded by an initial pore formed near the rim of the extended hemifusion diaphragm (HD), a rim-pore. This rim-pore is characterized by a nontoroidal shape that changes with size. To determine this shape as well as the free energy along the pathway of rim-pore expansion, we derived a simple analytical free energy model. We argue that dilation of HD material via expansion of a rim-pore is favored over a regular, circular pore. Further, the expanding rim-pore faces a free energy barrier that linearly increases with HD size. In contrast, the tension required to expand the rim-pore decreases with HD size. Pore flickering, followed by sudden opening, occurs when the tension in the HD competes with the line energy of the rim-pore, and the rim-pore reaches its equilibrium size before reaching the critical pore size. The experimental observation of flickering and closing fusion pores (kiss-and-run) is very well explained by the observed behavior of rim-pores. Finally, the free energy landscape of rim-pore expansion/HD dilation may very well explain why some cellular fusion reactions, in their attempt to minimize energetic costs, progress via alternative formation and dilation of microscopic hemifusion intermediates.

  4. An abiotic analogue of the nuclear pore complex hydrogel.

    PubMed

    Bird, Sean P; Baker, Lane A

    2011-09-12

    We describe an abiotic hydrogel that mimics selectivity of the nuclear pore complex. Copolymerization of peptide tetramers (phenylalanine-serine-phenylalanine-glycine, FSFG) with acrylamide results in hydrophobic interactions significant enough to allow the formation of freestanding hydrogel structures. Incorporation of FSFG motifs also renders the hydrogels selective. Selective binding of importins and nuclear transport receptor-cargo complexes is qualitatively demonstrated and compared with polyacrylamide, hydrogels prepared from a control peptide, and hydrogels prepared from the nuclear pore complex protein Nsp1. These abiotic hydrogels will enable further studies of the unique transport mechanisms of the nuclear pore complex and provide an interesting paradigm for the future development of synthetic platforms for separations and selective interfaces.

  5. Pore Topology Effects in Positron Annihilation Spectroscopy of Zeolites.

    PubMed

    Zubiaga, Asier; Warringham, Robbie; Mitchell, Sharon; Gerchow, Lars; Cooke, David; Crivelli, Paolo; Pérez-Ramírez, Javier

    2016-12-14

    Positron annihilation spectroscopy (PAS) is a powerful method to study the size and connectivity of pores in zeolites. The lifetime of positronium within the host material is commonly described by the Tao-Eldrup model. However, one of its largest limitations arises from the simple geometries considered for the shape of the pores, which cannot describe accurately the complex topologies in zeolites. Here, an atomic model that combines the Tao potential with the crystallographic structure is introduced to calculate the distribution and lifetime of Ps intrinsic to a given framework. A parametrization of the model is undertaken for a set of widely applied zeolite framework types (*BEA, FAU, FER, MFI, MOR, UTL), before extending the model to all known structures. The results are compared to structural and topological descriptors, and to the Tao-Eldrup model adapted for zeolites, demonstrating the intricate dependence of the lifetime on the pore architecture.

  6. Graphene-Induced Pore Formation on Cell Membranes

    NASA Astrophysics Data System (ADS)

    Duan, Guangxin; Zhang, Yuanzhao; Luan, Binquan; Weber, Jeffrey K.; Zhou, Royce W.; Yang, Zaixing; Zhao, Lin; Xu, Jiaying; Luo, Judong; Zhou, Ruhong

    2017-02-01

    Examining interactions between nanomaterials and cell membranes can expose underlying mechanisms of nanomaterial cytotoxicity and guide the design of safer nanomedical technologies. Recently, graphene has been shown to exhibit potential toxicity to cells; however, the molecular processes driving its lethal properties have yet to be fully characterized. We here demonstrate that graphene nanosheets (both pristine and oxidized) can produce holes (pores) in the membranes of A549 and Raw264.7 cells, substantially reducing cell viability. Electron micrographs offer clear evidence of pores created on cell membranes. Our molecular dynamics simulations reveal that multiple graphene nanosheets can cooperate to extract large numbers of phospholipids from the membrane bilayer. Strong dispersion interactions between graphene and lipid-tail carbons result in greatly depleted lipid density within confined regions of the membrane, ultimately leading to the formation of water-permeable pores. This cooperative lipid extraction mechanism for membrane perforation represents another distinct process that contributes to the molecular basis of graphene cytotoxicity.

  7. Pore design and engineering for filters and membranes.

    PubMed

    Holdich, Richard; Kosvintsev, Serguei; Cumming, Iain; Zhdanov, Sergey

    2006-01-15

    In filtration, the concept of pore size is not easy to define. In microfiltration, there are numerous advantages in employing a surface filtering membrane, rather than one relying on depth filtration mechanisms from a tortuous pore flow channel. Modern manufacturing techniques provide means to produce surface filtering membranes. For filtration, it is shown that a suitable pore design is an array of long thin slots. An analysis of fluid flow through the slots suggests that a short slot is adequate, but experimental data with suspended material indicates that slot length is important. Using long slots and careful control of the flow through the membrane it is possible to filter deforming particles such as oil drops from water.

  8. Pore size distribution in an uncompacted equilibrated ordinary chondrite

    SciTech Connect

    Friedrich, J.M.; Macke, R.J.; Wignarajah, D.P.; Rivers, M.L.; Britt, D.T.; Ebel, D.S.

    2008-05-30

    The extraordinarily uncompacted nature of the ordinary L chondrite fall Baszkowka gives a unique opportunity to investigate the potentially pre-compaction pore size distribution in an equilibrated ordinary chondrite. Using X-ray microtomography and helium pycnometry on two samples of Baszkowka, we have found that on average, two-thirds of the 19.0% porosity resides in inter- and intra-granular voids with volumes between {approx}3 x10{sup 05} and 3 mm{sup 3}. We show the cumulative number density of pore volumes observable by X-ray microtomography obeys a power law distribution function in this equilibrated ordinary chondrite. We foresee these data adding to our understanding of the impact processing of chondrites and their parent asteroids, where porosity and pore size play significant roles in the parameterization of impact events.

  9. Hydroxyapatite (HA) bone scaffolds with controlled macrochannel pores.

    PubMed

    Bae, Chang-Jun; Kim, Hae-Won; Koh, Young-Hag; Kim, Hyoun-Ee

    2006-06-01

    Hydroxyapatite (HA) macrochanneled porous scaffolds, with a controlled pore structure, were fabricated via a combination of the extrusion and lamination processes. The scaffold was architectured by aligning and laminating the extruded HA and carbon filaments. The macrochannel pores were formed by removing the carbon filaments after thermal treatments (binder removal and sintering). The porosity of the scaffolds was varied between 48 and 73% with a controlled pore size of approximately 450 microm, by adjusting the fractions of HA and carbon filaments. As the porosity was increased from 48 to 73%, the compressive strength decreased from 11.5 to 3.2 MPa. However, the osteoblast-like cell responses on the scaffold, such as the proliferation rate and alkaline phosphatase (ALP) activity, were significantly enhanced as the porosity was increased.

  10. Integration of pore features into the evaluation of fingerprint evidence.

    PubMed

    Anthonioz, Alexandre; Champod, Christophe

    2014-01-01

    Fingerprint practitioners rely on level 3 features to make decisions in relation to the source of an unknown friction ridge skin impression. This research proposes to assess the strength of evidence associated with pores when shown in (dis)agreement between a mark and a reference print. Based upon an algorithm designed to automatically detect pores, a metric is defined in order to compare different impressions. From this metric, the weight of the findings is quantified using a likelihood ratio. The results obtained on four configurations and 54 donors show the significant contribution of the pore features and translate into statistical terms what latent fingerprint examiners have developed holistically through experience. The system provides LRs that are indicative of the true state under both the prosecution and the defense propositions. Not only such a system brings transparency regarding the weight to assign to such features, but also forces a discussion in relation to the risks of such a model to mislead.

  11. Fines classification based on sensitivity to pore-fluid chemistry

    USGS Publications Warehouse

    Jang, Junbong; Santamarina, J. Carlos

    2016-01-01

    The 75-μm particle size is used to discriminate between fine and coarse grains. Further analysis of fine grains is typically based on the plasticity chart. Whereas pore-fluid-chemistry-dependent soil response is a salient and distinguishing characteristic of fine grains, pore-fluid chemistry is not addressed in current classification systems. Liquid limits obtained with electrically contrasting pore fluids (deionized water, 2-M NaCl brine, and kerosene) are combined to define the soil “electrical sensitivity.” Liquid limit and electrical sensitivity can be effectively used to classify fine grains according to their fluid-soil response into no-, low-, intermediate-, or high-plasticity fine grains of low, intermediate, or high electrical sensitivity. The proposed methodology benefits from the accumulated experience with liquid limit in the field and addresses the needs of a broader range of geotechnical engineering problems.

  12. Pore size of agarose gels by atomic force microscopy.

    PubMed

    Pernodet, N; Maaloum, M; Tinland, B

    1997-01-01

    The pore size of agarose gel in water at different concentrations was directly measured using atomic force microscopy (AFM). The experiment was specially designed to work under aqueous conditions and allows direct observation of the "unperturbed" gel without invasive treatment. The pore size a as a function of gel concentration C shows a power law dependence a approximately C-gamma, where gamma lies between the prediction of the Ogston model for a random array of straight chains, 0.5, and the value predicted by De Gennes for a network of flexible chains, 0.75. We confirm that gels present a wide pore size distribution and show that it narrows as the concentration increases.

  13. Pore Water Transport of Enterococci out of Beach Sediments

    PubMed Central

    Phillips, Matthew C.; Solo-Gabriele, Helena M.; Reniers, Adrianus J. H. M.; Wang, John D.; Kiger, Russell T.; Abdel-Mottaleb, Noha

    2011-01-01

    Enterococci are used to evaluate the safety of beach waters and studies have identified beach sands as a source of these bacteria. In order to study and quantify the release of microbes from beach sediments, flow column systems were built to evaluate flow of pore water out of beach sediments. Results show a peak in enterococci (average of 10% of the total microbes in core) released from the sand core within one pore water volume followed by a marked decline to below detection. These results indicate that few enterococci are easily removed and that factors other than simple pore water flow control the release of the majority of enterococci within beach sediments. A significantly larger quantity and release of enterococci were observed in cores collected after a significant rain event suggesting the influx of fresh water can alter the release pattern as compared to cores with no antecedent rainfall. PMID:21945015

  14. Translocation of an Incompressible Vesicle through a Pore

    PubMed Central

    Shojaei, Hamid R.; Muthukumar, Murugappan

    2016-01-01

    We have derived the free energy landscape for the translocation of a single vesicle through a narrow pore by accounting for bending and stretching of the vesicle, and the deformation of the vesicle by the pore. Emergence of a free energy barrier for translocation is a general result, and the magnitude of the barrier is calculated in terms of the various material parameters. The extent of the reduction in the barrier by the presence of an external constant force is calculated. Using the Fokker–Planck formalism, we have calculated the average translocation time corresponding to the various free energy landscapes representing different parameter sets. The dependencies of the average translocation time on the strength of the external force, vesicle size, bending and stretching moduli of the vesicle, and radius and length of the pore are derived, and the computed results are discussed. PMID:27089012

  15. Investigation of the Effect of the Tortuous Pore Structure on Water Diffusion through a Polymer Film Using Lattice Boltzmann Simulations.

