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Sample records for pore structure characterization

  1. 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.

  2. 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.

  3. Pore- and micro-structural characterization of a novel structural binder based on iron carbonation

    SciTech Connect

    Das, Sumanta; Stone, David; Convey, Diana; Neithalath, Narayanan

    2014-12-15

    The pore- and micro-structural features of a novel binding material based on the carbonation of waste metallic iron powder are reported in this paper. The binder contains metallic iron powder as the major ingredient, followed by additives containing silica and alumina to facilitate favorable reaction product formation. Compressive strengths sufficient for a majority of concrete applications are attained. The material pore structure is investigated primarily through mercury intrusion porosimetry whereas electron microscopy is used for microstructural characterization. Reduction in the overall porosity and the average pore size with an increase in carbonation duration from 1 day to 4 days is noticed. The pore structure features are used in predictive models for gas and moisture transport (water vapor diffusivity and moisture permeability) through the porous medium which dictates its long-term durability when used in structural applications. Comparisons of the pore structure with those of a Portland cement paste are also provided. The morphology of the reaction products in the iron-based binder, and the distribution of constituent elements in the microstructure are also reported. - Highlights: • Carbonation of iron produces a dense microstructure. • Pore volume in iron carbonate lower, critical size higher than those in OPC pastes • Reaction product contains iron, carbon, silicon, aluminum and calcium. • Power-law for porosity-moisture permeability relationship was established.

  4. 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.

  5. Characterizing pore sizes and water structure in stimuli-responsive hydrogels

    SciTech Connect

    Hoffman, A.S.; Antonsen, K.P.; Ashida, T.; Bohnert, J.L.; Dong, L.C.; Nabeshima, Y.; Nagamatsu, S.; Park, T.G.; Sheu, M.S.; Wu, X.S.; Yan, Q.

    1993-12-31

    Hydrogels have been extensively investigated as potential matrices for drug delivery. In particular, hydrogels responsive to pH and temperature changes have been of greatest interest most recently. Proteins and peptide drugs are especially relevant for delivery from such hydrogel matrices due to the relatively {open_quotes}passive{close_quotes} and biocompatible microenvironment which should exist within the hydrogel aqueous pores. The large molecular size of many proteins requires an interconnected large pore structure. Furthermore, the gel pore {open_quotes}walls{close_quotes} should not provide hydrophobic sites for strong interactions with proteins. In the special case of ion exchange release the protein would be attracted by opposite charges on the polymer backbones. Therefore, it is important both to control and to characterize the pore structure and the water character within a hydrogel to be used or protein or peptide drug delivery. This talk will critically review techniques for estimating these two key parameters in hydrogels.

  6. Limestone characterization to model damage from acidic precipitation: Effect of pore structure on mass transfer

    USGS Publications Warehouse

    Leith, S.D.; Reddy, M.M.; Irez, W.F.; Heymans, M.J.

    1996-01-01

    The pore structure of Salem limestone is investigated, and conclusions regarding the effect of the pore geometry on modeling moisture and contaminant transport are discussed based on thin section petrography, scanning electron microscopy, mercury intrusion porosimetry, and nitrogen adsorption analyses. These investigations are compared to and shown to compliment permeability and capillary pressure measurements for this common building stone. Salem limestone exhibits a bimodal pore size distribution in which the larger pores provide routes for convective mass transfer of contaminants into the material and the smaller pores lead to high surface area adsorption and reaction sites. Relative permeability and capillary pressure measurements of the air/water system indicate that Salem limestone exhibits high capillarity end low effective permeability to water. Based on stone characterization, aqueous diffusion and convection are believed to be the primary transport mechanisms for pollutants in this stone. The extent of contaminant accumulation in the stone depends on the mechanism of partitioning between the aqueous and solid phases. The described characterization techniques and modeling approach can be applied to many systems of interest such as acidic damage to limestone, mass transfer of contaminants in concrete and other porous building materials, and modeling pollutant transport in subsurface moisture zones.

  7. Smart Fluids in Hydrology: Use of Non-Newtonian Fluids for Pore Structure Characterization

    NASA Astrophysics Data System (ADS)

    Abou Najm, Majdi; Atallah, Nabil; Selker, John; Roques, Clément; Stewart, Ryan; Rupp, David; Saad, George; El-Fadel, Mutasem

    2016-04-01

    Classic porous media characterization relies on typical infiltration experiments with Newtonian fluids (i.e., water) to estimate hydraulic conductivity. However, such experiments are generally not able to discern important characteristics such as pore size distribution or pore structure. We show that introducing non-Newtonian fluids provides additional unique flow signatures that can be used for improved pore structure characterization. We present a new method that transforms results of N infiltration experiments using water and N-1 non-Newtonian solutions into a system of equations that yields N representative radii (Ri) and their corresponding percent contribution to flow (wi). Those radii and weights are optimized in terms of flow and porosity to represent the functional hydraulic behavior of real porous media. The method also allows for estimating the soil retention curve using only saturated experiments. Experimental and numerical validation revealed the ability of the proposed method to represent the water retention and functional infiltration behavior of real soils. The experimental results showed the ability of such fluids to outsmart Newtonian fluids and infer pore size distribution and unsaturated behavior using simple saturated experiments. Specifically, we demonstrate using synthetic porous media composed of different combinations of sizes and numbers of capillary tubes that the use of different non-Newtonian fluids enables the prediction of the pore structure. The results advance the knowledge towards conceptualizing the complexity of porous media and can potentially impact applications in fields like irrigation efficiencies, vadose zone hydrology, soil-root-plant continuum, carbon sequestration into geologic formations, soil remediation, petroleum reservoir engineering, oil exploration and groundwater modeling.

  8. Characterization of Tight Gas Reservoir Pore Structure Using USANS/SANS and Gas Adsorption Analysis

    SciTech Connect

    Clarkson, Christopher R; He, Lilin; Agamalian, Michael; Melnichenko, Yuri B; Mastalerz, Maria; Bustin, Mark; Radlinski, Andrzej Pawell; Blach, Tomasz P

    2012-01-01

    Small-angle and ultra-small-angle neutron scattering (SANS and USANS) measurements were performed on samples from the Triassic Montney tight gas reservoir in Western Canada in order to determine the applicability of these techniques for characterizing the full pore size spectrum and to gain insight into the nature of the pore structure and its control on permeability. The subject tight gas reservoir consists of a finely laminated siltstone sequence; extensive cementation and moderate clay content are the primary causes of low permeability. SANS/USANS experiments run at ambient pressure and temperature conditions on lithologically-diverse sub-samples of three core plugs demonstrated that a broad pore size distribution could be interpreted from the data. Two interpretation methods were used to evaluate total porosity, pore size distribution and surface area and the results were compared to independent estimates derived from helium porosimetry (connected porosity) and low-pressure N{sub 2} and CO{sub 2} adsorption (accessible surface area and pore size distribution). The pore structure of the three samples as interpreted from SANS/USANS is fairly uniform, with small differences in the small-pore range (< 2000 {angstrom}), possibly related to differences in degree of cementation, and mineralogy, in particular clay content. Total porosity interpreted from USANS/SANS is similar to (but systematically higher than) helium porosities measured on the whole core plug. Both methods were used to estimate the percentage of open porosity expressed here as a ratio of connected porosity, as established from helium adsorption, to the total porosity, as estimated from SANS/USANS techniques. Open porosity appears to control permeability (determined using pressure and pulse-decay techniques), with the highest permeability sample also having the highest percentage of open porosity. Surface area, as calculated from low-pressure N{sub 2} and CO{sub 2} adsorption, is significantly less

  9. Activated carbon from char obtained from vacuum pyrolysis of teak sawdust: pore structure development and characterization.

    PubMed

    Ismadji, S; Sudaryanto, Y; Hartono, S B; Setiawan, L E K; Ayucitra, A

    2005-08-01

    The preparation of activated carbon from vacuum pyrolysis char of teak sawdust was studied and the results are presented in this paper. The effects of process variables such as temperature and activation time on the pore structure of activated carbons were studied. The activated carbon prepared from char obtained by vacuum pyrolysis has higher surface area and pore volume than that from atmospheric pyrolysis char. The BET surface area and pore volume of activated carbon prepared from vacuum pyrolysis char were 1150 m2/g and 0.43 cm3/g, respectively.

  10. Pore Structure and Petrophysical Characterization of Hamelin Pool Stromatolites, Shark Bay, Western Australia

    NASA Astrophysics Data System (ADS)

    Karaca, E.; Eberli, G. P.; Weger, R. J.; Parke, E.

    2014-12-01

    Stromatolites are organic-sedimentary structures that form by trapping and binding of sediments and calcium carbonate precipitation through microbial activity. The largest modern stromatolite province is the hypersaline Hamelin Pool, Western Australia. Microbial precipitation generates a rigid framework with a wide range of porosities and pore sizes that influence the ultrasonic velocity permeability and resistivity in stromatolites. Stromatolites generally have simple and large pore structures and an impressive high permeability values. In the 55 core plugs, permeability varies from 0.5 D to 9 D, while porosity ranges from 17% to 46%. Ultrasonic velocity, measured under dry and saturated conditions, is generally high with a large scatter at any given porosity. Likewise large variations of porosity exist at any given velocity. For example, at 29% porosity, (dry) velocity ranges from 3611m/s to 5384m/s. Similarly at a velocity of 4048m/s the porosity ranges from 23% to 46%. Digital image analysis indicates that the main control on the variations is the pore complexity and size. Larger pores produce faster velocities at equal porosity. In saturated plugs compressional velocities increase up to 365m/s. In contrast, shear velocities show both a decrease (up to 578m/s) and an increase (up to 391m/s) in shear velocity (vs) with saturation. These changes in vsindicate that the stromatolites do change the shear modulus with saturation, thus violating the assumption by Gassmann. The cementation factor "m" (from Archie's equation, F = φ-m) determined from electrical resistivity varies in a narrow range from 2.1 to 2.6. This narrow range reduces the uncertainty in predicting the hydrocarbon/water saturation in stromatolites. The large range of porosities at a given velocity, however, makes porosity estimates from seismic inversion a challenge and, similarly, the shear moduli changes and the resultant shear strengthening and weakening add uncertainties to AVO analysis in

  11. Using X-Ray Computed Tomography in Pore Structure Characterization for a Berea Sandstone: Resolution Effect

    SciTech Connect

    Peng, Sheng; Hu, Qinhong; Dultz, Stefan; Zhang, Ming

    2012-11-23

    X-raycomputedtomography (XCT) is a powerful tool for detecting the micro-scale porestructure and has been applied to many natural and synthetic porous media. However, due to the resolution limitations, either non-representative view of the sample or inaccurate results can be produced from the XCT image processing. In this paper, two XCT (micro-CT and CT with synchrotron radiation) with different resolutions of 12.7 μm and 0.35 μm, as well as mercury intrusion porosimetry (MIP) with a minimum detection limit of 3 nm, were used for Berea sandstone to investigate the effect of detecting resolution on the porestructure. Several key porestructure parameters, including porosity, pore size distribution, pore connectivity, surface area, hydraulic radius, and aspect ratio were analyzed in a manner of quantitative comparison between different resolutions of XCT and MIP. The low resolution XCT can capture the large-pore porosity, while overestimates the pore size and pore connectivity. The high resolution XCT is more accurate in describing the pore shape, porosity, pore size; however, it is not representative since narrower detecting pore size range and small volume represented. A representative element volume related to large-pore porosity and probably large-pore connectivity with diameter and height of 2.8 mm is obtained through scale effect analysis. Therefore, selecting an appropriate resolution should be a compromise between the pore size and the representative element volume for the specific property or process of interest.

  12. Structural characterization of two pore-forming peptides: consequences of introducing a C-terminal tryptophan.

    PubMed

    Herrera, Alvaro I; Al-Rawi, Ahlam; Cook, Gabriel A; Gao, Jian; Iwamoto, Takeo; Prakash, Om; Tomich, John M; Chen, Jianhan

    2010-08-01

    Synthetic channel-forming peptides that can restore chloride conductance across epithelial membranes could provide a novel treatment of channelopathies such as cystic fibrosis. Among a series of 22-residue peptides derived from the second transmembrane segment of the glycine receptor alpha(1)-subunit (M2GlyR), p22-S22W (KKKKP ARVGL GITTV LTMTT QW) is particularly promising with robust membrane insertion and assembly. The concentration to reach one-half maximal short circuit current is reduced to 45 +/- 6 microM from that of 210 +/- 70 microM of peptide p22 (KKKKP ARVGL GITTV LTMTT QS). However, this is accompanied with nearly 50% reduction in conductance. Toward obtaining a molecular level understanding of the channel activities, we combine information from solution NMR, existing biophysical data, and molecular modeling to construct atomistic models of the putative pentameric channels of p22 and p22-S22W. Simulations in membrane bilayers demonstrate that these structural models, even though highly flexible, are stable and remain adequately open for ion conductance. The membrane-anchoring tryptophan residues not only rigidify the whole channel, suggesting increased stability, but also lead to global changes in the pore profile. Specifically, the p22-S22W pore has a smaller opening on average, consistent with lower measured conductance. Direct observation of several incidences of chloride transport suggests several qualitative features of how these channels might selectively conduct anions. The current study thus helps to rationalize the functional consequences of introducing a single C-terminal tryptophan. Availability of these structural models also paves the way for future work to rationally modify and improve M2GlyR-derived peptides toward potential peptide-based channel replacement therapy.

  13. Characterization of pore structure and hydraulic property alteration in pressurized unsaturated flow tests

    SciTech Connect

    McGrail, B. Peter; Lindenmeier, Clark W.; Martin, P F.

    1999-12-01

    The pressurized unsaturated flow (PUF) test is a new experimental method for the evaluation of the long-term corrosion behavior of waste forms and other engineered barrier materials. Essentially, the technique provides a means to flow water through a porous bed of test material or materials at elevated temperature and under hydraulically unsaturated conditions. Bulk volumetric content, effluent pH and electrical conductivity are monitored in real time using a computer control and data acquisition system. In previous papers, we have reported on the changes in bulk water content, effluent chemistry, and glass corrosion rates that result from the formation of alteration products during these tests. These measurements are now supplemented through the use of the ultracentrifugation apparatus (UFA) for hydraulic property measurements and high-resolution, x-ray microtomography (XMT) to provide 3-D spatial and temporal imaging of water distribution and pore structure alteration during these tests. Quantitative changes in the water retention characteristic were correlated with the onset of zeolite formation in the tests. Extensive alteration of the glass resulted in cementation of the glass grains near the bottom of the column, which was observed in situ using the XMT.

  14. Characterization of pore structure and hydraulic property alteration in pressurized unsaturated flow tests

    SciTech Connect

    McGrail, B.P.; Lindenmeier, C.W.; Martin, P.F.

    1999-07-01

    The pressurized unsaturated flow (PUF) test is a new experimental method for the evaluation of the long-term corrosion behavior of waste forms and other engineered barrier materials. Essentially, the technique provides a means to flow water through a porous bed of test material or materials at elevated temperature and under hydraulically unsaturated conditions. Bulk volumetric content, effluent pH and electrical conductivity are monitored in real time using a computer control and data acquisition system. In previous papers, the authors have reported on the changes in bulk water content, effluent chemistry, and glass corrosion rates that result from the formation of alteration products during these tests. These measurements are now supplemented through the use of the ultracentrifugation apparatus (UFA) for hydraulic property measurements and high-resolution, x-ray microtomography (XMT) to provide 3-D spatial and temporal imaging of water distribution and pore structure alteration during these tests. Quantitative changes in the water retention characteristic were correlated with the onset of zeolite formation in the tests. Extensive alteration of the glass resulted in cementation of the glass grains near the bottom of the column, which was observed in situ using the XMT.

  15. Characterization of pore structure and strain localization in Majella limestone by X-ray computed tomography and digital image correlation

    NASA Astrophysics Data System (ADS)

    Ji, Yuntao; Hall, Stephen A.; Baud, Patrick; Wong, Teng-fong

    2015-02-01

    Standard techniques for computed tomography 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 with 30 per cent porosity. Microtomography data acquired on this rock 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 microtomography images shows that in Majella limestone both the solid and intermediate domains are interconnected in a manner similar to that reported previously 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 significantly to its permeability. We then applied for the first time 3-D-volumetric digital image correlation (DIC) to characterize the mode of mechanical failure in this limestone. Samples were triaxially deformed over a wide range of confining pressures. Tomography imaging was performed on these samples before and after deformation. Inelastic compaction was observed at all tested pressures associated with both brittle and ductile behaviors. Our DIC analysis reveals the structure of compacting shear bands in Majella limestone deformed in the transitional regime. It also indicates an increase of geometric complexity with increasing confinement-from a planar shear band, to a curvilinear band, and ultimately to a diffuse multiplicity of bands, before shear localization is inhibited as the failure mode completes the transition to delocalized cataclastic flow.

  16. Preparation, characterization, and silanization of 3D microporous PDMS structure with properly sized pores for endothelial cell culture.

    PubMed

    Zargar, Reyhaneh; Nourmohammadi, Jhamak; Amoabediny, Ghassem

    2016-01-01

    Nowadays, application of porous polydimethylsiloxane (PDMS) structure in biomedical is becoming widespread, and many methods have been established to create such structure. Although the pores created through these methods are mostly developed on the outer surface of PDMS membrane, this study offers a simple and cost-efficient technique for creating three-dimensional (3D) microporous PDMS structure with appropriate pore size for endothelial cell culture. In this study, combination of gas foaming and particulate leaching methods, with NaHCO3 as effervescent salt and NaCl as progen are used to form a 3D PDMS sponge. The in situ chemical reaction between NaHCO3 and HCl resulted in the formation of small pores and channels. Moreover, soaking the samples in HCl solution temporarily improved the hydrophilicity of PDMS, which then facilitated the penetration of water for further leaching of NaCl. The surface chemical modification process was performed by (3-aminopropyl)triethoxysilane to culture endothelial cells on porous PDMS matrix. The results are an indication of positive response of endothelial cells to the fabricated PDMS sponge. Because of simplicity and practicality of this method for preparing PDMS sponge with appropriate pore size and biological properties, the fabricated matrix can perfectly be applied to future studies in blood-contacting devices.

  17. 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.

  18. Pore structure characterization of Chang-7 tight sandstone using MICP combined with N2GA techniques and its geological control factors

    PubMed Central

    Cao, Zhe; Liu, Guangdi; Zhan, Hongbin; Li, Chaozheng; You, Yuan; Yang, Chengyu; Jiang, Hang

    2016-01-01

    Understanding the pore networks of unconventional tight reservoirs such as tight sandstones and shales is crucial for extracting oil/gas from such reservoirs. Mercury injection capillary pressure (MICP) and N2 gas adsorption (N2GA) are performed to evaluate pore structure of Chang-7 tight sandstone. Thin section observation, scanning electron microscope, grain size analysis, mineral composition analysis, and porosity measurement are applied to investigate geological control factors of pore structure. Grain size is positively correlated with detrital mineral content and grain size standard deviation while negatively related to clay content. Detrital mineral content and grain size are positively correlated with porosity, pore throat radius and withdrawal efficiency and negatively related to capillary pressure and pore-to-throat size ratio; while interstitial material is negatively correlated with above mentioned factors. Well sorted sediments with high debris usually possess strong compaction resistance to preserve original pores. Although many inter-crystalline pores are produced in clay minerals, this type of pores is not the most important contributor to porosity. Besides this, pore shape determined by N2GA hysteresis loop is consistent with SEM observation on clay inter-crystalline pores while BJH pore volume is positively related with clay content, suggesting N2GA is suitable for describing clay inter-crystalline pores in tight sandstones. PMID:27830731

  19. Pore structure characterization of Chang-7 tight sandstone using MICP combined with N2GA techniques and its geological control factors

    NASA Astrophysics Data System (ADS)

    Cao, Zhe; Liu, Guangdi; Zhan, Hongbin; Li, Chaozheng; You, Yuan; Yang, Chengyu; Jiang, Hang

    2016-11-01

    Understanding the pore networks of unconventional tight reservoirs such as tight sandstones and shales is crucial for extracting oil/gas from such reservoirs. Mercury injection capillary pressure (MICP) and N2 gas adsorption (N2GA) are performed to evaluate pore structure of Chang-7 tight sandstone. Thin section observation, scanning electron microscope, grain size analysis, mineral composition analysis, and porosity measurement are applied to investigate geological control factors of pore structure. Grain size is positively correlated with detrital mineral content and grain size standard deviation while negatively related to clay content. Detrital mineral content and grain size are positively correlated with porosity, pore throat radius and withdrawal efficiency and negatively related to capillary pressure and pore-to-throat size ratio; while interstitial material is negatively correlated with above mentioned factors. Well sorted sediments with high debris usually possess strong compaction resistance to preserve original pores. Although many inter-crystalline pores are produced in clay minerals, this type of pores is not the most important contributor to porosity. Besides this, pore shape determined by N2GA hysteresis loop is consistent with SEM observation on clay inter-crystalline pores while BJH pore volume is positively related with clay content, suggesting N2GA is suitable for describing clay inter-crystalline pores in tight sandstones.

  20. Pore structure characterization of Chang-7 tight sandstone using MICP combined with N2GA techniques and its geological control factors.

    PubMed

    Cao, Zhe; Liu, Guangdi; Zhan, Hongbin; Li, Chaozheng; You, Yuan; Yang, Chengyu; Jiang, Hang

    2016-11-10

    Understanding the pore networks of unconventional tight reservoirs such as tight sandstones and shales is crucial for extracting oil/gas from such reservoirs. Mercury injection capillary pressure (MICP) and N2 gas adsorption (N2GA) are performed to evaluate pore structure of Chang-7 tight sandstone. Thin section observation, scanning electron microscope, grain size analysis, mineral composition analysis, and porosity measurement are applied to investigate geological control factors of pore structure. Grain size is positively correlated with detrital mineral content and grain size standard deviation while negatively related to clay content. Detrital mineral content and grain size are positively correlated with porosity, pore throat radius and withdrawal efficiency and negatively related to capillary pressure and pore-to-throat size ratio; while interstitial material is negatively correlated with above mentioned factors. Well sorted sediments with high debris usually possess strong compaction resistance to preserve original pores. Although many inter-crystalline pores are produced in clay minerals, this type of pores is not the most important contributor to porosity. Besides this, pore shape determined by N2GA hysteresis loop is consistent with SEM observation on clay inter-crystalline pores while BJH pore volume is positively related with clay content, suggesting N2GA is suitable for describing clay inter-crystalline pores in tight sandstones.

  1. Characterization of pore and crystal structure of synthesized LiBOB with varying quality of raw materials as electrolyte for lithium-ion battery

    NASA Astrophysics Data System (ADS)

    Lestariningsih, Titik; Ratri, Christin Rina; Wigayati, Etty Marty; Sabrina, Qolby

    2016-02-01

    Characterization of pore structure and crystal structure of the LiB(C2O4)2H2O or LIBOB compound has been performed in this study. These recent years, research regarding LiBOB electrolyte salt have been performed using analytical-grade raw materials, therefore this research was aimed to synthesized LiBOB electrolyte salt using the cheaper and abundant technical-grade raw materials. Lithium hydroxide (LiOH), oxalic acid dihydrate (H2C2O4.2H2O), and boric acid (H3BO3) both in technical-grade and analytical-grade quality were used as raw materials for the synthesis of LiBOB. Crystal structure characterization results of synthesized LiBOB from both technical-grade and analytical-grade raw materials have shown the existence of LiBOB and LiBOB hydrate phase with orthorombic structure. These results were also confirmed by FT-IR analysis, which showed the functional groups of LiBOB compounds. SEM analysis results showed that synthesized LiBOB has spherical structure, while commercial LiBOB has cylindrical structure. Synthesized LiBOB has a similar pore size of commercial LiBOB, i.e. 19 nm (mesoporous material). Surface area of synthesized LiBOB from analytical-grade raw materials and technical-grade materials as well as commercial LIBOB were 88.556 m2/g, 41.524 m2/g, and 108.776 m2/g, respectively. EIS analysis results showed that synthesized LiBOB from technical-grade raw materials has lower conductivity than synthesized LiBOB from analytical-grade raw materials.

  2. 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).

  3. 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.

  4. 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.

  5. 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.

  6. Comprehensive pore structure characterization of silica monoliths with controlled mesopore size and macropore size by nitrogen sorption, mercury porosimetry, transmission electron microscopy and inverse size exclusion chromatography.

    PubMed

    Lubda, Dieter; Lindner, Wolfgang; Quaglia, Milene; du Fresne von Hohenesche, Cedric; Unger, Klaus K

    2005-08-12

    The porosity of monolithic silica columns is measured by using different analytical methods. Two sets of monoliths were prepared with a given mesopore diameter of 10 and 25 nm, respectively and with gradated macropore diameters between 1.8 and 7.5 microm. After preparing the two sets of monolithic silica columns with different macro- and mesopores the internal, external and total porosity of these columns are determined by inverse size-exclusion chromatography (ISEC) using polystyrene samples of narrow molecular size distribution and known average molecular weight. The ISEC data from the 4.6 mm analytical monolithic silica columns are used to determine the structural properties of monolithic silica capillaries (100 microm I.D.) prepared as a third set of samples. The ISEC results illustrate a multimodal mesopore structure (mesopores are pores with stagnant zones) of the monoliths. It is found by ISEC that the ratio of the different types of pores is dependent on the change in diameter of the macropores (serve as flow-through pores). The porosity data achieved from the mercury penetration measurement and nitrogen adsorption as well of scanning electron microscopy (SEM) and transmission electron microscopy (TEM) pictures are correlated with the results we calculated from the ISEC measurements. The ISEC results, namely the multimodal pore structure of the monoliths, reported in several publications, are not confirmed analyzing the pore structures of the different silica monoliths using all other analytical methods.

  7. Characterizing the effects of elevated temperature on the air void pore structure of advanced gas-cooled reactor pressure vessel concrete using x-ray computed tomography

    NASA Astrophysics Data System (ADS)

    Stein, R. C.; Petkovski, M.; Engelberg, D. L.; Leonard, F.; Withers, P. J.

    2013-07-01

    X-ray computed tomography (X-ray CT) has been applied to nondestructively characterise changes in the microstructure of a concrete used in the pressure vessel structure of Advanced Gas-cooled Reactors (AGR) in the UK. Concrete specimens were conditioned at temperatures of 105 °C and 250 °C, to simulate the maximum thermal load expected to occur during a loss of coolant accident (LOCA). Following thermal treatment, these specimens along with an unconditioned control sample were characterised using micro-focus X-ray CT with a spatial resolution of 14.6 microns. The results indicate that the air void pore structure of the specimens experienced significant volume changes as a result of the increasing temperature. The increase in the porous volume was more prevalent at 250 °C. Alterations in air void size distributions were characterized with respect to the unconditioned control specimen. These findings appear to correlate with changes in the uni-axial compressive strength of the conditioned concrete.

  8. 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.

  9. 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.

  10. 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.

  11. The Description of Shale Reservoir Pore Structure Based on Method of Moments Estimation

    PubMed Central

    Li, Wenjie; Wang, Changcheng; Shi, Zejin; Wei, Yi; Zhou, Huailai; Deng, Kun

    2016-01-01

    Shale has been considered as good gas reservoir due to its abundant interior nanoscale pores. Thus, the study of the pore structure of shale is of great significance for the evaluation and development of shale oil and gas. To date, the most widely used approaches for studying the shale pore structure include image analysis, radiation and fluid invasion methods. The detailed pore structures can be studied intuitively by image analysis and radiation methods, but the results obtained are quite sensitive to sample preparation, equipment performance and experimental operation. In contrast, the fluid invasion method can be used to obtain information on pore size distribution and pore structure, but the relative simple parameters derived cannot be used to evaluate the pore structure of shale comprehensively and quantitatively. To characterize the nanoscale pore structure of shale reservoir more effectively and expand the current research techniques, we proposed a new method based on gas adsorption experimental data and the method of moments to describe the pore structure parameters of shale reservoir. Combined with the geological mixture empirical distribution and the method of moments estimation principle, the new method calculates the characteristic parameters of shale, including the mean pore size (x¯), standard deviation (σ), skewness (Sk) and variation coefficient (c). These values are found by reconstructing the grouping intervals of observation values and optimizing algorithms for eigenvalues. This approach assures a more effective description of the characteristics of nanoscale pore structures. Finally, the new method has been applied to analyze the Yanchang shale in the Ordos Basin (China) and Longmaxi shale from the Sichuan Basin (China). The results obtained well reveal the pore characteristics of shale, indicating the feasibility of this new method in the study of the pore structure of shale reservoir. PMID:26992168

  12. The Description of Shale Reservoir Pore Structure Based on Method of Moments Estimation.

    PubMed

    Li, Wenjie; Wang, Changcheng; Shi, Zejin; Wei, Yi; Zhou, Huailai; Deng, Kun

    2016-01-01

    Shale has been considered as good gas reservoir due to its abundant interior nanoscale pores. Thus, the study of the pore structure of shale is of great significance for the evaluation and development of shale oil and gas. To date, the most widely used approaches for studying the shale pore structure include image analysis, radiation and fluid invasion methods. The detailed pore structures can be studied intuitively by image analysis and radiation methods, but the results obtained are quite sensitive to sample preparation, equipment performance and experimental operation. In contrast, the fluid invasion method can be used to obtain information on pore size distribution and pore structure, but the relative simple parameters derived cannot be used to evaluate the pore structure of shale comprehensively and quantitatively. To characterize the nanoscale pore structure of shale reservoir more effectively and expand the current research techniques, we proposed a new method based on gas adsorption experimental data and the method of moments to describe the pore structure parameters of shale reservoir. Combined with the geological mixture empirical distribution and the method of moments estimation principle, the new method calculates the characteristic parameters of shale, including the mean pore size (mean), standard deviation (σ), skewness (Sk) and variation coefficient (c). These values are found by reconstructing the grouping intervals of observation values and optimizing algorithms for eigenvalues. This approach assures a more effective description of the characteristics of nanoscale pore structures. Finally, the new method has been applied to analyze the Yanchang shale in the Ordos Basin (China) and Longmaxi shale from the Sichuan Basin (China). The results obtained well reveal the pore characteristics of shale, indicating the feasibility of this new method in the study of the pore structure of shale reservoir.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. Effects of calcination temperature on the pore size and wall crystalline structure of mesoporous alumina.

    PubMed

    Sun, Zhong-Xi; Zheng, Ting-Ting; Bo, Qi-Bing; Du, Miao; Forsling, Willis

    2008-03-01

    In this paper, mesoporous alumina with different pore sizes and wall crystalline structures was synthesized at calcination temperatures over 550 degrees C. The characterization of the samples calcined at 550, 800, 1100, and 1300 degrees C, respectively, was performed using TEM, XRD, FTIR, TG/DTA, and N2 adsorption/desorption techniques. The correlation between pore size and wall crystalline structure on calcination temperature was systematically investigated.

  18. 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

  19. 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.

  20. 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

  1. 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].

  2. Characterization of a nuclear pore protein sheds light on the roles and composition of the Toxoplasma gondii nuclear pore complex.

    PubMed

    Courjol, Flavie; Mouveaux, Thomas; Lesage, Kevin; Saliou, Jean-Michel; Werkmeister, Elisabeth; Bonabaud, Maurine; Rohmer, Marine; Slomianny, Christian; Lafont, Franck; Gissot, Mathieu

    2017-01-30

    The nuclear pore is a key structure in eukaryotes regulating nuclear-cytoplasmic transport as well as a wide range of cellular processes. Here, we report the characterization of the first Toxoplasma gondii nuclear pore protein, named TgNup302, which appears to be the orthologue of the mammalian Nup98-96 protein. We produced a conditional knock-down mutant that expresses TgNup302 under the control of an inducible tetracycline-regulated promoter. Under ATc treatment, a substantial decrease of TgNup302 protein in inducible knock-down (iKD) parasites was observed, causing a delay in parasite proliferation. Moreover, the nuclear protein TgENO2 was trapped in the cytoplasm of ATc-treated mutants, suggesting that TgNup302 is involved in nuclear transport. Fluorescence in situ hybridization revealed that TgNup302 is essential for 18S RNA export from the nucleus to the cytoplasm, while global mRNA export remains unchanged. Using an affinity tag purification combined with mass spectrometry, we identified additional components of the nuclear pore complex, including proteins potentially interacting with chromatin. Furthermore, reverse immunoprecipitation confirmed their interaction with TgNup302, and structured illuminated microscopy confirmed the NPC localization of some of the TgNup302-interacting proteins. Intriguingly, facilitates chromatin transcription complex (FACT) components were identified, suggesting the existence of an NPC-chromatin interaction in T. gondii. Identification of TgNup302-interacting proteins also provides the first glimpse at the NPC structure in Apicomplexa, suggesting a structural conservation of the NPC components between distant eukaryotes.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  6. Fabrication, pore structure and compressive behavior of anisotropic porous titanium for human trabecular bone implant applications.