    PubMed

    Gebäck, Tobias; Marucci, Mariagrazia; Boissier, Catherine; Arnehed, Johan; Heintz, Alexei

    2015-04-23

    Understanding how the pore structure influences the mass transport through a porous material is important in several applications, not the least in the design of polymer film coatings intended to control drug release. In this study, a polymer film made of ethyl cellulose and hydroxypropyl cellulose was investigated. The 3D structure of the films was first experimentally characterized using confocal laser scanning microscopy data and then mathematically reconstructed for the whole film thickness. Lattice Boltzmann simulations were performed to compute the effective diffusion coefficient of water in the film and the results were compared to experimental data. The local porosities and pore sizes were also analyzed to determine how the properties of the internal film structure affect the water effective diffusion coefficient. The results show that the top part of the film has lower porosity, lower pore size, and lower connectivity, which results in a much lower effective diffusion coefficient in this part, largely determining the diffusion rate through the entire film. Furthermore, the local effective diffusion coefficients were not proportional to the local film porosity, indicating that the results cannot be explained by a single tortuosity factor. In summary, the proposed methodology of combining microscopy data, mass transport simulations, and pore space analysis can give valuable insights on how the film structure affects the mass transport through the film.

  16. Pore Scale Observations of Trapped CO2 in Mixed-Wet Carbonate Rock: Applications to Storage in Oil Fields.

    PubMed

    Al-Menhali, Ali S; Menke, Hannah P; Blunt, Martin J; Krevor, Samuel C

    2016-09-20

    Geologic CO2 storage has been identified as a key to avoiding dangerous climate change. Storage in oil reservoirs dominates the portfolio of existing projects due to favorable economics. However, in an earlier related work ( Al-Menhali and Krevor Environ. Sci. Technol. 2016 , 50 , 2727 - 2734 ) , it was identified that an important trapping mechanism, residual trapping, is weakened in rocks with a mixed wetting state typical of oil reservoirs. We investigated the physical basis of this weakened trapping using pore scale observations of supercritical CO2 in mixed-wet carbonates. The wetting alteration induced by oil provided CO2-wet surfaces that served as conduits to flow. In situ measurements of contact angles showed that CO2 varied from nonwetting to wetting throughout the pore space, with contact angles ranging 25° < θ < 127°; in contrast, an inert gas, N2, was nonwetting with a smaller range of contact angle 24° < θ < 68°. Observations of trapped ganglia morphology showed that this wettability allowed CO2 to create large, connected, ganglia by inhabiting small pores in mixed-wet rocks. The connected ganglia persisted after three pore volumes of brine injection, facilitating the desaturation that leads to decreased trapping relative to water-wet systems.

  17. Pore invasion dynamics during fluid front displacement in porous media determine functional pore size distribution and phase entrapment

    NASA Astrophysics Data System (ADS)

    Moebius, F.; Or, D.

    2012-12-01

    Dynamics of fluid fronts in porous media shape transport properties of the unsaturated zone and affect management of petroleum reservoirs and their storage properties. What appears macroscopically as smooth and continuous motion of a displacement fluid front may involve numerous rapid interfacial jumps often resembling avalanches of invasion events. Direct observations using high-speed camera and pressure sensors in sintered glass micro-models provide new insights on the influence of flow rates, pore size, and gravity on invasion events and on burst size distribution. Fundamental differences emerge between geometrically-defined pores and "functional" pores invaded during a single burst (invasion event). The waiting times distribution of individual invasion events and decay times of inertial oscillations (following a rapid interfacial jump) are characteristics of different displacement regimes. An invasion percolation model with gradients and including the role of inertia provide a framework for linking flow regimes with invasion sequences and phase entrapment. Model results were compared with measurements and with early studies on invasion burst sizes and waiting times distribution during slow drainage processes by Måløy et al. [1992]. The study provides new insights into the discrete invasion events and their weak links with geometrically-deduced pore geometry. Results highlight factors controlling pore invasion events that exert strong influence on macroscopic phenomena such as front morphology and residual phase entrapment shaping hydraulic properties after the passage of a fluid front.

  18. A theoretical analysis and prediction of pore size and pore size distribution in electrospun multilayer nanofibrous materials.

    PubMed

    Bagherzadeh, Roohollah; Najar, Saeed Shaikhzadeh; Latifi, Masoud; Tehran, Mohammad Amani; Kong, Lingxue

    2013-07-01

    Electrospinning process can fabricate nanomaterials with unique nanostructures for potential biomedical and environmental applications. However, the prediction and, consequently, the control of the porous structure of these materials has been impractical due to the complexity of the electrospinning process. In this research, a theoretical model for characterizing the porous structure of the electrospun nanofibrous network has been developed by combining the stochastic and stereological probability approaches. From consideration of number of fiber-to-fiber contacts in an electrospun nanofibrous assembly, geometrical and statistical theory relating morphological and structural parameters of the network to the characteristic dimensions of interfibers pores is provided. It has been shown that these properties are strongly influenced by the fiber diameter, porosity, and thickness of assembly. It is also demonstrated that at a given network porosity, increasing fiber diameter and thickness of the network reduces the characteristic dimensions of pores. It is also discussed that the role of fiber diameter and number of the layer in the assembly is dominant in controlling the pore size distribution of the networks. The theory has been validated experimentally and results compared with the existing theory to predict the pore size distribution of nanofiber mats. It is believed that the presented theory for estimation of pore size distribution is more realistic and useful for further studies of multilayer random nanofibrous assemblies.

  19. Evaluation of Colloid Retention Site Dominance in Variably Saturated Porous Media: An All Pores Pore-Scale Analysis

    NASA Astrophysics Data System (ADS)

    Morales, Veronica; Perez-Reche, Francisco; Holzner, Markus; Kinzelbach, Wolfgang

    2016-04-01

    It is well accepted that colloid and nanoparticle transport processes in porous media differ substantially between water saturated and unsaturated conditions. Differences are frequently ascribed to particle immobilization by association with interfaces with the gas, as well as to restrictions of the liquid medium through which colloids are transported. Yet, the current understanding of the importance of particle retention at gas interfaces is based on observations of single pores or two-dimensional pore network representations, leaving open the question of their statistical significance when all pores in the medium are considered. In order to address this question, column experiments were performed using a model porous medium of glass beads through which Silver particles were transported for conditions of varying water content and water chemistry. X-ray microtomography was subsequently employed as a non-destructive imaging technique to obtain pore-scale information of the entire column regarding: i) the presence and distribution of the main locations where colloids can become retained (interfaces with the water-solid, air-water, air-solid, and air-water-solid, grain-grain contacts, and the bulk liquid), ii) deposition profiles of colloids along the column classified by the available retention location, and iii) channel widths of 3-dimensional pore-water network representations. The results presented provide a direct statistical evaluation on the significance of colloid retention by attachment to interfaces or by strainig at contact points where multiple interfaces meet.

  20. Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases

    NASA Astrophysics Data System (ADS)

    Niether, Doreen; Afanasenkau, Dzmitry; Dhont, Jan K. G.

    2016-04-01

    Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007) Proc Natl Acad Sci USA 104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ˜85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of 10-310-3 wt % that is typical for concentrations in shallow lakes on early Earth.

  1. Benthic invertebrate bioassays with toxic sediment and pore water

    USGS Publications Warehouse

    Giesy, John P.; Rosiu, Cornell J.; Graney, Robert L.; Henry, Mary G.

    1990-01-01

    The relative sensitivities of bioassays to determine the toxicity of sediments were investigated and three methods of making the sample dilutions required to generate dose-response relationships were compared. The assays studied were: (a) Microtox®, a 15-min assay ofPhotobacterium phosphoreum bioluminescence inhibition by pore water; (b) 48-h Daphnia magnalethality test in pore water; (c) 10-d subchronic assay of lethality to and reduction of weight gain by Chironomus tentans performed in either whole sediment or pore water; (d) 168-h acute lethality assay of Hexagenia limbata in either whole sediment or pore water. The three methods of diluting sediments were: (a) extracting pore water from the toxic location and dilution with pore water from the control station; (b) diluting whole sediment from the toxic location with control whole sediment from a reference location, then extracting pore water; and (c) diluting toxic, whole sediment with whole sediment from a reference location, then using the whole sediment in bioassays. Based on lethality, H. limbata was the most sensitive organism to the toxicity of Detroit River sediment. Lethality of D. magna in pore water was similar to that of H. limbata in whole sediment and can be used to predict effects of whole sediment toxicity to H. limbata. The concentration required to cause a 50% reduction in C. tentans growth (10-d EC50) was approximately that which caused 50% lethality of D. magna (48-h LC50) and was similar to the toxicity that restricts benthic invertebrate colonization of contaminated sediments. While the three dilution techniques gave similar results with some assays, they gave very different results in other assays. The dose-response relationships determined by the three dilution techniques would be expected to vary with sediment, toxicant and bioassay type, and the dose-response relationship derived from each technique needs to be interpreted accordingly.

  2. Toward understanding the structure of the vertebrate nuclear pore complex.

    PubMed

    Beck, Martin; Glavy, Joseph S

    2014-01-01

    Nuclear pore complexes are large macromolecular assemblies that facilitate the nucleocytoplasmic exchange of macromolecules. Because of their intricate composition, membrane association, and sheer size, the integration of various, complementary structure determination approaches is a prerequisite for elucidating their structure. We have recently employed such an integrated strategy to analyze the scaffold structure of the cytoplasmic and nuclear rings of the human nuclear pore complex. In this extra view, we highlight two specific aspects of this work: the power of electron microscopy for bridging different resolution regimes and the importance of post-translational modifications for regulating nucleoporin interactions. We review recent technological developments and give a perspective toward future structure determination approaches.

  3. Probing single nanometer-scale pores with polymeric molecular rulers

    NASA Astrophysics Data System (ADS)

    Henrickson, Sarah E.; DiMarzio, Edmund A.; Wang, Qian; Stanford, Vincent M.; Kasianowicz, John J.

    2010-04-01

    We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus α-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the α-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.

  4. Multiscale characterization of pore size distributions using mercury porosimetry and nitrogen adsorption

    NASA Astrophysics Data System (ADS)

    Paz-Ferreiro, J.; Tarquis, A. M.; Miranda, J. G. V.; Vidal Vázquez, E.

    2009-04-01

    The soil pore space is a continuum extremely variable in size, including structures smaller than nanometres and as large as macropores or cracks with millimetres or even centimetres size. Pore size distributions (PSDs) affects important soil functions, such as those related with transmission and storage of water, and root growth. Direct and indirect measurements of PSDs are becoming increasingly used to characterize soil structure. Mercury injection porosimetry and nitrogen adsorption isotherms are techniques commonly employed for assessing equivalent pore size diameters in the range from about 50 nm to 100 m and 2 to 500 nm, respectively. The multifractal formalism was used to describe Hg injection curves and N2 adsorption isotherms from two series of a Mollisol cultivated under no tillage and minimum tillage. Soil samples were taken from 0-10, 10-20 and 20-30 cm depths in two experimental fields located in the north of Buenos Aires and South of Santa Fe provinces, Argentina. All the data sets analyzed from the two studied soil attributes showed remarkably good scaling trends as assessed by singularity spectrum and generalized dimension spectrum. Both, experimental Hg injection curves and N2 adsorption isotherms could be fitted reasonably well with multifractal models. A wide variety of singularity and generalized dimension spectra was found for the variables. The capacity dimensions, D0, for both Hg injection and N2 adsorption data were not significantly different from the Euclidean dimension. However, the entropy dimension, D1, and correlation dimension, D2, obtained from mercury injection and nitrogen adsorption data showed significant differences. So, D1 values were on average 0.868 and varied from 0.787 to 0.925 for Hg intrusion curves. Entropy dimension, D1, values for N2 adsorption isotherms were on average 0.582 significantly lower than those obtained when using the former technique. Twenty-three out of twenty-four N2 isotherms had D1 values in a

  5. Increase in capacitance by subnanometer pores in carbon

    SciTech Connect

    Jackel, Nicolas; Simon, Patrice; Gogotsi, Yury G.; Presser, Volker

    2016-11-21

    Electrical double-layer capacitors (EDLCs, also known as supercapacitors or ultracapacitors) store energy by electrosorption of ions at the electrode/electrolyte interface. In addition, to achieve a high-energy storage capacity, electrodes with a high surface area and well-developed pore structure in the range from several Angstroms to several tens of nanometers are required.

  6. Predicting pore pressure and porosity from VSP data

    SciTech Connect

    Stone, D.G.

    1984-04-01

    Presently, VSP is being used to predict interval velocity and depth beneath the drill bit. The method is to exploit special properties of the VSP to produce a successful inversion to acoustic impedance. Depth and interval velocity are derived from the acoustic impedance prediction. This technique is often a valuable aid in making drilling decisions. Other rock properties may be computed from the same data. Pore pressure is one such rock parameter that can be computed from interval transit times and depth. The product of interval transit times, depth, normal compaction ratios, and an area constant is pore pressure. Pore pressure prediction is as reliable as the predicted velocities and depths. In reservoir evaluation, and sometimes in the well completion program, porosity is the important rock property. The interval transit times predicted beneath the bit can be used to compute porosity. Unlike pore pressure, porosity computations require knowledge or assumptions about the rock matrix and shale percentages. For certain conditions these values are known. Further penetration of a reef in search of deeper porous zones is an example of a viable condition for porosity prediction. For both these rock properties the same conventions employed by well log analysis in modifying and interpreting results are needed. Where the parameters assumed fit the actual conditions, the results should have merit. If not, further interpretation is required.

  7. FOULING OF FINE PORE DIFFUSED AERATORS: AN INTER- PLANT COMPARISON

    EPA Science Inventory

    There has been increasing interest in fine pore aeration systems, along with concerned about diffuser fouling and the subsequent loss of aeration efficiency. The objective of this study was to assess the relative fouling tendency of fine bubble diffusers t nine activated sludge ...

  8. Bi-directionally draining pore fluid extraction vessel

    DOEpatents

    Prizio, Joseph; Ritt, Alexander; Mower, Timothy E.; Rodine, Lonn

    1991-01-01

    The invention is used to extract pore fluid from porous solids through a combination of mechanical compression and inert-gas injection and comprises a piston for axially compressing samples to force water out, and top and bottom drainage plates for capturing the exuded water and using inert gas to force water to exit when the limits of mechanical compression have been reached.

  9. Pore-scale Modelling of Capillarity in Swelling Granular Materials

    NASA Astrophysics Data System (ADS)

    Hassanizadeh, S. M.; Sweijen, T.; Nikooee, E.; Chareyre, B.

    2015-12-01

    Capillarity in granular porous media is a common and important phenomenon in earth materials and industrial products, and therefore has been studied extensively. To model capillarity in granular porous media, one needs to go beyond current models which simulate either two-phase flow in porous media or mechanical behaviour in granular media. Current pore-scale models for two-phase flow such as pore-network models are tailored for rigid pore-skeletons, even though in many applications, namely hydro-mechanical coupling in soils, printing, and hygienic products, the porous structure does change during two-phase flow. On the other hand, models such as Discrete Element Method (DEM), which simulate the deformable porous media, have mostly been employed for dry or saturated granular media. Here, the effects of porosity change and swelling on the retention properties was studied, for swelling granular materials. A pore-unit model that was capable to construct the capillary pressure - saturation curve was coupled to DEM. Such that the capillary pressure - saturation curve could be constructed for varying porosities and amounts of absorbed water. The study material was super absorbent polymer particles, which are capable to absorb water 10's to 200 times their initial weight. We have simulated quasi-static primary imbibition for different porosities and amounts of absorbed water. The results reveal a 3 dimensional surface between capillary pressure, saturation, and porosity, which can be normalized by means of the entry pressure and the effective water saturation to a unique curve.

  10. Pore Water Pumping by Upside-Down Jellyfish

    NASA Astrophysics Data System (ADS)

    Gaddam, Manikantam; Santhanakrishnan, Arvind

    2016-11-01

    Patchy aggregations of Cassiopea medusae, commonly called upside-down jellyfish, are found in sheltered marine environments with low-speed ambient flows. These medusae exhibit a sessile, non-swimming lifestyle, and are oriented such that their bells are attached to the substrate and oral arms point towards sunlight. Pulsations of their bells are used to generate currents for suspension feeding. Their pulsations have also been proposed to generate forces that can release sediment locked nutrients into the surrounding water. The goal of this study is to examine pore water pumping by Cassiopea individuals in laboratory aquaria, as a model for understanding pore water pumping in unsteady flows. Planar laser-induced fluorescence (PLIF) measurements were conducted to visualize the release of pore water via bell motion, using fluorescent dye introduced underneath the substrate. 2D particle image velocimetry (PIV) measurements were conducted on the same individuals to correlate PLIF-based concentration profiles with the jets generated by pulsing of medusae. The effects of varying bell diameter on pore water release and pumping currents will be discussed.

  11. Pore structure development in oxidized IG-110 nuclear graphite

    NASA Astrophysics Data System (ADS)

    Wang, Peng; Contescu, Cristian I.; Yu, Suyuan; Burchell, Timothy D.

    2012-11-01

    The oxidation-induced porosity development in nuclear graphite has great effect on its mechanical behavior, thus it is very important to understand the pore structure development of nuclear graphite during oxidation. This paper reports on the oxidation kinetics of grade IG-110 nuclear graphite and the porosity development in oxidized samples. The distribution of the oxidized layer in IG-110 specimens oxidized at 600-750 °C was studied using optical microscopy coupled with automated image analysis technique, and the mechanism of porosity development was determined. The thickness of oxidized layer decreased with the oxidation temperature but was independent of the weight loss level. Oxidation caused consumption of graphite structure and development of porosity, which was initiated from the binder phase. Statistical analysis indicated that generation and growth of pores was dominant at low temperatures, while merging and collapse of pores was the main effect at high temperatures. Compared with medium-grained PCEA graphite, the fine-grained IG-110 graphite demonstrates deeper penetration of the oxidant because of its higher pore density and greater porosity.

  12. Pore structure development in oxidized IG-110 nuclear graphite

    SciTech Connect

    Wang, Peng; Contescu, Cristian I; Yu, Suyuan; Burchell, Timothy D

    2012-01-01

    The oxidation-induced porosity development in nuclear graphite has great effect on its mechanical behavior, thus it is very important to understand the pore structure development of nuclear graphite during oxidation. This paper reports on the oxidation kinetics of grade IG-110 nuclear graphite and the porosity development in oxidized samples. The distribution of the oxidized layer in IG-110 specimens oxidized at 600-750 C was studied using optical microscopy coupled with automated image analysis technique, and the mechanism of porosity development was determined. The thickness of oxidized layer decreased with the oxidation temperature but was independent of the weight loss level. Oxidation caused consumption of graphite structure and development of porosity, which was initiated from the binder phase. Statistical analysis indicated that generation and growth of pores was dominant at low temperatures, while merging and collapse of pores was the main effect at high temperatures. Compared with medium-grained PCEA graphite, the fine-grained IG-110 graphite demonstrates deeper penetration of the oxidant because of its higher pore density and lager porosity.

  13. Microstructural characterization and pore structure analysis of nuclear graphite

    NASA Astrophysics Data System (ADS)

    Kane, J.; Karthik, C.; Butt, D. P.; Windes, W. E.; Ubic, R.

    2011-08-01

    Graphite will be used as a structural and moderator material in next-generation nuclear reactors. While the overall nature of the production of nuclear graphite is well understood, the historic nuclear grades of graphite are no longer available. This paper reports the virgin microstructural characteristics of filler particles and macro-scale porosity in virgin nuclear graphite grades of interest to the Next Generation Nuclear Plant program. Optical microscopy was used to characterize filler particle size and shape as well as the arrangement of shrinkage cracks. Computer aided image analysis was applied to optical images to quantitatively determine the variation of pore structure, area, eccentricity, and orientation within and between grades. The overall porosity ranged between ˜14% and 21%. A few large pores constitute the majority of the overall porosity. The distribution of pore area in all grades was roughly logarithmic in nature. The average pore was best fit by an ellipse with aspect ratio of ˜2. An estimated 0.6-0.9% of observed porosity was attributed to shrinkage cracks in the filler particles. Finally, a preferred orientation of the porosity was observed in all grades.

  14. Microstructural Characterization and Pore Structure Analysis of Nuclear Graphite

    SciTech Connect

    J. Kane; C. Karthik; D. P. Butt; W. E. Windes; R. Ubic

    2011-08-01

    Graphite will be used as a structural and moderator material in next-generation nuclear reactors. While the overall nature of the production of nuclear graphite is well understood, the historic nuclear grades of graphite are no longer available. This paper reports the virgin microstructural characteristics of filler particles and macro-scale porosity in virgin nuclear graphite grades of interest to the Next Generation Nuclear Plant program. Optical microscopy was used to characterize filler particle size and shape as well as the arrangement of shrinkage cracks. Computer aided image analysis was applied to optical images to quantitatively determine the variation of pore structure, area, eccentricity, and orientation within and between grades. The overall porosity ranged between {approx}14% and 21%. A few large pores constitute the majority of the overall porosity. The distribution of pore area in all grades was roughly logarithmic in nature. The average pore was best fit by an ellipse with aspect ratio of {approx}2. An estimated 0.6-0.9% of observed porosity was attributed to shrinkage cracks in the filler particles. Finally, a preferred orientation of the porosity was observed in all grades.