    PubMed

    Li, Fuping; Li, Jinshan; Xu, Guangsheng; Liu, Gejun; Kou, Hongchao; Zhou, Lian

    2015-06-01

    Porous titanium with average pore size of 100-650 μm and porosity of 30-70% was fabricated by diffusion bonding of titanium meshes. Pore structure was characterized by Micro-CT scan and SEM. Compressive behavior of porous titanium in the out-of-plane direction was studied. The effect of porosity and pore size on the compressive properties was also discussed based on the deformation mode. The results reveal that the fabrication process can control the porosity precisely. The average pore size of porous titanium can be tailored by adjusting the pore size of titanium meshes. The fabricated porous titanium possesses an anisotropic structure with square pores in the in-plane direction and elongated pores in the out-of-plane direction. The compressive Young's modulus and yield stress are in the range of 1-7.5 GPa and 10-110 MPa, respectively. The dominant compressive deformation mode is buckling of mesh wires, but some uncoordinated buckling is present in porous titanium with lower porosity. Relationship between compressive properties and porosity conforms well to the Gibson-Ashby model. The effect of pore size on compressive properties is fundamentally ascribed to the aspect ratio of titanium meshes. Porous titanium with 60-70% porosity has potential for trabecular bone implant applications.

  7. 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.

  8. 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.

  9. Characterizing Hydrogen Storage Media: Understanding the Interior Pore Structure of a Cu3BTC2 Metal-Organic Framework Infiltrated with NaAlH4

    SciTech Connect

    Kirmiz, A; Bhakta, R K; Allendorf, M D; Majzoub, E H; Behrens, R; Herberg, J

    2010-04-15

    Preliminary results support the nano-confinement of sodium alanate within the pores of a Cu{sub 3}BTC{sub 2} MOF substrate. Increased {sup 1}H and {sup 27}Al NMR T{sub 1} relaxation rates indicate a close proximity of infiltrated sodium alante to the paramagnetic Cu{sup 2+} ions on the BTC paddlewheel units. This is in support of the theory that an interaction due to the electronegative framework with the sodium alanate facilitates thermodynamically-favorable hydrogen adsorption and desorption. Further studies can elucidate the local electronic environment of the sodium ions, further supporting a charge-transfer mechanism as the driving force for thermodynamically-favorable hydrogen adsorption and desorption.

  10. Effects of Coke Calcination Level on Pore Structure in Carbon Anodes

    NASA Astrophysics Data System (ADS)

    Fang, Ning; Xue, Jilai; Lang, Guanghui; Bao, Chongai; Gao, Shoulei

    2016-02-01

    Effects of coke calcination levels on pore structure of carbon anodes have been investigated. Bench anodes were prepared by 3 types of cokes with 4 calcination temperatures (800°C, 900°C, 1000°C and 1100°C). The cokes and anodes were characterized using hydrostatic method, air permeability determination, mercury porosimetry, image analysis and confocal microscopy (CSLM). The cokes with different calcination levels are almost the same in LC values (19-20 Å) and real density (1.967-1.985 g/cm3), while the anode containing coke calcined at 900°C has the lowest open porosity and air permeability. Pore size distribution (represented by Anode H sample) can be roughly divided into two ranges: small and medium pores in diameter of 10-400 μm and large pores of 400-580 μm. For the anode containing coke calcined at 800°C, a number of long, narrow pores in the pore size range of 400-580 μm are presented among cokes particles. Formation of these elongated pores may be attributed to coke shrinkages during the anode baking process, which may develop cracking in the anode under cell operations. More small or medium rounded pores with pore size range of 10-400 μm emerge in the anodes with coke calcination temperatures of 900°C, 1000°C and 1100°C, which may be generated due to release of volatiles from the carbon anode during baking. For the anode containing coke calcined at 1100°C, it is found that many rounded pores often closely surround large coke particles, which have potential to form elongated, narrow pores.

  11. Advanced NMR-based techniques for pore structure analysis of coal. Final project report

    SciTech Connect

    Smith, D.M.; Hua, D.W.

    1996-02-01

    During the 3 year term of the project, new methods have been developed for characterizing the pore structure of porous materials such as coals, carbons, and amorphous silica gels. In general, these techniques revolve around; (1) combining multiple techniques such as small-angle x-ray scattering (SAXS) and adsorption of contrast-matched adsorbates or {sup 129}Xe NMR and thermoporometry (the change in freezing point with pore size), (2) combining adsorption isotherms over several pressure ranges to obtain a more complete description of pore filling, or (3) applying NMR ({sup 129}Xe, {sup 14}N{sub 2}, {sup 15}N{sub 2}) techniques with well-defined porous solids with pores in the large micropore size range (>1 nm).

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  13. Pore Structure of Macroporous Polymers Using Polystyrene/Silica Composite Particles as Pickering Stabilizers.

    PubMed

    Tu, Shuhua; Zhu, Chenxu; Zhang, Lingyun; Wang, Haitao; Du, Qiangguo

    2016-12-13

    A novel approach for the preparation of interconnected macroporous polymers with a controllable pore structure was reported. The method was based on the polymerization of water-in-oil Pickering high internal phase emulsion (HIPE) stabilized by polystyrene (PS)/silica composite particles. The composite Pickering stabilizers were facilely obtained by mixing positively charged PS microspheres and negatively charged silica nanoparticles, and their amphiphilicity could be delicately tailored by varying the ratio of PS and silica. The droplet size of Pickering HIPEs was characterized using an optical microscope. The pore structure of polymer foams was observed using a scanning electron microscope. The interconnectivity of macroporous polymers was evaluated upon their gas permeability, which was greatly improved after etching PS microspheres included in the Pickering stabilizers with tetrahydrofuran. As a result, fine tailoring of the pore structure of polymer foams could be realized by simply tuning the ratio of PS to silica particles in the composite stabilizer.

  14. Importance of lipid-pore loop interface for potassium channel structure and function.

    PubMed

    van der Cruijsen, Elwin A W; Nand, Deepak; Weingarth, Markus; Prokofyev, Alexander; Hornig, Sönke; Cukkemane, Abhishek Arun; Bonvin, Alexandre M J J; Becker, Stefan; Hulse, Raymond E; Perozo, Eduardo; Pongs, Olaf; Baldus, Marc

    2013-08-06

    Potassium (i.e., K(+)) channels allow for the controlled and selective passage of potassium ions across the plasma membrane via a conserved pore domain. In voltage-gated K(+) channels, gating is the result of the coordinated action of two coupled gates: an activation gate at the intracellular entrance of the pore and an inactivation gate at the selectivity filter. By using solid-state NMR structural studies, in combination with electrophysiological experiments and molecular dynamics simulations, we show that the turret region connecting the outer transmembrane helix (transmembrane helix 1) and the pore helix behind the selectivity filter contributes to K(+) channel inactivation and exhibits a remarkable structural plasticity that correlates to K(+) channel inactivation. The transmembrane helix 1 unwinds when the K(+) channel enters the inactivated state and rewinds during the transition to the closed state. In addition to well-characterized changes at the K(+) ion coordination sites, this process is accompanied by conformational changes within the turret region and the pore helix. Further spectroscopic and computational results show that the same channel domain is critically involved in establishing functional contacts between pore domain and the cellular membrane. Taken together, our results suggest that the interaction between the K(+) channel turret region and the lipid bilayer exerts an important influence on the selective passage of potassium ions via the K(+) channel pore.

  15. 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.

  16. 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.

  17. Synthesis, characterization, and evaluation of a superficially porous particle with unique, elongated pore channels normal to the surface.

    PubMed

    Wei, Ta-Chen; Mack, Anne; Chen, Wu; Liu, Jia; Dittmann, Monika; Wang, Xiaoli; Barber, William E

    2016-04-01

    In recent years, superficially porous particles (SPPs) have drawn great interest because of their special particle characteristics and improvement in separation efficiency. Superficially porous particles are currently manufactured by adding silica nanoparticles onto solid cores using either a multistep multilayer process or one-step coacervation process. The pore size is mainly controlled by the size of the silica nanoparticles and the tortuous pore channel geometry is determined by how those nanoparticles randomly aggregate. Such tortuous pore structure is also similar to that of all totally porous particles used in HPLC today. In this article, we report on the development of a next generation superficially porous particle with a unique pore structure that includes a thinner shell thickness and ordered pore channels oriented normal to the particle surface. The method of making the new superficially porous particles is a process called pseudomorphic transformation (PMT), which is a form of micelle templating. Porosity is no longer controlled by randomly aggregated nanoparticles but rather by micelles that have an ordered liquid crystal structure. The new particle possesses many advantages such as a narrower particle size distribution, thinner porous layer with high surface area and, most importantly, highly ordered, non-tortuous pore channels oriented normal to the particle surface. This PMT process has been applied to make 1.8-5.1μm SPPs with pore size controlled around 75Å and surface area around 100m(2)/g. All particles with different sizes show the same unique pore structure with tunable pore size and shell thickness. The impact of the novel pore structure on the performance of these particles is characterized by measuring van Deemter curves and constructing kinetic plots. Reduced plate heights as low as 1.0 have been achieved on conventional LC instruments. This indicates higher efficiency of such particles compared to conventional totally porous and

  18. 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

  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. Synthesis and Characterization of Bionanoparticle-Silica Composites and Mesoporous Silica with Large Pores

    SciTech Connect

    Niu, Z.; Yang, L.; Kabisatpathy, S.; He, J.; Lee, A.; Ron, J.; Sikha, G.; Popov, B.N.; Emrick, T.; Russell, T. P.; Wang. Q.

    2009-03-24

    A sol-gel process has been developed to incorporate bionanoparticles, such as turnip yellow mosaic virus, cowpea mosaic virus, tobacco mosaic virus, and ferritin into silica, while maintaining the integrity and morphology of the particles. The structures of the resulting materials were characterized by transmission electron microscopy, small angle X-ray scattering, and N{sub 2} adsorption-desorption analysis. The results show that the shape and surface morphology of the bionanoparticles are largely preserved after being embedded into silica. After removal of the bionanoparticles by calcination, mesoporous silica with monodisperse pores, having the shape and surface morphology of the bionanoparticles replicated inside the silica, was produced,. This study is expected to lead to both functional composite materials and mesoporous silica with structurally well-defined large pores.

  1. Effects of the Al content on pore structures of porous TieAl alloys

    SciTech Connect

    Jaing, Y; He, Y H; Xu, N P; Zou, J; Huang, B; Lui, C T

    2008-01-01

    Porous TieAl alloys with different nominal compositions were fabricated through a reactive synthesis of Ti and Al elemental powders. It has been found that the pore parameters vary with the Al contents, indicating that the nature of the pores can be manipulated through changing the Al contents. In addition, detailed structural characterizations showed that the fabricated porous TieAl alloys can have three crystalline phases (i.e., a2-Ti3Al, g-TiAl, and TiAl3) when using different compositions. The fundamental reasons behind these phenomena have been explored.

  2. Effect of Processing Parameters on Pore Structure and Thickness of Anodic Aluminum Oxide (AAO) Tubular Membranes

    PubMed Central

    Belwalkar, A.; Grasing, E.; Huang, Z.; Misiolek, W.Z.

    2008-01-01

    Nanoporous anodic aluminum oxide (AAO) tubular membranes were fabricated from aluminum alloy tubes in sulfuric and oxalic acid electrolytes using a two-step anodization process. The membranes were investigated for characteristics such as pore size, interpore distance and thickness by varying applied voltage and electrolyte concentration. Morphology of the membranes was examined using light optical and scanning electron microscopy and characterized using ImageJ software. Results showed that membranes having narrow pore size and uniform pore distribution with parallel channel arrays were obtained. The pore sizes were ranging from 14 to 24 nm and the wall thicknesses as high as 76 µm. It was found that the pore size increased in direct proportion with the applied voltage and inversely with the electrolyte concentration while the interpore distance increased linearly with the applied voltage. It was also observed that increase in acid concentration increased tubular membrane wall thickness that improved mechanical handling. By using anodic alumina technology, robust ceramic tubes with uniformly distributed pore-structure and parallel nano-channels of lengths and sizes practical for industrial applications were reliably produced in quantity. PMID:19578471

  3. 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

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

    SciTech Connect

    Wang, Hsiu-Wen; Anovitz, Lawrence {Larry} M; Burg, Avihu; Cole, David; Allard Jr, Lawrence Frederick; Jackson, Andrew J; Stack, Andrew G; Rother, Gernot; Ciarlette, Diane D

    2013-01-01

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

  5. Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore

    NASA Astrophysics Data System (ADS)

    Song, Langzhou; Hobaugh, Michael R.; Shustak, Christopher; Cheley, Stephen; Bayley, Hagan; Gouaux, J. Eric

    1996-12-01

    The structure of the Staphylococcus aureus α-hemolysin pore has been determined to 1.9 overset{circ}{mathrm A} resolution. Contained within the mushroom-shaped homo-oligomeric heptamer is a solvent-filled channel, 100 overset{circ}{mathrm A} in length, that runs along the sevenfold axis and ranges from 14 overset{circ}{mathrm A} to 46 overset{circ}{mathrm A} in diameter. The lytic, transmembrane domain comprises the lower half of a 14-strand antiparallel β barrel, to which each protomer contributes two β strands, each 65 overset{circ}{mathrm A} long. The interior of the β barrel is primarily hydrophilic, and the exterior has a hydrophobic belt 28 overset{circ}{mathrm A} wide. The structure proves the heptameric subunit stoichiometry of the α-hemolysin oligomer, shows that a glycine-rich and solvent-exposed region of a water-soluble protein can self-assemble to form a transmembrane pore of defined structure, and provides insight into the principles of membrane interaction and transport activity of β barrel pore-forming toxins.

  6. Processing and Characterization of Porous Ti2AlC with Controlled Porosity and Pore Size

    DTIC Science & Technology

    2012-09-11

    fabricated by spark plasma sintering , were also characterized. The effects of porosity and/or pore size on the room temperature elastic moduli...pressureless- sintered without NaCl pore former, or fabricated by spark plasma sintering , were also characterized. The effects of porosity and/or pore size...as well as several samples sintered using spark plasma sintering (SPS). Furthermore, we demon- strate that the developed methodology can be implemented

  7. Using radial NMR profiles to characterize pore size distributions

    NASA Astrophysics Data System (ADS)

    Deriche, Rachid; Treilhard, John

    2012-02-01

    Extracting information about axon diameter distributions in the brain is a challenging task which provides useful information for medical purposes; for example, the ability to characterize and monitor axon diameters would be useful in diagnosing and investigating diseases like amyotrophic lateral sclerosis (ALS)1 or autism.2 Three families of operators are defined by Ozarslan,3 whose action upon an NMR attenuation signal extracts the moments of the pore size distribution of the ensemble under consideration; also a numerical method is proposed to continuously reconstruct a discretely sampled attenuation profile using the eigenfunctions of the simple harmonic oscillator Hamiltonian: the SHORE basis. The work presented here extends Ozarlan's method to other bases that can offer a better description of attenuation signal behaviour; in particular, we propose the use of the radial Spherical Polar Fourier (SPF) basis. Testing is performed to contrast the efficacy of the radial SPF basis and SHORE basis in practical attenuation signal reconstruction. The robustness of the method to additive noise is tested and analysed. We demonstrate that a low-order attenuation signal reconstruction outperforms a higher-order reconstruction in subsequent moment estimation under noisy conditions. We propose the simulated annealing algorithm for basis function scale parameter estimation. Finally, analytic expressions are derived and presented for the action of the operators on the radial SPF basis (obviating the need for numerical integration, thus avoiding a spectrum of possible sources of error).

  8. Crystal structure of human nuclear pore complex component NUP43.

    PubMed

    Xu, Chao; Li, Zhihong; He, Hao; Wernimont, Amy; Li, Yanjun; Loppnau, Peter; Min, Jinrong

    2015-10-24

    Nuclear pore complexes (NPC) form nuclear pores that cross the nuclear envelope and allow molecules to transport between the nucleus and the cytoplasm. We solved the crystal structure of human Nup43 (hNUP43), an important component in the Nup107 subcomplex of NPC. hNup43 adopts a seven-bladed β-propeller fold. We confirmed by ITC that neither human Nup37 (hNup37) nor human Nup133 (hNup133) interacts with hNup43. We demonstrated by analytical gel filtration that the human Nup85-Seh1L binary complex recruits hNup43 to form a ternary complex. Based on amino acid sequence analysis, we predicted the hNup85-hSeh1L binding surface of hNup43.

  9. Pore structure of the activated coconut shell charcoal carbon

    NASA Astrophysics Data System (ADS)

    Budi, E.; Nasbey, H.; Yuniarti, B. D. P.; Nurmayatri, Y.; Fahdiana, J.; Budi, A. S.

    2014-09-01

    The development of activated carbon from coconut shell charcoal has been investigated by using physical method to determine the influence of activation parameters in term of temperature, argon gas pressure and time period on the pore structure of the activated carbon. The coconut shell charcoal was produced by pyrolisis process at temperature of about 75 - 150 °C for 6 hours. The charcoal was activated at various temperature (532, 700 and 868 °C), argon gas pressure (6.59, 15 and 23.4 kgf/cm2) and time period of (10, 60 and 120 minutes). The results showed that the pores size were reduced and distributed uniformly as the activation parameters are increased.

  10. In situ structural analysis of the human nuclear pore complex.

    PubMed

    von Appen, Alexander; Kosinski, Jan; Sparks, Lenore; Ori, Alessandro; DiGuilio, Amanda L; Vollmer, Benjamin; Mackmull, Marie-Therese; Banterle, Niccolo; Parca, Luca; Kastritis, Panagiotis; Buczak, Katarzyna; Mosalaganti, Shyamal; Hagen, Wim; Andres-Pons, Amparo; Lemke, Edward A; Bork, Peer; Antonin, Wolfram; Glavy, Joseph S; Bui, Khanh Huy; Beck, Martin

    2015-10-01

    Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations.

  11. The Structure Inventory of the Nuclear Pore Complex.

    PubMed

    Schwartz, Thomas U

    2016-05-22

    The nuclear pore complex (NPC) is the principal gateway for molecular exchange between nucleus and cytoplasm across the nuclear envelope. Due to its sheer size of estimated 50-112MDa and its complex buildup from about 500-1000 individual proteins, it is a difficult object to study for structural biologists. Here, I review the extensive ensemble of high-resolution structures of the building blocks of the NPC. Concurrent with the increase in size and complexity, these latest, large structures and assemblies can now be used as the basis for hybrid approaches, primarily in combination with cryo-electron microscopic analysis, generating the first structure-based assembly models of the NPC. Going forward, the structures will be critically important for a detailed analysis of the NPC, including function, evolution, and assembly.

  12. The effect of pore structure on ebullition from peat

    NASA Astrophysics Data System (ADS)

    Ramirez, Jorge A.; Baird, Andy J.; Coulthard, Tom J.

    2016-06-01

    The controls on methane (CH4) bubbling (ebullition) from peatlands are uncertain, but evidence suggests that physical factors related to gas transport and storage within the peat matrix are important. Variability in peat pore size and the permeability of layers within peat can produce ebullition that ranges from steady to erratic in time and can affect the degree to which CH4 bubbles bypass consumption by methanotrophic bacteria and enter the atmosphere. Here we investigate the role of peat structure on ebullition in structurally different peats using a physical model that replicates bubble production using air injection into peat. We find that the frequency distributions of number of ebullition events per time and the magnitude of bubble loss from the physical model were similar in shape to ebullition from peatlands and incubated peats. This indicates that the physical model could be a valid proxy for naturally occurring ebullition from peat. For the first time, data on bubble sizes from peat were collected to conceptualize ebullition, and we find that peat structure affects bubble sizes. Using a new method to measure peat macrostructure, we collected evidence that supports the hypothesis that structural differences in peat determine if bubble release is steady or erratic and extreme. Collected pore size data suggest that erratic ebullition occurs when large amounts of gas stored at depth easily move through shallower layers of open peat. In contrast, steady ebullition occurs when dense shallower layers of peat regulate the flow of gas emitted from peat.

  13. Effect of pore structure on gas trapping in porous media

    NASA Astrophysics Data System (ADS)

    Mohammadian, Sadjad; Geistlinger, Helmut; Vogel, Hans-Jörg

    2014-05-01

    Capillary trapping of nonwetting phase in porous media plays an important role in many geological processes. For example, large portions of hydrocarbons cannot be extracted from reservoirs due to capillary forces, while in carbon sequestration processes; capillary trapping might improve the storage efficiency. An important case is when the wetting phase (mostly water) displaces a low-viscosity low-density fluid. In such cases, like water encroachment into gas reservoirs or rising of water table in soils, competition of gravity, viscous, and capillary forces determines the final configuration of the fluids in invaded zone. The trapped nonwetting phase and its distribution within the porous media will affect many other processes such as flow of the other fluids and mass transfer phenomena. Thus, investigating the parameters affecting phase trapping and distribution, especially their relation to pore structure, which controls the capillary action, is required. The aim is to predict gas trapping from structural properties of the material. We conducted a series of column experiments, in which water displaces air at a range of flow rates in different glass-bead packs. The final 3D configuration and morphology of fluids was observed using X-Ray Computed Tomography (CT). We extracted 3D structure of porous media as well as of the trapped gas phase, and quantified them in terms of volume ratios, interfacial area, and morphology. Then we investigated the relations of the trapped phase to capillary forces (pore structure) and viscous forces (front velocity). The results give us new insights to explore the flow and dissolution processes: We found no systematic dependency of the front velocity of the invading water phase in the velocity range from 0.1 to 0.6 cm/min what corresponds to capillary numbers from 2 to 12 ×10^-6. Our experimental results indicate that the capillary trapping mechanism is controlled by the local pore structure and local connectivity and not by

  14. Atomic structure of the Y complex of the nuclear pore.

    PubMed

    Kelley, Kotaro; Knockenhauer, Kevin E; Kabachinski, Greg; Schwartz, Thomas U

    2015-05-01

    The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. Here we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved core of the Y complex has six rather than seven members. Evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.

  15. Influence of biochar on soil pore structure and denitrification

    NASA Astrophysics Data System (ADS)

    Maenhout, Peter; Sleutel, Steven; Ameloot, Nele; De Neve, Stefaan

    2014-05-01

    Incorporation of biochar into soils has frequently been found to reduce soil emission of the greenhouse gas N2O, formed as an intermediate during microbial denitrification. The exact mechanism that regulates N2O emission reduction after biochar incorporation is still unknown and diverse hypotheses on either chemical, physical or biological controls over soil denitrification exist. The porous structure of biochar may directly and indirectly influence the soil pore structure upon its incorporation. Firstly biochar may increase soil aeration and thereby reduce denitrification which requires an anaerobic atmosphere to continue. In order to investigate this hypothesis we incorporated 4 biochar types in a sandy loam soil and collected undisturbed soil cores after 8 months of field incorporation. We then crushed half of the soil cores and replaced them. We followed N2O emissions from undisturbed and disturbed biochar amended soil cores by GC headspace analysis. From the disturbed soil cores no emission reduction was expected because soil pore structure was severely disrupted. However, both disturbed and undisturbed soil cores showed emission reductions when compared to the soil cores without biochar amendment. This allowed us to reject the hypothesis that biochar would affect soil denitrification through increased soil aeration. We moved to investigate a second hypothesis, viz. 'Through the retention of water in its finer pores, biochar could create local anaerobic 'denitrification hot spots' in soils. It could be hypothesized that the final further reduction of N2O into N2 is stimulated. We tested this hypothesis by comparing N2+N2O (acetylene inhibition) and N2O emissions from undisturbed soil cores with or without biochar amended, at 70 and 90 % WFPS. At 70% WFPS we expected higher N2 emissions in biochar amended soils compared to the unamended control cores, through the action of anaerobic hot spots in biochar. In contrast, at 90% WFPS anaerobicity would be general in

  16. 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.

  17. 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

  18. An improvement of the fractal theory and its application in pore structure evaluation and permeability estimation

    NASA Astrophysics Data System (ADS)

    Ge, Xinmin; Fan, Yiren; Deng, Shaogui; Han, Yujiao; Liu, Jiaxiong

    2016-09-01

    We present an improved fractal model for pore structure evaluation and permeability estimation based on the high pressure mercury porosimetry data. An accumulative fractal equation is introduced to characterize the piecewise nature of the capillary pressure and the mercury saturation. The iterative truncated singular value decomposition algorithm is developed to solve the accumulative fractal equation and obtain the fractal dimension distributions. Furthermore, the fractal dimension distributions and relevant parameters are used to characterize the pore structure and permeability. The results demonstrate that the proposed model provides better characterization of the mercury injection capillary pressure than conventional monofractal theory. In addition, there is a direct relationship between the pore structure types and the fractal dimension spectrums. What is more, the permeability is strongly correlated with the geometric and the arithmetic mean values of fractal dimensions, and the permeability estimated using these new fractal dimension parameters achieve excellent result. The improved model and solution give a fresh perspective of the conventional monofractal theory, which may be applied in many geological and geophysical fields.

  19. Effect of Pore Structure on Diffusion of Sorbates in Zeolites.

    NASA Astrophysics Data System (ADS)

    Nivarthi, Sriram Satyamurthy

    1995-01-01

    This thesis describes the application of nuclear magnetic resonance (NMR) techniques to measure the dynamics of sorbates in the constrained geometries presented by zeolite molecular sieve micropores. Molecular simulations have been used to further probe the effect of structural modifications of the zeolite on the siting and energetics of the adsorbed phase. The aim of this research effort has been to understand the relationship between the pore structure of the zeolite and the mobility of sorbates. The issues addressed in this research are relevant to the application of zeolites in shape selective catalysis and separations. The self-diffusion of simple probe sorbate molecules like methane and ethylene has been studied in zeolites of varying pore architecture using the pulsed field gradient (PFG) NMR technique. Using NMR inversion recovery measurements, we estimated the rate of intercage hopping of xenon in zeolite NaA and found it to decrease with pore crowding. The effect of dealumination on adsorption and diffusion in mordenite was studied using a combination of experiments and grand canonical Monte Carlo simulations. Experimental studies using methane as sorbate indicated that diffusional constraints were relieved by dealumination. Simulations revealed an octahedral lattice of sorption sites for xenon in mordenite which remained virtually unchanged by dealumination. Diffusion measurements of methane in large crystals of the anisotropic molecular sieve AlPO_4 -5 established the motion of methane to be unidirectional, but not single-file. Finally, we have carried out multicomponent diffusion measurements in large Y and silicalite crystals. Blocking caused by the presence of strongly coadsorbed molecules like benzene and ethylene was found to strongly suppress the diffusion of the relatively mobile methane in NaY. Excellent agreement was found between the experimental diffusivity data and the prediction based on the effective medium approximation to the percolation

  20. Integrated structural analysis of the human nuclear pore complex scaffold.

    PubMed

    Bui, Khanh Huy; von Appen, Alexander; DiGuilio, Amanda L; Ori, Alessandro; Sparks, Lenore; Mackmull, Marie-Therese; Bock, Thomas; Hagen, Wim; Andrés-Pons, Amparo; Glavy, Joseph S; Beck, Martin

    2013-12-05

    The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC. We show that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC. This arrangement may explain how changes of the diameter are realized that would accommodate transport of huge cargoes.

  1. The nuclear pore complex: understanding its function through structural insight.

    PubMed

    Beck, Martin; Hurt, Ed

    2017-02-01

    Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. They are large macromolecular assemblies with a complex composition and diverse functions. Apart from facilitating nucleocytoplasmic transport, NPCs are involved in chromatin organization, the regulation of gene expression and DNA repair. Understanding the molecular mechanisms underlying these functions has been hampered by a lack of structural knowledge about the NPC. The recent convergence of crystallographic and biochemical in vitro analysis of nucleoporins (NUPs), the components of the NPC, with cryo-electron microscopic imaging of the entire NPC in situ has provided first pseudo-atomic view of its central core and revealed that an unexpected network of short linear motifs is an important spatial organization principle. These breakthroughs have transformed the way we understand NPC structure, and they provide an important base for functional investigations, including the elucidation of the molecular mechanisms underlying clinically manifested mutations of the nucleocytoplasmic transport system.

  2. Towards reconciling structure and function in the nuclear pore complex

    PubMed Central

    Aebi, Ueli; Fahrenkrog, Birthe

    2008-01-01

    The spatial separation between the cytoplasm and the cell nucleus necessitates the continuous exchange of macromolecular cargo across the double-membraned nuclear envelope. Being the only passageway in and out of the nucleus, the nuclear pore complex (NPC) has the principal function of regulating the high throughput of nucleocytoplasmic transport in a highly selective manner so as to maintain cellular order and function. Here, we present a retrospective review of the evidence that has led to the current understanding of both NPC structure and function. Looking towards the future, we contemplate on how various outstanding effects and nanoscopic characteristics ought to be addressed, with the goal of reconciling structure and function into a single unified picture of the NPC. PMID:18228033

  3. Structure and gating of the nuclear pore complex

    NASA Astrophysics Data System (ADS)

    Eibauer, Matthias; Pellanda, Mauro; Turgay, Yagmur; Dubrovsky, Anna; Wild, Annik; Medalia, Ohad

    2015-06-01

    Nuclear pore complexes (NPCs) perforate the nuclear envelope and allow the exchange of macromolecules between the nucleus and the cytoplasm. To acquire a deeper understanding of this transport mechanism, we analyse the structure of the NPC scaffold and permeability barrier, by reconstructing the Xenopus laevis oocyte NPC from native nuclear envelopes up to 20 Å resolution by cryo-electron tomography in conjunction with subtomogram averaging. In addition to resolving individual protein domains of the NPC constituents, we propose a model for the architecture of the molecular gate at its central channel. Furthermore, we compare and contrast this native NPC structure to one that exhibits reduced transport activity and unveil the spatial properties of the NPC gate.

  4. Structure and gating of the nuclear pore complex.

    PubMed

    Eibauer, Matthias; Pellanda, Mauro; Turgay, Yagmur; Dubrovsky, Anna; Wild, Annik; Medalia, Ohad

    2015-06-26

    Nuclear pore complexes (NPCs) perforate the nuclear envelope and allow the exchange of macromolecules between the nucleus and the cytoplasm. To acquire a deeper understanding of this transport mechanism, we analyse the structure of the NPC scaffold and permeability barrier, by reconstructing the Xenopus laevis oocyte NPC from native nuclear envelopes up to 20 Å resolution by cryo-electron tomography in conjunction with subtomogram averaging. In addition to resolving individual protein domains of the NPC constituents, we propose a model for the architecture of the molecular gate at its central channel. Furthermore, we compare and contrast this native NPC structure to one that exhibits reduced transport activity and unveil the spatial properties of the NPC gate.

  5. Real Time Pore Structure Evolution during Olivine Mineral Carbonation

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Aqueous carbonation of ultramafic rocks has been proposed as a promising method for long-term, secure sequestration of carbon dioxide. While chemical kinetics data indicate that carbonation reaction in olivine is one of the fastest among the mg-bearing minerals, in practice, the factors that limit the extent and rate of carbonation in ultramafic rocks are fluid supply and flux. On the one hand, reaction products could produce passivating layer that prohibits further reactions. On the other hand, the increases in solid volume during carbonation could lead to cracking and create new fluid paths. Whether carbonation in ultramafic rocks is self-limiting or self-sustaining has been hotly debated. Experimental evidence of precipitation of reaction products during olivine carbonation was reported. To date, reaction-driven cracking has not been observed. In this paper, we present the first real-time pore structure evolution data using the x-ray synchrotron microtomography. Sodium bicarbonate (NaHCO3) solution was injected into porous olivine aggregates and in-situ pore structure change during olivine carbonation at a constant confining pressure (12 MPa) and a temperature of 200oC was captured at 30 min. interval for ~160 hours. Shortly after the experiment started, filling-in of the existing pores by precipitation of reaction products was visible. The size of the in-fills kept increasing as reactions continued. After ~48 hours, cracking around the in-fill materials became visible. After ~60 hours, these cracks started to show a clear polygonal pattern, similar to the crack patterns usually seen on the surface of drying mud. After ~72 hours, some of the cracks coalesced into large fractures that cut-through the olivine aggregates. New fractures continued to develop and at the end of the experiment, the sample was completely disintegrated by these fractures. We also conducted nanotomography experiments on a sub-volume of the reacted olivine aggregate. Orthogonal sets of

  6. Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes.