  15. The Outer Pore and Selectivity Filter of TRPA1

    PubMed Central

    Christensen, Adam P.; Corey, David P.

    2016-01-01

    TRPA1 (transient-receptor-potential-related ion channel with ankyrin domains) is a direct receptor or indirect effector for a wide variety of nociceptive signals, and thus is a compelling target for development of analgesic pharmaceuticals such as channel blockers. Recently, the structure of TRPA1 was reported, providing insights into channel assembly and pore architecture. Here we report whole-cell and single-channel current recordings of wild-type human TRPA1 as well as TRPA1 bearing point mutations of key charged residues in the outer pore. These measurements demonstrate that the glutamate at position 920 plays an important role in collecting cations into the mouth of the pore, by changing the effective surface potential by ~16 mV, while acidic residues further out have little effect on permeation. Electrophysiology experiments also confirm that the aspartate residue at position 915 represents a constriction site of the TRPA1 pore and is critical in controlling ion permeation. PMID:27824920

  16. Microporous polyphenylenes with tunable pore size for hydrogen storage.

    PubMed

    Yuan, Shengwen; Dorney, Brian; White, Desiree; Kirklin, Scott; Zapol, Peter; Yu, Luping; Liu, Di-Jia

    2010-07-07

    A series of highly porous polymers with similar BET surface areas of higher than 1000 m(2) g(-1) but tunable pore ranging from 0.7 nm to 0.9 nm were synthesized through facile ethynyl trimerization reaction to demonstrate the surface property-hydrogen adsorption relationship.

  17. Improving pore interconnectivity in polymeric scaffolds for tissue engineering.

    PubMed

    Aydin, H M; El Haj, A J; Pişkin, E; Yang, Y

    2009-08-01

    A new scaffold fabrication technique aiming to enhance pore interconnectivity for tissue engineering has been developed. Medical grade poly(lactic acid) was utilized to generate scaffolds by a solvent-evaporating/particulate-leaching technique, using a new dual-porogen system. Water-soluble sodium chloride particles were used to control macro-pore size in the range 106-255 microm, while organic naphthalene was utilized as a porogen to increase pore interconnections. The three-dimensional (3D) morphology of the scaffolds manufactured with and without naphthalene was examined by optical coherence tomography and scanning electron microscopy. The mechanical properties of the scaffolds were characterized by compression tests. MG63 osteoblast cells were seeded in the scaffolds to study the cell attachment and viability evaluated by confocal microscopy. It was revealed that introducing naphthalene as the second porogen in the solvent-evaporating/particulate-leaching process resulted in improvement of the pore interconnectivity. Cells grew in both scaffolds fabricated with and without naphthalene. They exhibited strong green fluorescence when using a live/dead fluorescent dye kit, indicating that the naphthalene in the scaffold process did not affect cell viability.

  18. Hydrochromic conjugated polymers for human sweat pore mapping

    PubMed Central

    Lee, Joosub; Pyo, Minkyeong; Lee, Sang-hwa; Kim, Jaeyong; Ra, Moonsoo; Kim, Whoi-Yul; Park, Bum Jun; Lee, Chan Woo; Kim, Jong-Man

    2014-01-01

    Hydrochromic materials have been actively investigated in the context of humidity sensing and measuring water contents in organic solvents. Here we report a sensor system that undergoes a brilliant blue-to-red colour transition as well as ‘Turn-On’ fluorescence upon exposure to water. Introduction of a hygroscopic element into a supramolecularly assembled polydiacetylene results in a hydrochromic conjugated polymer that is rapidly responsive (<20 μs), spin-coatable and inkjet-compatible. Importantly, the hydrochromic sensor is found to be suitable for mapping human sweat pores. The exceedingly small quantities (sub-nanolitre) of water secreted from sweat pores are sufficient to promote an instantaneous colorimetric transition of the polymer. As a result, the sensor can be used to construct a precise map of active sweat pores on fingertips. The sensor technology, developed in this study, has the potential of serving as new method for fingerprint analysis and for the clinical diagnosis of malfunctioning sweat pores. PMID:24781362

  19. Nanoporous carbide-derived carbon with tunable pore size

    NASA Astrophysics Data System (ADS)

    Gogotsi, Yury; Nikitin, Alexei; Ye, Haihui; Zhou, Wei; Fischer, John E.; Yi, Bo; Foley, Henry C.; Barsoum, Michel W.

    2003-09-01

    Porous solids are of great technological importance due to their ability to interact with gases and liquids not only at the surface, but throughout their bulk. Although large pores can be produced and well controlled in a variety of materials, nanopores in the range of 2 nm and below (micropores, according to IUPAC classification) are usually achieved only in carbons or zeolites. To date, major efforts in the field of porous materials have been directed towards control of the size, shape and uniformity of the pores. Here we demonstrate that porosity of carbide-derived carbons (CDCs) can be tuned with subångström accuracy in a wide range by controlling the chlorination temperature. CDC produced from Ti3SiC2 has a narrower pore-size distribution than single-wall carbon nanotubes or activated carbons; its pore-size distribution is comparable to that of zeolites. CDCs are produced at temperatures from 200-1,200 °C as a powder, a coating, a membrane or parts with near-final shapes, with or without mesopores. They can find applications in molecular sieves, gas storage, catalysts, adsorbents, battery electrodes, supercapacitors, water/air filters and medical devices.

  20. Nanoporous carbide-derived carbon with tunable pore size.

    PubMed

    Gogotsi, Yury; Nikitin, Alexei; Ye, Haihui; Zhou, Wei; Fischer, John E; Yi, Bo; Foley, Henry C; Barsoum, Michel W

    2003-09-01

    Porous solids are of great technological importance due to their ability to interact with gases and liquids not only at the surface, but throughout their bulk. Although large pores can be produced and well controlled in a variety of materials, nanopores in the range of 2 nm and below (micropores, according to IUPAC classification) are usually achieved only in carbons or zeolites. To date, major efforts in the field of porous materials have been directed towards control of the size, shape and uniformity of the pores. Here we demonstrate that porosity of carbide-derived carbons (CDCs) can be tuned with subångström accuracy in a wide range by controlling the chlorination temperature. CDC produced from Ti3SiC2 has a narrower pore-size distribution than single-wall carbon nanotubes or activated carbons; its pore-size distribution is comparable to that of zeolites. CDCs are produced at temperatures from 200-1,200 degrees C as a powder, a coating, a membrane or parts with near-final shapes, with or without mesopores. They can find applications in molecular sieves, gas storage, catalysts, adsorbents, battery electrodes, supercapacitors, water/air filters and medical devices.

  1. Pore-size distributions of N-isopropylacrylamide (NIPA) hydrogels

    SciTech Connect

    Walther, D.H.; Blanch, H.W.; Prausnitz, J.M. |

    1993-11-01

    Pore-size distributions have been measured for N-isopropylacrylamide (NIPA) hydrogels at 25 and 32{degrees}C with swelling capacities 11.3 and 6.0 g swollen gel per g dry gel. The mixed-solute-exclusion method (introduced by Kuga) was used to obtain the experimental solute-exclusion curve which represents the amount of imbibed liquid inside the gel inaccessible for a solute of radius r. The pore-size distributions were obtained by using Casassa`s Brownian-motion model and numerically solving the Fredholm integral equation. The pore-size distributions of temperature-sensitive NIPA hydrogels are strongly dependent on temperature which determines swelling capacity. With increasing swelling capacity (from 6.0 to 11.3), the pore-size distribution shifts to higher mode values (27.3 to 50.6 {angstrom}) and to higher variance (1.07{center_dot}10{sup 3} to 3.58{center_dot}10{sup 3} {angstrom}{sup 2}).

  2. Capillary condensation of 4He in cylindrical pores

    NASA Astrophysics Data System (ADS)

    Urrutia, Ignacio; Szybisz, Leszek

    2004-10-01

    The adsorption of superfluid 4He confined into cylindrical pores of alkali metals is illustrated by looking at the case of Na. A density functional formalism is utilized for the theoretical description. The energetics and density profiles are determined as a function of the radius of cylinders and the filling fraction. These results are compared with those provided by a simple model recently proposed.

  3. Effects of pore-scale precipitation on permeability and flow

    NASA Astrophysics Data System (ADS)

    Noiriel, Catherine; Steefel, Carl I.; Yang, Li; Bernard, Dominique

    2016-09-01

    The effects of calcite precipitation on porous media permeability and flow were evaluated with a combined experimental and modeling approach. X-ray microtomography images of two columns packed with glass beads and calcite (spar crystals) or aragonite (Bahamas ooids) injected with a supersaturated solution (log Ω = 1.42) were processed in order to calculate rates of calcite precipitation with a spatial resolution of 4.46 μm. Identification and localization of the newly precipitated crystals on the 3D images was performed and results used to calculate the crystal growth rates and velocities. The effects of carbonate precipitation were also evaluated in terms of the integrated precipitation rate over the length of the column, crystal shape, surface area and pore roughness changes. While growth was epitaxial on calcite spar, calcite rhombohedra formed on glass beads and clusters of polyhedrons formed on aragonite ooids. Near the column inlet, calcite precipitation occurred preferentially on carbonate grains compared to glass beads, with almost 100% of calcite spar surface area covered by new crystals versus 92% in the case of aragonite and 11% in the case of glass beads. Although the experimental chemistry and flow boundary conditions in the two columns were similar, their porosity-permeability evolution was different because the nucleation and subsequent crystal growth on the two substrates (i.e., calcite spar and aragonite ooids) was very different. The impact of mineral precipitation on pore-scale flow and permeability was evaluated using a pore-scale Stokes solver that accounted for the changes in pore geometry. For similar magnitude reductions in porosity, the decrease in permeability was highest within the sample that experienced the greatest increase in pore roughness. Various porous media models were generated to show the impact of different crystal growth patterns and pore roughness changes on flow and permeability-porosity relationship. Under constant flow

  4. How Lipid Membranes Affect Pore Forming Toxin Activity.

    PubMed

    Rojko, Nejc; Anderluh, Gregor

    2015-12-15

    Pore forming toxins (PFTs) evolved to permeate the plasma membrane of target cells. This is achieved in a multistep mechanism that usually involves binding of soluble protein monomer to the lipid membrane, oligomerization at the plane of the membrane, and insertion of part of the polypeptide chain across the lipid membrane to form a conductive channel. Introduced pores allow uncontrolled transport of solutes across the membrane, inflicting damage to the target cell. PFTs are usually studied from the perspective of structure-function relationships, often neglecting the important role of the bulk membrane properties on the PFT mechanism of action. In this Account, we discuss how membrane lateral heterogeneity, thickness, and fluidity influence the pore forming process of PFTs. In general, lipid molecules are more accessible for binding in fluid membranes due to steric reasons. When PFT specifically binds ordered domains, it usually recognizes a specific lipid distribution pattern, like sphingomyelin (SM) clusters or SM/cholesterol complexes, and not individual lipid species. Lipid domains were also suggested to act as an additional concentration platform facilitating PFT oligomerization, but this is yet to be shown. The last stage in PFT action is the insertion of the transmembrane segment across the membranes to build the transmembrane pore walls. Conformational changes are a spontaneous process, and sufficient free energy has to be available for efficient membrane penetration. Therefore, fluid bilayers are permeabilized more readily in comparison to highly ordered and thicker liquid ordered lipid phase (Lo). Energetically more costly insertion into the Lo phase can be driven by the hydrophobic mismatch between the thinner liquid disordered phase (Ld) and large protein complexes, which are unable to tilt like single transmembrane segments. In the case of proteolipid pores, membrane properties can directly modulate pore size, stability, and even selectivity. Finally

  5. The evolution of pore connectivity in magma: Insights on eruptive processes

    NASA Astrophysics Data System (ADS)

    Colombier, Mathieu; Scheu, Bettina; Kueppers, Ulrich; Gurioli, Lucia; Di Muro, Andrea; Wadsworth, Fabian; Vasseur, Jeremie; Dingwell, Donald

    2016-04-01

    The evolution of pore space in magma as well as its connectivity is subjected to continuous changes over an eruptive cycle from magma ascent to eruption and emplacement. Main processes contributing to this evolution are vesiculation (bubble nucleation, growth, coalescence) and densification (bubble collapse, crystallization, compaction, sintering). The evolution of connectivity with respect to porosity during these processes is investigated based on a database compiled from new data acquired by Helium pycnometry and literature data. The database comprises more than 2500 analyses of rock samples covering a broad range of eruptive styles and incorporates the effects of crystallinity, glass H2O content and chemistry. Further it is supplemented by textural images in 2D and 3D and permeability data. We evaluate the trends of the natural samples from our database in the light of experiments on vesiculation (Okumura et al. 2008) and densification (Okumura et al. 2013; Vasseur et al. 2013). In general, we find that pumices from Plinian, sub-Plinian and Phreatoplinian eruptions and scoria from Hawaiian and Strombolian eruptions plot together at high porosity and cover a broad range of connectivity. The high porosity and the abrupt increase of connectivity with porosity observed for these datasets suggest a high percolation threshold above 40 %. Pumices and breadcrust bombs from Vulcanian eruptions form a cluster at intermediate porosities. They follow the experimental vesiculation trend with an increase of connectivity with porosity suggesting much a lower percolation threshold at around 20-30%. Finally, dense volcanic rocks from lava domes, lavas and block and ash flow deposits follow the experimental densification trend. In contrast with permeability, connectivity is not sensitive to pore aperture and tortuosity but only depends on the degree of pore nucleation, coalescence and collapse. We propose that this metric of connectivity permits diagnostic differentiation of

  6. The Water Retention Curves in THF Hydrate-Bearing Sediments - Experimental Measurement and Pore Scale Simulation

    NASA Astrophysics Data System (ADS)

    Mahabadi, N.; Zheng, X.; Dai, S.; Seol, Y.; Zapata, C.; Yun, T.; Jang, J.

    2015-12-01

    The water retention curve (WRC) of hydrate-bearing sediments is critically important to understand the behaviour of hydrate dissociation for gas production. Most gas hydrates in marine environment have been formed from an aqueous phase (gas-dissolved water). However, the gas hydrate formation from an aqueous phase in a laboratory requires long period due to low gas solubility in water and is also associated with many experimental difficulties such as hydrate dissolution, difficult hydrate saturation control, and dynamic hydrate dissolution and formation. In this study, tetrahydrofuran (THF) is chosen to form THF hydrate because the formation process is faster than gas hydrate formation and hydrate saturation is easy to control. THF hydrate is formed at water-excess condition. Therefore, there is only water in the pore space after a target THF hydrate saturation is obtained. The pore habit of THF hydrate is investigated by visual observation in a transparent micromodel and X-ray computed tomography images; and the water retention curves are obtained under different THF hydrate saturation conditions. Targeted THF hydrate saturations are Sh=0, 0.2, 0.4, 0.6 and 0.8. Results shown that at a given water saturation the capillary pressure increases as THF hydrate saturation increases. And the gas entry pressure increases with increasing hydrate saturation. The WRC obtained by experiments is also compared with the results of a pore-network model simulation and Lattice Boltzmann Method. The fitting parameters of van Genuchten equation for different hydrate saturation conditions are suggested for the use as input parameters of reservoir simulators.

  7. Characterization of Gas-Hydrate Sediment: In Situ Evaluation of Hydrate Saturation in Pores of Pressured Sedimental Samples

    NASA Astrophysics Data System (ADS)

    Jin, Y.; Konno, Y.; Kida, M.; Nagao, J.

    2014-12-01

    Hydrate saturation of gas-hydrate bearing sediment is a key of gas production from natural gas-hydrate reservoir. Developable natural gas-hydrates by conventional gas/oil production apparatus almost exist in unconsolidated sedimental layer. Generally, hydrate saturations of sedimental samples are directly estimated by volume of gas generated from dissociation of gas hydrates in pore spaces, porosity data and volume of the sediments. Furthermore, hydrate saturation can be also assessed using velocity of P-wave through sedimental samples. Nevertheless, hydrate saturation would be changed by morphological variations (grain-coating, cementing and pore-filling model) of gas hydrates in pore spaces. Jin et al.[1,2] recently observed the O-H stretching bands of H2O molecules of methane hydrate in porous media using an attenuated total reflection IR (ATR-IR) spectra. They observed in situ hydrate formation/dissociation process in sandy samples (Tohoku Keisya number 8, grain size of ca. 110 μm). In this presentation, we present IR spectroscopy approach to in situ evaluation of hydrate saturation of pressured gas-hydrate sediments. This work was supported by funding from the Research Consortium for Methane Hydrate Resources in Japan (MH21 Research Consortium) planned by the Ministry of Economy, Trade and Industry (METI), Japan. [1] Jin, Y.; Konno, Y.; Nagao, J. Energy Fules, 2012, 26, 2242-2247. [2] Jin, Y.; Oyama, H.; Nagao, J. Jpn. J. Appl. Phys. 2009, 48, No. 108001.

  8. Events leading to the opening and closing of the exocytotic fusion pore have markedly different temperature dependencies. Kinetic analysis of single fusion events in patch-clamped mouse mast cells.

    PubMed Central

    Oberhauser, A F; Monck, J R; Fernandez, J M

    1992-01-01

    The earliest event in exocytosis is the formation of a fusion pore, an aqueous channel that connects the lumen of a secretory granule with the extracellular space. We can observe the formation of individual fusion pores and their subsequent dilation or closure by measuring the changes in the admittance of patch-clamped mast cells during GTP gamma S-stimulated exocytotic fusion. To investigate the molecular structure of the fusion pore, we have studied the temperature dependency of the rate constants for fusion pore formation and closure. An Arrhenius plot of the rate of fusion pore formation shows a simple linear relationship with an apparent activation energy of 23 kcal/mol. In contrast, the Arrhenius plot of the rate of closure of the fusion pore is discontinuous, with the break at approximately 13 degrees C. Above the break point, the rate of closure has a weak temperature dependence (7 kcal/mol), whereas below 13 degrees C the rate of closure is temperature independent. This type of temperature dependency is characteristic of events that depend on diffusion in a lipid phase that undergoes a fluid-solid phase transition. We propose that the formation of the fusion pore is regulated by the conformational change of a molecular structure with a high activation energy, whereas the closure of the fusion pore is regulated by lipids that become phase separated at 13 degrees C. PMID:1504250

  9. Explaining glomerular pores with fiber matrices. A visualization study based on computer modeling.

    PubMed Central

    Booth, J W; Lumsden, C J

    1993-01-01

    The extracellular space of the glomerular capillary wall is occupied by a complex meshwork of fibrous molecules. Little is understood about how the size, shape, and charge recognition properties of glomerular ultrafiltration arise from this space-filling fiber matrix. We studied the problem of size recognition by visualizing the void volume accessible to hard spheres in computer-generated three-dimensional homogeneous random fiber matrices. The spatial organization of the void volume followed a complex "blob-and-throat" pattern in which circumscribed cavities of free space within the matrix ("blobs") were joined to adjacent cavities by narrower throats of void space. For sufficiently small solutes, chains of blobs and throats traversed the matrix, providing pathways for trans-matrix permeation. The matrices showed threshold or gating properties with respect to permeation: solutes whose radius exceeded a critical value, at which a throat on the last connected trans-matrix pathway pinched off, could not cross, whereas smaller solutes had nonzero permeability. The thresholds may give the glomerular fiber matrix porelike response properties and explain why pore models have been such a useful means of treating permselectivity. Images FIGURE 4 FIGURE 5 PMID:8369404

  10. Structural Insights into Clostridium perfringens Delta Toxin Pore Formation.

    PubMed

    Huyet, Jessica; Naylor, Claire E; Savva, Christos G; Gibert, Maryse; Popoff, Michel R; Basak, Ajit K

    2013-01-01

    Clostridium perfringens Delta toxin is one of the three hemolysin-like proteins produced by C. perfringens type C and possibly type B strains. One of the others, NetB, has been shown to be the major cause of Avian Nectrotic Enteritis, which following the reduction in use of antibiotics as growth promoters, has become an emerging disease of industrial poultry. Delta toxin itself is cytotoxic to the wide range of human and animal macrophages and platelets that present GM2 ganglioside on their membranes. It has sequence similarity with Staphylococcus aureus β-pore forming toxins and is expected to heptamerize and form pores in the lipid bilayer of host cell membranes. Nevertheless, its exact mode of action remains undetermined. Here we report the 2.4 Å crystal structure of monomeric Delta toxin. The superposition of this structure with the structure of the phospholipid-bound F component of S. aureus leucocidin (LukF) revealed that the glycerol molecules bound to Delta toxin and the phospholipids in LukF are accommodated in the same hydrophobic clefts, corresponding to where the toxin is expected to latch onto the membrane, though the binding sites show significant differences. From structure-based sequence alignment with the known structure of staphylococcal α-hemolysin, a model of the Delta toxin pore form has been built. Using electron microscopy, we have validated our model and characterized the Delta toxin pore on liposomes. These results highlight both similarities and differences in the mechanism of Delta toxin (and by extension NetB) cytotoxicity from that of the staphylococcal pore-forming toxins.