    PubMed

    Bestembayeva, Aizhan; Kramer, Armin; Labokha, Aksana A; Osmanović, Dino; Liashkovich, Ivan; Orlova, Elena V; Ford, Ian J; Charras, Guillaume; Fassati, Ariberto; Hoogenboom, Bart W

    2015-01-01

    The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ∼5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC. Although the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins, and is therefore not well understood. Here, we show that stiffness topography with sharp atomic force microscopy tips can generate nanoscale cross-sections of the NPC. The cross-sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel.

  7. Comparative study of pore structure evolution during solvent and thermal debinding of powder injection molded parts

    SciTech Connect

    Hwang, K.S.; Hsieh, Y.M.

    1996-02-01

    The solvent debinding process has been widely accepted in the powder injection molding (PIM) industry due to its short debinding cycle. In the current study, specimens were immersed in a heptane bath for different lengths of time, and the pore structure evolvement in the compact was analyzed. Mercury porosimetry analyses and scanning electron micrographs showed that the binder extraction started from the surface and progressed toward the center of the compacts. As the debinding continued, the pores grew and were widely distributed in size. This pore structure evolvement was different from that of straight thermal debinding in which the pore size distribution was quite narrow and the mean pore diameter shifted toward smaller sizes as debinding time increased. After the soluble binders were extracted, parts were subjected to a subsequent thermal debinding during which these pores served as conduits for decomposed gas to escape. Concurrently, the remaining binder became fluidlike and was redistributed within the compact due to capillarity. This pore structure, as observed from the mercury intrusion curves, showed a sharp increase in the pore volume at the 0.8-{micro}m size, followed by a series of fine pores, which is different from the pore structure of straight thermal debinding. The difference in the pore structure evolvement between solvent and thermal debinding and its effect on the debinding rate are discussed.

  8. Exceptional structural and mechanical flexibility of the nuclear pore complex.

    PubMed

    Liashkovich, Ivan; Meyring, Anne; Kramer, Armin; Shahin, Victor

    2011-03-01

    Nuclear pore complexes (NPCs) mediate all transport between the cytosol and the nucleus and therefore take centre stage in physiology. While transport through NPCs has been extensively investigated little is known about their structural and barley anything about their mechanical flexibility. Structural and mechanical flexibility of NPCs, however, are presumably of key importance. Like the cell and the cell nucleus, NPCs themselves are regularly exposed to physiological mechanical forces. Besides, NPCs reveal striking transport properties which are likely to require fairly high structural flexibility. The NPC transports up to 1,000 molecules per second through a physically 9 nm wide channel which repeatedly opens to accommodate macromolecules significantly larger than its physical diameter. We hypothesised that NPCs possess remarkable structural and mechanical stability. Here, we tested this hypothesis at the single NPC level using the nano-imaging and probing approach atomic force microscopy (AFM). AFM presents the NPC as a highly flexible structure. The NPC channel dilates by striking 35% on exposure to trans-cyclohexane-1,2-diol (TCHD), which is known to transiently collapse the hydrophobic phase in the NPC channel like receptor-cargo complexes do in transit. It constricts again to its initial size after TCHD removal. AFM-based nano-indentation measurements show that the 50 nm long NPC basket can astonishingly be squeezed completely into the NPC channel on exposure to incremental mechanical loads but recovers its original vertical position within the nuclear envelope plane when relieved. We conclude that the NPC possesses exceptional structural and mechanical flexibility which is important to fulfilling its functions.

  9. 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.

  10. 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

  11. Highly ordered porous alumina with tailor-made pore structures fabricated by pulse anodization.

    PubMed

    Lee, Woo; Kim, Jae-Cheon

    2010-12-03

    A new anodization method for the preparation of nanoporous anodic aluminum oxide (AAO) with pattern-addressed pore structure was developed. The approach is based on pulse anodization of aluminum employing a series of potential waves that consist of two or more different pulses with designated periods and amplitudes, and provides unique tailoring capability of the internal pore structure of anodic alumina. Pores of the resulting AAOs exhibit a high degree of directional coherency along the pore axes without branching, and thus are suitable for fabricating novel nanowires or nanotubes, whose diameter modulation patterns are predefined by the internal pore geometry of AAO. It is found from microscopic analysis on pulse anodized AAOs that the effective electric field strength at the pore base is a key controlling parameter, governing not only the size of pores, but also the detailed geometry of the barrier oxide layer.

  12. Analysis of the pore structure of activated carbons produced from paper mill sludge using small angle neutron scattering data

    SciTech Connect

    Sandi, G.; Khalil, N. R.; Littrell, K.; Thiyagarajan, P.

    1999-12-13

    A novel, cost-effective, and environmentally benign process was developed to produce highly efficient carbon-based adsorbents (CBAs) from paper mill sludge. The production process required chemical activation of sludge using zinc chloride and pyrolysis at 750 C in N{sub 2} gas. The produced CBAs were characterized according to their surface area and pore size distribution using N{sub 2}-BET adsorption isotherm data. Further characterization of the surface and pore structure was conducted using a unified exponential/power law approach applied to small angle neutron scattering (SANS) data. The structural features analyzed by SANS revealed the dependence of porosity with zinc chloride concentration. The presence of inaccessible pores was also determined by contrast-match experiments.

  13. Assessment of the 3 D Pore Structure and Individual Components of Preshaped Catalyst Bodies by X-Ray Imaging.

    PubMed

    da Silva, Julio C; Mader, Kevin; Holler, Mirko; Haberthür, David; Diaz, Ana; Guizar-Sicairos, Manuel; Cheng, Wu-Cheng; Shu, Yuying; Raabe, Jörg; Menzel, Andreas; van Bokhoven, Jeroen A

    2015-02-01

    Porosity in catalyst particles is essential because it enables reactants to reach the active sites and it enables products to leave the catalyst. The engineering of composite-particle catalysts through the tuning of pore-size distribution and connectivity is hampered by the inability to visualize structure and porosity at critical-length scales. Herein, it is shown that the combination of phase-contrast X-ray microtomography and high-resolution ptychographic X-ray tomography allows the visualization and characterization of the interparticle pores at micro- and nanometer-length scales. Furthermore, individual components in preshaped catalyst bodies used in fluid catalytic cracking, one of the most used catalysts, could be visualized and identified. The distribution of pore sizes, as well as enclosed pores, which cannot be probed by traditional methods, such as nitrogen physisorption and isotherm analysis, were determined.

  14. Investigating the effects of stress on the pore structures of nuclear grade graphites

    NASA Astrophysics Data System (ADS)

    Taylor, Joshua E. L.; Hall, Graham N.; Mummery, Paul M.

    2016-03-01

    Graphite is used as a moderating material and as a structural component in a number of current generation nuclear reactors. During reactor operation stresses develop in the graphite components, causing them to deform. It is important to understand how the microstructure of graphite affects the material's response to these stresses. A series of experiments were performed to investigate how the pore structures of Pile Grade A and Gilsocarbon graphites respond to loading stresses. A compression rig was used to simulate the build-up of operational stresses in graphite components, and a confocal laser microscope was used to study variation of a number of important pore properties. Values of elastic modulus and Poisson's ratio were calculated and compared to existing literature to confirm the validity of the experimental techniques. Mean pore areas were observed to decrease linearly with increasing applied load, mean pore eccentricity increased linearly, and a small amount of clockwise pore rotation was observed. The response to build-up of stresses was dependent on the orientation of the pores and basal planes and the shapes of the pores with respect to the loading axis. It was proposed that pore closure and pore reorientation were competing processes. Pore separation was quantified using 'nearest neighbour' and Voronoi techniques, and non-pore regions were found to shrink linearly with increasing applied load.

  15. Investigation of electrolyte wetting in lithium ion batteries: Effects of electrode pore structures and solution

    NASA Astrophysics Data System (ADS)

    Sheng, Yangping

    and surface tension of electrolyte is used to reflect performance of electrolyte wetting. There are very few reports about quantitative measurement about electrolyte wetting. Moreover, there are only simple qualitative observations, good, poor, and fair, were reported on the wettability of microporous separators. Therefore, development of a quantitative analysis method is critical to help understand the mechanism of how electrolyte wetting is affected by material properties and manufacturing processes. In this dissertation, a quantitative test method is developed to analyze the electrolyte wetting performance. Wetting rate, measured by wetting balance method, is used to quantitatively measure the speed of electrolyte wetting. The feasibility of the wetting rate is demonstrated by repeated test of wetting rate between electrolytes and electrodes. Various electrolytes from single solvents to complicated industrial level electrolytes are measured with baseline electrodes. Electrodes with different composition, active materials and manufacturing process, separator sheets with different materials and additives are also measured with baseline electrolyte. The wetting behaviors for different materials and manufacturing processes could be used to help improve the optimization of production process. It is very necessary to reveal the mechanism underlying electrolyte wetting, especially the effects of electrode pore microstructure. The Electrodes, which are composed of active material, binder and carbon black, are formed by production process (rheological processing, coating, drying), and post-production process (calendaring and slicing etc.). The pore structure is also complicated by the broad size range of pores from nanometer to tens micrometer. In this dissertation, a pore network concept, as revealed in the MIP test (mercury intrusion porosimetry), is employed to characterize the electrode pore structure. It is composed by the random pore cavity and connected part of pores

  16. Description and Reconstruction of Soil Structure Using Correlation Functions: Morphological and Pore-Scale Modeling Study

    NASA Astrophysics Data System (ADS)

    Karsanina, M.; Gerke, K.; Vasilyev, R.; Skvortsova, E. B.; Korost, D. V.; Mallants, D.

    2013-12-01

    It is now well-established that structure of porous or composite media (i.e., distribution of different materials or phases) defines all physical properties, including multi-phase flow and solute transport. To characterize soil structure conventional soil science uses such metrics as grain size distribution, morphology or numerous classifications. However, all these descriptors provide only limited and often qualitative information about structural properties, cannot be used to reconstruct real structure or predict physical properties. With the progress of modern non-destructive analysis tools we can obtain detailed 3D structure information and use it for calculation of any physical property. Such 3D data is a valuable verification dataset to check the usefulness of soil structure description using stochastic measures such as correlation functions. Any potential soil structure descriptor should possess two main features: 1) represent structure in some mathematical way, 2) reconstruction based on this mathematical function alone should be statistically equal to the original structure (e.g., have similar pore size distributions, physical properties, etc.). To check the applicability to soil science, we choose different 2D and 3D segmented soil images and calculated their correlation function. The modified Yeong-Torquato procedure was then used to reconstruct images based on calculated correlation functions. This method was applied to three different soil datasets: 1) a set of 2D thin-sections, 2) 3D images of soils with known hydraulic properties (Ksat and WRC), 3) 3D images of soils and aggregates from the same soil profile, but different genetic horizons. In the first case, we use conventional morphological descriptors in 2D original and reconstructed images (pore size, shapes and orientations) to quantify reconstructions quality. In the second case, we use pore-network models extracted from original and reconstructed 3D images to calculate Ksat, WRC and relative

  17. Synaptic fusion pore structure and AMPA receptor activation according to Brownian simulation of glutamate diffusion.

    PubMed

    Ventriglia, Francesco; Maio, Vito Di

    2003-03-01

    The rising phase of fast, AMPA-mediated Excitatory Post Synaptic Currents (EPSCs) has a primary role in the computational ability of neurons. The structure and radial expansion velocity of the fusion pore between the vesicle and the presynaptic membrane could be important factors in determining the time course of the EPSC. We have used a Brownian simulation model for glutamate neurotransmitter diffusion to test two hypotheses on the fusion pore structure, namely, the proteinaceous pore and the purely lipidic pore. Three more hypotheses on the radial expansion velocity were also tested. The rising phases of the EPSC, computed under various conditions, were compared with experimental data from the literature. Our present results show that a proteinaceous fusion pore should produce a more marked foot at the beginning of the rising phase of the EPSC. They also confirm the hypothesis that the structure of the fusion pore and its radial expansion velocity play significant roles in shaping the fast EPSC time course.

  18. 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.

  19. Ultrasonic characterization of structural ceramics

    NASA Technical Reports Server (NTRS)

    Klima, S. J.; Baaklini, G. Y.

    1986-01-01

    Ultrasonic velocity and attenuation measurements were used to characterize density and microstructure in monolithic silicon nitride and silicon carbide. Research samples of these structural ceramics exhibited a wide range of density and microstructural variations. It was shown that bulk density variations correlate with and can be estimated by velocity measurements. Variations in microstructural features such as grain size or shape and pore morphology had a minor effect on velocity. However, these features had a pronounced effect on ultrasonic attenuation. The ultrasonic results are supplemented by low-energy radiography and scanning laser acoustic microscopy.

  20. 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.

  1. Preparation of Ni-doped carbon nanospheres with different surface chemistry and controlled pore structure

    NASA Astrophysics Data System (ADS)

    Zubizarreta, L.; Arenillas, A.; Pis, J. J.

    2008-04-01

    In classic carbon supports is very difficult to control pore size, pore size distribution, and surface chemical properties at the same time. In this work microporous carbons derived from furfuryl alcohol are used as support to prepare Ni-doped carbon materials. The N 2 flow rate used during the carbonisation process of the precursor influences on the size of the nanospheres obtained but not in their textural properties. Microporous carbon nanospheres have been synthesised with a narrow pore size distribution centred in 5.5 Å. The surface chemistry of these materials can be easily modified by different treatments without detriment of the pore structure of the doped carbon nanospheres.

  2. Porous hydrogels with well-defined pore structure for biomaterials applications

    NASA Astrophysics Data System (ADS)

    Marshall, Andrew J.

    When any medical device is implanted inside the body, the natural inflammatory response causes the device to be encapsulated with a thin layer of dense, relatively avascular fibrous tissue, effectively sealing off the device from the surrounding tissue and isolating it from the rest of the body. For medical devices such as electrodes and glucose sensors, where functionality depends on the ability of the device to interact with the surrounding biochemistry, the "foreign body response" poses a formidable obstacle. Previous studies have demonstrated that porous materials with pore dimensions on the order of cell dimensions can induce a modified foreign body response, resulting in more vascularized capsule tissue. However, the utility of these studies is limited because the materials used had broad pore size distributions and poorly defined pore geometries. This thesis is motivated by the unavailability of biomaterials with well-defined and controlled pore size, and by the lack of understanding of the relationships between pore dimensions and the foreign body response. Our sphere templating technology permits the fabrication of open-pore structures with precisely controlled pore dimensions. We can produce these sphere-templated pore structures out of a variety of polymeric materials, including poly(2-hydroxyethyl methacrylate) (polyHEMA), silicone rubber, and degradable copolymers of polyHEMA and poly(epsilon-caprolactone). We applied our precision-engineered pore structures in vivo to investigate the role of pore size in the foreign body response. We implanted porous polyHEMA with various pore geometries under the skin of mice and found that the level of intra-pore vascularization increases with decreasing pore size, with vascular density directly proportional to the specific surface area of the implant, and that the threshold pore throat diameter for rapid tissue in-growth is approximately 8 mum. Based on our empirical results coupled with first principles, we

  3. Structure of the sodium channel pore revealed by serial cysteine mutagenesis.

    PubMed Central

    Pérez-García, M T; Chiamvimonvat, N; Marban, E; Tomaselli, G F

    1996-01-01

    The pores of voltage-gated cation channels are formed by four intramembrane segments that impart selectivity and conductance. Remarkably little is known about the higher order structure of these critical pore-lining or P segments. Serial cysteine mutagenesis reveals a pattern of side-chain accessibility that contradicts currently favored structural models based on alpha-helices or beta-strands. Like the active sites of many enzymes of known structure, the sodium channel pore consists of irregular loop regions. Images Fig. 1 Fig. 4 PMID:8552626

  4. 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

  5. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 9, October 1, 1993--December 30, 1993

    SciTech Connect

    Smith, D.M.

    1993-12-31

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultra-micro pores but they also exhibit meso and macroporosity. Conventional pore size techniques (adsorption/condensation, mercury porosimetry) are limited because of this broad pore size range, microporosity, reactive nature of coal, samples must be completely dried, and network/percolation effects. Small angle scattering is limited because it probes both open and dosed pores. Although one would not expect any single technique to provide a satisfactory description of a coal`s structure, it is apparent that better techniques are necessary. Small angle scattering could be improved by combining scattering and adsorption measurements. Also, the measurement of NMR parameters of various gas phase and adsorbed phase NMR active probes can provide pore structure information. We will investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules ({sup 129}Xe, {sup 3}He, {sup 14}N{sub 2}, {sup 14}NH{sub 3}, {sup 15}N{sub 2}, {sup 13}CH{sub 4}, {sup 13}CO{sub 2}) and pore surface. Our current work may be divided into three areas: small-angle X-ray scattering (SAXS), adsorption, and NMR.

  6. Evolution of the pore structure during the early stages of the alkali-activation reaction: An in situ small-angle neutron scattering investigation

    DOE PAGES

    White, Claire E.; Olds, Daniel P.; Hartl, Monika; ...

    2017-02-01

    The long-term durability of cement-based materials is influenced by the pore structure and associated permeability at the sub-micrometre length scale. With the emergence of new types of sustainable cements in recent decades, there is a pressing need to be able to predict the durability of these new materials, and therefore nondestructive experimental techniques capable of characterizing the evolution of the pore structure are increasingly crucial for investigating cement durability. Here, small-angle neutron scattering is used to analyze the evolution of the pore structure in alkali-activated materials over the initial 24 h of reaction in order to assess the characteristic poremore » sizes that emerge during these short time scales. By using a unified fitting approach for data modeling, information on the pore size and surface roughness is obtained for a variety of precursor chemistries and morphologies (metakaolin- and slag-based pastes). Furthermore, the impact of activator chemistry is elucidatedviathe analysis of pastes synthesized using hydroxide- and silicate-based activators. It is found that the main aspect influencing the size of pores that are accessible using small-angle neutron scattering analysis (approximately 10–500 Å in diameter) is the availability of free silica in the activating solution, which leads to a more refined pore structure with smaller average pore size. Furthermore, as the reaction progresses the gel pores visible using this scattering technique are seen to increase in size.« less

  7. Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation

    PubMed Central

    Lawrence, Sara L.; Feil, Susanne C.; Morton, Craig J.; Farrand, Allison J.; Mulhern, Terrence D.; Gorman, Michael A.; Wade, Kristin R.; Tweten, Rodney K.; Parker, Michael W.

    2015-01-01

    Pore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world’s leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface. PMID:26403197

  8. 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.

  9. Characterization of pores in high pressure die cast aluminum using active thermography and computed tomography

    NASA Astrophysics Data System (ADS)

    Maierhofer, Christiane; Myrach, Philipp; Röllig, Mathias; Jonietz, Florian; Illerhaus, Bernhard; Meinel, Dietmar; Richter, Uwe; Miksche, Ronald

    2016-02-01

    Larger high pressure die castings (HPDC) and decreasing wall thicknesses are raising the issue of casting defects like pores in aluminum structures. Properties of components are often strongly influenced by inner porosity. As these products are being established more and more in lightweight construction (e.g. automotive and other transport areas), non-destructive testing methods, which can be applied fast and on-site, are required for quality assurance. In this contribution, the application of active thermography for the direct detection of larger pores is demonstrated. The analysis of limits and accuracy of the method are completed by numerical simulation and the method is validated using computed tomography.

  10. Structural basis for self-assembly of a cytolytic pore lined by protein and lipid

    NASA Astrophysics Data System (ADS)

    Tanaka, Koji; Caaveiro, Jose M. M.; Morante, Koldo; González-Mañas, Juan Manuel; Tsumoto, Kouhei

    2015-02-01

    Pore-forming toxins (PFT) are water-soluble proteins that possess the remarkable ability to self-assemble on the membrane of target cells, where they form pores causing cell damage. Here, we elucidate the mechanism of action of the haemolytic protein fragaceatoxin C (FraC), a α-barrel PFT, by determining the crystal structures of FraC at four different stages of the lytic mechanism, namely the water-soluble state, the monomeric lipid-bound form, an assembly intermediate and the fully assembled transmembrane pore. The structure of the transmembrane pore exhibits a unique architecture composed of both protein and lipids, with some of the lipids lining the pore wall, acting as assembly cofactors. The pore also exhibits lateral fenestrations that expose the hydrophobic core of the membrane to the aqueous environment. The incorporation of lipids from the target membrane within the structure of the pore provides a membrane-specific trigger for the activation of a haemolytic toxin.

  11. Preparation and Pore Structure Stability at High Temperature of Porous Fe-Al Intermetallics

    NASA Astrophysics Data System (ADS)

    Shen, P. Z.; Gao, H. Y.; Song, M.; He, Y. H.

    2013-12-01

    Porous Fe-Al intermetallics with different nominal compositions (from Fe-8 wt.% Al to Fe-50 wt.% Al) were fabricated by Fe and Al elemental powders through reaction synthesis. The effects of the Al content on the pore structure properties, and the comparison of pore structure stabilities at high-temperatures among the porous Fe-Al intermetallics and porous Ti, Ni, 316L stainless steel samples, were systematically studied. Results showed that the open porosity, maximum pore size, and permeability vary with the Al content. Porous Fe-(25-30 wt.%) Al intermetallics show good shape controllability and excellent pore structure stability at 1073 K in air, which suggests that these porous Fe-Al intermetallics could be used for filtration at high temperatures.

  12. Pore-scale flow characterization of low-interfacial tension flow through mixed-wet porous media with different pore geometries

    SciTech Connect

    Yadali Jamaloei, Benyamin; Asghari, Koorosh; Kharrat, Riyaz

    2011-01-15

    The low-interfacial tension flow through porous media occurs in surfactant-based enhanced oil recovery (EOR), soil clean-up, underground removal of the non-aqueous phase liquid and dense non-aqueous phase liquid, etc. In surfactant-based EOR processes, numerous works have been carried out to characterize - either qualitatively or quantitatively - the micro- and macro-scale flow behavior. What has been lacking is to link the statistics of oil blobs population (e.g., distribution of blob length and diameter) to the pore-scale phenomena and macro-scale quantities. In particular, no work has been reported to elucidate the effect of the ratio of pore body to throat diameter (i.e., aspect ratio) on the pore-scale characterization based on the blobs population statistics. The significance of the aspect ratio lies in that it describes the geometry of a porous medium and is one of the foremost morphological features. The aspect ratio is also one of the fundamental factors governing the pore-level events. This study presents the effect of aspect ratio on the statistical distribution of the blob length and equivalent diameter and links the blobs population statistics to the observed pore-level events. The pore-scale variation of the ratio of viscous-to-capillary forces acted on the oil blobs at the threshold of displacement is utilized to characterize the effect of blob length distribution at different aspect ratios. It also provides some insight into correlating the change in oil recovery efficiency and capillary number, by change in aspect ratio, with the change in blobs population statistics. (author)

  13. Synthesis and characterization of thermally stable large-pore mesoporous nanocrystallineanatase

    SciTech Connect

    Ermokhina, Natalia I.; Nevinskiy, Vitaly A.; Manorik, Piotr A.; Ilyin, Vladimir G.; Novichenko, Viktor N.; Shcherbatiuk, Mykola M.; Klymchuk, Dmitro O.; Tsyba, Mykola M.; Puziy, Alexander M.

    2013-04-15

    Thermally stable mesoporous nanocrystalline TiO{sub 2} with a pure anatase structure was obtained by sol–gel synthesis (in combination with hydrothermal treatment) using titanium tetrabutoxide and dibenzo-18-crown-6 as a structure-directing agent in presence of surfactant and/or La{sup 3+} ions additives. Nanocrystalline TiO{sub 2} demonstrates various textures with a well-defined spherical morphology (micro- and nanospheres), a crystallite size of no greater than 10 nm (XRD), and a narrow pore size distribution. Spherical particles of micrometer scale in the presence of La{sup 3+} ions do not form. TiO{sub 2} calcined (at 500 °C) after hydrothermal treatment (at 175 °C) has a significantly more developed porous structure as compared with TiO{sub 2} which was not treated hydrothermally. For example, specific surface area amounts 137 m{sup 2} g{sup −1} and 69 m{sup 2} g{sup −1}, pore volume 0.98 cm{sup 3} g{sup −1} and 0.21 cm{sup 3} g{sup −1}, pore diameter 17.5 nm and 12.5 nm respectively for samples hydrothermally treated and not treated. - Graphical abstract: Large-pore mesoporous nanocristalline anatase. Highlights: ► Large-pore mesoporous nanocrystalline TiO{sub 2} was obtained by sol–gel synthesis. ► Crown ether was used as template in presence of surfactant and/or La{sup 3+} ions. ► Anatase (crystalline size<11 nm) is the only crystalline phase present in TiO{sub 2}. ► TiO{sub 2} shows well-defined homogeneous spherical morphology (micro- and nano-spheres)

  14. Survival and relaxation time, pore size distribution moments, and viscous permeability in random unidirectional fiber structures

    NASA Astrophysics Data System (ADS)

    Tomadakis, Manolis M.; Robertson, Teri J.

    2005-03-01

    Computer simulation results are presented for the mean survival time, principal relaxation time, mean pore size, and mean square pore size, for random porous structures consisting of parallel nonoverlapping or partially overlapping fibers. The numerical procedure is based on a discrete step-by-step random walk mechanism simulating the Brownian diffusion trajectories of molecules in the porous media. Numerical results on the viscous permeability of these structures are computed with a method based on electrical conduction principles and compared to a variational bound derived from the mean survival time. The results show that nonoverlapping fiber structures exhibit lower values of the dimensionless mean survival time, principal relaxation time, mean pore size, and mean square pore size than randomly overlapping fiber structures of the same porosity, while partially overlapping fiber structures show behavior intermediate to those of the two extreme cases. The mean square pore size (second moment of the pore size distribution) is found to be a very good predictor of the mean survival time for non-, partially, and randomly overlapping fiber structures. Dimensionless groups representing the deviation of variational bounds from our simulation results vary in practically the same range as the corresponding values reported earlier for beds of spherical particles. A universal scaling expression of the literature relating the mean survival time to structural properties [S. Torquato and C. L. Y. Yeong, J. Chem. Phys. 106, 8814 (1997)] agrees very well with our results for all examined fiber structures, thus validated for the first time for porous media formed by partially overlapping particles. The permeability behavior of partially overlapping fiber structures resembles that of nonoverlapping fiber structures for flow parallel to the fibers, but not for transverse flow, where percolation phenomena prevail. The permeability results for beds of unidirectional partially

  15. Survival and relaxation time, pore size distribution moments, and viscous permeability in random unidirectional fiber structures.

    PubMed

    Tomadakis, Manolis M; Robertson, Teri J

    2005-03-01

    Computer simulation results are presented for the mean survival time, principal relaxation time, mean pore size, and mean square pore size, for random porous structures consisting of parallel nonoverlapping or partially overlapping fibers. The numerical procedure is based on a discrete step-by-step random walk mechanism simulating the Brownian diffusion trajectories of molecules in the porous media. Numerical results on the viscous permeability of these structures are computed with a method based on electrical conduction principles and compared to a variational bound derived from the mean survival time. The results show that nonoverlapping fiber structures exhibit lower values of the dimensionless mean survival time, principal relaxation time, mean pore size, and mean square pore size than randomly overlapping fiber structures of the same porosity, while partially overlapping fiber structures show behavior intermediate to those of the two extreme cases. The mean square pore size (second moment of the pore size distribution) is found to be a very good predictor of the mean survival time for non-, partially, and randomly overlapping fiber structures. Dimensionless groups representing the deviation of variational bounds from our simulation results vary in practically the same range as the corresponding values reported earlier for beds of spherical particles. A universal scaling expression of the literature relating the mean survival time to structural properties [S. Torquato and C. L. Y. Yeong, J. Chem. Phys. 106, 8814 (1997)] agrees very well with our results for all examined fiber structures, thus validated for the first time for porous media formed by partially overlapping particles. The permeability behavior of partially overlapping fiber structures resembles that of nonoverlapping fiber structures for flow parallel to the fibers, but not for transverse flow, where percolation phenomena prevail. The permeability results for beds of unidirectional partially

  16. Influence of lyophilization factors and gelatin concentration on pore structures of atelocollagen/gelatin sponge biomaterial.

    PubMed

    Yang, Longqiang; Tanabe, Koji; Miura, Tadashi; Yoshinari, Masao; Takemoto, Shinji; Shintani, Seikou; Kasahara, Masataka

    2017-03-08

    This study aimed to investigate influences of lyophilization factors and gelatin concentration on pore structures of ACG sponge. ACG sponges of different freezing temperatures (-30, -80 and -196(o)C), freezing times (1, 2 and 24 h), gelatin concentrations (0.6%AC+0.15%G, 0.6%AC+0.6%G and 0.6%AC+2.4%G), and with 500 μM fluvastatin were fabricated. Pore structures including porosity and pore size were analyzed by scanning electron microscopy and ImageJ. The cytotoxic effects of ACG sponges were evaluated in vitro. Freezing temperature did not affect porosity while high freezing temperature (-30(o)C) increased pore size. The high gelatin concentration group (0.6%AC+2.4%G) had decreased porosity and pore size. Freezing time and 500 μM fluvastatin did not affect pore structures. The cytotoxicity and cell proliferation assays revealed that ACG sponges had no cytotoxic effects on human mesenchymal stromal cell growth and proliferation. These results indicate that ACG sponge may be a good biomaterial scaffold for bone regeneration.

  17. 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.

  18. 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.

  19. Pore structure of hydrating cement paste by magnetic resonance relaxation analysis and freezing.

    PubMed

    Jehng, J Y; Sprague, D T; Halperin, W P

    1996-01-01

    Nuclear magnetic resonance relaxation analysis has been applied to interpret the evolution of microstructure in a cement paste during hydration. A basic understanding of the wet-dry and freeze-thaw processes of cement pastes has been developed. The pore structure evolution has been studied by the suppression of the freezing temperature of water and compared with spin-spin relaxation analysis performed at room temperature. Both methods consistently show that hydrating cement pastes have two principal components in their size distribution. The NMR relaxation times provide a measure of the characteristic pore sizes. Their interpretation is made in the context of a fast exchange model. Supercooling and thawing point depression of confined water has been studied systematically. The depression of the freezing point of liquid water confined within a pore was found to be dependent on the pore size, with capillary pore water freezing at 240 K and the remaining gel pore water freezing over a temperature range extending to as low as 160 K.A modified Gibbs-Thompson analysis was used to determine pore volume distributions from the distribution of thawing temperatures.

  20. The pore wall structure of porous semi-crystalline anatase TiO2.

    SciTech Connect

    Kim, Dr Man-Ho; Han, Seong Chul; Chae, Keun Hwa; Yu, Byung-Yong; Hong, Kyung Tea; Jackson, Andrew; Anovitz, Lawrence {Larry} M

    2011-01-01

    The structure of porous TiO2 prepared by electrochemical anodization in a fluoride-containing ethylene glycol electrolyte solution was quantitatively studied using small-angle neutron scattering (SANS) and ultra-small-angle neutron scattering (USANS). The cylindrical pores along the coaxial direction were somewhat irregular in shape, were widely distributed in diameter, and seemed to have a broadly pseudo-hexagonal arrangement. The scattering from the pore wall showed a negative deviation from Porod scattering, indicating that the interface between TiO2 and the pore was not sharp. A density gradient of around 40 60 A at the pore wall (i.e. the interface between the pore and the TiO2 matrix) was estimated using both constant and semi-sigmoidal interface models. This gradient may be due to the presence of fluorine and carbon partially absorbed by the pore wall from the fluoride-containing electrolyte or to sorbed water molecules on the wall. The neutron contrast-matching point between the TiO2 matrix and the pores filled with liquid H2O/D2O mixtures was 51/49%(v/v) H2O/D2O, yielding an estimated mass density of 3.32 g cm3. The specific surface area of the sample derived from the (U)SANS data was around 939 1003 m2 cm3 (283 302 m2 g1).

  1. The pore wall structure of porous semi-crystalline anatase TiO2

    SciTech Connect

    Kim, Dr Man-Ho; Han, Seong Chul; Chae, Keun Hwa; Yu, Byung-Yong; Hong, Kyung Tea; Jackson, Andrew; Anovitz, Lawrence {Larry} M

    2011-01-01

    The structure of porous TiO2 prepared by electrochemical anodization in a fluoride-containing ethylene glycol electrolyte solution was quantitatively studied using small angle neutron scattering (SANS) and ultra small angle neutron scattering (USANS). The cylindrical pores along the coaxial direction were somewhat irregular shape, were broadly distributed in diameter, and seemed to have a broadly pseudo-hexagonal arrangement. The scattering from the pore wall showed a negative deviation from Porod scattering, indicating the interface between TiO2 and the pore was not sharp. A density gradient of around 40 ~ 60 at the pore wall (i.e. interface between the pore and the TiO2 matrix) was estimated using both constant and semi-sigmoidal interface models. This may be due to the presence of fluorine and carbon partially absorbed by the pore wall from the fluoride-containing electrolyte and sorbed water molecules on the wall. The neutron contrast-matching point between the TiO2 matrix and the pores filled with liquid H2O/D2O mixtures was 51/49 vol/vol H2O/D2O, yielding an estimated mass density of 3.32 g/cm3. The specific surface area of the sample derived from the (U)SANS data, S/V, was around 939 ~ 1003 m2/cm3 (283~ 302m2/g).

  2. Microporous metal organic framework [M{sub 2}(hfipbb){sub 2}(ted)] (M=Zn, Co; H{sub 2}hfipbb=4,4-(hexafluoroisopropylidene)-bis(benzoic acid); ted=triethylenediamine): Synthesis, structure analysis, pore characterization, small gas adsorption and CO{sub 2}/N{sub 2} separation properties

    SciTech Connect

    Xu, William W.; Pramanik, Sanhita; Zhang, Zhijuan; Emge, Thomas J.; Li, Jing

    2013-04-15

    Carbon dioxide is a greenhouse gas that is a major contributor to global warming. Developing methods that can effectively capture CO{sub 2} is the key to reduce its emission to the atmosphere. Recent research shows that microporous metal organic frameworks (MOFs) are emerging as a promising family of adsorbents that may be promising for use in adsorption based capture and separation of CO{sub 2} from power plant waste gases. In this work we report the synthesis, crystal structure analysis and pore characterization of two microporous MOF structures, [M{sub 2}(hfipbb){sub 2}(ted)] (M=Zn (1), Co (2); H{sub 2}hfipbb=4,4-(hexafluoroisopropylidene)-bis(benzoic acid); ted=triethylenediamine). The CO{sub 2} and N{sub 2} adsorption experiments and IAST calculations are carried out on [Zn{sub 2}(hfipbb){sub 2}(ted)] under conditions that mimic post-combustion flue gas mixtures emitted from power plants. The results show that the framework interacts with CO{sub 2} strongly, giving rise to relatively high isosteric heats of adsorption (up to 28 kJ/mol), and high adsorption selectivity for CO{sub 2} over N{sub 2}, making it promising for capturing and separating CO{sub 2} from CO{sub 2}/N{sub 2} mixtures. - Graphical abstract: Microporous [Zn{sub 2}(hfipbb){sub 2}(ted)] demonstrates high adsorption selectivity for CO{sub 2} over N{sub 2} under conditions that mimic flue gas mixtures. Highlights: ► Two new porous MOFs were synthesized and characterized by rational design. ► The small pore size leads to greatly enhanced CO{sub 2}–MOF interaction. ► High adsorption selectivity of the Zn–MOF for CO{sub 2} over N{sub 2} is achieved.

  3. Fractal characterization of seepage-pores of coals from China: An investigation on permeability of coals

    NASA Astrophysics Data System (ADS)

    Yao, Yanbin; Liu, Dameng; Tang, Dazhen; Tang, Shuheng; Huang, Wenhui; Liu, Zhihua; Che, Yao

    2009-06-01

    To better understand the characteristics of seepage-pores (pore radius larger than 100 nanometers) and their influence on the permeability of coals, we have conducted fractal analyses for 34 fresh coal samples (mean maximum vitrinite reflectance Ro,max from 0.43% to 4.21%) from North, Northwest and Northeast China. Mercury porosimetry data indicate that the coals are fractal, with pore radius ranging from 0.1 to 50 μm. Calculated fractal dimensions of these coals range from 2.61 to 2.98, higher than those from other kinds of rocks such as sandstone, shale, and carbonate. The data suggest that the coals have more complicated and inhomogeneous pore structures than other rocks. The fractal dimension has a negative correlation with the petrologic permeability of coals, particularly for higher rank coals (with 1.47-4.21% Ro,max), from which a strong negative linear correlation ( R2=0.85) between fractal dimension and permeability is observed. A 'U-shaped' trend between fractal dimensions and coal ranks is observed, with the minimum fractal dimensions occurring at 1.1-1.3% Ro,max. The sub-bituminous, high volatile bituminous, semi-anthracite, and anthracite have higher fractal dimensions. The effects of coal rank upon fractal dimensions are mainly due to the variety of micropore contents and aromaticity of coals with coalification.

  4. Effect of calcium magnesium acetate on the forming property and fractal dimension of sludge pore structure during combustion.

    PubMed

    Zhang, Lihui; Duan, Feng; Huang, Yaji; Chyang, Chiensong

    2015-12-01

    The changes in pore structure characteristics of sewage sludge particles under effect of calcium magnesium acetate (CMA) during combustion were investigated, the samples were characterized by N2 isothermal absorption method, and the data were used to analyze the fractal properties of the obtained samples. Results show that reaction time and the mole ratio of calcium to sulfur (Ca/S ratio) have notable impact on the pore structure and morphology of solid sample. The Brunauer-Emmett-Teller (BET) specific surface area (SBET) of sample increases with Ca/S ratio, while significant decreases with reaction time. The fractal dimension D has the similar trend with that of SBET, indicating that the surface roughness of sludge increases under the effect of CMA adding, resulting in improved the sludge combustion and the desulfurization process.

  5. Synthesis and characterization of thermally stable large-pore mesoporous nanocrystallineanatase

    NASA Astrophysics Data System (ADS)

    Ermokhina, Natalia I.; Nevinskiy, Vitaly A.; Manorik, Piotr A.; Ilyin, Vladimir G.; Novichenko, Viktor N.; Shcherbatiuk, Mykola M.; Klymchuk, Dmitro O.; Tsyba, Mykola M.; Puziy, Alexander M.

    2013-04-01

    Thermally stable mesoporous nanocrystalline ТiО2 with a pure anatase structure was obtained by sol-gel synthesis (in combination with hydrothermal treatment) using titanium tetrabutoxide and dibenzo-18-crown-6 as a structure-directing agent in presence of surfactant and/or La3+ ions additives. Nanocrystalline TiO2 demonstrates various textures with a well-defined spherical morphology (micro- and nanospheres), a crystallite size of no greater than 10 nm (XRD), and a narrow pore size distribution. Spherical particles of micrometer scale in the presence of La3+ ions do not form. TiO2 calcined (at 500 °C) after hydrothermal treatment (at 175 °C) has a significantly more developed porous structure as compared with TiO2 which was not treated hydrothermally. For example, specific surface area amounts 137 m2 g-1 and 69 m2 g-1, pore volume 0.98 cm3 g-1 and 0.21 cm3 g-1, pore diameter 17.5 nm and 12.5 nm respectively for samples hydrothermally treated and not treated.

  6. Characteristics of pore structures in Selma Chalk using dual FIB-SEM 3D imaging and Lattice Boltzmann Modeling

    NASA Astrophysics Data System (ADS)

    Yoon, H.; Dewers, T. A.

    2012-12-01

    Accurate prediction of coupled geophysical and chemical processes at the pore scale requires realistic representation of pore structures. This is especially true for chalk materials, where pore networks are small and complex, and often characterized at sub-micron scale. Common techniques such as X-ray microtomography, microscopic imaging, or mercury intrusion porosimetry often show a limit on determining pore throat distributions and seal analysis of such fine-grained rocks. Focused ion beam-scanning electron microscope (FIB-SEM) and laser scanning confocal microscopy methods are used for 3D imaging of nanometer-to-micron scale microcrack and pore distributions in samples of the Cretaceous Selma Group Chalk. The Selma Chalk is considered the seal for oil and gas fields in the Mississippi Interior Salt Basin and a proposed regional-scale seal identified for CO2 sequestration sites. A series of image analysis techniques is used to process raw images in order to recover both nano-scale pore structure and continuous fracture networks. We apply 3D imaging techniques in interpreting FIB-SEM binary data for characterizing geometric pore body and throat distributions and other topological properties, and lattice-Boltzmann method (LBM) for obtaining permeability at several different scales. In particular, comparison of primary flow paths obtained from 3D image analysis and LBM demonstrates that image analysis results may have too many equally plausible flow paths, compared to LBM results. Upscaling of permeability and LB multiphase flow results with image dataset will be discussed with emphasis on understanding microfracture-matrix interaction during multiphase flow, and seal analysis for geologic CO2 storage. 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

  7. Assessing the effects of microbial metabolism and metabolities on reservoir pore structure

    USGS Publications Warehouse

    Udegbunam, E.O.; Adkins, J.P.; Knapp, R.M.; McInerney, M.J.; Tanner, R.S.

    1991-01-01

    The effect of microbial treatment on pore structure of sandstone and carbonatereservoirs was determined. Understanding how different bacterial strains and their metabolic bioproducts affect reservoir pore structure will permit the prudent application of microorganisms for enhanced oil recovery. The microbial strains tested included Clostridium acetobutylicum, a polymer-producing Bacillus strain, and an unidentified halophilic anaerobe that mainly produced acids and gases. Electrical conductivity, absolute permeability, porosity and centrifuge capillary pressure were used to examine rock pore structures. Modifications of the pore structure observed in the laboratory cores included pore enlargement due to acid dissolution of carbonates and poare throat reduction due to biomass plugging. This paper shows that careful selection of microbes based on proper understanding of the reservoir petrophysical characteristics is necessary for applications of microbially enhanced oil recovery. These methods and results can be useful to field operators and laboratory researchers involved in design and screening of reservoirs for MEOR. The methods are also applicable in evaluation of formation damage caused by drilling, injection or completion fluids or stimulation caused by acids.

  8. Role of uniform pore structure and high positive charges in the arsenate adsorption performance of Al13-modified montmorillonite.

    PubMed

    Zhao, Shou; Feng, Chenghong; Huang, Xiangning; Li, Baohua; Niu, Junfeng; Shen, Zhenyao

    2012-02-15

    Four modified montmorillonite adsorbents with varied Al(13) contents (i.e., Na-Mont, AC-Mont, PAC(20)-Mont, and Al(13)-Mont) were synthesized and characterized by N(2) adsorption/desorption, X-ray diffraction, and Fourier-transform infrared analyses. The arsenate adsorption performance of the four adsorbents were also investigated to determine the role of intercalated Al(13), especially its high purity, high positive charge (+7), and special Keggin structure. With increased Al(13) content, the physicochemical properties (e.g., surface area, structural uniformity, basal spacing, and pore volume) and adsorption performance of the modified montmorillonites were significantly but disproportionately improved. The adsorption data well fitted the Freundlich and Redlich-Peterson isotherm model, whereas the kinetic data better correlated with the pseudo-second-order kinetic model. The arsenate sorption mechanism of the montmorillonites changed from physical to chemisorption after intercalation with Al(13). Increasing charges of the intercalated ions enhanced the arsenate adsorption kinetics, but had minimal effect on the structural changes of the montmorillonites. The uniform pore structure formed by intercalation with high-purity Al(13) greatly enhanced the pore diffusion and adsorption rate of arsenate, resulting in the high adsorption performance of Al(13)-Mont.

  9. Asymmetric block copolymer membranes with ultrahigh porosity and hierarchical pore structure by plain solvent evaporation.

    PubMed

    Yu, H; Qiu, X; Behzad, A R; Musteata, V; Smilgies, D-M; Nunes, S P; Peinemann, K-V

    2016-10-04

    Membranes with a hierarchical porous structure could be manufactured from a block copolymer blend by pure solvent evaporation. Uniform pores in a 30 nm thin skin layer supported by a macroporous structure were formed. This new process is attractive for membrane production because of its simplicity and the lack of liquid waste.

  10. Method for forming porous sintered bodies with controlled pore structure

    DOEpatents

    Whinnery, LeRoy Louis; Nichols, Monte Carl

    2000-01-01

    The present invention is based, in part, on a method for combining a mixture of hydroxide and hydride functional siloxanes to form a polysiloxane polymer foam, that leaves no residue (zero char yield) upon thermal decomposition, with ceramic and/or metal powders and appropriate catalysts to produce porous foam structures having compositions, densities, porosities and structures not previously attainable. The siloxanes are mixed with the ceramic and/or metal powder, wherein the powder has a particle size of about 400 .mu.m or less, a catalyst is added causing the siloxanes to foam and crosslink, thereby forming a polysiloxane polymer foam having the metal or ceramic powder dispersed therein. The polymer foam is heated to thermally decompose the polymer foam and sinter the powder particles together. Because the system is completely nonaqueous, this method further provides for incorporating reactive metals such as magnesium and aluminum, which can be further processed, into the foam structure.

  11. Preparation of microporous films with sub nanometer pores and their characterization using stress and FTIR measurements

    SciTech Connect

    Samuel, J.; Hurd, A.J.; Swoll, F. van; Frink, L.J.D.; Contakes, S.C.; Brinker, C.J. |

    1996-06-01

    The authors have used a novel technique, measurement of stress isotherms in microporous thin films, as a means of characterizing porosity. The stress measurement was carried out by applying sol-gel thin films on a thin silicon substrate and monitoring the curvature of the substrate under a controlled atmosphere of various vapors. The magnitude of macroscopic bending stress developed in microporous films depends on the relative pressure and molar volume of the adsorbate and reaches a value of 180 MPa for a relative vapor pressure, P/Po = 0.001, of methanol. By using a series of molecules, and observing both the magnitude and the kinetics of stress development while changing the relative pressure, they have determined the pore size of microporous thin films. FTIR measurements were used to acquire adsorption isotherms and to compare pore emptying to stress development, about 80% of the change in stress takes place with no measurable change in the amount adsorbed. The authors show that for sol-gel films, pore diameters can be controlled in the range of 5--8 {angstrom} by ``solvent templating``.

  12. Effect of the hydroaffinity and topology of pore walls on the structure and dynamics of confined water

    SciTech Connect

    Harrach, Michael F. Klameth, Felix; Drossel, Barbara; Vogel, Michael

    2015-01-21

    We perform molecular dynamics simulations to observe the structure and dynamics of SPC/E water in amorphous silica pores and amorphous ice pores with radii slightly larger than 10 Å. In addition to atomically rough pores, we construct completely smooth pores such that the potential felt at a given distance from the pore wall is an averaged atomic potential. As compared to rough walls, smooth walls induce stronger distortions of water structure for both silica and ice confinements. On the other hand, unlike the smooth pores, the rough pores strongly slow down water dynamics at the pore wall. The slowdown vanishes when reducing the atomic charges in the wall, i.e., when varying the hydroaffinity, while keeping the surface topology, indicating that it is not a geometric effect. Rather, it is due to the fact that the wall atoms provide a static energy landscape along the surface, e.g., fixed anchor-points for hydrogen bonds, to which the water molecules need to adapt, blocking channels for structural rearrangement. In the smooth pores, water dynamics can be faster than in the bulk liquid not only at the pore wall but also in the pore center. Changes in the tetrahedral order rather than in the local density are identified as the main cause for this change of the dynamical behavior in the center of smooth pores.

  13. Pore Structure Model for Predicting Elastic Wavespeeds in Fluid-Saturated Sandstones

    NASA Astrophysics Data System (ADS)

    Zimmerman, R. W.; David, E. C.

    2011-12-01

    During hydrostatic compression, in the elastic regime, ultrasonic P and S wave velocities measured on rock cores generally increase with pressure, and reach asymptotic values at high pressures. The pressure dependence of seismic velocities is generally thought to be due to the closure of compliant cracks, in which case the high-pressure velocities must reflect only the influence of the non-closable, equant "pores". Assuming that pores can be represented by spheroids, we can relate the elastic properties to the pore structure using an effective medium theory. Moreover, the closure pressure of a thin crack-like pore is directly proportional to its aspect ratio. Hence, our first aim is to use the pressure dependence of seismic velocities to invert the aspect ratio distribution. We use a simple analytical algorithm developed by Zimmerman (Compressibility of Sandstones, 1991), which can be used for any effective medium theory. Previous works have used overly restrictive assumptions, such as assuming that the stiff pores are spherical, or that the interactions between pores can be neglected. Here, we assume that the rock contains an exponential distribution of crack aspect ratios, and one family of stiff pores having an aspect ratio lying somewhere between 0.01 and 1. We develop our model in two versions, using the Differential Scheme, and the Mori-Tanaka scheme. The inversion is done using data obtained in dry experiments, since pore fluids have a strong effect on velocities and tend to mask the effect of the pore geometry. This avoids complicated joint inversion of dry and wet data, such as done by Cheng and Toksoz (JGR, 1979). Our results show that for many sets of data on sandstones, we can fit very well the dry velocities. Our second aim is to predict the saturated velocities from our pore structure model, noting that at a given differential stress, the pore structure should be the same as for a dry test. Our results show that the Biot-Gassmann predictions always

  14. Effect of surface pore structure of nerve guide conduit on peripheral nerve regeneration.

    PubMed

    Oh, Se Heang; Kim, Jin Rae; Kwon, Gu Birm; Namgung, Uk; Song, Kyu Sang; Lee, Jin Ho

    2013-03-01

    Polycaprolactone (PCL)/Pluronic F127 nerve guide conduits (NGCs) with different surface pore structures (nano-porous inner surface vs. micro-porous inner surface) but similar physical and chemical properties were fabricated by rolling the opposite side of asymmetrically porous PCL/F127 membranes. The effect of the pore structure on peripheral nerve regeneration through the NGCs was investigated using a sciatic nerve defect model of rats. The nerve fibers and tissues were shown to have regenerated along the longitudinal direction through the NGC with a nano-porous inner surface (Nanopore NGC), while they grew toward the porous wall of the NGC with a micro-porous inner surface (Micropore NGC) and, thus, their growth was restricted when compared with the Nanopore NGC, as investigated by immunohistochemical evaluations (by fluorescence microscopy with anti-neurofilament staining and Hoechst staining for growth pattern of nerve fibers), histological evaluations (by light microscopy with Meyer's modified trichrome staining and Toluidine blue staining and transmission electron microscopy for the regeneration of axon and myelin sheath), and FluoroGold retrograde tracing (for reconnection between proximal and distal stumps). The effect of nerve growth factor (NGF) immobilized on the pore surfaces of the NGCs on nerve regeneration was not so significant when compared with NGCs not containing immobilized NGF. The NGC system with different surface pore structures but the same chemical/physical properties seems to be a good tool that is used for elucidating the surface pore effect of NGCs on nerve regeneration.

  15. Forecast of geometric characteristics of low-temperature ceramics with multilevel hierarchical pore structure

    NASA Astrophysics Data System (ADS)

    Leytsin, Vladimir N.; Dmitrieva, Mariya A.; Ivonin, Ivan V.; Ponomarev, Sergey V.; Polyushko, V. A.

    2016-11-01

    On the base of micromechanics of heterogeneous media the approach of computer simulation of the process of low-temperature ceramic sintering being synthesized by additive technologies of layer-by-layer build-up of the original polydisperse mixture and subsequent sintering is offered. The possibility of refractory component skeleton formation at different structural levels, being determined by particle fraction size is taken into account. Formation of the skeleton of refractory components of interacting particles causes the formation of the pore structure, and non-uniform distribution of pores in the layer thickness determines the initial anisotropy of shrinkage of sintered ceramics.

  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. Micro- and nano-X-ray computed-tomography: A step forward in the characterization of the pore network of a leached cement paste

    SciTech Connect

    Bossa, Nathan; Chaurand, Perrine; Vicente, Jérôme; Borschneck, Daniel; Levard, Clément; Aguerre-Chariol, Olivier; Rose, Jérôme

    2015-01-15

    Pore structure of leached cement pastes (w/c = 0.5) was studied for the first time from micro-scale down to the nano-scale by combining micro- and nano-X-ray computed tomography (micro- and nano-CT). This allowed assessing the 3D heterogeneity of the pore network along the cement profile (from the core to the altered layer) of almost the entire range of cement pore size, i.e. from capillary to gel pores. We successfully quantified an increase of porosity in the altered layer at both resolutions. Porosity is increasing from 1.8 to 6.1% and from 18 to 58% at the micro-(voxel = 1.81 μm) and nano-scale (voxel = 63.5 nm) respectively. The combination of both CT allowed to circumvent weaknesses inherent of both investigation scales. In addition the connectivity and the channel size of the pore network were also evaluated to obtain a complete 3D pore network characterization at both scales.

  18. Quantitative multi-scale analysis of mineral distributions and fractal pore structures for a heterogeneous Junger Basin shale

    NASA Astrophysics Data System (ADS)

    Wang, Y. D.; Liu, K. Y.; Yang, Y. S.; Ren, Y. Q.; Hu, T.; Deng, B.; Xiao, T. Q.

    2016-04-01

    Three dimensional (3D) characterization of shales has recently attracted wide attentions in relation to the growing importance of shale oil and gas. Obtaining a complete 3D compositional distribution of shale has proven to be challenging due to its multi-scale characteristics. A combined multi-energy X-ray micro-CT technique and data-constrained modelling (DCM) approach has been used to quantitatively investigate the multi-scale mineral and porosity distributions of a heterogeneous shale from the Junger Basin, northwestern China by sub-sampling. The 3D sub-resolution structures of minerals and pores in the samples are quantitatively obtained as the partial volume fraction distributions, with colours representing compositions. The shale sub-samples from two areas have different physical structures for minerals and pores, with the dominant minerals being feldspar and dolomite, respectively. Significant heterogeneities have been observed in the analysis. The sub-voxel sized pores form large interconnected clusters with fractal structures. The fractal dimensions of the largest clusters for both sub-samples were quantitatively calculated and found to be 2.34 and 2.86, respectively. The results are relevant in quantitative modelling of gas transport in shale reservoirs.

  19. Towards understanding nuclear pore complex architecture and dynamics in the age of integrative structural analysis.

    PubMed

    Hurt, Ed; Beck, Martin

    2015-06-01

    Determining the functional architecture of the nuclear pore complex, that remains only partially understood, requires bridging across different length scales. Recent technological advances in quantitative and cross-linking mass spectrometry, super-resolution fluorescence microscopy and electron microscopy have enormously accelerated the integration of different types of data into coherent structural models. Moreover, high-resolution structural analysis of nucleoporins and their in vitro reconstitution into complexes is now facilitated by the use of thermostable orthologs. In this review we highlight how the application of such technologies has led to novel insights into nuclear pore architecture and to a paradigm shift. Today nuclear pores are not anymore seen as static facilitators of nucleocytoplasmic transport but ensembles of multiple overlaying functional states that are involved in various cellular processes.

  20. Porous carbon and carbon/metal oxide microfibers with well-controlled pore structure and interface.

    PubMed

    Shi, Qihui; Liang, Hongjun; Feng, Dan; Wang, Jianfang; Stucky, Galen D

    2008-04-16

    A "brick-and-mortar" assembly approach for creating porous carbon and carbon/metal oxide fibers on the micron scale with well-defined pore structure and interface is presented. A series of monodisperse silica@polyacrylonitrile (PAN) and silica@metal oxide@PAN core/shell particles were synthesized by emulsion polymerization and assembled into organic-inorganic composite fibers through a simple ice-templating strategy with the assistance of polyvinyl alcohol. Porous carbon and carbon/metal oxide fibers with well-controlled pores and interfaces were created by oxidative stabilization and carbonization of composite fibers followed by removal of silica cores with hydrofluoric acid or concentrated alkali. The pore structure and the carbon/metal oxide interfaces of the fibers impart to the fibers' lightweight and potential applications in catalysis, electrochemical energy, and gas or liquid separations and storage.

  1. Nuclear pore proteins regulate chromatin structure and transcriptional memory by a conserved mechanism.

    PubMed

    Light, William H; Brickner, Jason H

    2013-01-01

    Previous experience alters the rate of transcriptional induction of many genes in yeast and this phenomenon persists through several cell division cycles. This phenomenon is called epigenetic transcriptional memory. For the yeast gene INO1, transcriptional memory requires a physical interaction with the nuclear pore complex (NPC) and changes in the chromatin structure of the promoter. These changes lead to binding of a preinitiation form of RNA Polymerase II (RNAPII) to the INO1 promoter, bypassing the need to recruit RNAPII to the promoter during reactivation. In our recent study, we found that in human cells, hundreds of interferon-γ responsive genes exhibit a mechanistically similar form of transcriptional memory. Transcriptional memory requires a homologous nuclear pore protein in yeast and humans, which interacts with the promoters of genes that exhibit transcriptional memory and promotes both alteration of chromatin structure and binding of RNAPII. Whereas the interaction of yeast genes with nuclear pore proteins occurs at the NPC, the interaction of human genes with nuclear pore proteins occurs in the nucleoplasm. Thus, the interaction of nuclear pore proteins with genes plays an important and conserved role in affecting long-term epigenetic changes in transcriptional regulation.

  2. Structural basis for pore-forming mechanism of staphylococcal α-hemolysin.

    PubMed

    Sugawara, Takaki; Yamashita, Daichi; Kato, Koji; Peng, Zhao; Ueda, Junki; Kaneko, Jun; Kamio, Yoshiyuki; Tanaka, Yoshikazu; Yao, Min

    2015-12-15

    Staphylococcal α-hemolysin (α-HL) is a β-barrel pore-forming toxin (PFT) expressed by Staphylococcus aureus. α-HL is secreted as a water-soluble monomeric protein, which binds to target membranes and forms membrane-inserted heptameric pores. To explore the pore-forming mechanism of α-HL in detail, we determined the crystal structure of the α-HL monomer and prepore using H35A mutant and W179A/R200A mutant, respectively. Although the overall structure of the monomer was similar to that of other staphylococcal PFTs, a marked difference was observed in the N-terminal amino latch, which bent toward the prestem. Moreover, the prestem was fastened by the cap domain with a key hydrogen bond between Asp45 and Tyr118. Prepore structure showed that the transmembrane region is roughly formed with flexibility, although the upper half of the β-barrel is formed appropriately. Structure comparison among monomer, prepore and pore revealed a series of motions, in which the N-terminal amino latch released upon oligomerization destroys its own key hydrogen bond between Asp45-Tyr118. This action initiated the protrusion of the prestem. Y118F mutant and the N-terminal truncated mutant markedly decreased in the hemolytic activity, indicating the importance of the key hydrogen bond and the N-terminal amino latch on the pore formation. Based on these observations, we proposed a dynamic molecular mechanism of pore formation for α-HL.

  3. The pore structure and gating mechanism of K2P channels

    PubMed Central

    Piechotta, Paula L; Rapedius, Markus; Stansfeld, Phillip J; Bollepalli, Murali K; Erhlich, Gunter; Andres-Enguix, Isabelle; Fritzenschaft, Hariolf; Decher, Niels; Sansom, Mark S P; Tucker, Stephen J; Baukrowitz, Thomas

    2011-01-01

    Two-pore domain (K2P) potassium channels are important regulators of cellular electrical excitability. However, the structure of these channels and their gating mechanism, in particular the role of the bundle-crossing gate, are not well understood. Here, we report that quaternary ammonium (QA) ions bind with high-affinity deep within the pore of TREK-1 and have free access to their binding site before channel activation by intracellular pH or pressure. This demonstrates that, unlike most other K+ channels, the bundle-crossing gate in this K2P channel is constitutively open. Furthermore, we used QA ions to probe the pore structure of TREK-1 by systematic scanning mutagenesis and comparison of these results with different possible structural models. This revealed that the TREK-1 pore most closely resembles the open-state structure of KvAP. We also found that mutations close to the selectivity filter and the nature of the permeant ion profoundly influence TREK-1 channel gating. These results demonstrate that the primary activation mechanisms in TREK-1 reside close to, or within the selectivity filter and do not involve gating at the cytoplasmic bundle crossing. PMID:21822218

  4. Fabrication and Cell Responsive Behavior of Macroporous PLLA/Gelatin Composite Scaffold with Hierarchical Micro-Nano Pore Structure

    PubMed Central

    Song, Kedong; Ji, Lili; Zhang, Jingying; Wang, Hai; Jiao, Zeren; Mayasari, Lim; Fu, Xiaoyan; Liu, Tianqing

    2015-01-01

    Scaffolds providing a 3D environment which can effectively promote the adhesion, proliferation and differentiation of cells are crucial to tissue regeneration. In this study, the polyllactic acid (PLLA) scaffold with hierarchical pore structural was fabricated via two-step thermally induced phase separation (TIPS). To mimic both physical architecture and chemical composite of natural bone extracellular matrix (ECM), gelatin fibers were introduced into the pores of PLLA scaffolds and formed 3D network structure via TIPS. Human adipose tissue-derived stem cells (ADSCs) were harvested and seeded into PLLA/gel hybrid scaffolds and cultured in vitro for biocompatibility assay. The surface morphology, porosity and compressive modulus of scaffolds were characterized by scanning electron microscopy (SEM), density analysis and compression test respectively. The results showed that hybrid scaffolds had high porosity (91.62%), a good compressive modulus (2.79 ± 0.20 MPa), nanometer fibers (diameter around 186.39~354.30 nm) and different grades of pore size from 7.41 ± 2.64 nm to 387.94 ± 102.48 nm. The scaffolds with mild hydrolysis by NaOH were modified by 1-ethyl-3-(3-dimethyl ami-nopropyl) carbodiimide/N-hydroxysuccinimide (EDC/NHS). Gelatin was performed onto PLLA scaffold via TIPS aiming at enhancement cell-material interaction. In comparison with PLLA scaffold, the PLLA/gel scaffold had better biological performance and the mechanical properties because the gelatin fibers homogeneously distributed in each pore of PLLA scaffold and formed 3D network structure.

  5. 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.

  6. Perfringolysin O structure and mechanism of pore formation as a paradigm for cholesterol-dependent cytolysins.

    PubMed

    Johnson, Benjamin B; Heuck, Alejandro P

    2014-01-01

    Cholesterol-dependent cytolysins (CDCs) constitute a family of pore forming toxins secreted by Gram-positive bacteria. These toxins form transmembrane pores by inserting a large β-barrel into cholesterol-containing membrane bilayers. Binding of water-soluble CDCs to the membrane triggers the formation of oligomers containing 35-50 monomers. The coordinated insertion of more than seventy β-hairpins into the membrane requires multiple structural conformational changes. Perfringolysin O (PFO), secreted by Clostridium perfringens, has become the prototype for the CDCs. In this chapter, we will describe current knowledge on the mechanism of PFO cytolysis, with special focus on cholesterol recognition, oligomerization, and the conformational changes involved in pore formation.

  7. High Structural Stability of Textile Implants Prevents Pore Collapse and Preserves Effective Porosity at Strain

    PubMed Central

    Klinge, Uwe; Otto, Jens; Mühl, Thomas

    2015-01-01

    Reinforcement of tissues by use of textiles is encouraged by the reduced rate of recurrent tissue dehiscence but for the price of an inflammatory and fibrotic tissue reaction to the implant. The latter mainly is affected by the size of the pores, whereas only sufficiently large pores are effective in preventing a complete scar entrapment. Comparing two different sling implants (TVT and SIS), which are used for the treatment of urinary incontinence, we can demonstrate that the measurement of the effective porosity reveals considerable differences in the textile construction. Furthermore the changes of porosity after application of a tensile load can indicate a structural instability, favouring pore collapse at stress and questioning the use for purposes that are not “tension-free.” PMID:25973427

  8. Toward the atomic structure of the nuclear pore complex: when top down meets bottom up.

    PubMed

    Hoelz, André; Glavy, Joseph S; Beck, Martin

    2016-07-01

    Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, owing to its sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom-up approaches rely on biochemical interaction studies and crystal-structure determination of NPC components, top-down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, thereby bridging the resolution gap from the higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function.

  9. Towards the atomic structure of the Nuclear Pore Complex: When top down meets bottom up

    PubMed Central

    Hoelz, André; Glavy, Joseph S.; Beck, Martin

    2016-01-01

    Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, due to sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom up approaches rely on biochemical interaction studies and crystal structure determination of NPC components, top down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, bridging the resolution gap from higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function. PMID:27273515

  10. On dependence of mechanical properties of brittle material on partial concentrations of different sized pores in its structure in a wide range of porosity

    NASA Astrophysics Data System (ADS)

    Konovalenko, Igor S.; Smolin, Alexey Yu.; Psakhie, Sergey G.

    2015-10-01

    2D and 3D models of mechanical behavior of brittle porous material under uniaxial compression loading were developed in the framework of the movable cellular automaton method. The considered material was characterized by pore size distribution function having two maxima. On the basis of simulation results the dependence of the strength properties of brittle porous material on its total porosity and partial porosities corresponding to pores with different size was revealed. The change in internal structure of material in a wide range of mentioned parameters was analyzed. The main structural factors influencing compression strength of the material at various combinations of values of porosity parameters were identified.