  11. Single nuclear pores visualized by confocal microscopy and image processing.

    PubMed Central

    Kubitscheck, U; Wedekind, P; Zeidler, O; Grote, M; Peters, R

    1996-01-01

    How nuclear pore complexes, mediating the transport of nucleic acids, proteins, and metabolites between cell nucleus and cytoplasm, are arranged in the nuclear envelope is essentially unknown. Here we describe a method combining high-resolution confocal imaging with image processing and pattern recognition to visualize single nuclear pore complexes (120 nm diameter), determine their relative positions with nanometer accuracy, and analyze their distribution in situ. The method was tested by means of a model system in which the very same sample areas could be imaged by confocal and electron microscopy. It was thus found that single fluorescent beads of 105 nm nominal diameter could be localized with a lateral accuracy of <20 nm and an axial accuracy of approximately 20 nm. The method was applied to digitonin-permeabilized 3T3 cells, whose nuclear pore complexes were fluorescently labeled with the anti-nucleoporin antibody mAb414. Stacks of optical sections were generated by confocal imaging at high resolution. Herein the nuclear pore complexes appeared as bright diffraction-limited spots whose centers were localized by fitting them by three-dimensional gaussians. The nearest-neighbor distribution function and the pair correlation function were calculated and found to agree well with those of randomly distributed hard cylinders of 138 +/- 17 nm diameter, but not with those of randomly distributed points or nonrandomly distributed cylinders. This was supported by a cluster analysis. Implications for the direct observation of the transport of single particles and molecules through individual nuclear pore complexes are discussed. Images FIGURE 1 FIGURE 2 FIGURE 4 PMID:9172731

  12. Pore fabric geometry inferred from magnetic and acoustic anisotropies in rocks with various mineralogy, permeability and porosity

    NASA Astrophysics Data System (ADS)

    Robion, Philippe; David, Christian; Dautriat, Jérémie; Colombier, Jean-Christian; Zinsmeister, Louis; Collin, Pierre-Yves

    2014-08-01

    The ferrofluid impregnation technique combined with anisotropy of magnetic susceptibility measurements (AMSff) is one of the ways to analyze the 3-D geometry of the pore space in a rock and indirectly to infer the anisotropy of permeability. We applied this method on different types of rocks (sandstones and carbonates) with a range of different porosity values (10-30%) and permeability (1 mD to 1 D). To get additional information on both the pore aspect ratio and the directional anisotropy we used another technique, measuring the anisotropy of P-waves velocity (APV) in dry and water saturated conditions. Comparing between both methods shows that despite the good agreement in directional data, inferring the true shape of the porosity is not straightforward. Modeling the presence of an elastic anisotropy in the solid matrix for sandstones allows one to get more consistent values for the pore aspect ratio obtained from both APV and AMSff. However for the carbonate rocks, due to an intricate distribution of microstructures, the aspect ratios obtained show significant discrepancies between the two methods. The ferrofluid method is very sensitive to the quality of the impregnation and suffers from a major drawback which is the threshold size of investigation, limited by the size of the magnetite nanoparticles (10 nm) and probably this method doesn't see all the porosity. On the other hand with acoustic methods, the range of porosity investigated is probably larger but several microstructural attributes can contribute to the elastic anisotropy which makes the pore shape effect more difficult to decipher. Therefore, we promote the combined use of both methods in order to get more reliable information on the pore shape in porous media.

  13. Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly

    NASA Astrophysics Data System (ADS)

    Podobnik, Marjetka; Savory, Peter; Rojko, Nejc; Kisovec, Matic; Wood, Neil; Hambley, Richard; Pugh, Jonathan; Wallace, E. Jayne; McNeill, Luke; Bruce, Mark; Liko, Idlir; Allison, Timothy M.; Mehmood, Shahid; Yilmaz, Neval; Kobayashi, Toshihide; Gilbert, Robert J. C.; Robinson, Carol V.; Jayasinghe, Lakmal; Anderluh, Gregor

    2016-05-01

    The invertebrate cytolysin lysenin is a member of the aerolysin family of pore-forming toxins that includes many representatives from pathogenic bacteria. Here we report the crystal structure of the lysenin pore and provide insights into its assembly mechanism. The lysenin pore is assembled from nine monomers via dramatic reorganization of almost half of the monomeric subunit structure leading to a β-barrel pore ~10 nm long and 1.6-2.5 nm wide. The lysenin pore is devoid of additional luminal compartments as commonly found in other toxin pores. Mutagenic analysis and atomic force microscopy imaging, together with these structural insights, suggest a mechanism for pore assembly for lysenin. These insights are relevant to the understanding of pore formation by other aerolysin-like pore-forming toxins, which often represent crucial virulence factors in bacteria.

  14. Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly

    PubMed Central

    Podobnik, Marjetka; Savory, Peter; Rojko, Nejc; Kisovec, Matic; Wood, Neil; Hambley, Richard; Pugh, Jonathan; Wallace, E. Jayne; McNeill, Luke; Bruce, Mark; Liko, Idlir; Allison, Timothy M.; Mehmood, Shahid; Yilmaz, Neval; Kobayashi, Toshihide; Gilbert, Robert J. C.; Robinson, Carol V.; Jayasinghe, Lakmal; Anderluh, Gregor

    2016-01-01

    The invertebrate cytolysin lysenin is a member of the aerolysin family of pore-forming toxins that includes many representatives from pathogenic bacteria. Here we report the crystal structure of the lysenin pore and provide insights into its assembly mechanism. The lysenin pore is assembled from nine monomers via dramatic reorganization of almost half of the monomeric subunit structure leading to a β-barrel pore ∼10 nm long and 1.6–2.5 nm wide. The lysenin pore is devoid of additional luminal compartments as commonly found in other toxin pores. Mutagenic analysis and atomic force microscopy imaging, together with these structural insights, suggest a mechanism for pore assembly for lysenin. These insights are relevant to the understanding of pore formation by other aerolysin-like pore-forming toxins, which often represent crucial virulence factors in bacteria. PMID:27176125

  15. A specific two-pore domain potassium channel blocker defines the structure of the TASK-1 open pore.

    PubMed

    Streit, Anne K; Netter, Michael F; Kempf, Franca; Walecki, Magdalena; Rinné, Susanne; Bollepalli, Murali K; Preisig-Müller, Regina; Renigunta, Vijay; Daut, Jürgen; Baukrowitz, Thomas; Sansom, Mark S P; Stansfeld, Phillip J; Decher, Niels

    2011-04-22

    Two-pore domain potassium (K(2P)) channels play a key role in setting the membrane potential of excitable cells. Despite their role as putative targets for drugs and general anesthetics, little is known about the structure and the drug binding site of K(2P) channels. We describe A1899 as a potent and highly selective blocker of the K(2P) channel TASK-1. As A1899 acts as an open-channel blocker and binds to residues forming the wall of the central cavity, the drug was used to further our understanding of the channel pore. Using alanine mutagenesis screens, we have identified residues in both pore loops, the M2 and M4 segments, and the halothane response element to form the drug binding site of TASK-1. Our experimental data were used to validate a K(2P) open-pore homology model of TASK-1, providing structural insights for future rational design of drugs targeting K(2P) channels.

  16. A Study of Pore Geometry Effects on Anisotropy in Hydraulic Permeability Using the Lattice-Boltzmann Method

    SciTech Connect

    Stewart, Mark L.; Ward, Andy L.; Rector, David R.

    2006-09-01

    We hypothesize that anisotropy in soil properties arises from pore-scale heterogeneity caused by the alignment of aspherical soil particles. We developed a method to predict the permeability tensor from particle shape and packing structure. Digital geometry maps were created for the pore space in regular cubic and random packs of particles with various aspect ratios using a numerical packing algorithm. The lattice-Boltzmann method was used to simulate saturated flow through these packs, and the effect of particle shape and degree of alignment on the permeability tensor was characterized. Results show that the degree of anisotropy in permeability depends not only upon particle shape and alignment, but also on the three-dimensional structure of the pack. In random packs, more oblate particles and higher degrees of particle alignment lead to reduced permeability perpendicular to the direction of particle alignment compared to the direction parallel to particle alignment.

  17. Single Hepatitis-B Virus Core Capsid Binding to Individual Nuclear Pore Complexes in HeLa Cells

    PubMed Central

    Lill, Yoriko; Lill, Markus A.; Fahrenkrog, Birthe; Schwarz-Herion, Kyrill; Paulillo, Sara; Aebi, Ueli; Hecht, Bert

    2006-01-01

    We investigate the interaction of hepatitis B virus capsids lacking a nuclear localization signal with nuclear pore complexes (NPCs) in permeabilized HeLa cells. Confocal and wide-field optical images of the nuclear envelope show well-spaced individual NPCs. Specific interactions of capsids with single NPCs are characterized by extended residence times of capsids in the focal volume which are characterized by fluorescence correlation spectroscopy. In addition, single-capsid-tracking experiments using fast wide-field fluorescence microscopy at 50 frames/s allow us to directly observe specific binding via a dual-color colocalization of capsids and NPCs. We find that binding occurs with high probability on the nuclear-pore ring moiety, at 44 ± 9 nm radial distance from the central axis. PMID:16877503

  18. Analysis of dispersion and absorption characteristics of shear waves in sinusoidally corrugated elastic medium with void pores

    PubMed Central

    Kundu, Santimoy; Gupta, Shishir

    2017-01-01

    This theoretical work reports the dispersion and absorption characteristics of horizontally polarized shear wave (SH-wave) in a corrugated medium with void pores sandwiched between two dissimilar half-spaces. The dispersion and absorption equations have been derived in a closed form using the method of separation of variables. It has been established that there are two different kinds of wavefronts propagating in the proposed media. One of the wavefronts depends on the modulus of rigidity of elastic matrix of the medium and satisfies the dispersion equation of SH-waves. The second wavefront depends on the changes in volume fraction of the pores. Numerical computation of the obtained relations has been performed and the results are depicted graphically. The influence of corrugation, sandiness on the phase velocity and the damped velocity of SH-wave has been studied extensively. PMID:28386416

  19. Effective porosity and pore-throat sizes of Conasauga Group mudrock: Application, test and evaluation of petrophysical techniques

    SciTech Connect

    Dorsch, J.; Katsube, T.J.; Sanford, W.E. |; Dugan, B.E.; Tourkow, L.M.

    1996-04-01

    Effective porosity (specifically referring to the interconnected pore space) was recently recognized as being essential in determining the effectiveness and extent of matrix diffusion as a transport mechanism within fractured low-permeability rock formations. The research presented in this report was performed to test the applicability of several petrophysical techniques for the determination of effective porosity of fine-grained siliciclastic rocks. In addition, the aim was to gather quantitative data on the effective porosity of Conasauga Group mudrock from the Oak Ridge Reservation (ORR). The quantitative data reported here include not only effective porosities based on diverse measurement techniques, but also data on the sizes of pore throats and their distribution, and specimen bulk and grain densities. The petrophysical techniques employed include the immersion-saturation method, mercury and helium porosimetry, and the radial diffusion-cell method.