  11. Pitch-based activated carbon fibers: The effect of precursor composition on pore structure

    NASA Astrophysics Data System (ADS)

    Tekinalp, Halil Levent

    Although researchers have previously investigated the effect of precursor differences on the final properties of activated carbon fibers (ACFs), those precursors were not well-characterized. In particular, detailed information about their molecular composition and anisotropy was not available. In this study, seven oligomeric fractions, each of well-defined composition and molecular weight (mol wt) distribution, were isolated from a commercially produced isotropic petroleum pitch (i.e., Marathon M-50) and used for the production of ACFs. Four of these precursors of varying oligomeric composition were fully isotropic and three contained different levels of mesophase, so that the effects of molecular composition and molecular order were successfully isolated from each other. After the precursors were melt-spun into fibers and stabilized, they were processed by so-called "direct activation", whereby carbonization and activation occurred simultaneously. Separate carbonization tests were also carried out in order to separate out the effects of carbonization vs. activation. Carbonization weight loss was found to be higher for fibers prepared from lower average mol wt (480--550 Da) precursors. The presence of mesophase per se did not affect weight loss during carbonization. On the other hand, activation weight loss (˜28 percent) was found to be essentially independent of precursor mol wt for all isotropic fibers. (Activation weight loss for mesophase-containing fibers was much lower.) The micropore volume of the ACFs was found to increase with decreasing precursor mol wt. However, the ratio of pores smaller than 7 A (i.e., the desired pore size for hydrogen storage) to the total pore volume (3.9--30 A) was found to be essentially constant for all isotropic precursors, suggesting that a similar activation mechanism occurred for all of these materials, with both new pore formation and pore widening proceeding at similar rates. For mesophase-containing precursors, on the

  12. Polar organic compounds in pore waters of the Chesapeake Bay impact structure, Eyreville core hole: Character of the dissolved organic carbon and comparison with drilling fluids

    USGS Publications Warehouse

    Rostad, C.E.; Sanford, W.E.

    2009-01-01

    Pore waters from the Chesapeake Bay impact structure cores recovered at Eyreville Farm, Northampton County, Virginia, were analyzed to characterize the dissolved organic carbon. After squeezing or centrifuging, a small volume of pore water, 100 ??L, was taken for analysis by electrospray ionization-mass spectrometry. Porewater samples were analyzed directly without filtration or fractionation, in positive and negative mode, for polar organic compounds. Spectra in both modes were dominated by low-molecular-weight ions. Negative mode had clusters of ions differing by -60 daltons, possibly due to increasing concentrations of inorganic salts. The numberaverage molecular weight and weight-average molecular weight values for the pore waters from the Chesapeake Bay impact structure are higher than those reported for other aquatic sources of natural dissolved organic carbon as determined by electrospray ionization-mass spectrometry. In order to address the question of whether drilling mud fluids may have contaminated the pore waters during sample collection, spectra from the pore waters were compared to spectra from drilling mud fluids. Ions indicative of drilling mud fluids were not found in spectra from the pore waters, indicating there was no detectable contamination, and highlighting the usefulness of this analytical technique for detecting potential contamination during sample collection. ?? 2009 The Geological Society of America.

  13. Structural determinants for membrane insertion, pore formation and translocation of Clostridium difficile toxin B.

    PubMed

    Genisyuerek, Selda; Papatheodorou, Panagiotis; Guttenberg, Gregor; Schubert, Rolf; Benz, Roland; Aktories, Klaus

    2011-03-01

    Clostridium difficile toxins A and B bind to eukaryotic target cells, are endocytosed and then deliver their N-terminal glucosyltransferase domain after processing into the cytosol. Whereas glucosyltransferase, autoprocessing and cell-binding domains are well defined, structural features involved in toxin delivery are unknown. Here, we studied structural determinants that define membrane insertion, pore formation and translocation of toxin B. Deletion analyses revealed that a large region, covering amino acids 1501-1753 of toxin B, is dispensable for cytotoxicity in Vero cells. Accordingly, a chimeric toxin, consisting of amino acids 1-1550 and the receptor-binding domain of diphtheria toxin, caused cytotoxic effects. A large N-terminal part of toxin B (amino acids 1-829) was not essential for pore formation (measured by (86) Rb(+) release in mammalian cells). Studies using C-terminal truncation fragments of toxin B showed that amino acid residues 1-990 were still capable of inducing fluorescence dye release from large lipid vesicles and led to increased electrical conductance in black lipid membranes. Thereby, we define the minimal pore-forming region of toxin B within amino acid residues 830 and 990. Moreover, we identify within this region a crucial role of the amino acid pair glutamate-970 and glutamate-976 in pore formation of toxin B.

  14. Mechanical properties and in vitro cell compatibility of hydroxyapatite ceramics with graded pore structure.

    PubMed

    Werner, Jan; Linner-Krcmar, Britta; Friess, Wolfgang; Greil, Peter

    2002-11-01

    In order to improve the mechanical strength of hydroxyapatite (HA) ceramics used as osteoimplants and to enhance cellular penetration functionally graded ceramics with a transition in porosity from the surface towards the centre were designed. The multilayer structures were prepared by multiple tape casting based on an aqueous HA slurry containing polybutylmethacrylate (PBMA) spheres with diameters ranging from 100 to 300 microns. After burning out the PBMA, pores of 70-200 microns were generated. The pore-graded laminates were sintered at temperatures between 1250 degrees C and 1450 degrees C. Bending strength of the pore-graded ceramics was approximately 50% higher as compared to HA of the same pore volume fraction but without gradient structure. The materials were tested in vitro for attachment and activity of osteoblast-like MC3T3-E1 cells over a period of 3 weeks. Cells formed confluent layers on the ceramic surface, penetrated into the graded porosity ranging from 100-150 microns to 250-300 microns in size and showed increasing alkaline phosphatase activity over 3 weeks. The results demonstrated initial in vitro cell compatibility of the functionally graded HA materials and their potential as osteoimplants.

  15. Capillary Rise in Granitic Rocks: Interpretation of Kinetics on the Basis of Pore Structure.

    PubMed

    Mosquera; Rivas; Prieto; Silva

    2000-02-01

    The capillary transport of water into granitic rocks has been interpreted on the basis of the structure of its porous network. An effective pore radius has been calculated from a three-sized single-pore model proposed by F. A. L. Dullien, El-Sayed, and V. K. Batra (J. Colloid Interface Sci. 60, 497, 1977) Considering the porous network of granites as consisting of fissures grouped in two size types, macro- and microfissures, an effective radius was found from the characteristic radii for each type and the average of these two values. Good agreement between the effective radius calculated and the radius estimated using a capillary rate value measured experimentally provides a suitable basis for identifying interrelationships between the pore structure and moisture capillary rise. In fact, it is possible to predict the process rate from only two characteristic pore sizes, corresponding to the radii of macrofissures and microfissures. The abnormally low rate of capillary rise observed in one of the granites studied could be easily interpreted as due to the involvement exclusively of the macrofissures of its porous network in capillary transport. Copyright 2000 Academic Press.

  16. Porous silicon structures with high surface area/specific pore size

    DOEpatents

    Northrup, M. Allen; Yu, Conrad M.; Raley, Norman F.

    1999-01-01

    Fabrication and use of porous silicon structures to increase surface area of heated reaction chambers, electrophoresis devices, and thermopneumatic sensor-actuators, chemical preconcentrates, and filtering or control flow devices. In particular, such high surface area or specific pore size porous silicon structures will be useful in significantly augmenting the adsorption, vaporization, desorption, condensation and flow of liquids and gasses in applications that use such processes on a miniature scale. Examples that will benefit from a high surface area, porous silicon structure include sample preconcentrators that are designed to adsorb and subsequently desorb specific chemical species from a sample background; chemical reaction chambers with enhanced surface reaction rates; and sensor-actuator chamber devices with increased pressure for thermopneumatic actuation of integrated membranes. Examples that benefit from specific pore sized porous silicon are chemical/biological filters and thermally-activated flow devices with active or adjacent surfaces such as electrodes or heaters.

  17. Porous silicon structures with high surface area/specific pore size

    DOEpatents

    Northrup, M.A.; Yu, C.M.; Raley, N.F.

    1999-03-16

    Fabrication and use of porous silicon structures to increase surface area of heated reaction chambers, electrophoresis devices, and thermopneumatic sensor-actuators, chemical preconcentrates, and filtering or control flow devices. In particular, such high surface area or specific pore size porous silicon structures will be useful in significantly augmenting the adsorption, vaporization, desorption, condensation and flow of liquids and gases in applications that use such processes on a miniature scale. Examples that will benefit from a high surface area, porous silicon structure include sample preconcentrators that are designed to adsorb and subsequently desorb specific chemical species from a sample background; chemical reaction chambers with enhanced surface reaction rates; and sensor-actuator chamber devices with increased pressure for thermopneumatic actuation of integrated membranes. Examples that benefit from specific pore sized porous silicon are chemical/biological filters and thermally-activated flow devices with active or adjacent surfaces such as electrodes or heaters. 9 figs.

  18. Nuclear pore scaffold structure analyzed by super-resolution microscopy and particle averaging.

    PubMed

    Szymborska, Anna; de Marco, Alex; Daigle, Nathalie; Cordes, Volker C; Briggs, John A G; Ellenberg, Jan

    2013-08-09

    Much of life's essential molecular machinery consists of large protein assemblies that currently pose challenges for structure determination. A prominent example is the nuclear pore complex (NPC), for which the organization of its individual components remains unknown. By combining stochastic super-resolution microscopy, to directly resolve the ringlike structure of the NPC, with single particle averaging, to use information from thousands of pores, we determined the average positions of fluorescent molecular labels in the NPC with a precision well below 1 nanometer. Applying this approach systematically to the largest building block of the NPC, the Nup107-160 subcomplex, we assessed the structure of the NPC scaffold. Thus, light microscopy can be used to study the molecular organization of large protein complexes in situ in whole cells.

  19. Structural basis for assembly and function of the Nup82 complex in the nuclear pore scaffold

    PubMed Central

    Gaik, Monika; Flemming, Dirk; von Appen, Alexander; Kastritis, Panagiotis; Mücke, Norbert; Fischer, Jessica; Stelter, Philipp; Ori, Alessandro; Bui, Khanh Huy; Baßler, Jochen; Barbar, Elisar

    2015-01-01

    Nuclear pore complexes (NPCs) are huge assemblies formed from ∼30 different nucleoporins, typically organized in subcomplexes. One module, the conserved Nup82 complex at the cytoplasmic face of NPCs, is crucial to terminate mRNA export. To gain insight into the structure, assembly, and function of the cytoplasmic pore filaments, we reconstituted in yeast the Nup82–Nup159–Nsp1–Dyn2 complex, which was suitable for biochemical, biophysical, and electron microscopy analyses. Our integrative approach revealed that the yeast Nup82 complex forms an unusual asymmetric structure with a dimeric array of subunits. Based on all these data, we developed a three-dimensional structural model of the Nup82 complex that depicts how this module might be anchored to the NPC scaffold and concomitantly can interact with the soluble nucleocytoplasmic transport machinery. PMID:25646085

  20. Development of Layered Sediment Structure and its Effects on Pore Water Transport and Hyporheic Exchange

    SciTech Connect

    Packman, Aaron I.; Marion, Andrea; Zaramella, Mattia; Chen, Cheng; Gaillard, Jean-François; Keane, Denis T.

    2008-04-15

    Hyporheic exchange is known to provide an important control on nutrient and contaminant fluxes across the stream-subsurface interface. Similar processes also mediate interfacial transport in other permeable sediments. Recent research has focused on understanding the mechanics of these exchange processes and improving estimation of exchange rates in natural systems. While the structure of sediment beds obviously influences pore water flow rates and patterns, little is known about the interplay of typical sedimentary structures, hyporheic exchange, and other transport processes in fluvial/alluvial sediments. Here we discuss several processes that contribute to local-scale sediment heterogeneity and present results that illustrate the interaction of overlying flow conditions, the development of sediment structure, pore water transport, and stream-subsurface exchange. Layered structures are shown to develop at several scales within sediment beds. Surface sampling is used to analyze the development of an armor layer in a sand-and-gravel bed, while innovative synchrotron-based X-ray microtomography is used to observe patterns of grain sorting within sand bedforms. We show that layered bed structures involving coarsening of the bed surface increase interfacial solute flux but produce an effective anisotropy that favors horizontal pore water transport while limiting vertical penetration.

  1. 3D modeling to characterize lamina cribrosa surface and pore geometries using in vivo images from normal and glaucomatous eyes.

    PubMed

    Sredar, Nripun; Ivers, Kevin M; Queener, Hope M; Zouridakis, George; Porter, Jason

    2013-07-01

    En face adaptive optics scanning laser ophthalmoscope (AOSLO) images of the anterior lamina cribrosa surface (ALCS) represent a 2D projected view of a 3D laminar surface. Using spectral domain optical coherence tomography images acquired in living monkey eyes, a thin plate spline was used to model the ALCS in 3D. The 2D AOSLO images were registered and projected onto the 3D surface that was then tessellated into a triangular mesh to characterize differences in pore geometry between 2D and 3D images. Following 3D transformation of the anterior laminar surface in 11 normal eyes, mean pore area increased by 5.1 ± 2.0% with a minimal change in pore elongation (mean change = 0.0 ± 0.2%). These small changes were due to the relatively flat laminar surfaces inherent in normal eyes (mean radius of curvature = 3.0 ± 0.5 mm). The mean increase in pore area was larger following 3D transformation in 4 glaucomatous eyes (16.2 ± 6.0%) due to their more steeply curved laminar surfaces (mean radius of curvature = 1.3 ± 0.1 mm), while the change in pore elongation was comparable to that in normal eyes (-0.2 ± 2.0%). This 3D transformation and tessellation method can be used to better characterize and track 3D changes in laminar pore and surface geometries in glaucoma.

  2. Structural and functional analysis of the pore-forming toxin NetB from Clostridium perfringens.

    PubMed

    Yan, Xu-Xia; Porter, Corrine J; Hardy, Simon P; Steer, David; Smith, A Ian; Quinsey, Noelene S; Hughes, Victoria; Cheung, Jackie K; Keyburn, Anthony L; Kaldhusdal, Magne; Moore, Robert J; Bannam, Trudi L; Whisstock, James C; Rood, Julian I

    2013-02-05

    Clostridium perfringens is an anaerobic bacterium that causes numerous important human and animal diseases, primarily as a result of its ability to produce many different protein toxins. In chickens, C. perfringens causes necrotic enteritis, a disease of economic importance to the worldwide poultry industry. The secreted pore-forming toxin NetB is a key virulence factor in the pathogenesis of avian necrotic enteritis and is similar to alpha-hemolysin, a β-barrel pore-forming toxin from Staphylococcus aureus. To address the molecular mechanisms underlying NetB-mediated tissue damage, we determined the crystal structure of the monomeric form of NetB to 1.8 Å. Structural comparisons with other members of the alpha-hemolysin family revealed significant differences in the conformation of the membrane binding domain. These data suggested that NetB may recognize different membrane receptors or use a different mechanism for membrane-protein interactions. Consistent with this idea, electrophysiological experiments with planar lipid bilayers revealed that NetB formed pores with much larger single-channel conductance than alpha-hemolysin. Channel conductance varied with phospholipid net charge. Furthermore, NetB differed in its ion selectivity, preferring cations over anions. Using hemolysis as a screen, we carried out a random-mutagenesis study that identified several residues that are critical for NetB-induced cell lysis. Mapping of these residues onto the crystal structure revealed that they were clustered in regions predicted to be required for oligomerization or membrane binding. Together these data provide an insight into the mechanism of NetB-mediated pore formation and will contribute to our understanding of the mode of action of this important toxin. IMPORTANCE Necrotic enteritis is an economically important disease of the worldwide poultry industry and is mediated by Clostridium perfringens strains that produce NetB, a β-pore-forming toxin. We carried out

  3. Mercury Porosimetry: Contact Angle Hysteresis of Materials with Controlled Pore Structure.

    PubMed

    Salmas, Constantinos; Androutsopoulos, George

    2001-07-01

    Mercury Porosimetry (MP) hysteresis is a commonly observed phenomenon in which mercury retention disguises further the overall hysteresis picture. This article introduces a new interpretation of the MP hysteresis based on the combined effect of pore structure networking and mercury contact angle variation occurring between the mercury penetration and retraction operations. To distinguish the contribution of each factor the following investigations were carried out. Nitrogen sorption (NP) and MP experiments were performed on samples of an anodic aluminum membrane and the results were interpreted in terms of the Corrugated Pore Structure Model (CPSM), i.e., CPSM-Nitrogen and CPSM-Mercury models, respectively. The simulation of the observed hysteresis data using the CPSM model enabled the evaluation of an identical for the two methods intrinsic pore size distribution (PSD) and cumulative surface area in perfect agreement with the respective BET value. Additionally, the CPSM analysis of data resulted in the evaluation of mercury contact angles, i.e., θ(p)=143 degrees and θ(r)=101.7 degrees for the MP penetration and retraction branches of the hysteresis loop, respectively. Moreover, CPSM-Mercury simulations of literature MP hysteresis data, valid for controlled-pore glasses and nuclepore membranes, led to the evaluation of contact angles, i.e., glasses: θ(p)=143 degrees, θ(r)=100.5-107.5 degrees and nuclepore: θ(p)=143 degrees, θ(r)=118- 121 degrees. The latter values are comparable with relevant literature data and approximate those determined for the anodic aluminum membrane. The CPSM model employed herein proved to be a flexible and reliable model for simulating the pertinent hysteresis loops by combining pore networking and contact angle hysteresis phenomena. Copyright 2001 Academic Press.

  4. Salt marsh pore water geochemistry does not correlate with microbial community structure

    NASA Astrophysics Data System (ADS)

    Koretsky, Carla M.; Van Cappellen, Philippe; DiChristina, Thomas J.; Kostka, Joel E.; Lowe, Kristi L.; Moore, Charles M.; Roychoudhury, Alakendra N.; Viollier, Eric

    2005-01-01

    Spatial and temporal trends in pore water geochemistry and sediment microbial community structure are compared at three intertidal sites of a saltmarsh on Sapelo Island, GA. The sites include a heavily bioturbated, unvegetated creek bank, a levee with dense growth of Spartina alterniflora, and a more sparsely vegetated ponded marsh site. The redox chemistry of the pore waters ranges from sulfide-dominated at the ponded marsh site to suboxic at the creek bank site. At the three sites, the vertical redox stratification of the pore waters is more compressed in summer than in winter. The trends in redox chemistry reflect opposing effects of sediment respiration and pore water irrigation. Intense and deep burrowing activity by fiddler crabs at the creek bank site results in the efficient oxidation of reduced byproducts of microbial metabolism and, hence, the persistence of suboxic conditions to depths of 50 cm below the sediment surface. Increased supply of labile organic substrates at the vegetated sites promotes microbial degradation processes, leading to sharper redox gradients. At the levee site, this is partly offset by the higher density and deeper penetration of roots and macrofaunal burrows. Surprisingly, the microbial community structure shows little correlation with the variable vertical redox zonation of the pore waters across the saltmarsh. At the three sites, the highest population densities of aerobic microorganisms, iron- plus manganese-reducing bacteria, and sulfate reducers coexist within the upper 10 cm of sediment. The absence of a clear vertical separation of these microorganisms is ascribed to the high supply of labile organic matter and intense mixing of the topmost sediment via bioturbation.

  5. Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family

    PubMed Central

    Pino-Angeles, Almudena; Leveritt, John M.; Lazaridis, Themis

    2016-01-01

    Magainin 2 and PGLa are among the best-studied cationic antimicrobial peptides. They bind preferentially to negatively charged membranes and apparently cause their disruption by the formation of transmembrane pores, whose detailed structure is still unclear. Here we report the results of 5–9 μs all-atom molecular dynamics simulations starting from tetrameric transmembrane helical bundles of these two peptides, as well as their stoichiometric mixture, and the analog MG-H2 in DMPC or 3:1 DMPC/DMPG membranes. The simulations produce pore structures that appear converged, although some effect of the starting peptide arrangement (parallel vs. antiparallel) is still observed on this timescale. The peptides remain mostly helical and adopt tilted orientations. The calculated tilt angles for PGLa are in excellent agreement with recent solid state NMR experiments. The antiparallel dimer structure in the magainin 2 simulations resembles previously determined NMR and crystal structures. More transmembrane orientations and a larger and more ordered pore are seen in the 1:1 heterotetramer with an antiparallel helix arrangement. Insights into the mechanism of synergy between these two peptides are obtained via implicit solvent modeling of homo- and heterodimers and analysis of interactions in the atomistic simulations. This analysis suggests stronger pairwise interactions in the heterodimer than in the two homodimers. PMID:26727376

  6. Cadmium-cysteine coordination in the BK inner pore region and its structural and functional implications.

    PubMed

    Zhou, Yu; Xia, Xiao-Ming; Lingle, Christopher J

    2015-04-21

    To probe structure and gating-associated conformational changes in BK-type potassium (BK) channels, we examined consequences of Cd(2+) coordination with cysteines introduced at two positions in the BK inner pore. At V319C, the equivalent of valine in the conserved Kv proline-valine-proline (PVP) motif, Cd(2+) forms intrasubunit coordination with a native glutamate E321, which would place the side chains of V319C and E321 much closer together than observed in voltage-dependent K(+) (Kv) channel structures, requiring that the proline between V319C and E321 introduces a kink in the BK S6 inner helix sharper than that observed in Kv channel structures. At inner pore position A316C, Cd(2+) binds with modest state dependence, suggesting the absence of an ion permeation gate at the cytosolic side of BK channel. These results highlight fundamental structural differences between BK and Kv channels in their inner pore region, which likely underlie differences in voltage-dependent gating between these channels.

  7. 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.

  8. EFFICIENT CONTROL OVER THE PORE STRUCTURE OF Fe3O4-nSiO2-mSiO2 CORE-SHELL NANOPARTICLES

    NASA Astrophysics Data System (ADS)

    Liu, Feng; Tian, Hua; He, Junhui; Liu, Hongying

    2012-01-01

    In this paper, magnetic mesoporous silica nanoparticles (Fe3O4-nSiO2-mSiO2) were synthesized using trimethylbenzene (TMB) as a swelling agent. These composite nanoparticles have a typical sandwich structure with a magnetic core, a nonporous silica middle layer and an ordered mesoporous silica outer shell. The experimental results indicate that the magnetic mesoporous silica nanoparticles have high specific surface area (510 m2/g), large pore size (3.8 nm) and pore volume (1.04 cm3/g). The thickness and pore structure of the out shell can also be easily tailored by adjusting the reaction conditions. The obtained nanomaterials were characterized by X-ray diffraction, transmission electron microscopy and nitrogen adsorption-desorption measurements.

  9. The nuclear pore complex--structure and function at a glance.

    PubMed

    Kabachinski, Greg; Schwartz, Thomas U

    2015-02-01

    Nuclear pore complexes (NPCs) are indispensable for cell function and are at the center of several human diseases. NPCs provide access to the nucleus and regulate the transport of proteins and RNA across the nuclear envelope. They are aqueous channels generated from a complex network of evolutionarily conserved proteins known as nucleporins. In this Cell Science at a Glance article and the accompanying poster, we discuss how transport between the nucleoplasm and the cytoplasm is regulated, what we currently know about the structure of individual nucleoporins and the assembled NPC, and how the cell regulates assembly and disassembly of such a massive structure. Our aim is to provide a general overview on what we currently know about the nuclear pore and point out directions of research this area is heading to.

  10. Pore structure and reactivity changes in hot coal gas desulfurization sorbents

    SciTech Connect

    Sotirchos, S.V.

    1991-05-01

    The primary objective of the project was the investigation of the pore structure and reactivity changes occurring in metal/metal oxide sorbents used for desulfurization of hot coal gas during sulfidation and regeneration, with particular emphasis placed on the effects of these changes on the sorptive capacity and efficiency of the sorbents. Commercially available zinc oxide sorbents were used as model solids in our experimental investigation of the sulfidation and regeneration processes.

  11. Effects of catalyst pore structure and acid properties on the dehydration of glycerol.

    PubMed

    Choi, Youngbo; Park, Hongseok; Yun, Yang Sik; Yi, Jongheop

    2015-03-01

    Hierarchical porous catalysts have recently attracted increasing interest because of the enhanced accessibility to active sites on such materials. In this context, previously reported hierarchically mesoporous ASN and ASPN materials are evaluated by applying them to the dehydration of glycerol, and demonstrate excellent catalytic performance. In addition, a comprehensive understanding of the effects of pore structures and the acid properties on the reaction through comparative studies with microporous HZSM-5 and mesoporous AlMCM-41 is provided.

  12. CAPILLARY CONDENSATION IN MMS AND PORE STRUCTURE CHARACTERIZATION. (R825959)

    EPA Science Inventory

    Phenomena of capillary condensation and desorption in siliceous mesoporous molecular sieves (MMS) with cylindrical channels are studied by means of the non-local density functional theory (NLDFT). The results are compared with macroscopic thermodynamic approaches based on Kelv...

  13. Adsorption performance of salicylic acid on a novel resin with distinctive double pore structure.

    PubMed

    Xiao, Guqing; Wen, Ruiming; Liu, Aijiao; He, Guowen; Wu, Dan

    2017-05-05

    Two approaches were used to synthesize two resins with different pore structures. In one way, the CH2Cl groups in macroporous chloromethylated polystyrene resin were transformed to methylene bridges, and achieved a hypercrosslinked resin with plentiful micropores (denoted GQ-06). In the other way, 50% of the CH2Cl groups in chloromethylated polystyrene resin was used to produce micropores, while the residual 50% of the CH2Cl groups was reacted with 2-aminopyridine, and prepared another resin with double pore structure of hypercrosslinked resin and macroporous resin (denoted GQ-11). The adsorption of salicylic acid (SA) on GQ-11 was investigated using GQ-06 as the reference adsorbent. The effect of pH on the adsorption of SA on GQ-06 was consistent with the dissociation curve of SA. The maximum adsorption capacity of SA on GQ-11 was observed at the solution pH of 2.64. The greater adsorption rate of SA on GQ-11 than that of GQ-06 was attributed to its double pore structure. The multifunctional adsorption mechanism of anion exchange and hydrophobic interaction resulted in the larger equilibrium capacity of SA on GQ-11 than that of GQ-06. GQ-06 and GQ-11 could be regenerated by absolute alcohol and 80% of alcohol -0.5mol/L of sodium hydroxide aqueous solution, respectively.

  14. A method for fabricating a micro-structured surface of polyimide with open and closed pores

    NASA Astrophysics Data System (ADS)

    Ma, Yong-Won; Oh, Jae Yong; Ahn, Seokyoung; Shin, Bo Sung

    2016-08-01

    A new approach for fabricating open and closed porous structures based on laser processing is presented. Liquid polyimide (PI) was mixed with azodicarbonamide which is a chemical blowing agent (CBA), and the mixture was spin-coated and pre-cured in order to fabricate solid PI films. Porous PI was prepared by irradiating PI films mixed with azodicarbonamide. The PI film with azodicarbonamide was etched by using laser ablation, and the azodicarbonamide was decomposed due to the heat induced by the absorbed laser energy. At higher laser beam irradiation, more pores were fabricated due to the resulting increase in the CBA decomposition from 27 mJ/cm2 to 40 mJ/cm2 per single pulse. A fluence of about 50 mJ/cm2 resulted in fewer and larger open pores, which were formed by the coalescence of small pores. In contrast, a closed porous structure was fabricated at a fluence of less than 1 mJ/cm2 because PI was barely etched. The proposed method can be used to create open and closed porous structures selectively and is not limited to thermosetting polymers, but is also effective with thermoplastic polymers.

  15. Collaborative Research: Evolution of Pore Structure and Permeability of Rocks Under Hydrothermal Conditions

    SciTech Connect

    Zhu, Wenlu; Evans, J. Brian

    2007-04-15

    The physical and transport properties of porous rocks can be altered by a variety of diagenetic, metamorphic, and tectonic processes, and the changes that result are of critical importance to such industrial applications as resource recovery, carbon dioxide sequestration, and waste isolation in geologic formations. These inter-relationships between rocks, pore fluids, and deformation are also the key to understanding many natural processes, including: dynamic metamorphism, fault mechanics, fault stability, and pressure solution deformation. Here, we propose work to investigate the changes of permeability and pore geometry owing to inelastic deformation by solution-transfer, brittle fracturing, and dislocation creep. The work would study the relationship of deformation and permeability reduction in fluid-filled quartz and calcite rocks and investigate the effects of loading configuration on the evolution of porosity and permeability under hydrothermal conditions. We would use a combination of techniques, including laboratory experiments, numerical calculations, and observations of rock microstructure. The laboratory experiments provide mechanical and transport data under conditions that isolate each particular mechanism. Our apparatus are designed to provide simultaneous measurements of pore volume, permeability, axial and volumetric strain rates while being loaded under isostatic or conventional triaxial loading. Temperatures up to 1400 K may be obtained, while confining pressures and pore pressures are maintained independently up to 500 MPa. Observations of the structure will be made with standard optical, scanning electron, and laser confocal scanning optical microscopes. The data obtained will be used to quantify changes in surface roughness, porosity, pore dimensions, and their spatial fluctuations. The results of the experiments and the image data are then used in network, finite-difference and other numerical models to verify the validity of experimentally

  16. The lamellar structure of reactive mixtures in porous media: Pore scale experimental imaging and upscaling

    NASA Astrophysics Data System (ADS)

    Le Borgne, T.; De Anna, P.; Turuban, R.; Jimenez-Martinez, J.; Tabuteau, H.; Meheust, Y.; Ginn, T. R.; Dentz, M.

    2014-12-01

    Effective reaction rates in porous media are controlled by the spatial organization of chemical species concentrations at the pore scale. From high resolution millifluidic pore scale imaging of reactive tracers we report experimental evidence of the formation of well-developed lamellar structures in reactive mixtures transported through porous media (de Anna et al., Environ. Sci. Technol., 2014). The latter are highlighted by a chemioluminescent reaction producing photons that localize along spatially coherent lines, representing hotspots of mixing and reaction at pore scale. These elongated spatial structures are naturally created by the stretching action of the pore scale velocity field, which induces a dynamic deformation of the material elements carrying solutes (Le Borgne et al., Phys. Rev. Lett., 2013). This particular spatial organization is shown to have a major impact on global reactivity by increasing the surface available for reactive mixing and by enhancing local chemical gradients (de Anna et al., Geophys. Res. Lett. 2014). We quantify this phenomenon for different flow topologies using a reactive lamella representation, which links fluid deformation, diffusion and reaction at the elementary scale. The upscaled reaction rates, estimated by integrating the distribution of local deformation rates, are shown to follow different temporal behavior depending on the distribution of local velocity gradients. This approach allows for the systematic evaluation of the temporal evolution of upscaled reaction rates, and establishes a direct link between the global reaction efficiency and the spatial characteristics of the underlying pore scale flow field.References:[1] P. de Anna, J. Jimenez-Martinez, H. Tabuteau, R. Turuban, T. Le Borgne, M. Derrien,and Yves Méheust, Mixing and reaction kinetics in porous media : an experimental pore scale quantification, Environ. Sci. Technol.48, 508-516, 2014. [2] de Anna, P., Dentz, M., Tartakovsky A. and Le Borgne, T., The

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  18. Controllable synthesis of ordered mesoporous NiFe₂O₄ with tunable pore structure as a bifunctional catalyst for Li-O₂ batteries.

    PubMed

    Li, Yuan; Guo, Kun; Li, Jun; Dong, Xiaowen; Yuan, Ting; Li, Xiaowei; Yang, Hui

    2014-12-10

    Three-dimensional ordered mesoporous (3DOM) NiFe2O4 materials with tunable pore size ranging from 5.0 to 25.1 nm have been synthesized via a hard template and used as bifunctional electrocatalysts for rechargeable Li-O2 batteries. Characterization of the catalysts by X-ray diffraction and transmission electron microscopy confirms the formation of a single-phase 3DOM NiFe2O4 structure. Linear scanning voltammetry measurements reveal that Ketjen black (KB) carbon-supported 3DOM NiFe2O4 exhibits a decreased overpotential for both oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) than commonly used KB. A reduction in both the ORR and OER overpotentials increases with the mean pore size of 3DOM NiFe2O4 materials. Importantly, Li-O2 batteries with 3DOM NiFe2O4 materials as the cathode catalysts exhibit a significant enhancement in the discharge capacity, rate capability, and cyclability, and these performances increases with the mean pore size of 3DOM NiFe2O4 materials. For a Li-O2 battery equipped with a 3DOM NiFe2O4 catalyst with a maximum mean pore size of 25.1 nm, a long cycling life of up to 100 cycles under the limiting capacity of 1000 mAh gC(-1) is achieved, strongly indicating that the mesoporous size of the bifunctional catalysts plays a crucial role in enhancing the performance of Li-O2 batteries. The combined use of 3DOM NiFe2O4 with a maximal pore size of 25.1 nm and a poly(vinylidene difluoride hexafluoropropylene) separator with a tuned pore structure further improves the Li-O2 battery performance, highlighting the importance of the pore structure in the development of bifunctional catalysts and separators.