  20. Analysis of dispersion and absorption characteristics of shear waves in sinusoidally corrugated elastic medium with void pores

    NASA Astrophysics Data System (ADS)

    Pandit, Deepak Kr.; Kundu, Santimoy; Gupta, Shishir

    2017-02-01

    This theoretical work reports the dispersion and absorption characteristics of horizontally polarized shear wave (SH-wave) in a corrugated medium with void pores sandwiched between two dissimilar half-spaces. The dispersion and absorption equations have been derived in a closed form using the method of separation of variables. It has been established that there are two different kinds of wavefronts propagating in the proposed media. One of the wavefronts depends on the modulus of rigidity of elastic matrix of the medium and satisfies the dispersion equation of SH-waves. The second wavefront depends on the changes in volume fraction of the pores. Numerical computation of the obtained relations has been performed and the results are depicted graphically. The influence of corrugation, sandiness on the phase velocity and the damped velocity of SH-wave has been studied extensively.

  1. Simulating the biofilm-induced evolution of pore-scale flow in porous media

    NASA Astrophysics Data System (ADS)

    Ostvar, S.

    2015-12-01

    We present results on the influence of biofilms on hydraulic conductivity. In thiswork, we use computational methods to compute the hydraulic conductivity onbiofilms of Shewanella onedensis grown in bead packs. The biofilm and beads wereimaged using X-ray computed microtomography, and the change in hydraulic con-ductivity was measured from the change in pressure drop across the column duringflow. Our numerical analysis is based on fully-resolved immersed boundary directnumerical simulations of pre- and post-growth flow fields for three experiments inpolydisperse sphere packings with Re = 0.1, 1, and 10. Correpondence betweenthe experiments and the simulations is established by matching the effective hy-draulic conductivity of the columns that is calculated via (1) simulations usingthe pore geometries that are derived directly from the micro-CT images, and (2)differential pressure transducer measurments. We discuss several aspects of howthe simulations are set up, including the representation of the biofilm surface andinterfacial boundary conditions, and study the structural changes to the flow fieldas a result of biofilm growth. We also use these numerical data to further validatethe method of volume averaging with closure as a viable tool for predicting thehydraulic conductivity from knowledge of the pore space geometry.

  2. Electrical behavior and pore accumulation in a multicellular model for conventional and supra-electroporation

    SciTech Connect

    Gowrishankar, T.R.; Weaver, James C. . E-mail: jcw@mit.edu

    2006-10-20

    Extremely large but very short (20 kV/cm, 300 ns) electric field pulses were reported recently to non-thermally destroy melanoma tumors. The stated mechanism for field penetration into cells is pulse characteristic times faster than charge redistribution (displacement currents). Here we use a multicellular model with irregularly shaped, closely spaced cells to show that instead overwhelming pore creation (supra-electroporation) is dominant, with field penetration due to pores (ionic conduction currents) during most of the pulse. Moreover, the model's maximum membrane potential (about 1.2 V) is consistent with recent experimental observations on isolated cells. We also use the model to show that conventional electroporation resulting from 100 microsecond, 1 kV/cm pulses yields a spatially heterogeneous electroporation distribution. In contrast, the melanoma-destroying pulses cause nearly homogeneous electroporation of cells and their nuclear membranes. Electropores can persist for times much longer than the pulses, and are likely to be an important mechanism contributing to cell death.

  3. Micro- and meso-scale pore structure in mortar in relation to aggregate content

    SciTech Connect

    Gao, Yun; De Schutter, Geert; Ye, Guang

    2013-10-15

    Mortar is often viewed as a three-phase composite consisting of aggregate, bulk paste, and an interfacial transition zone (ITZ). However, this description is inconsistent with experimental findings because of the basic assumption that larger pores are only present within the ITZ. In this paper, we use backscattered electron (BSE) imaging to investigate the micro- and meso-scale structure of mortar with varying aggregate content. The results indicate that larger pores are present not only within the ITZ but also within areas far from aggregates. This phenomenon is discussed in detail based on a series of analytical calculations, such as the effective water binder ratio and the inter-aggregate spacing. We developed a modified computer model that includes a two-phase structure for bulk paste. This model interprets previous mercury intrusion porosimetry data very well. -- Highlights: •Based on BSE, we examine the HCSS model. •We develop the HCSS-DBLB model. •We use the modified model to interpret the MIP data.

  4. Control of Mechanical Properties of Three-Dimensional Ti-6Al-4V Products Fabricated by Electron Beam Melting with Unidirectional Elongated Pores

    NASA Astrophysics Data System (ADS)

    Ikeo, Naoko; Ishimoto, Takuya; Serizawa, Ai; Nakano, Takayoshi

    2014-09-01

    Aligned, unidirectional, elongated pores were incorporated in Ti-6Al-4V products fabricated by electron beam melting in order to control the mechanical properties of the products such that they became suitable for biomedical applications. Unidirectional pores were successfully produced when the scan spacing of the electron beam was greater than the diameter of the beam. By changing the scan spacing of the electron beam, the size of the unidirectional pores could be varied. As a result, both the Young's moduli and the yield stresses of the products with unidirectional pores decreased linearly with an increase in their porosity, owing to the stress concentration coefficient being 1 in the equation representing the relation between strength and porosity for porous materials. Further, low (<35 GPa) Young's moduli were obtained when the scan spacing was 1 mm or higher, with these values being were close to the typical Young's modulus of human cortical bone. This suggested that these porous materials could be used to fabricate customized bone implants that exhibited desired mechanical properties and suppressed the stress shielding of bone that is normally noticed when implants made of Ti alloys are used.

  5. Rock Pore Structure as Main Reason of Rock Deterioration

    NASA Astrophysics Data System (ADS)

    Ondrášik, Martin; Kopecký, Miloslav

    2014-03-01

    Crashed or dimensional rocks have been used as natural construction material, decoration stone or as material for artistic sculptures. Especially old historical towns not only in Slovakia have had experiences with use of stones for construction purposes for centuries. The whole buildings were made from dimensional stone, like sandstone, limestone or rhyolite. Pavements were made especially from basalt, andesite, rhyolite or granite. Also the most common modern construction material - concrete includes large amounts of crashed rock, especially limestone, dolostone and andesite. However, rock as any other material if exposed to exogenous processes starts to deteriorate. Especially mechanical weathering can be very intensive if rock with unsuitable rock properties is used. For long it had been believed that repeated freezing and thawing in relation to high absorption is the main reason of the rock deterioration. In Slovakia for many years the high water absorption was set as exclusion criterion for use of rocks and stones in building industry. Only after 1989 the absorption was accepted as merely informational rock property and not exclusion. The reason of the change was not the understanding of the relationship between the porosity and rock deterioration, but more or less good experiences with some high porous rocks used in constructions exposed to severe weather conditions and proving a lack of relationship between rock freeze-thaw resistivity and water absorption. Results of the recent worldwide research suggest that understanding a resistivity of rocks against deterioration is hidden not in the absorption but in the structure of rock pores in relation to thermodynamic properties of pore water and tensile strength of rocks and rock minerals. Also this article presents some results of research on rock deterioration and pore structure performed on 88 rock samples. The results divide the rocks tested into two groups - group N in which the pore water does not freeze

  6. Pore connectivity effects on solute transport in rocks

    SciTech Connect

    Hu, Qinhong; Ewing, Robert P.

    2001-11-30

    Retardation of nuclear contaminants in rock matrices can lead to long retention times, allowing substantial radionuclide decay prior to eventual release. Imbibition and diffusion into the rock matrix can move contaminants away from an active fracture, thereby contributing to their retardation. However, diffusive transport in some rocks may behave anomalously because of their sparsely connected porespace, in contrast to diffusion in rocks with denser pore connections. We examined imbibition of weakly sorbing tracers into welded tuff and Indiana sandstone, and water imbibition into metagraywacke and Berea sandstone. Tuff samples were initially equilibrated to 12% and 76% water (v/v) within controlled humidity chambers, while the other rocks were air-dried. For imbibition, one face was exposed to water, with or without tracer, and uptake was measured over time. Following imbibition, tracer concentration measurements were made at fine (1 mm) increments. Three anomalous results were observed: (1) Indiana sandstone and metagraywacke showed mass of imbibed water scaling as time{sup 0.26}, while tuff and Berea sandstone showed the more classical scaling with time{sup 0.5}; (2) tracer movement into dry (2% initial saturation) Indiana sandstone showed a dispersion pattern similar to that expected during tracer movement into moist (76% initial saturation) tuff; and (3) tracer concentrations at the inlet face of the tuff sample were approximately twice those deeper inside the sample. The experiment was then modeled using random walk methods on a 3-D lattice with different values of pore coordination. Network model simulations that used a pore coordination of 1.49 for Indiana sandstone and 1.56 for metagraywacke showed similar temporal scaling, a result of their porespace being close to the percolation threshold. Tracer concentration profiles in Indiana sandstone and tuff were closely matched by simulations that used pore coordinations of 1.49 and 1.68, respectively, because of

  7. Unstable Pore-Water Flow in Intertidal Wetlands

    NASA Astrophysics Data System (ADS)

    Barry, D. A.; Shen, C.; Li, L.

    2014-12-01

    Salt marshes are important intertidal wetlands strongly influenced by interactions between surface water and groundwater. Bordered by coastal water, the marsh system undergoes cycles of inundation and exposure driven by the tide. This leads to dynamic, complex pore-water flow and solute transport in the marsh soil. Pore-water circulations occur over vastly different spatial and temporal scales with strong link to the marsh topography. These circulations control solute transport between the marsh soil and the tidal creek, and ultimately affect the overall nutrient exchange between the marsh and coastal water. The pore-water flows also dictate the soil condition, particularly aeration, which influences the marsh plant growth. Numerous studies have been carried out to examine the pore-water flow process in the marsh soil driven by tides, focusing on stable flow with the assumption of homogeneity in soil and fluid properties. This assumption, however, is questionable given the actual inhomogeneous conditions in the field. For example, the salinity of surface water in the tidal creek varies temporally and spatially due to the influence of rainfall and evapotranspiration as well as the freshwater input from upland areas to the estuary, creating density gradients across the marsh surface and within the marsh soil. Many marshes possess soil stratigraphy with low-permeability mud typically overlying high-permeability sandy deposits. Macropores such as crab burrows are commonly distributed in salt marsh sediments. All these conditions are prone to the development of non-uniform, unstable preferential pore-water flow in the marsh soil, for example, funnelling and fingering. Here we present results from laboratory experiments and numerical simulations to explore such unstable flow. In particular, the analysis aims to address how the unstable flow modifies patterns of local pore-water movement and solute transport, as well as the overall exchange between the marsh soil and

  8. Direct Measurements of Pore Fluid Density by Vibrating Tube Densimetry

    SciTech Connect

    Gruszkiewicz, Miroslaw {Mirek} S; Rother, Gernot; Wesolowski, David J; Cole, David R; Wallacher, Dirk

    2012-01-01

    The densities of pore-confined fluids were measured for the first time by means of a vibrating tube method. Isotherms of total adsorption capacity were measured directly making the method complementary to the conventional gravimetric or volumetric/piezometric adsorption techniques, which yield the excess adsorption (the Gibbsian surface excess). A custom-made high-pressure, high-temperature vibrating tube densimeter (VTD) was used to measure the densities of subcritical and supercritical propane (between 35 C and 97 C) and supercritical carbon dioxide (between 32 C and 50 C) saturating hydrophobic silica aerogel (0.2 g/cm3, 90% porosity) synthesized inside Hastelloy U-tubes. Additionally, excess adsorption isotherms for supercritical CO2 and the same porous solid were measured gravimetrically using a precise magnetically-coupled microbalance. Pore fluid densities and total adsorption isotherms increased monotonically with increasing density of the bulk fluid, in contrast to excess adsorption isotherms, which reached a maximum at a subcritical density of the bulk fluid, and then decreased towards zero or negative values at supercritical densities. Compression of the confined fluid significantly beyond the density of the bulk liquid at the same temperature was observed at subcritical temperatures. The features of the isotherms of confined fluid density are interpreted to elucidate the observed behavior of excess adsorption. The maxima of excess adsorption were found to occur below the critical density of the bulk fluid at the conditions corresponding to the beginning of the plateau of total adsorption, marking the end of the transition of pore fluid to a denser, liquid-like pore phase. The results for propane and carbon dioxide showed similarity in the sense of the principle of corresponding states. No measurable effect of pore confinement on the liquid-vapor critical point was found. Quantitative agreement was obtained between excess adsorption isotherms determined

  9. Correlation between gas permeability and pore structure of coal matrix

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Yang, J.; Gao, F.; Li, Y.; Niu, H.; Gao, H.