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

    PubMed

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

    2016-03-01

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

  20. Nuclear pore complex protein sequences determine overall copolymer brush structure and function.

    PubMed

    Ando, David; Zandi, Roya; Kim, Yong Woon; Colvin, Michael; Rexach, Michael; Gopinathan, Ajay

    2014-05-06

    The transport of cargo across the nuclear membrane is highly selective and accomplished by a poorly understood mechanism involving hundreds of nucleoporins lining the inside of the nuclear pore complex (NPC). Currently, there is no clear picture of the overall structure formed by this collection of proteins within the pore, primarily due to their disordered nature. We perform coarse-grained simulations of both individual nucleoporins and grafted rings of nups mimicking the in vivo geometry of the NPC and supplement this with polymer brush modeling. Our results indicate that different regions or blocks of an individual NPC protein can have distinctly different forms of disorder and that this property appears to be a conserved functional feature. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture that can exist in distinct morphologies depending on the effective interaction energy between the phenylalanine glycine (FG) domains of different nups. Because the interactions between FG domains may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability.

  1. Porous Copolymer Resins: Tuning Pore Structure and Surface Area with Non Reactive Porogens

    PubMed Central

    Mohamed, Mohamed H.; Wilson, Lee D.

    2012-01-01

    In this review, the preparation of porous copolymer resin (PCR) materials via suspension polymerization with variable properties are described by tuning the polymerization reaction, using solvents which act as porogens, to yield microporous, mesoporous, and macroporous materials. The porogenic properties of solvents are related to traditional solubility parameters which yield significant changes in the surface area, porosity, pore volume, and morphology of the polymeric materials. The mutual solubility characteristics of the solvents, monomer units, and the polymeric resins contribute to the formation of porous materials with tunable pore structures and surface areas. The importance of the initiator solubility, surface effects, the temporal variation of solvent composition during polymerization, and temperature effects contribute to the variable physicochemical properties of the PCR materials. An improved understanding of the factors governing the mechanism of formation for PCR materials will contribute to the development and design of versatile materials with tunable properties for a wide range of technical applications. PMID:28348302

  2. Characterization of variants of the pore-forming toxin ClyA from Escherichia coli controlled by a redox switch.

    PubMed

    Roderer, Daniel; Benke, Stephan; Müller, Marcus; Fäh-Rechsteiner, Helene; Ban, Nenad; Schuler, Benjamin; Glockshuber, Rudi

    2014-10-14

    The α-pore-forming toxin Cytolysin A (ClyA) is responsible for the hemolytic phenotype of several Escherichia coli and Salmonella enterica strains. ClyA is a soluble, 34 kDa monomer that assembles into a dodecameric pore complex in the presence of membranes or detergent. The comparison of the X-ray structures of monomeric ClyA and the ClyA protomer in the pore complex revealed one of the largest conformational transitions observed so far in proteins, involving the structural rearrangement of more than half of all residues, which is consistent with the finding that conversion from the monomer to the assembly competent protomer is rate-limiting for pore assembly. Here, we introduced artificial disulfide bonds at two distinct sites into the ClyA monomer that both prevent a specific structural rearrangement required for protomer formation. Using electron microscopy and hemolytic activity assays, we show that the engineered disulfides indeed trap these ClyA variants in an assembly incompetent state. Assembly of the variants into functional pore complexes can be completely recovered by disulfide reduction. The assembly kinetics of the ClyA variants recorded with circular dichroism and fluorescence spectroscopy revealed the same mechanism of protomer formation that was observed for wild-type ClyA, proceeding via an intermediate with decreased secondary structure content.

  3. Structure Determination of the Nuclear Pore Complex with Three-Dimensional Cryo electron Microscopy.

    PubMed

    von Appen, Alexander; Beck, Martin

    2016-05-22

    Determining the structure of the nuclear pore complex (NPC) imposes an enormous challenge due to its size, intricate composition and membrane-embedded nature. In vertebrates, about 1000 protein building blocks assemble into a 110-MDa complex that fuses the inner and outer membranes of a cell's nucleus. Here, we review the recent progress in understanding the in situ architecture of the NPC with a specific focus on approaches using three-dimensional cryo electron microscopy. We discuss technological benefits and limitations and give an outlook toward obtaining a high-resolution structure of the NPC.

  4. Effects of pore structure and electrolyte on the capacitive characteristics of steam- and KOH-activated carbons for supercapacitors

    NASA Astrophysics Data System (ADS)

    Wu, Feng-Chin; Tseng, Ru-Ling; Hu, Chi-Chang; Wang, Chen-Ching

    Four kinds of activated carbons (denoted as ACs) with specific surface area of ca. 1050 m 2 g -1 were fabricated from fir wood and pistachio shell by means of steam activation or chemical activation with KOH. Pore structures of ACs were characterized by a t-plot method based on N 2 adsorption isotherms. The amount of mesopores within KOH-activated carbons ranged from 9.2 to 15.3% while 33.3-49.5% of mesopores were obtained for the steam-activated carbons. The pore structure, surface functional groups, and raw materials of ACs, as well as pH and the supporting electrolyte were also found to be significant factors determining the capacitive characteristics of ACs. The excellent capacitive characteristics in both acidic and neutral media and the weak dependence of the specific capacitance on the scan rate of cyclic voltammetry (CV) for the ACs derived from the pistachio shell with steam activation (denoted as P-H 2O-AC) revealed their promising potential in the application of supercapacitors. The ACs derived from fir wood with KOH activation (denoted as F-KOH-AC), on the other hand, showed the best capacitive performance in H 2SO 4 due to excellent reversibility and high specific capacitance (180 F g -1 measured at 10 mV s -1), which is obviously larger than 100 F g -1 (a typical value of activated carbons with specific surface areas equal to/above 1000 m 2 g -1).

  5. Lennard-Jones fluids in two-dimensional nano-pores. Multi-phase coexistence and fluid structure

    NASA Astrophysics Data System (ADS)

    Yatsyshin, Petr; Savva, Nikos; Kalliadasis, Serafim

    2014-03-01

    We present a number of fundamental findings on the wetting behaviour of nano-pores. A popular model for fluid confinement is a one-dimensional (1D) slit pore formed by two parallel planar walls and it exhibits capillary condensation (CC): a first-order phase transition from vapour to capillary-liquid (Kelvin shift). Capping such a pore at one end by a third orthogonal wall forms a prototypical two-dimensional (2D) pore. We show that 2D pores possess a wetting temperature such that below this temperature CC remains of first order, above it becomes a continuous phase transition manifested by a slab of capillary-liquid filling the pore from the capping wall. Continuous CC exhibits hysteresis and can be preceded by a first-order capillary prewetting transition. Additionally, liquid drops can form in the corners of the 2D pore (remnant of 2D wedge prewetting). The three fluid phases, vapour, capillary-liquid slab and corner drops, can coexist at the pore triple point. Our model is based on the statistical mechanics of fluids in the density functional formulation. The fluid-fluid and fluid-substrate interactions are dispersive. We analyze in detail the microscopic fluid structure, isotherms and full phase diagrams. Our findings also suggest novel ways to control wetting of nano-pores. We are grateful to the European Research Council via Advanced Grant No. 247031 for support.

  6. Structural features of the pore formed by Staphylococcus aureus alpha-toxin inferred from chemical modification and primary structure analysis.

    PubMed

    Menestrina, G; Belmonte, G; Parisi, V; Morante, S

    1992-09-01

    Staphylococcus aureus alpha-toxin makes cells and model membranes permeable to ions and uncharged molecules by opening oligomeric pores of uniform size. Its primary sequence reveals peculiar features which give some hints on the structure of the pore. A flexible region separating the toxin into two halves, several amphiphilic beta-strands and two amphiphilic alpha-helices long enough to span the hydrophobic core of the lipid bilayer are predicted. In analogy to bacterial porins, we propose that the inner walls of the pore are, at least in part, built by an amphiphilic beta-barrel. The model is consistent with circular dichroism data and with the electrophysiological properties of the pore. Functional information on this toxin were obtained by chemical modification of its four histidine residues. Specific carbethoxylation suggested they have different roles: one is required for specific receptor binding, one for oligomerisation and two for unspecific lipid binding. A tentative assignment of each histidine to its specific role is done on the basis of the structural predictions. A functionally related hemolysin, Aeromonas hydrophyla aerolysin, reveals remarkably similar features including the presence and location of histidines involved in receptor binding and oligomerisation.

  7. Effect of torrefaction on the properties of rice straw high temperature pyrolysis char: Pore structure, aromaticity and gasification activity.

    PubMed

    Chen, Handing; Chen, Xueli; Qin, Yueqiang; Wei, Juntao; Liu, Haifeng

    2017-03-01

    The influence of torrefaction on the physicochemical characteristics of char during raw and water washed rice straw pyrolysis at 800-1200°C is investigated. Pore structure, aromaticity and gasification activity of pyrolysis chars are compared between raw and torrefied samples. For raw straw, BET specific surface area decreases with the increased torrefaction temperature at the same pyrolysis temperature and it approximately increases linearly with weight loss during pyrolysis. The different pore structure evolutions relate to the different volatile matters and pore structures between raw and torrefied straw. Torrefaction at higher temperature would bring about a lower graphitization degree of char during pyrolysis of raw straw. Pore structure and carbon crystalline structure evolutions of raw and torrefied water washed straw are different from these of raw straw during pyrolysis. For both raw and water washed straw, CO2 gasification activities of pyrolysis chars are different between raw and torrefied samples.

  8. Evaporation-based method for preparing gelatin foams with aligned tubular pore structures.

    PubMed

    Frazier, Shane D; Srubar, Wil V

    2016-05-01

    Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5-30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05-0.22 g/cm(3)) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming.

  9. Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi.

    PubMed

    Balasubramaniam, D; Arockiasamy, Arulandu; Kumar, P D; Sharma, Amit; Krishnaswamy, S

    2012-06-01

    OmpF is a major general diffusion porin of Salmonella typhi, a Gram-negative bacterium, which is an obligatory human pathogen causing typhoid. The structure of S. typhi Ty21a OmpF (PDB Id: 3NSG) determined at 2.8 Å resolution by X-ray crystallography shows a 16-stranded β-barrel with three β-barrel monomers associated to form a trimer. The packing observed in S. typhi Ty21a rfOmpF crystals has not been observed earlier in other porin structures. The variations seen in the loop regions provide a starting point for using the S. typhi OmpF for structure-based multi-valent vaccine design. Along one side of the S. typhi Ty21a OmpF pore there exists a staircase arrangement of basic residues (20R, 60R, 62K, 65R, 77R, 130R and 16K), which also contribute, to the electrostatic potential in the pore. This structure suggests the presence of asymmetric electrostatics in the porin oligomer. Moreover, antibiotic translocation, permeability and reduced uptake in the case of mutants can be understood based on the structure paving the way for designing new antibiotics.

  10. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.

    PubMed

    Sampathkumar, Parthasarathy; Kim, Seung Joong; Upla, Paula; Rice, William J; Phillips, Jeremy; Timney, Benjamin L; Pieper, Ursula; Bonanno, Jeffrey B; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Ketaren, Natalia E; Matsui, Tsutomu; Weiss, Thomas M; Stokes, David L; Sauder, J Michael; Burley, Stephen K; Sali, Andrej; Rout, Michael P; Almo, Steven C

    2013-04-02

    The nuclear pore complex, composed of proteins termed nucleoporins (Nups), is responsible for nucleocytoplasmic transport in eukaryotes. Nuclear pore complexes (NPCs) form an annular structure composed of the nuclear ring, cytoplasmic ring, a membrane ring, and two inner rings. Nup192 is a major component of the NPC's inner ring. We report the crystal structure of Saccharomyces cerevisiae Nup192 residues 2-960 [ScNup192(2-960)], which adopts an α-helical fold with three domains (i.e., D1, D2, and D3). Small angle X-ray scattering and electron microscopy (EM) studies reveal that ScNup192(2-960) could undergo long-range transition between "open" and "closed" conformations. We obtained a structural model of full-length ScNup192 based on EM, the structure of ScNup192(2-960), and homology modeling. Evolutionary analyses using the ScNup192(2-960) structure suggest that NPCs and vesicle-coating complexes are descended from a common membrane-coating ancestral complex. We show that suppression of Nup192 expression leads to compromised nuclear transport and hypothesize a role for Nup192 in modulating the permeability of the NPC central channel.

  11. Morphology and Gas-Sensing Properties of Tin Oxide Foams with Dual Pore Structure

    NASA Astrophysics Data System (ADS)

    Nam, Kyungju; Kim, Hyeong-Gwan; Choi, Hyelim; Park, Hyeji; Kang, Jin Soo; Sung, Yung-Eun; Lee, Hee Chul; Choe, Heeman

    2017-01-01

    Tin oxide is a commonly used gas-sensing material, which can be applied as an n- or p-type gas sensor. To improve the gas-sensing performance of tin oxide, we successfully synthesized tin oxide foam via an ice-templating or freeze-casting method. The tin oxide foam samples showed different morphological features depending on the major processing parameters, which include sintering temperature, sintering time, and the amount of added powder. Based on scanning electron microscopy images, we could identify dual pore structure of tin oxide foam containing `wall' pores ranging from 5.3 μm to 10.7 μm, as well as smaller secondary pores (a few micrometers in size) on the wall surfaces. Gas-sensing performance tests for the synthesized tin oxide foams reveal a sensitivity of 13.1, a response time of 192 s, and a recovery time of 160 s at an ethanol gas concentration of 60 ppm at 300°C. This is a remarkable result given that it showed p-type semiconductor behavior and was used without the addition of any catalyst.

  12. Effects of rock mineralogy and pore structure on stress-dependent permeability of shale samples.

    PubMed

    Al Ismail, Maytham I; Zoback, Mark D

    2016-10-13

    We conducted pulse-decay permeability experiments on Utica and Permian shale samples to investigate the effect of rock mineralogy and pore structure on the transport mechanisms using a non-adsorbing gas (argon). The mineralogy of the shale samples varied from clay rich to calcite rich (i.e. clay poor). Our permeability measurements and scanning electron microscopy images revealed that the permeability of the shale samples whose pores resided in the kerogen positively correlated with organic content. Our results showed that the absolute value of permeability was not affected by the mineral composition of the shale samples. Additionally, our results indicated that clay content played a significant role in the stress-dependent permeability. For clay-rich samples, we observed higher pore throat compressibility, which led to higher permeability reduction at increasing effective stress than with calcite-rich samples. Our findings highlight the importance of considering permeability to be stress dependent to achieve more accurate reservoir simulations especially for clay-rich shale reservoirs.This article is part of the themed issue 'Energy and the subsurface'.

  13. Pore-pressure diffusion based on analysis and characterization of microseismicity in central Arkansas

    NASA Astrophysics Data System (ADS)

    Ogwari, Paul Otieno

    Part 1: Between August 2010 and June 2011, an intense sequence of induced earthquakes occurred along the Guy-Greenbrier fault in central Arkansas due to fluid injection at nearby waste disposal wells. A previous study by Horton (2010) limited to ˜1,000 earthquakes having md > ˜2.0 illuminated the ˜13km fault. We present an updated catalogue of 17,395 earthquakes that appears complete between 0 <= ml <= 4.4 for the initial part of the sequence between August 2010 and October 20, 2010 located using an updated 1D velocity model for the region. The inclusion of the small magnitude events reveals that seismicity starts below the SRE injection well a month earlier than estimated using only md >2 events. During this period of time, the seismicity migrated from north to south enhancing the resolution of three joined sections that form the northern ˜7.3km portion of the fault, which plunges southwards. The seismogenic zone covers the lower portion of the Paleozoic sedimentary layers and extends into the crystalline Precambrian basement (˜3km < z 3 events constrained within the basement. A b-value of 1.1 was obtained for the updated catalog during this period with the b-value varying between 1.45 and 0.74 for different clusters of events. The seismicity pattern at depth is coincident with structural geologic features observed within the Fayetteville Shale (at ˜1500m depth). Part 2: We model pore-pressure diffusion caused by pressurized waste-fluid injection at two nearby wells, and then compare the build-up of pressure with the observed initiation and migration of earthquakes during the early part of the 2010-2011 Guy-Greenbrier earthquake swarm. Pore pressure diffusion is calculated using MODFLOW 2005 that allows the actual injection histories (volume/day) at the two wells to diffuse through a fractured and faulted 3D aquifer system representing the eastern Arkoma basin. The aquifer system is calibrated using the observed well "drawup" following well shut-in at three

  14. 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.

  15. 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.

  16. Atomic Structure of the Y-Complex of the Nuclear Pore

    PubMed Central

    Kabachinski, Greg; Schwartz, Thomas U.

    2015-01-01

    The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40 MDa ring-like structure. Here we present the 4.1 Å crystal structure of a heterotetrameric core element (‘hub’) of the Y-complex, the essential NPC building block, from Myceliophthora thermophila. Using the ‘hub’ structure together with known Y-complex fragments we built the entire ~0.5 MDa Y-complex. Our data reveal that the conserved core of the Y-complex has 6, rather than 7 members. Evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes. PMID:25822992

  17. Determination of the pore size of woven structures through image analysis

    NASA Astrophysics Data System (ADS)

    Angelova, R. A.

    2012-03-01

    The paper presents an experimental procedure developed for determination of the pore size, shape and distribution in a single layer woven fabric, for the construction of a virtual model to be incorporated in a future CFD software package. The procedure is based on non-destructive observation and analysis of woven samples. 14 different samples of gray fabrics of 100 % cotton in plain and twill weaves are investigated. The results obtained allow the creation of reality more realistic virtual model of the woven structure, and theoretical investigation of its porosity and permeability through computer simulation.

  18. Influence of the pore structure and surface chemical properties of activated carbon on the adsorption of mercury from aqueous solutions.

    PubMed

    Lu, Xincheng; Jiang, Jianchun; Sun, Kang; Wang, Jinbiao; Zhang, Yanping

    2014-01-15

    Reactivation and chemical modification were used to obtain modified activated carbons with different pore structure and surface chemical properties. The samples were characterized by nitrogen absorption-desorption, Fourier transform infrared spectroscopy and the Bothem method. Using mercury chloride as the target pollutant, the Hg(2+) adsorption ability of samples was investigated. The results show that the Hg(2+) adsorption capacity of samples increased significantly with increases in micropores and acidic functional groups and that the adsorption process was exothermic. Different models and thermodynamic parameters were evaluated to establish the mechanisms. It was concluded that the adsorption occurred through a monolayer mechanism by a two-speed process involving both rapid adsorption and slow adsorption. The adsorption rate was determined by chemical reaction.

  19. Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein

    PubMed Central

    Bokori-Brown, Monika; Martin, Thomas G.; Naylor, Claire E.; Basak, Ajit K.; Titball, Richard W.; Savva, Christos G.

    2016-01-01

    Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel. PMID:27048994

  20. Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein

    NASA Astrophysics Data System (ADS)

    Bokori-Brown, Monika; Martin, Thomas G.; Naylor, Claire E.; Basak, Ajit K.; Titball, Richard W.; Savva, Christos G.

    2016-04-01

    Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel.

  1. Functional Characterization of Sticholysin I and W111C Mutant Reveals the Sequence of the Actinoporin’s Pore Assembly

    PubMed Central

    Antonini, Valeria; Pérez-Barzaga, Victor; Bampi, Silvia; Pentón, David; Martínez, Diana; Serra, Mauro Dalla; Tejuca, Mayra

    2014-01-01

    The use of pore-forming toxins in the construction of immunotoxins against tumour cells is an alternative for cancer therapy. In this protein family one of the most potent toxins are the actinoporins, cytolysins from sea anemones. We work on the construction of tumour proteinase-activated immunotoxins using sticholysin I (StI), an actinoporin isolated from the sea anemone Stichodactyla helianthus. To accomplish this objective, recombinant StI (StIr) with a mutation in the membrane binding region has been employed. In this work, it was evaluated the impact of mutating tryptophan 111 to cysteine on the toxin pore forming capability. StI W111C is still able to permeabilize erythrocytes and liposomes, but at ten-fold higher concentration than StI. This is due to its lower affinity for the membrane, which corroborates the importance of residue 111 for the binding of actinoporins to the lipid bilayer. In agreement, other functional characteristics not directly associated to the binding, are essentially the same for both variants, that is, pores have oligomeric structures with similar radii, conductance, cation-selectivity, and instantaneous current-voltage behavior. In addition, this work provides experimental evidence sustaining the toroidal protein-lipid actinoporins lytic structures, since the toxins provoke the trans-bilayer movement (flip–flop) of a pyrene-labeled analogue of phosphatidylcholine in liposomes, indicating the existence of continuity between the outer and the inner membrane leaflet. Finally, our planar lipid membranes results have also contributed to a better understanding of the actinoporin’s pore assembly mechanism. After the toxin binding and the N-terminal insertion in the lipid membrane, the pore assembly occurs by passing through different transient sub-conductance states. These states, usually 3 or 4, are due to the successive incorporation of N-terminal α-helices and lipid heads to the growing pores until a stable toroidal oligomeric

  2. Functional characterization of sticholysin I and W111C mutant reveals the sequence of the actinoporin's pore assembly.

    PubMed

    Antonini, Valeria; Pérez-Barzaga, Victor; Bampi, Silvia; Pentón, David; Martínez, Diana; Dalla Serra, Mauro; Tejuca, Mayra

    2014-01-01

    The use of pore-forming toxins in the construction of immunotoxins against tumour cells is an alternative for cancer therapy. In this protein family one of the most potent toxins are the actinoporins, cytolysins from sea anemones. We work on the construction of tumour proteinase-activated immunotoxins using sticholysin I (StI), an actinoporin isolated from the sea anemone Stichodactyla helianthus. To accomplish this objective, recombinant StI (StIr) with a mutation in the membrane binding region has been employed. In this work, it was evaluated the impact of mutating tryptophan 111 to cysteine on the toxin pore forming capability. StI W111C is still able to permeabilize erythrocytes and liposomes, but at ten-fold higher concentration than StI. This is due to its lower affinity for the membrane, which corroborates the importance of residue 111 for the binding of actinoporins to the lipid bilayer. In agreement, other functional characteristics not directly associated to the binding, are essentially the same for both variants, that is, pores have oligomeric structures with similar radii, conductance, cation-selectivity, and instantaneous current-voltage behavior. In addition, this work provides experimental evidence sustaining the toroidal protein-lipid actinoporins lytic structures, since the toxins provoke the trans-bilayer movement (flip-flop) of a pyrene-labeled analogue of phosphatidylcholine in liposomes, indicating the existence of continuity between the outer and the inner membrane leaflet. Finally, our planar lipid membranes results have also contributed to a better understanding of the actinoporin's pore assembly mechanism. After the toxin binding and the N-terminal insertion in the lipid membrane, the pore assembly occurs by passing through different transient sub-conductance states. These states, usually 3 or 4, are due to the successive incorporation of N-terminal α-helices and lipid heads to the growing pores until a stable toroidal oligomeric structure

  3. Characterization of pore evolution in ceramics during creep failure and densification. Final report, April 15, 1984--April 14, 1995

    SciTech Connect

    Page, R.A.; Chan, K.S.

    1995-04-01

    This research program was divided into two phases, one involving creep cavitation, the other cavity evolution during sintering. In the former, work was aimed at determining the effect of microstructure and stress state upon creep cavitation, while in the latter, the principal objective was the characterization of pore evolution during sintering. In order to meet these objectives, the creep cavitation portion of the program was centered around small-angle neutron scattering, supplemented by electron microscopy and precision density measurements. The neutron scattering measurements yielded cavity nucleation and growth rates, and average pore, size, distribution, and morphology. These data were used to evaluate current cavitation models, and to implement improved modelling efforts. Additionally, stereoimaging analysis was used to determine grain boundary sliding displacements, which appear to be the critical driving force responsible for cavity nucleation and early growth. Effort in the pore sintering phase focussed on characterization of pore evolution during intermediate and final stage sintering of alumina using both single and multiple scattering techniques. Electron microscopy, density measurements, and mercury intrusion porosimetry measurements complemented the scattering results. The effects of sintering trajectory, green state, powder morphology, and additives were evaluated. These results were compared to current sintering models.

  4. Laser scanning confocal microscopy characterization of water repellent distribution in a sandstone pore network.

    PubMed

    Zoghlami, Karima; Gómez-Gras, David; Corbella, Mercè; Darragi, Fadila

    2008-11-01

    In the present work, we propose the use of the Laser Scanning Confocal Microscopy (LSCM) to determine the effect of water repellents on rock's pore-network configuration and interconnection. The rocks studied are sandstones of Miocene age, a building material that is commonly found in the architectural heritage of Tunisia. The porosity quantitative data of treated and untreated samples, obtained by mercury porosimetry tests, were compared. The results show a slight decrease in total porosity with the water repellent treatment, which reduced both microporosity and macroporosity. This reduction produced a modification in pore size distribution and a shift of the pore access size mode interval toward smaller pore diameters (from the 30-40 microm to the 20-30 microm intervals). The water repellent was observed in SEM images as a continuous film coating grain surfaces; moreover, it was easily visualized in LSCM, by staining the water repellent with Epodye fluorochrome, and the coating thickness was straightforwardly measured (1.5-2 microm). In fact, the combination of mercury intrusion porosimetry data and LSCM observations suggests that the porosity reduction and the shift of the pore diameter mode were mainly due to the general reduction of pore diameters, but also to the plugging of the smallest pores (less than 3-4 microm in diameter) by the water repellent film. Finally, the LSCM technique enabled the reconstruction of 3D views of the water repellent coating film in the pore network, indicating that its distribution was uniform and continuous over the 100 microm thick sample. The LSCM imaging facilitates the integration and interpretation of mercury porosimetry and SEM data.

  5. Mitochondrial chloride channels: electrophysiological characterization and pH induction of channel pore dilation.

    PubMed

    Misak, Anton; Grman, Marian; Malekova, Lubica; Novotova, Marta; Markova, Jana; Krizanova, Olga; Ondrias, Karol; Tomaskova, Zuzana

    2013-09-01

    Physiological and pathological functions of mitochondria are highly dependent on the properties and regulation of mitochondrial ion channels. There is still no clear understanding of the molecular identity, regulation, and properties of anion mitochondrial channels. The inner membrane anion channel (IMAC) was assumed to be equivalent to mitochondrial centum picosiemens (mCS). However, the different properties of IMAC and mCS channels challenges this opinion. In our study, we characterized the single-channel anion selectivity and pH regulation of chloride channels from purified cardiac mitochondria. We observed that channel conductance decreased in the order: Cl⁻ > Br⁻ > I⁻ > chlorate ≈ formate > acetate, and that gluconate did not permeate under control conditions. The selectivity sequence was Br⁻ ≥ chlorate ≥ I⁻ ≥ Cl⁻ ≥ formate ≈ acetate. Measurement of the concentration dependence of chloride conductance revealed altered channel gating kinetics, which was demonstrated by prolonged mean open time value with increasing chloride concentration. The observed mitochondrial chloride channels were in many respects similar to those of mCS, but not those of IMAC. Surprisingly, we observed that acidic pH increased channel conductance and that an increase of pH from 7.4 to 8.5 reduced it. The gluconate current appeared and gradually increased when pH decreased from pH 7.0 to 5.6. Our results indicate that pH regulates the channel pore diameter in such a way that dilation increases with more acidic pH. We assume this newly observed pH-dependent anion channel property may be involved in pH regulation of anion distribution in different mitochondrial compartments.

  6. Structural alterations, pore generation, and deacetylation of α- and β-chitin submitted to steam explosion.

    PubMed

    Tan, Too Shen; Chin, Hui Yen; Tsai, Min-Lang; Liu, Chao-Lin

    2015-05-20

    The purpose of this study was to use an environmentally friendly steam explosion method to achieve α- and β-chitin structural alterations, pore generation, and deacetylation, enhancing the degree of deacetylation (DD) in chitin and extending its applications. The samples of α- and β-chitin possessing various moisture contents that were exploded at 9 kg/cm(2) exhibited higher DDs, lower densities, lower crystallinity and more porous structures compared to unexploded chitin. After explosion, β-chitin exhibited a larger expansion ratio, lower crystallinity and contained a larger proportion of small-sized particles compared to α-chitin. The highest DD values of exploded α- and β-chitin with 75% moisture content were 42.9% and 43.7%, respectively. The exploded chitin samples with lower moisture content exhibited lower DDs, densities, crystallinity indices, smaller particle sizes, and higher expansion ratios than the chitin samples with higher moisture content. The chitin samples with lower moisture content also contained larger and more numerous pores.

  7. Synthesis of carbon core–shell pore structures and their performance as supercapacitors

    DOE PAGES

    Ariyanto, Teguh; Dyatkin, Boris; Zhang, Gui-Rong; ...

    2015-07-15

    High-power supercapacitors require excellent electrolyte mobility within the pore network and high electrical conductivity for maximum capacitance and efficiency. Achieving high power typically requires sacrificing energy densities, as the latter demands a high specific surface area and narrow porosity that impedes ion transport. Here, we present a novel solution for this optimization problem: a nanostructured core–shell carbonaceous material that exhibits a microporous carbon core surrounded by a mesoporous, graphitic shell. The tunable synthesis parameters yielded a structure that features either a sharp or a gradual transition between the core and shell sections. Electrochemical supercapacitor testing using organic electrolyte revealed thatmore » these novel core–shell materials outperform carbons with homogeneous pore structures. The hybrid core–shell materials showed a combination of good capacitance retention, typical for the carbon present in the shell and high specific capacitance, typical for the core material. These materials achieved power densities in excess of 40 kW kg-1 at energy densities reaching 27 Wh kg-1.« less

  8. Synthesis of carbon core–shell pore structures and their performance as supercapacitors

    SciTech Connect

    Ariyanto, Teguh; Dyatkin, Boris; Zhang, Gui-Rong; Kern, Andreas; Gogotsi, Yury; Etzold, Bastian J. M.

    2015-07-15

    High-power supercapacitors require excellent electrolyte mobility within the pore network and high electrical conductivity for maximum capacitance and efficiency. Achieving high power typically requires sacrificing energy densities, as the latter demands a high specific surface area and narrow porosity that impedes ion transport. Here, we present a novel solution for this optimization problem: a nanostructured core–shell carbonaceous material that exhibits a microporous carbon core surrounded by a mesoporous, graphitic shell. The tunable synthesis parameters yielded a structure that features either a sharp or a gradual transition between the core and shell sections. Electrochemical supercapacitor testing using organic electrolyte revealed that these novel core–shell materials outperform carbons with homogeneous pore structures. The hybrid core–shell materials showed a combination of good capacitance retention, typical for the carbon present in the shell and high specific capacitance, typical for the core material. These materials achieved power densities in excess of 40 kW kg-1 at energy densities reaching 27 Wh kg-1.

  9. Nuclear Pore Complex Protein Sequences Determine Overall Copolymer Brush Structure and Function?

    NASA Astrophysics Data System (ADS)

    Ando, David; Kim, Yongwoon; Zandi, Roya; Colvin, Michael; Rexach, Michael; Gopinathan, Ajay

    2015-03-01

    Disordered proteins are an interesting class of unfolded protein biopolymers which are functionally versatile. Their sequences are unconstrained by a sequence-structure relationship, and allow for a wide range of chemical and physical polymer properties. The Nuclear Pore Complex (NPC) contains over one hundred of such proteins (FG nups), which collectively function to regulate the exchange of all materials between the nucleus and cytoplasm. We perform coarse grained simulations of both individual FG nups and grafted rings of nups mimicking the in vivo geometry of the NPC, supplemented with polymer brush modeling. Our results indicate that different regions or ``blocks'' of an individual FG nup can have distinctly different forms of disorder, and that this property appears to be a conserved feature across eukarya. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture. Because the interactions between FG nups may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability.

  10. Probing a Structural Model of the Nuclear Pore Complex Channel through Molecular Dynamics

    PubMed Central

    Miao, Lingling; Schulten, Klaus

    2010-01-01

    Abstract The central pore of a nuclear pore complex (NPC) is filled with unstructured proteins that contain many FG-repeats separated by hydrophilic regions. An example of such protein is nsp1. By simulating an array of nsp1 segments, we identified, in an earlier study, a spontaneously formed brushlike structure that promises to explain selective transport in the NPC channel. Here we report four (350,000 atom, 200 ns) simulations probing this structure via its interaction with transport receptor NTF2 as well as with an inert protein. NTF2 dimers are observed to gradually enter the brush, but the inert protein is not. Both NTF2 and the inert protein are found to bind to FG-repeats, but binding periods lasted more briefly for the inert protein. A simulation also investigated the behavior of a brush made of mutant nsp1 that is known to be less effective in NPC-selective transport, finding that this brush does not attract NTF2. PMID:20409487

  11. 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.

  12. Visualization of soil structure and pore structure modifications by pioneering ground beetles (Cicindelidae) in surface sediments of an artificial catchment

    NASA Astrophysics Data System (ADS)

    Badorreck, Annika; Gerke, Horst H.; Weller, Ulrich; Vontobel, Peter

    2010-05-01

    An artificial catchment was constructed to study initial soil and ecosystem development. As a key process, the pore structure dynamics in the soil at the surface strongly influences erosion, infiltration, matter dynamics, and vegetation establishment. Little is known, however, about the first macropore formation in the very early stage. This presentation focuses on observations of soil pore geometry and its effect on water flow at the surface comparing samples from three sites in the catchment and in an adjacent "younger" site composed of comparable sediments. The surface soil was sampled in cylindrical plastic rings (10 cm³) down to 2 cm depth in three replicates each site and six where caves from pioneering ground-dwelling beetles Cicindelidae were found. The samples were scanned with micro-X-ray computed tomography (at UFZ-Halle, Germany) with a resolution of 0.084 mm. The infiltration dynamics were visualized with neutronradiography (at Paul-Scherer-Institute, Switzerland) on slab-type soil samples in 2D. The micro-tomographies exhibit formation of surface sealing whose thickness and intensity vary with silt and clay content. The CT images show several coarser- and finer-textured micro-layers at the sample surfaces that were formed as a consequence of repeated washing in of finer particles in underlying coarser sediment. In micro-depressions, the uppermost layers consist of sorted fine sand and silt due to wind erosion. Similar as for desert pavements, a vesicular pore structure developed in these sediments on top, but also scattered in fine sand- and silt-enriched micro-layers. The ground-dwelling activity of Cicindelidae beetles greatly modifies the soil structure through forming caves in the first centimetres of the soil. Older collapsed caves, which form isolated pores within mixed zones, were also found. The infiltration rates were severely affected both, by surface crusts and activity of ground-dwelling beetles. The observations demonstrate relatively

  13. Structures of lysenin reveal a shared evolutionary origin for pore-forming proteins and its mode of sphingomyelin recognition.

    PubMed

    De Colibus, Luigi; Sonnen, Andreas F-P; Morris, Keith J; Siebert, C Alistair; Abrusci, Patrizia; Plitzko, Jürgen; Hodnik, Vesna; Leippe, Matthias; Volpi, Emanuela; Anderluh, Gregor; Gilbert, Robert J C

    2012-09-05

    Pore-forming proteins insert from solution into membranes to create lesions, undergoing a structural rearrangement often accompanied by oligomerization. Lysenin, a pore-forming toxin from the earthworm Eisenia fetida, specifically interacts with sphingomyelin (SM) and may confer innate immunity against parasites by attacking their membranes to form pores. SM has important roles in cell membranes and lysenin is a popular SM-labeling reagent. The structure of lysenin suggests common ancestry with other pore-forming proteins from a diverse set of eukaryotes and prokaryotes. The complex with SM shows the mode of its recognition by a protein in which both the phosphocholine headgroup and one acyl tail are specifically bound. Lipid interaction studies and assays using viable target cells confirm the functional reliance of lysenin on this form of SM recognition.

  14. 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

  15. 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

  16. 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

  17. Dendritic silica nanomaterials (KCC-1) with fibrous pore structure possess high DNA adsorption capacity and effectively deliver genes in vitro.

    PubMed

    Huang, Xiaoxi; Tao, Zhimin; Praskavich, John C; Goswami, Anandarup; Al-Sharab, Jafar F; Minko, Tamara; Polshettiwar, Vivek; Asefa, Tewodros

    2014-09-16

    The pore size and pore structure of nanoporous materials can affect the materials' physical properties, as well as potential applications in different areas, including catalysis, drug delivery, and biomolecular therapeutics. KCC-1, one of the newest members of silica nanomaterials, possesses fibrous, large pore, dendritic pore networks with wide pore entrances, large pore size distribution, spacious pore volume and large surface area--structural features that are conducive for adsorption and release of large guest molecules and biomacromolecules (e.g., proteins and DNAs). Here, we report the results of our comparative studies of adsorption of salmon DNA in a series of KCC-1-based nanomaterials that are functionalized with different organoamine groups on different parts of their surfaces (channel walls, external surfaces or both). For comparison the results of our studies of adsorption of salmon DNA in similarly functionalized, MCM-41 mesoporous silica nanomaterials with cylindrical pores, some of the most studied silica nanomaterials for drug/gene delivery, are also included. Our results indicate that, despite their relatively lower specific surface area, the KCC-1-based nanomaterials show high adsorption capacity for DNA than the corresponding MCM-41-based nanomaterials, most likely because of KCC-1's large pores, wide pore mouths, fibrous pore network, and thereby more accessible and amenable structure for DNA molecules to diffuse through. Conversely, the MCM-41-based nanomaterials adsorb much less DNA, presumably because their outer surfaces/cylindrical channel pore entrances can get blocked by the DNA molecules, making the inner parts of the materials inaccessible. Moreover, experiments involving fluorescent dye-tagged DNAs suggest that the amine-grafted KCC-1 materials are better suited for delivering the DNAs adsorbed on their surfaces into cellular environments than their MCM-41 counterparts. Finally, cellular toxicity tests show that the KCC-1-based

  18. Influence of Boehmite Precursor on Aluminosilicate Aerogel Pore Structure, Phase Stability and Resistance to Densification at High Temperatures

    NASA Technical Reports Server (NTRS)

    Hurwitz, Frances I.; Guo, Haiquan; Newlin, Katy N.

    2011-01-01

    Aluminosilicate aerogels are of interest as constituents of thermal insulation systems for use at temperatures higher than those attainable with silica aerogels. It is anticipated that their effectiveness as thermal insulators will be influenced by their morphology, pore size distribution, physical and skeletal densities. The present study focuses on the synthesis of aluminosilicate aerogel from a variety of Boehmite (precursors as the Al source, and tetraethylorthosilicate (TEOS) as the Si source, and the influence of starting powder on pore structure and thermal stability.

  19. 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

  20. 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.

  1. 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.

  2. Relationship of pore structure to fluid behavior in low permeability gas sands. Final report

    SciTech Connect

    Morrow, N.R.

    1984-01-01

    This is the final report of a three-year project concerned with the pore structure of low permeability gas sands. The report is divided into five sections: (1) Pressure Sensitivity of Permeability, (2) Effects of Fluid, Confining Pressure, and Temperature on Absolute Permeabiities of Low Permeability Sandstones, (3) Effect of Acid Leaching and Presence of Fractures, (4) Adsorption, and, (5) Mathematical Modelling and Correlations. In the first section, a data base of core properties is developed with measurements of permeability vs. confining pressure for three suites of cores as the main feature. The third section describes an initial investigation into (a) the effects of removing carbonate cement by leaching cores with acetic acid, (b) the effects of calcite-filled fractures on permeability and pressure sensitivity. Dramatic increase in permeability and decrease in pressure sensitivity were observed to result from leaching. For cores containing calcite-filled fractures, it was found that the fracture was neither a permeability barrier to flow across the fracture or a highly conductive region for flow along the fracture. Results presented in the fourth section on relationships between relative pressure and amount of adsorption provide careful information about the existence and extent of microporous material contained in tight gas sands. The fifth section on mathematical modelling presents results in which the diffusive contribution to flow is calculated for crack-shaped pores in series, and for two- and three-dimensional networks. 93 figures, 20 tables.

  3. Intumescence and pore structure of alkali-activated volcanic glasses upon exposure to high temperatures

    NASA Astrophysics Data System (ADS)

    Erdogan, S. T.

    2015-12-01

    Structures formed with ground perlite, a natural volcanic glass, activated with NaOH solutions, are shown to possess the ability to expand up to ~225 % of their original volumes upon exposure to temperatures in the 200-600 °C range. Porous solid with 3-7 MPa compressive strength and ˜450 kg/m3 or higher density are obtained. The observed expansion is believed to occur due to a loss of silanol condensation water, as vapor and is accompanied by an up to ~20 % loss in mass. A drop in pH to near-neutral values supports this idea. The size and total amount of pores in the final solid are controlled by concentration of the NaOH solution and thermal processing conditions. The pores formed are observed to be ~1-10 μm to mm-sized. The ability of perlite-based solids to intumesce over specific temperature ranges could be beneficial in applications where absorption of thermal energy is necessary, such as passive fire protection.

  4. Structural characterization of submerged granular packings.

    PubMed

    Jakšić, Z M; Šćepanović, J R; Lončarević, I; Budinski-Petković, Lj; Vrhovac, S B; Belić, A

    2014-12-01

    We consider the impact of the effective gravitational acceleration on microstructural properties of granular packings through experimental studies of spherical granular materials saturated within fluids of varying density. We characterize the local organization of spheres in terms of contact connectivity, distribution of the Delaunay free volumes, and the shape factor (parameter of nonsphericity) of the Voronoï polygons. The shape factor gives a clear physical picture of the competition between less and more ordered domains of particles in experimentally obtained packings. As the effective gravity increases, the probability distribution of the shape factor becomes narrower and more localized around the lowest values of the shape factor corresponding to regular hexagon. It is found that curves of the pore distributions are asymmetric with a long tail on the right-hand side, which progressively reduces while the effective gravity gets stronger for lower densities of interstitial fluid. We show that the distribution of local areas (Voronoï cells) broadens with decreasing value of the effective gravity due to the formation of lose structures such as large pores and chainlike structures (arches or bridges). Our results should be particularly helpful in testing the newly developed simulation techniques involving liquid-related forces associated with immersed granular particles.

  5. Structural characterization of submerged granular packings

    NASA Astrophysics Data System (ADS)

    Jakšić, Z. M.; Šćepanović, J. R.; Lončarević, I.; Budinski-Petković, Lj.; Vrhovac, S. B.; Belić, A.

    2014-12-01

    We consider the impact of the effective gravitational acceleration on microstructural properties of granular packings through experimental studies of spherical granular materials saturated within fluids of varying density. We characterize the local organization of spheres in terms of contact connectivity, distribution of the Delaunay free volumes, and the shape factor (parameter of nonsphericity) of the Voronoï polygons. The shape factor gives a clear physical picture of the competition between less and more ordered domains of particles in experimentally obtained packings. As the effective gravity increases, the probability distribution of the shape factor becomes narrower and more localized around the lowest values of the shape factor corresponding to regular hexagon. It is found that curves of the pore distributions are asymmetric with a long tail on the right-hand side, which progressively reduces while the effective gravity gets stronger for lower densities of interstitial fluid. We show that the distribution of local areas (Voronoï cells) broadens with decreasing value of the effective gravity due to the formation of lose structures such as large pores and chainlike structures (arches or bridges). Our results should be particularly helpful in testing the newly developed simulation techniques involving liquid-related forces associated with immersed granular particles.

  6. Synthesis and study on pore structure of SiO{sub 2}/Al{sub 2}O{sub 3} aerogel

    SciTech Connect

    Bakina, O. V. Glazkova, E. A. Svarovskaya, N. V. Lozhkomoev, A. S. Lerner, M. I.; Petrova, T. M. Ponomarev, Y. N. Solodov, A. A. Solodov, A. M.

    2015-10-27

    In the current paper, the mixed SiO{sub 2}/Al{sub 2}O{sub 3} aerogel was synthesized by sol-gel method with subcritical drying and characterized. Tetraethoxysilane was used as a precursor of silicon sol. The flower-shaped alumina suspension was peptized to produce alumina sol. The aerogel texture, morphology, and structure were determined using scanning electron microscopy, X-ray diffraction, low-temperature nitrogen adsorption, and high-resolution spectroscopy. A special attention was paid to the pore structure of aerogel, and aerogel framework was formed by the spherical agglomerates containing spherical particles of silicon oxide and alumina nanopetals. The pore size distribution was bimodal with peaks of 5.5 nm and 77 nm.

  7. Evaluation of pore structures and cracking in cement paste exposed to elevated temperatures by X-ray computed tomography

    SciTech Connect

    Kim, Kwang Yeom; Yun, Tae Sup; Park, Kwang Pil

    2013-08-15

    When cement-based materials are exposed to the high temperatures induced by fire, which can rapidly cause temperatures of over 1000 °C, the changes in pore structure and density prevail. In the present study, mortar specimens were subjected to a series of increasing temperatures to explore the temperature-dependent evolution of internal pore structure. High-performance X-ray computed tomography (CT) was used to observe the evolution of temperature-induced discontinuities at the sub-millimeter level. X-ray diffraction (XRD) and scanning electron microscopy (SEM) were employed to investigate the cause of physical changes in the heated mortar specimens. Results exhibit the changes in pore structure caused by elevated temperatures, and thermally induced fractures. We discuss the progressive formation of thermally induced fracture networks, which is a prerequisite for spalling failure of cement-based materials by fire, based on visual observations of the 3D internal structures revealed by X-ray CT.

  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. Effect of Pore Structure of Macroporous Poly(Lactide-co-Glycolide) Scaffolds on the in Vivo Enrichment of Dendritic Cells

    PubMed Central

    2015-01-01

    The in vivo enrichment of dendritic cells (DCs) in implanted macroporous scaffolds is an emerging strategy to modulate the adaptive immune system. The pore architecture is potentially one of the key factors in controlling enrichment of DCs. However, there have been few studies examining the effects of scaffold pore structure on in vivo DC enrichment. Here we present the effects of surface porosity, pore size, and pore volume of macroporous poly(lactide-co-glycolide) (PLG) scaffolds encapsulating granulocyte macrophage colony-stimulating factor (GM-CSF), an inflammatory chemoattractant, on the in vivo enrichment of DCs. Although in vitro cell seeding studies using PLG scaffolds without GM-CSF showed higher cell infiltration in scaffolds with higher surface porosity, in vivo results revealed higher DC enrichment in GM-CSF loaded PLG scaffolds with lower surface porosity despite a similar level of GM-CSF released. The diminished compressive modulus of high surface porosity scaffolds compared to low surface porosity scaffolds lead to the significant shrinkage of these scaffolds in vivo, suggesting that the mechanical strength of scaffolds was critical to maintain a porous structure in vivo for accumulating DCs. The pore volume was also found to be important in total number of recruited cells and DCs in vivo. Varying the pore size significantly impacted the total number of cells, but similar numbers of DCs were found as long as the pore size was above 10–32 μm. Collectively, these results suggested that one can modulate in vivo enrichment of DCs by altering the pore architecture and mechanical properties of PLG scaffolds. PMID:24844318

  10. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform.

    PubMed

    Fernandez-Martinez, Javier; Kim, Seung Joong; Shi, Yi; Upla, Paula; Pellarin, Riccardo; Gagnon, Michael; Chemmama, Ilan E; Wang, Junjie; Nudelman, Ilona; Zhang, Wenzhu; Williams, Rosemary; Rice, William J; Stokes, David L; Zenklusen, Daniel; Chait, Brian T; Sali, Andrej; Rout, Michael P

    2016-11-17

    The last steps in mRNA export and remodeling are performed by the Nup82 complex, a large conserved assembly at the cytoplasmic face of the nuclear pore complex (NPC). By integrating diverse structural data, we have determined the molecular architecture of the native Nup82 complex at subnanometer precision. The complex consists of two compositionally identical multiprotein subunits that adopt different configurations. The Nup82 complex fits into the NPC through the outer ring Nup84 complex. Our map shows that this entire 14-MDa Nup82-Nup84 complex assembly positions the cytoplasmic mRNA export factor docking sites and messenger ribonucleoprotein (mRNP) remodeling machinery right over the NPC's central channel rather than on distal cytoplasmic filaments, as previously supposed. We suggest that this configuration efficiently captures and remodels exporting mRNP particles immediately upon reaching the cytoplasmic side of the NPC.

  11. Water vapor weathering of Taurus-Littrow orange soil - A pore-structure analysis

    NASA Technical Reports Server (NTRS)

    Cadenhead, D. A.; Mikhail, R. S.

    1975-01-01

    A pore-volume analysis was performed on water vapor adsorption data previously obtained on a fresh sample of Taurus-Littrow orange soil, and the analysis was repeated on the same sample after its exposure to moist air for a period of approximately six months. The results indicate that exposure of an outgassed sample to high relative pressures of water vapor can result in the formation of substantial micropore structure, the precise amount being dependent on the sample pretreatment, particularly the outgassing temperature. Micropore formation is explained in terms of water penetration into surface defects. In contrast, long-term exposure to moist air at low relative pressures appears to reverse the process with the elimination of micropores and enlargement of mesopores possibly through surface diffusion of metastable adsorbent material. The results are considered with reference to the storage of lunar samples.

  12. Structure-Assisted Functional Anchor Implantation in Robust Metal–Organic Frameworks with Ultralarge Pores

    SciTech Connect

    Park, Jihye; Feng, Dawei; Zhou, Hong-Cai

    2015-02-04

    A facile functionalization assisted by the structural attributes of PCN-333 has been studied while maintaining the integrity of the parent MOF including ultralarge pores, chemical robustness, and crystallinity. Herein we thoroughly analyzed ligand exchange phenomena in PCN-333 and demonstrate that the extent of exchange can be tailored by varying the exchange conditions as potential applications may require. Through this method a variety of functional groups are incorporated into PCN-333. To further show the capabilities of this system introduction of a BODIPY fluorophore as a secondary functionality was performed to the functionalized framework via a click reaction. We anticipate the PCN-333 with functional anchor can serve as a stable platform for further chemistry to be explored in future applications.

  13. Structure-Assisted Functional Anchor Implantation in Robust Metal-Organic Frameworks with Ultra large Pores

    SciTech Connect

    Park, J; Feng, DW; Zhou, HC

    2015-02-04

    A facile functionalization assisted by the structural attributes of PCN-333 has been studied while maintaining the integrity of the parent MOF including ultralarge pores, chemical robustness, and crystallinity. Herein we thoroughly analyzed ligand exchange phenomena in PCN-333 and demonstrate that the extent of exchange can be tailored by varying the exchange conditions as potential applications may require. Through this method a variety of functional groups are incorporated into PCN-333. To further show the capabilities of this system introduction of a BODIPY fluorophore as a secondary functionality was performed to the functionalized framework via a click reaction. We anticipate the PCN-333 with functional anchor can serve as a stable platform for further chemistry to be explored in future applications

  14. Functional insights from studies on the structure of the nuclear pore and coat protein complexes.

    PubMed

    Schwartz, Thomas

    2013-07-01

    The nuclear envelope (NE) is a specific extension of the endoplasmic reticulum (ER) that wraps around the nucleus and enables the spatial separation of gene transcription and protein translation, one of the signature features of eukaryotes. Rather than being completely closed, the double lipid bilayer of the NE is perforated at sites where the inner and outer nuclear membranes fuse, resulting in circular openings lined with sharply bent membranes. These openings are filled with nuclear pore complexes (NPCs), enormous protein assemblies that facilitate nuclear transport. The scaffold components of the NPC surprisingly share interesting similarities with elements of coat protein complexes, which have general implications for function and evolution of these membrane-coating complexes. Here I discuss, from a structural perspective, what these findings might teach us.

  15. Effect of polymers pore-filling on structural, optical and electrical properties of porous silicon

    NASA Astrophysics Data System (ADS)

    Kulathuraan, K.; Jeyakumar, P.; Ramadas, V.; Natarajan, B.

    2014-04-01

    We fabricate the heterojunction device by filling Porous Silicon (PS) with Polystyrene and Polyvinylchloride (PVC) in the present investigation. The rectifying characteristics of the Al/PS/c-Si/Al and Al/Polymers/PS/c-Si/Al were measured. Analyses of the structural properties using SEM and AFM have demonstrated that the PS layer filled with polymers have no significant changes in the structures except that the polymers were infiltrated in the pores. The refractive index values of the PS and Polymers/PS composites as a function of porosity were determined by Effective Medium Approximation (EMA) method. The Photoluminescence (PL) of the structures at room temperature showed that the emission intensity was very high as compared with that of the polymer films on PS layer. The PL peak in polymers/PS composites structures were not caused any blue shift of the PL peak energy. The band gap energy of PS device was determined from PL. This heterojunction device, especially due to charge storage in PS surface, which will be useful in sensor applications and diode in addition, it also possesses potential applications in the optoelectronic fields.

  16. 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

  17. Investigation of the pore geometrical structure of nanofibrous membranes using statistical modelling

    NASA Astrophysics Data System (ADS)

    Khanmohammadi Khoshui, Sedigheh; Hosseini Ravandi, Seyed Abdolkarim; Bagherzadeh, Roohollah; Saberi, Zahra; Karimi, Mohammad

    2016-10-01

    The pore size and its distribution are the two main geometrical properties of nanofibrous membranes in various applications such as filtration and tissue engineering. In the current paper, a modified approach (model) is suggested to predict pore size and its distribution in nanofibrous membranes. In the present work, inter-fibre pores are considered as polygons arising from the fibre contacts. For the first time, these polygons are assumed to be three-, four- and five-gons, and the hydraulic radius of the pores was obtained instead of the equal radius. The pore size of multilayer mats was provided with a different insight. The pore mean size and its distribution were obtained by statistical methods. In order to validate the model, polycaprolactone (PCL) nanofibrous mats were electrospun, and the mean pore size and its distribution were measured using porosimetry. It was found that the probability distribution function of the pore size in both single and multi nanofibrous layers was the Gamma function with two parameters. The effect of the fibre width and porosity raise was increasing of mean pore diameter of multilayer networks. A comparison between the modified model and previous models revealed that the modified approach was more realistic.

  18. Electrochemical and analytical characterization of three corrosion inhibitors of steel in simulated concrete pore solutions

    NASA Astrophysics Data System (ADS)

    Shi, Jin-Jie; Sun, Wei

    2012-01-01

    Corrosion inhibitors for steel, such as sodium phosphate (Na3PO4), sodium nitrite (NaNO2), and benzotriazole (BTA), in simulated concrete pore solutions (saturated Ca(OH)2) were investigated. Corrosion behaviors of steel in different solutions were studied by means of corrosion potential ( E corr), linear polarization resistance (LPR), electrochemical impedance spectroscopy (EIS), and potentiodynamic polarization (PDP). A field emission scanning electron microscope (FESEM) equipped with energy dispersive X-ray analysis (EDXA) was used for observing the microstructures and morphology of corrosion products of steel. The results indicate that, compared with the commonly used nitrite-based inhibitors, Na3PO4 is not a good inhibitor, while BTA may be a potentially effective inhibitor to prevent steel from corrosion in simulated concrete pore solutions.

  19. Optimization of pore structure and particle morphology of mesoporous silica for antibody adsorption for use in affinity chromatography

    NASA Astrophysics Data System (ADS)

    Hikosaka, Ryouichi; Nagata, Fukue; Tomita, Masahiro; Kato, Katsuya

    2016-10-01

    Antibodies have received significant attention for use as antibody drugs, because they bind the objective protein (antigen) via antigen-antibody reactions. Recently, many reports have appeared on various monoclonal antibodies that recognize a single antigen. In this study, monoclonal antibodies are used as adsorbates on mesoporous silica (MPS) for affinity chromatography. MPS has high surface area and large pore volume; moreover, pore diameter, pore structure, and particle morphology are relatively easy to tune by adjusting the conditions of synthesis. The pore structure (two-dimensional (2D) hexagonal and three-dimensional cubic) and particle morphology (spherical and polyhedral) of MPS are optimized for use in a monoclonal antibody/MPS composite. When anti-IgG (one of the monoclonal antibodies) adsorbs on the MPS material and IgG (antigen) binds to anti-IgG/MPS composites, MCM-41p with a 2D-hexagonal pore structure and polyhedral particle morphology has the highest IgG binding efficiency. In addition, the antibody/MPS composites remain stable in chaotropic and low-pH solutions and can be cycled at least five times without decreasing IgG elution. In purification and removal tests, the use of the antibody/MPS composites allows only the objective protein from protein mixtures to be bound and eluted.

  20. Molecular characterization of dissolved organic matter in pore water of continental shelf sediments

    NASA Astrophysics Data System (ADS)

    Schmidt, Frauke; Elvert, Marcus; Koch, Boris P.; Witt, Matthias; Hinrichs, Kai-Uwe

    2009-06-01

    Dissolved organic matter (DOM) in sediment pore water is a complex molecular mixture reflecting various sources and biogeochemical processes. In order to constrain those sources and processes, molecular variations of pore water DOM in surface sediments from the NW Iberian shelf were analyzed by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and compared to river and marine water column DOM. Weighted average molecular element ratios of oxygen to carbon ((O/C) wa) and hydrogen to carbon ((H/C) wa) provided general information about DOM sources. DOM in local rivers was more oxygenated ((O/C) wa 0.52) and contained less hydrogen ((H/C) wa 1.15) than marine pore water DOM (mean (O/C) wa 0.50, mean (H/C) wa 1.26). The relative abundance of specific compound groups, such as highly oxygenated aromatic compounds or nitrogen-bearing compounds with low H/C ratios, correspond to a high concentration of lignin phenols (160 μg/g sediment dry weight) and a high TOC/TN ratio (13.3) in the sedimentary organic matter and were therefore assigned to terrestrial sources. The lower degree of unsaturation and a higher relative abundance of nitrogen-bearing compounds in the pore water DOM reflected microbial activity within the sediment. One sampling site on the shelf with a high sediment accumulation, and a humic-rich river sample showed a wide range of sulfur compounds in the DOM, accompanied by a higher abundance of lipid biomarkers for sulfate-reducing bacteria, probably indicating early diagenetic sulfurization of organic matter.

  1. Water transport in the nano-pore of the calcium silicate phase: reactivity, structure and dynamics.

    PubMed

    Hou, Dongshuai; Li, Zongjin; Zhao, Tiejun; Zhang, Peng

    2015-01-14

    Reactive force field molecular dynamics was utilized to simulate the reactivity, structure and dynamics of water molecules confined in calcium-silicate-hydrate (C-S-H) nano-pores of 4.5 nm width. Due to the highly reactive C-S-H surface, hydrolytic reactions occur in the solid-liquid interfacial zone, and partially surface adsorbed water molecules transforming into the Si-OH and Ca-OH groups are strongly embedded in the C-S-H structure. Due to the electronic charge difference, the silicate and calcium hydroxyl groups have binomial distributions of the dipolar moment and water orientation. While Ca-OH contributes to the Ow-downward orientation, the ONB atoms in the silicate chains prefer to accept H-bonds from the surface water molecules. Furthermore, the defective silicate chains and solvated Caw atoms near the surface contribute to the glassy nature of the surface water molecules, with large packing density, pronounced orientation preference, and distorted organization. The stable H-bonds connected with the Ca-OH and Si-OH groups also restrict the mobility of the surface water molecules. The significant reduction of the diffusion coefficient matches well with the experimental results obtained by NMR, QENS and PCFR techniques. Upon increasing the distance from the channel, the structural and dynamic behavior of the water molecules varies and gradually translates into bulk water properties at distances of 10-15 Å from the liquid-solid interface.

  2. Structure-function mapping of a heptameric module in the nuclear pore complex.

    PubMed

    Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D; Diaz-Avalos, Ruben; Velazquez-Muriel, Javier; Franke, Josef D; Williams, Rosemary; Stokes, David L; Chait, Brian T; Sali, Andrej; Rout, Michael P

    2012-02-20

    The nuclear pore complex (NPC) is a multiprotein assembly that serves as the sole mediator of nucleocytoplasmic exchange in eukaryotic cells. In this paper, we use an integrative approach to determine the structure of an essential component of the yeast NPC, the ~600-kD heptameric Nup84 complex, to a precision of ~1.5 nm. The configuration of the subunit structures was determined by satisfaction of spatial restraints derived from a diverse set of negative-stain electron microscopy and protein domain-mapping data. Phenotypic data were mapped onto the complex, allowing us to identify regions that stabilize the NPC's interaction with the nuclear envelope membrane and connect the complex to the rest of the NPC. Our data allow us to suggest how the Nup84 complex is assembled into the NPC and propose a scenario for the evolution of the Nup84 complex through a series of gene duplication and loss events. This work demonstrates that integrative approaches based on low-resolution data of sufficient quality can generate functionally informative structures at intermediate resolution.

  3. Simulations of the Pore Structures for a M2GlyR Derived Channel Forming Peptide in Different Membrane Environments

    NASA Astrophysics Data System (ADS)

    Al-Rawi, A.; Herrera, A.; Tomich, J.; Rahman, T.

    2007-03-01

    As part of an effort to develop a peptide-based compound suitable for clinical use as a channel replacement therapeutic for treating channelopathies such as cystic fibrosis, we present a reductionist model that appears to grasp the characteristics of ion channeling peptides. In particular we present the observed changes in the functional characteristics of NK4-M2GlyR p22 (KKKKPARVGLGITTVLTMTTQS), a M2 GlyR derived channel forming peptide. Starting with a structure determined by multidimensional NMR (800 MHz) in SDS, a potential from CHARMM force-field was used to relax the structure of NK4-M2GlyR p22. Following the relaxation, numerous pore structures were generated for the symmetric five-helix assembly with geometries varying from cylindrical to conical. As it is difficult a priori to assign accurately the orientation of the hydrophilic portion of M2GlyR derived amphipath towards the inside of the pore, we tilted and rotated the helical structure by five different angles about the backbone axis before forming the pore. Energy minimization of the channel was performed in vacuum, in phosphotidylcholine (POPC) membrane, and 60% POPC 30% phosphotidylethanolamine (POPE) in order to determine the effect of the environment surrounding on the structure on its energy minimization. We will present the various pore assemblies, in the different membrane environments, used to predict the most probably membrane bound structure.

  4. Effects of mineral composition and pore structure in HC potential of reservoir rocks in the Western Foothill Belt, Taiwan

    NASA Astrophysics Data System (ADS)

    Lin, J. M.; Tsai, L. Y.

    2014-12-01

    The exploration of unconventional gas resource achieved a successful breakthrough in USA due to the innovation of hydraulic fracturing and horizontal drilling since 1995. The production of shale gas dramatically changed the energy structure and released the demand of fossil fuel in USA. Many studies about the unconventional oil-gas resource were performed worldwide especially in China, which provide very useful characterization for unconventional gas reservoirs. Since Taiwan has a strong energy demand and still highly relied on imported fossil fuel, the development of unconventional gas resource needs to be concerned. Therefore, the objective of this study is to evaluate the potential of unconventional oil-gas in Taiwan. In this study, we examine mineral composition and pore structure of Miocene oil-gas bearing strata from the Western Foothill Belt in Taiwan. Sandstone samples were collected from Cholan Fm, Yutengpin ss, Kuantaoshan ss, Shangfuchi ss, Tungkeng Fm, Guanyinshang ss and Peiliao Fm; whereas shale samples were collected from Chinshui sh and Talu sh, as well as outcropped coal sample from Nanchung Fm. The porosity, permeability, TOC, thermal maturity, and mineral composition of samples are examined after a series of geochemical experiments. Finally, after comparing the data with their gas sorption capacity, the reservoir with the strongest potential in unconventional gas resource can be identified.

  5. New x-ray parallel beam facility XPBF 2.0 for the characterization of silicon pore optics

    NASA Astrophysics Data System (ADS)

    Krumrey, Michael; Müller, Peter; Cibik, Levent; Collon, Max; Barrière, Nicolas; Vacanti, Giuseppe; Bavdaz, Marcos; Wille, Eric

    2016-07-01

    A new X-ray parallel beam facility (XPBF 2.0) has been installed in the laboratory of the Physikalisch-Technische Bundesanstalt at the synchrotron radiation facility BESSY II in Berlin to characterize silicon pore optics (SPOs) for the future X-ray observatory ATHENA. As the existing XPBF which is operated since 2005, the new beamline provides a pencil beam of very low divergence, a vacuum chamber with a hexapod system for accurate positioning of the SPO to be investigated, and a vertically movable CCD-based camera system to register the direct and the reflected beam. In contrast to the existing beamline, a multilayer-coated toroidal mirror is used for beam monochromatization at 1.6 keV and collimation, enabling the use of beam sizes between about 100 μm and at least 5 mm. Thus the quality of individual pores as well as the focusing properties of large groups of pores can be investigated. The new beamline also features increased travel ranges for the hexapod to cope with larger SPOs and a sample to detector distance of 12 m corresponding to the envisaged focal length of ATHENA.