    2012-04-01

    The sequestration of CO2 in unminable coal seams represents a promising option for CO2 geologic storage, because the injected CO2 may enhance coalbed methane recovery (CO2-ECBM), which could partly offset the costs of the storage process. The CO2-ECBM technology is based on the relative affinity of CO2 and CH4 to coals under given pressure and temperature conditions. The excess sorption capacity of coals for CO2 is generally higher than the sorption capacity for methane. The coal seams are characterized by a dual porosity structure including cleat and matrix pores. The cleats in the coal seams are considered as highways for gas and water flow, while the matrix is the storage location of gas by adsorption. The slow transport process of gas in coal matrix may constrain the efficiency of the displacement of CH4 by CO2 due to the compacted pore structure of the coal matrix. Therefore, a detailed understanding of the correlation between permeability of gas and pore structure in coal matrix is crucial for the CO2-ECBM processes. Yangquan coals originating from the Qingshui basin, which contains gas-rich coals in China, were selected for the tests in this study. Yangquan coals are classified as anthracite. In order to avoid the influence of coal cleats on fluid flow, small coal plugs (~6 mm in diameter, ~13 mm in length) were selected and fixed in the sample compartment by special glue. A test system for simultaneously measuring adsorption-porosity-permeability on the coal matrix blocks in its free state is constructed. The permeability of gas and porosity in coal plugs to He under different gas pressure and temperature conditions were simultaneously investigated. The permeability and excess sorption capacity of the coal plugs to He, N2, CH4 and CO2 were compared at a constant gas pressure and temperature. It is expected that gas break through a cleat-plug is much faster than that through a coal matrix-plug. Different sample plugs with the different pore structure results

  10. Pore Connectivity Effects on Solute Transport in Rocks

    SciTech Connect

    Oinhong Hu

    2001-12-05

    Retardation of nuclear contaminants in rock matrices can lead to long retention times, allowing substantial radionuclide decay prior to eventual release. Imbibition and diffusion into the rock matrix can move contaminants away from an active fracture, thereby contributing to their retardation. However, diffusive transport in some rocks may behave anomalously because of their sparsely connected porespace, in contrast to diffusion in rocks with denser pore connections. We examined imbibition of weakly sorbing tracers into welded tuff and Indiana sandstone, and water imbibition into metagraywacke and Berea sandstone. Tuff samples were initially equilibrated to 12% and 76% water (v/v) within controlled humidity chambers, while the other rocks were air-dried. For imbibition, one face was exposed to water, with or without tracer, and uptake was measured over time. Following imbibition, tracer concentration measurements were made at fine (1 mm) increments. Three anomalous results were observed: (1) Indiana sandstone and metagraywacke showed mass of imbibed water scaling as time{sup 0.26}, while tuff and Berea sandstone showed the more classical scaling with time{sup 0.05}; (2) tracer movement into dry (2% initial saturation) Indiana sandstone showed a dispersion pattern similar to that expected during tracer movement into moist (76% initial saturation) tuft and (3) tracer concentrations at the inlet face of the tuff sample were approximately twice those deeper inside the sample. The experiment was then modeled using random walk methods on a 3-D lattice with different values of pore coordination. Network model simulations that used a pore coordination of 1.49 for Indiana sandstone and 1.56 for metagraywacke showed similar temporal scaling, a result of their porespace being close to the percolation threshold. Tracer concentration profiles in Indiana sandstone and tuff were closely matched by simulations that used pore coordinations of 1.49 and 1.68, respectively, because of

  11. Molecular Dynamics Modeling of Tethered Organics in Confined Spaces

    SciTech Connect

    Waksburg, Avi; Nguyen, M; Chaffe, Alan; Kidder, Michelle; Buchanan III, A C; Britt, Phillip F

    2011-01-01

    A computational method for constructing and evaluating the dynamic behaviour of functionalised hexagonal mesoporous silica (HMS) MCM-41 models is reported. HMS with three pore diameters (1.7, 2.2 and 2.9 nm) were prepared, and, from these, two series of derivative structures were constructed - one with 1,3-diphenylpropyl (DPP) tethers and the other with smaller dimethylsilyl (DMS) tethers attached to the mesopores internal surfaces. Comparison with experimental data shows that simulation results correctly predict the maximum tether density that can be achieved for each tether and each pore diameter. For the smaller pore models, the extent of DPP functionalisation that can be achieved is limited by the available pore volume. However, for the larger pore model, the extent of functionalisation is limited by access to potentially reactive sites on the pore surface. The dynamic behaviour of the models was investigated over a range of temperatures (240-648 K). At lower temperatures (< 400 K), the mobility of DPP tethers in the 2.9 nm model is actually less than that observed in either the 2.2 nm model or the 1.7 nm model due to the extensive non-bonded interactions that are able to develop between tethers and the silica surface at this diameter. At higher temperatures, the free ends of these tethers break away from the surface, extend further into the pore space and the DPP mobility in the 2.9 nm model is higher than in the smaller pore systems.

  12. Formation of texturally equilibrated pores: is salt always a hydrocarbon seal?

    NASA Astrophysics Data System (ADS)

    Ghanbarzadeh, S.; Prodanovic, M.; Hesse, M. A.

    2012-12-01

    Evaporation of salt-rich waters in basins can result in the deposition of thick layers of rock salt. Over time, denser sediments cover the layer of salt and bury it under an increasingly large overburden. Hydraulic properties of evaporites change during burial process. The porosity decrease as the depth increases and permeability decreases upon burial at a greater rate providing excellent sealing capabilities. However, there are pieces of evidence that permeability of rock salt may increase once burial becomes deep enough. At such depth these salt beds could have permeability comparable to sandstones. This means that salt beds could be acting as fluid conduits. Two processes are known to increase permeability in rock salts. The first is microcracking and associated dilation due to dynamic recrystallization and the second is the formation of topologically connected pores due to changes in interfacial tension between brine and rock salt with increasing pressure and temperature allowing the brine to wet the crystal edges. The wetting properties are characterized by the dihedral angle, the angle measured in the brine at a brine-salt-salt triple junction. For angles less than 60, porosity becomes connected along crystal triple junctions, whereas at angles greater than 60, porosity is virtually isolated. Computing 3D configuration of the texturally equilibrated pore space can provide the basic information for advanced models of physical properties of rock salt. Knowing connectivity/permeability can help improving sub-salt imaging by tuning in the input velocity models for seismic imaging. Also, this provides better understanding of fluid migration paths at great depth in sedimentary basins. Current models of texturally equilibrated pore geometries are limited to simple periodic geometries. This study presents a novel numerical method to describe the texturally equilibrated 2D pore shapes in polycrystalline rock salt and brine systems. Textural equilibrium is achieved

  13. NOTE: Hydrodynamic effects on the solute transport across endothelial pores and hepatocyte membranes

    NASA Astrophysics Data System (ADS)

    Popescu, Dumitru; Movileanu, Liviu; Ion, Stelian; Flonta, Maria-Luiza

    2000-11-01

    In this short note we propose a simple and rapid procedure to calculate the net quantity of metabolites absorbed by hepatocytes from blood plasma. The blood movement through sinusoids determines an opposed circulation of plasma through the space of Disse. Hydrodynamic considerations lead to the conclusion that hepatocytes absorb for their own synthesis processes a quantity of metabolites in a volume flow of the order of 10-12 nl s-1 through a sieve plate surface with an area of 1 µm2. At pathological temperature (40 °C), the excess of the net absorbed volume flow for the entire sinusoidal surface of the mammalian liver may be as high as 1.9 nl s-1. Some observations on the effect of red and white blood cells on the chylomicron traffic through endothelial pores are made.

  14. Evaporation of suspensions to form an incompressible cake and to fill filter pores with solid particles

    NASA Astrophysics Data System (ADS)

    Khuzhayorov, B. Kh.

    2011-11-01

    Equations of filtration of suspensions to form an incompressible cake of particles on the surface of the filter with simultaneous passage of a certain share of the particles from the cake to the filter's pore space and next to the region of a filtered liquid are derived from the principles of the mechanics of multiphase media. The influence of the travel of the particles in the region of the cake and the filter on the dynamics of growth of the cake bed is investigated. An analysis of the derived dynamic filtration equations shows that allowance for the factors of travel and accumulation of particles in the cake and the filter causes their total filtration resistance, in particular the resistance in the inertial component of the filtration law, to decrease.

  15. Nanometer-Scale Pore Characteristics of Lacustrine Shale, Songliao Basin, NE China

    PubMed Central

    Wang, Min; Yang, Jinxiu; Wang, Zhiwei; Lu, Shuangfang

    2015-01-01

    In shale, liquid hydrocarbons are accumulated mainly in nanometer-scale pores or fractures, so the pore types and PSDs (pore size distributions) play a major role in the shale oil occurrence (free or absorbed state), amount of oil, and flow features. The pore types and PSDs of marine shale have been well studied; however, research on lacustrine shale is rare, especially for shale in the oil generation window, although lacustrine shale is deposited widely around the world. To investigate the relationship between nanometer-scale pores and oil occurrence in the lacustrine shale, 10 lacustrine shale core samples from Songliao Basin, NE China were analyzed. Analyses of these samples included geochemical measurements, SEM (scanning electron microscope) observations, low pressure CO2 and N2 adsorption, and high-pressure mercury injection experiments. Analysis results indicate that: (1) Pore types in the lacustrine shale include inter-matrix pores, intergranular pores, organic matter pores, and dissolution pores, and these pores are dominated by mesopores and micropores; (2) There is no apparent correlation between pore volumes and clay content, however, a weak negative correlation is present between total pore volume and carbonate content; (3) Pores in lacustrine shale are well devel