  6. A direct and quantitative three-dimensional reconstruction of the internal structure of disordered mesoporous carbon with tailored pore size.

    PubMed

    Balach, Juan; Soldera, Flavio; Acevedo, Diego F; Mücklich, Frank; Barbero, César A

    2013-06-01

    A new technique that allows direct three-dimensional (3D) investigations of mesopores in carbon materials and quantitative characterization of their physical properties is reported. Focused ion beam nanotomography (FIB-nt) is performed by a serial sectioning procedure with a dual beam FIB-scanning electron microscopy instrument. Mesoporous carbons (MPCs) with tailored mesopore size are produced by carbonization of resorcinol-formaldehyde gels in the presence of a cationic surfactant as a pore stabilizer. A visual 3D morphology representation of disordered porous carbon is shown. Pore size distribution of MPCs is determined by the FIB-nt technique and nitrogen sorption isotherm methods to compare both results. The obtained MPCs exhibit pore sizes of 4.7, 7.2, and 18.3 nm, and a specific surface area of ca. 560 m(2)/g.

  7. Structure of the food-poisoning Clostridium perfringens enterotoxin reveals similarity to the aerolysin-like pore-forming toxins.

    PubMed

    Briggs, David C; Naylor, Claire E; Smedley, James G; Lukoyanova, Natalya; Robertson, Susan; Moss, David S; McClane, Bruce A; Basak, Ajit K

    2011-10-14

    Clostridium perfringens enterotoxin (CPE) is a major cause of food poisoning and antibiotic-associated diarrhea. Upon its release from C. perfringens spores, CPE binds to its receptor, claudin, at the tight junctions between the epithelial cells of the gut wall and subsequently forms pores in the cell membranes. A number of different complexes between CPE and claudin have been observed, and the process of pore formation has not been fully elucidated. We have determined the three-dimensional structure of the soluble form of CPE in two crystal forms by X-ray crystallography, to a resolution of 2.7 and 4.0 Å, respectively, and found that the N-terminal domain shows structural homology with the aerolysin-like β-pore-forming family of proteins. We show that CPE forms a trimer in both crystal forms and that this trimer is likely to be biologically relevant but is not the active pore form. We use these data to discuss models of pore formation.

  8. Facile synthesis of diverse graphene nanomeshes based on simultaneous regulation of pore size and surface structure

    PubMed Central

    Zhang, Jia; Song, Huaibing; Zeng, Dawen; Wang, Hao; Qin, Ziyu; Xu, Keng; Pang, Aimin; Xie, Changsheng

    2016-01-01

    Recently, graphene nanomesh (GNM) has attracted great attentions due to its unique porous structure, abundant active sites, finite band gap and possesses potential applications in the fields of electronics, gas sensor/storage, catalysis, etc. Therefore, diverse GNMs with different physical and chemical properties are required urgently to meet different applications. Herein we demonstrate a facile synthetic method based on the famous Fenton reaction to prepare GNM, by using economically fabricated graphene oxide (GO) as a starting material. By precisely controlling the reaction time, simultaneous regulation of pore size from 2.9 to 11.1 nm and surface structure can be realized. Ultimately, diverse GNMs with tunable band gap and work function can be obtained. Specially, the band gap decreases from 4.5–2.3 eV for GO, which is an insulator, to 3.9–1.24 eV for GNM-5 h, which approaches to a semiconductor. The dual nature of electrophilic addition and oxidizability of HO• is responsible for this controllable synthesis. This efficient, low-cost, inherently scalable synthetic method is suitable for provide diverse and optional GNMs, and may be generalized to a universal technique. PMID:27561350

  9. Facile synthesis of diverse graphene nanomeshes based on simultaneous regulation of pore size and surface structure

    NASA Astrophysics Data System (ADS)

    Zhang, Jia; Song, Huaibing; Zeng, Dawen; Wang, Hao; Qin, Ziyu; Xu, Keng; Pang, Aimin; Xie, Changsheng

    2016-08-01

    Recently, graphene nanomesh (GNM) has attracted great attentions due to its unique porous structure, abundant active sites, finite band gap and possesses potential applications in the fields of electronics, gas sensor/storage, catalysis, etc. Therefore, diverse GNMs with different physical and chemical properties are required urgently to meet different applications. Herein we demonstrate a facile synthetic method based on the famous Fenton reaction to prepare GNM, by using economically fabricated graphene oxide (GO) as a starting material. By precisely controlling the reaction time, simultaneous regulation of pore size from 2.9 to 11.1 nm and surface structure can be realized. Ultimately, diverse GNMs with tunable band gap and work function can be obtained. Specially, the band gap decreases from 4.5–2.3 eV for GO, which is an insulator, to 3.9–1.24 eV for GNM-5 h, which approaches to a semiconductor. The dual nature of electrophilic addition and oxidizability of HO• is responsible for this controllable synthesis. This efficient, low-cost, inherently scalable synthetic method is suitable for provide diverse and optional GNMs, and may be generalized to a universal technique.

  10. Structure and dynamics of the pore of inwardly rectifying K(ATP) channels.

    PubMed

    Loussouarn, G; Makhina, E N; Rose, T; Nichols, C G

    2000-01-14

    Inwardly rectifying K(+) currents are generated by a complex of four Kir (Kir1-6) subunits. Pore properties are conferred by the second transmembrane domain (M2) of each subunit. Using cadmium ions as a cysteine-interacting probe, we examined the accessibility of substituted cysteines in M2 of the Kir6.2 subunit of inwardly rectifying K(ATP) channels. The ability of Cd(2+) ions to inhibit channels was used as the estimate of accessibility. The distribution of Cd(2+) accessibility is consistent with an alpha-helical structure of M2. The apparent surface of reactivity is broad, and the most reactive residues correspond to the solvent-accessible residues in the bacterial KcsA channel crystal structure. In several mutants, single channel measurements indicated that inhibition occurred by a single transition from the open state to a zero-conductance state. Analysis of currents expressed from mixtures of control and L164C mutant subunits indicated that at least three cysteines are required for coordination of the Cd(2+) ion. Application of phosphatidylinositol 4,5-diphosphate to inside-out membrane patches stabilized the open state of all mutants and also reduced cadmium sensitivity. Moreover, the Cd(2+) sensitivity of several mutants was greatly reduced in the presence of inhibitory ATP concentrations. Taken together, these results are consistent with state-dependent accessibility of single Cd(2+) ions to coordination sites within a relatively narrow inner vestibule.

  11. Effects of tubificid bioturbation on pore structures in sediment and the migration of sediment particles.

    PubMed

    Li, Yaorui; Hua, Xiuyi; Zheng, Fang; Dong, Deming; Liang, Dapeng; Guo, Zhiyong

    2016-04-01

    In this study, the effects of tubificid bioturbation near the water-sediment interface on pore structures and the migration of sediment particles were evaluated using a series of simulations. In these experiments, the distribution and variation of the tubificid burrows and the macropores in the sediment were investigated by X-ray computed tomography (CT) and digital image collecting, without sampling or disturbing the sediment. The migration of the sediment particles was also determined using CT by adding BaSO4 microspheres to the sediment as a tracer. The effects of tubificid bioturbation on the distribution and migration of contaminants in the sediment were verified by adding Pb-containing sediment layers to the sediment. The results indicate that after the addition of the tubificids, both the burrows and the macropores in the sediments increased with time, and the rate of increase slowed gradually. With the increased worm density, the burrows and the pore structures also increased. The in-depth distribution of the burrows and macropores was determined by the settlement time of the worms: with the settlement time increasing from 3 to 19 days, the depth of the zone with the highest density of burrows and macropores increased from 0-30 to 30-50 mm and from 0-10 to 30-60 mm, respectively. The distribution of the burrows and macropores was closely related to the distribution of the tubificids. Thickening of the oxidized zones in the superficial sediments in the presence of tubificid bioturbation was also observed. The main action of tubificids on the sediment particles was the transport of particles from the inner sediment (especially in the range of 30-50 mm in depth) to the water-sediment interface. The migration of Pb in the contaminated sediment with tubificid bioturbation could be interpreted by the variation in the burrows and macropores and the migration of sediment particles. Both the formation and the variation in the burrows and macropores, as well as

  12. 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

  13. Isolation and characterization of OmpC porin mutants with altered pore properties

    SciTech Connect

    Misra, R.; Benson, S.A.

    1988-02-01

    The LamB protien is normally required for the uptake of maltodextrins. Starting with a LamB/sup -/ OmpF/sup -/ strain, we have isolated mutants that will grow on maltodextrins. The mutation conferring the Dex/sup +/ phenotype in the majority of these mutants has been mapped to the ompC locus. These mutants, unlike LamB/sup -/ OmpF/sup -/ strains, grew on maltotriose and maltotetraose, but not on maltopentaose, and showed a significantly higher rate of (/sup 14/C) maltose uptake than the parent strain did. In addition, these mutants showed increased sensitivity to certain ..beta..-lactam antibiotics and sodium dodecyl sulfate, but did not exhibit an increase in sensitivity to other antibiotics and detergents. The nucleotide sequence of these mutants has been determined. In all cases, residue 74 (arginine) of the mature OmpC protein was affected. The results suggest that this region of the OmpC protein is involved in the pore domain and that the alterations lead to an increased pore size.

  14. Vertical structure of pore pressure under surface gravity waves on a steep, megatidal, mixed sand-gravel-cobble beach

    NASA Astrophysics Data System (ADS)

    Guest, Tristan B.; Hay, Alex E.

    2017-01-01

    The vertical structure of surface gravity wave-induced pore pressure is investigated within the intertidal zone of a natural, steeply sloping, megatidal, mixed sand-gravel-cobble beach. Results from a coherent vertical array of buried pore pressure sensors are presented in terms of signal phase lag and attenuation as functions of oscillatory forcing frequency and burial depth. Comparison of the observations with the predictions of a theoretical poro-elastic bed response model indicates that the large observed phase lags and attenuation are attributable to interstitial trapped air. In addition to the dependence on entrapped air volume, the pore pressure phase and attenuation are shown to be sensitive to the hydraulic conductivity of the sediment, to the changing mean water depth during the tidal cycle, and to the redistribution/rearrangement of beach face material by energetic wave action during storm events. The latter result indicates that the effects on pore pressure of sediment column disturbance during instrument burial can persist for days to weeks, depending upon wave forcing conditions. Taken together, these results raise serious questions as to the practicality of using pore pressure measurements to estimate the kinematic properties of surface gravity waves on steep, mixed sand-gravel beaches.

  15. Multi-scale analysis in carbonates by X-ray microtomography: Characterization of the porosity and pore size distribution

    NASA Astrophysics Data System (ADS)

    Fernandes, Jaquiel S.; Nagata, Rodrigo; Moreira, Anderson C.; Fernandes, Celso P.; Appoloni, Carlos R.

    2013-05-01

    The porous systems of reservoir rocks present a complex geometry, involving aspects of shape of pores (morphology) and connectivity between the pores (topology). The macroscopic physical properties of these materials are strongly dependent of their microstructures. Based on these aspects, the present study has as main objective the characterization of the porous system geometry and computational determination of petrophysics properties of carbonate reservoir rocks through the X-ray microtomography methodology. Samples were microtomographed with the microtomographs Skyscan model 1172, installed at the PETROBRAS Research and Development Center (CENPES), Rio de Janeiro-RJ, Brazil and model 1173, installed at Sedimentary Geology Laboratory (LAGESD) in the Federal University of Rio de Janeiro (UFRJ). Two samples of carbonates were measured, Travertine and Dolomite, with spatial resolutions of 7 μm and 9.8 μm and 1.3 μm, 7 μm and 17 μm, respectively for the travertine and dolomite. With the data collected in the acquisitions, 900 transversal sections were reconstructed for each one of the referred resolutions. For the sample of dolomite, the average porosity found was 21.64%, 20.92% and 15.97% for resolutions of 1.3 μm, 7 μm and 17 μm, respectively. For the sample of travertine, the average porosity was 7.80 % and 7.52 % for resolutions of 7 μm and 9.8 μm, respectively. For the sample of dolomite, the pore size distribution showed that 50 % of the porous phase has pores with radius up to 37.6 μm, 84.6 μm and 84.4 μm, for the spatial resolutions of 1.3 μm, 7 μm and 17 μm, respectively. For the sample of travertine, 50 % of the pores have radius up to 148.1 μm and 158.1 μm, for the spatial resolutions of 7 μm and 9.8 μm.

  16. Supercapacitor electrode materials with hierarchically structured pores from carbonization of MWCNTs and ZIF-8 composites.

    PubMed

    Li, Xueqin; Hao, Changlong; Tang, Bochong; Wang, Yue; Liu, Mei; Wang, Yuanwei; Zhu, Yihua; Lu, Chenguang; Tang, Zhiyong

    2017-02-09

    Due to their high specific surface area and good electric conductivity, nitrogen-doped porous carbons (NPCs) and carbon nanotubes (CNTs) have attracted much attention for electrochemical energy storage applications. In the present work, we firstly prepared MWCNT/ZIF-8 composites by decoration of zeolitic imidazolate frameworks (ZIF-8) onto the surface of multi-walled CNTs (MWCNTs), then obtained MWCNT/NPCs by the direct carbonization of MWCNT/ZIF-8. By controlling the reaction conditions, MWCNT/ZIF-8 with three different particle sizes were synthesized. The effect of NPCs size on capacitance performance has been evaluated in detail. The MWCNT/NPC with large-sized NPC (MWCNT/NPC-L) displayed the highest specific capacitance of 293.4 F g(-1) at the scan rate of 5 mV s(-1) and only lost 4.2% of capacitance after 10 000 cyclic voltammetry cycles, which was attributed to the hierarchically structured pores, N-doping and high electrical conductivity. The studies of symmetric two-electrode supercapacitor cells also confirmed MWCNT/NPC-L as efficient electrode materials that have good electrochemical performance, especially for high-rate applications.

  17. An invasive podosome-like structure promotes fusion pore formation during myoblast fusion

    PubMed Central

    Sens, Kristin L.; Zhang, Shiliang; Jin, Peng; Duan, Rui; Zhang, Guofeng; Luo, Fengbao; Parachini, Lauren

    2010-01-01

    Recent studies in Drosophila have implicated actin cytoskeletal remodeling in myoblast fusion, but the cellular mechanisms underlying this process remain poorly understood. Here we show that actin polymerization occurs in an asymmetric and cell type–specific manner between a muscle founder cell and a fusion-competent myoblast (FCM). In the FCM, a dense F-actin–enriched focus forms at the site of fusion, whereas a thin sheath of F-actin is induced along the apposing founder cell membrane. The FCM-specific actin focus invades the apposing founder cell with multiple finger-like protrusions, leading to the formation of a single-channel macro fusion pore between the two muscle cells. Two actin nucleation–promoting factors of the Arp2/3 complex, WASP and Scar, are required for the formation of the F-actin foci, whereas WASP but not Scar promotes efficient foci invasion. Our studies uncover a novel invasive podosome-like structure (PLS) in a developing tissue and reveal a previously unrecognized function of PLSs in facilitating cell membrane juxtaposition and fusion. PMID:21098115

  18. Pore structure and limit pressure of gas slippage effect in tight sandstone.

    PubMed

    You, Lijun; Xue, Kunlin; Kang, Yili; Liao, Yi; Kong, Lie

    2013-01-01

    Gas slip effect is an important mechanism that the gas flow is different from liquid flow in porous media. It is generally considered that the lower the permeability in porous media is, the more severe slip effect of gas flow will be. We design and then carry out experiments with the increase of backpressure at the outlet of the core samples based on the definition of gas slip effect and in view of different levels of permeability of tight sandstone reservoir. This study inspects a limit pressure of the gas slip effect in tight sandstones and analyzes the characteristic parameter of capillary pressure curves. The experimental results indicate that gas slip effect can be eliminated when the backpressure reaches a limit pressure. When the backpressure exceeds the limit pressure, the measured gas permeability is a relatively stable value whose range is less than 3% for a given core sample. It is also found that the limit pressure increases with the decreasing in permeability and has close relation with pore structure of the core samples. The results have an important influence on correlation study on gas flow in porous medium, and are beneficial to reduce the workload of laboratory experiment.

  19. Copper Nanowire Based Aerogel with Tunable Pore Structure and Its Application as Flexible Pressure Sensor.

    PubMed

    Xu, Xiaojuan; Wang, Ranran; Nie, Pu; Cheng, Yin; Lu, Xiaoyu; Shi, Liangjing; Sun, Jing

    2017-04-11

    Aerogel is a kind of material with high porosity and low density. However, the research on metal-based aerogel with good conductivity is quite limited, which hinders its usage in electronic devices, such as flexible pressure sensors. In this work, we successfully fabricate copper nanowire (CuNW) based aerogel through a one-pot method, and the dynamics for the assembly of CuNWs into hydrogel is intensively investigated. The "bubble controlled assembly" mechanism is put forward for the first time, according to which tunable pore structures and densities (4.3 mg cm-3~7.5 mg cm-3) of the nanowire aerogel is achieved. Subsequently, ultralight flexible pressure sensors with tunable sensitivities (0.02 kPa-1 to 0.7 kPa-1) are fabricated from the Cu NWs aerogels, and the negative correlation behavior of the sensitivity to the density of the aerogel sensors is disclosed systematically. This work provides a versatile strategy for the fabrication of nanowire based aerogels, which greatly broadens their application potential.

  20. The effect of adding SiO2 on the pore structure and the color fastness to washing of PVA sponge

    NASA Astrophysics Data System (ADS)

    Chang, Y. I.; Lin, T. Y.; Cheng, W. Y.; Jang, L.

    2015-12-01

    The present study investigates the role of pore-forming SiO2 particles on the pore structure, and color fastness following washing of a porous PVA sponge. We found that the SiO2 micron particle consideration plays a decisive role on the pore-structural type and the color fastness. Moreover, the particles also influence the mechanical modulus and the water adsorption capacity.

  1. Pore geometry in woven fiber structures: 0{degree}/90{degree} plain-weave cloth layup preform

    SciTech Connect

    Lee, S.; Stock, S.R.; Butts, M.D.; Starr, T.L.; Breunig, T.M.; Kinney, J.H.

    1998-05-01

    Composite preform fiber architectures range from the very simple to the complex, and the extremes are typified by parallel continuous fibers and complicated three-dimensional woven structures. Subsequent processing of these preforms to produce dense composites may depend critically on the geometry of the interfiber porosity. The goal of this study is to fully characterize the structure of a 0{degree}/90{degree} cloth layup preform using x-ray tomographic microscopy (XTM). This characterization includes the measurement of intercloth channel widths and their variability, the transverse distribution of through-cloth holes, and the distribution of preform porosity. The structure of the intercloth porosity depends critically on the magnitude and direction of the offset between adjacent cloth layers. The structures observed include two-dimensional networks of open pipes linking adjacent holes, arrays of parallel one-dimensional pipes linking holes, and relatively closed channels exhibiting little structure, and these different structures would appear to offer very different resistances to gas flow through the preform. These measurements, and future measurements for different fiber architectures, will yield improved understanding of the role of preform structure on processing. {copyright} {ital 1998 Materials Research Society.}

  2. Silicon-on-glass pore network micromodels with oxygen-sensing fluorophore films for chemical imaging and defined spatial structure.

    PubMed

    Grate, Jay W; Kelly, Ryan T; Suter, Jonathan; Anheier, Norm C

    2012-11-21

    Pore network microfluidic models were fabricated by a silicon-on-glass technique that provides the precision advantage of dry etched silicon while creating a structure that is transparent across all microfluidic channels and pores, and can be imaged from either side. A silicon layer is bonded to an underlying borosilicate glass substrate and thinned to the desired height of the microfluidic channels and pores. The silicon is then patterned and through-etched by deep reactive ion etching (DRIE), with the underlying glass serving as an etch stop. After bonding on a transparent glass cover plate, one obtains a micromodel in oxygen impermeable materials with water-wet surfaces where the microfluidic channels are transparent and structural elements such as the pillars creating the pore network are opaque. The advantageous features of this approach in a chemical imaging application are demonstrated by incorporating a Pt porphyrin fluorophore in a PDMS film serving as the oxygen-sensing layer and a bonding surface, or in a polystyrene film coated with a PDMS layer for bonding. The sensing of a dissolved oxygen gradient was demonstrated using fluorescence lifetime imaging, and it is shown that different matrix polymers lead to optimal use in different ranges of oxygen concentration. Imaging with the opaque pillars in between the observation direction and the continuous fluorophore film yields images that retain defined spatial structure in the sensor image.

  3. The Pivotal Role of Alumina Pore Structure in HF Capture and Fluoride Return in Aluminum Reduction

    NASA Astrophysics Data System (ADS)

    McIntosh, Grant J.; Agbenyegah, Gordon E. K.; Hyland, Margaret M.; Metson, James B.

    2016-09-01

    Fluoride emissions during primary aluminum production are mitigated by dry scrubbing on alumina which, as the metal feedstock, also returns fluoride to the pots. This ensures stable pot operation and maintains process efficiency but requires careful optimization of alumina for both fluoride capture and solubility. The Brunauer-Emmett-Teller (BET) surface area of 70-80 m2 g-1 is currently accepted. However, this does not account for pore accessibility. We demonstrate using industry-sourced data that pores <3.5 nm are not correlated with fluoride return. Reconstructing alumina pore size distributions (PSDs) following hydrogen fluoride (HF) adsorption shows surface area is not lost by pore diameter shrinkage, but by blocking the internal porosity. However, this alone cannot explain this 3.5 nm threshold. We show this is a consequence of surface diffusion-based inhibition with surface chemistry probably playing an integral role. We advocate new surface area estimates for alumina which account for pore accessibility by explicitly ignoring <3.5 nm pores.

  4. Relations between structural parameters and adsorption characterization of templated nanoporous materials with cubic symmetry

    SciTech Connect

    Ravikovitch, P.I.; Neimark, A.V.

    2000-03-21

    A systematic approach is proposed to structural characterization of templated nanoporous materials with cubic symmetry by gas adsorption. The authors hypothesize that regular structures of these materials can be described in terms of triply periodic minimal surfaces (TPMS), similarly to bicontinuous mesophases observed in oil-water, lipid, block copolymer, and other amphiphilic systems. The authors relate topological characteristics of TPMS to the pore structure parameters evaluated from adsorption measurements, such as the specific surface area, pore volume, mean pore size, and also pore wall thickness. The relations obtained can be used for discrimination of possible TPMS morphologies. The method developed is used for characterization of newly synthesized MCM-48 mesoporous materials by low-temperature nitrogen adsorption. They show that adsorption data fully support the minimal gyroid model of MCM-48 structure (Ia3d space group) established earlier by the X-ray diffraction (XRD) and transmission electron microscopy studies. The mean pore size of MCM-48 can be accurately described by the hydraulic diameter calculated from the capillary condensation region of nitrogen adsorption isotherms by the nonlocal density functional theory method. Moreover, the adsorption method allows one to estimate the pore wall thickness, which cannot be done by XRD. For a series of high-quality MCM-48 materials reported recently in the literature, the calculated mean wall thickness varied from 0.8 to 1.2 nm. The adsorption method developed is recommended as a complement to X-ray diffraction and electron microscopy techniques for characterization of nanoporous materials.

  5. Silicon-on-glass pore network micromodels with oxygen-sensing fluorophore films for chemical imaging and defined spatial structure

    SciTech Connect

    Grate, Jay W.; Kelly, Ryan T.; Suter, Jonathan D.; Anheier, Norman C.

    2012-11-21

    Pore network microfluidic models were fabricated by a silicon-on-glass technique that provides the precision advantage of dry etched silicon while creating a structure that is transparent across all microfluidic channels and pores, and can be imaged from either side. A silicon layer is bonded to an underlying borosilicate glass substrate and thinned to the desired height of the microfluidic channels and pores. The silicon is then patterned and through-etched by deep reactive ion etching (DRIE), with the underlying glass serving as an etch stop. After bonding on a transparent glass cover plate, one obtains a micromodel in oxygen impermeable materials with water wet surfaces where the microfluidic channels are transparent and structural elements such as the pillars creating the pore network are opaque. The micromodel can be imaged from either side. The advantageous features of this approach in a chemical imaging application are demonstrated by incorporating a Pt porphyrin fluorophore in a PDMS film serving as the oxygen sensing layer and a bonding surface, or in a polystyrene film coated with a PDMS layer for bonding. The sensing of a dissolved oxygen gradient was demonstrated using fluorescence lifetime imaging, and it is shown that different matrix polymers lead to optimal use in different ranges dissolved oxygen concentration. Imaging with the opaque pillars in between the observation direction and the continuous fluorophore film yields images that retain spatial information in the sensor image.

  6. Structural model of FeoB, the iron transporter from Pseudomonas aeruginosa, predicts a cysteine lined, GTP-gated pore

    PubMed Central

    Seyedmohammad, Saeed; Fuentealba, Natalia Alveal; Marriott, Robert A.J.; Goetze, Tom A.; Edwardson, J. Michael; Barrera, Nelson P.; Venter, Henrietta

    2016-01-01

    Iron is essential for the survival and virulence of pathogenic bacteria. The FeoB transporter allows the bacterial cell to acquire ferrous iron from its environment, making it an excellent drug target in intractable pathogens. The protein consists of an N-terminal GTP-binding domain and a C-terminal membrane domain. Despite the availability of X-ray crystal structures of the N-terminal domain, many aspects of the structure and function of FeoB remain unclear, such as the structure of the membrane domain, the oligomeric state of the protein, the molecular mechanism of iron transport, and how this is coupled to GTP hydrolysis at the N-terminal domain. In the present study, we describe the first homology model of FeoB. Due to the lack of sequence homology between FeoB and other transporters, the structures of four different proteins were used as templates to generate the homology model of full-length FeoB, which predicts a trimeric structure. We confirmed this trimeric structure by both blue-native-PAGE (BN-PAGE) and AFM. According to our model, the membrane domain of the trimeric protein forms a central pore lined by highly conserved cysteine residues. This pore aligns with a central pore in the N-terminal GTPase domain (G-domain) lined by aspartate residues. Biochemical analysis of FeoB from Pseudomonas aeruginosa further reveals a putative iron sensor domain that could connect GTP binding/hydrolysis to the opening of the pore. These results indicate that FeoB might not act as a transporter, but rather as a GTP-gated channel. PMID:26934982

  7. Biophysical characterization of Vpu from HIV-1 suggests a channel-pore dualism.

    PubMed

    Mehnert, T; Routh, A; Judge, P J; Lam, Y H; Fischer, D; Watts, A; Fischer, W B

    2008-03-01

    Vpu from HIV-1 is an 81 amino acid type I integral membrane protein which consists of a cytoplasmic and a transmembrane (TM) domain. The TM domain is known to alter membrane permeability for ions and substrates when inserted into artificial membranes. Peptides corresponding to the TM domain of Vpu (Vpu(1-32)) and mutant peptides (Vpu(1-32)-W23L, Vpu(1-32)-R31V, Vpu(1-32)-S24L) have been synthesized and reconstituted into artificial lipid bilayers. All peptides show channel activity with a main conductance level of around 20 pS. Vpu(1-32)-W23L has a considerable flickering pattern in the recordings and longer open times than Vpu(1-32). Whilst recordings for Vpu(1-32)-R31V are almost indistinguishable from those of the WT peptide, recordings for Vpu(1-32)-S24L do not exhibit any noticeable channel activity. Recordings of WT peptide and Vpu(1-32)-W23L indicate Michaelis-Menten behavior when the salt concentration is increased. Both peptide channels follow the Eisenman series I, indicative for a weak ion channel with almost pore like characteristics.

  8. Electrochemical synthesis and optical characterization of copper selenide nanowire arrays within the alumina pores

    NASA Astrophysics Data System (ADS)

    Jagminas, A.; Juškėnas, R.; Gailiūtė, I.; Statkutė, G.; Tomašiūnas, R.

    2006-09-01

    By choosing an appropriate aqueous solution containing CuSO 4, H 2SeO 3, MgSO 4, and H 2SO 4 the suitable composition for two- or one-phase copper selenide deposition within the alumina pores under alternating current (AC) electrolysis conditions was created. X-ray diffraction spectra recorded within 15-55° 2 Θ range revealed fabrication of Cu 3Se 2+Cu 2-xSe or almost pure Cu 2-xSe crystalline material. The compositional and morphological studies using XRD, EDX, SEM, and TEM techniques show fabrication of nearly pure Cu 2-xSe with some deficiency of copper, say, Cu 1.75Se, nanowires in length up to several microns when the selenious acid to copper-ion ratio is close to 1:2 and pH of the bath is <1.25. The fundamental absorption spectrum for this nanostructured material was shown to be formed by allowed direct and indirect interband transitions with the evaluated energy band gaps 2.3 and 1.1 eV, respectively.

  9. Characterizing two-phase flow relative permeabilities in chemicalflooding using a pore-scale network model

    SciTech Connect

    Liu, Qingjie; Shen, Pingping; Wu, Yu-Shu

    2004-03-15

    A dynamic pore-scale network model is presented for investigating the effects of interfacial tension and oil-water viscosity on relative permeability during chemical flooding. This model takes into account both viscous and capillary forces in analyzing the impact of chemical properties on flow behavior or displacement configuration, as opposed to the conventional or invasion percolation algorithm which incorporates capillary pressure only. The study results indicate that both water and oil relative-permeability curves are dependent strongly on interfacial tension as well as an oil-water viscosity ratio. In particular, water and oil relative-permeability curves are both found to shift upward as interfacial tension is reduced, and they both tend to become linear versus saturation once interfacial tension is at low values. In addition, the oil-water viscosity ratio appears to have only a small effect under conditions of high interfacial tension. When the interfacial tension is low, however, water relative permeability decreases more rapidly (with the increase in the aqueous-phase viscosity) than oil relative permeability. The breakthrough saturation of the aqueous phase during chemical flooding tends to decrease with the reduction of interfacial tension and may also be affected by the oil-water viscosity ratio.

  10. Relationship between chemical structure of soil organic matter and intra-aggregate pore structure: evidence from X-ray computed micro-tomography

    NASA Astrophysics Data System (ADS)

    Kravchenko, Alexandra; Grandy, Stuart A.

    2014-05-01

    Understanding chemical structure of soil organic matter (SOM) and factors that affect it are vital for gaining understanding of mechanisms of C sequestration by soil. Physical protection of C by adsorption to mineral particles and physical disconnection between C sources and microbial decomposers is now regarded as the key component of soil C sequestration. Both of the processes are greatly influenced by micro-scale structure and distribution of soil pores. However, because SOM chemical structure is typically studied in disturbed (ground and sieved) soil samples the experimental evidence of the relationships between soil pore structure and chemical structure of SOM are still scarce. Our study takes advantage of the X-ray computed micro-tomography (µ-CT) tools that enable non-destructive analysis of pore structure in intact soil samples. The objective of this study is to examine the relationship between SOM chemical structure and pore-characteristics in intact soil macro-aggregates from two contrasting long-term land uses. The two studied land use treatments are a conventionally tilled corn-soybean-wheat rotation treatment and a native succession vegetation treatment removed from agricultural use >20 years ago. The study is located in southwest Michigan, USA, on sandy-loam Typic Hapludalfs. For this study we used soil macro-aggregates 4-6 mm in size collected at 0-15 cm depth. The aggregate size was selected so as both to enable high resolution of µ-CT and to provide sufficient amount of soil for C measurements. X-ray µ-CT scanning was conducted at APS Argonne at a scanning resolution of 14 µm. Two scanned aggregates (1 per treatment) were used in this preliminary study. Each aggregate was cut into 7 "geo-referenced" sections. Analyses of pore characteristics in each section were conducted using 3DMA and ImageJ image analysis tools. SOM chemistry was analyzed using pyrolysis/gas chromatography-mass spectroscopy. Results demonstrated that the relationships

  11. Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145

    SciTech Connect

    Sampathkumar, Parthasarathy; Ozyurt, Sinem A.; Do, Johnny; Bain, Kevin T.; Dickey, Mark; Rodgers, Logan A.; Gheyi, Tarun; Sali, Andrej; Kim, Seung Joong; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D.; Martel, Anne; Tsuruta, Hiro; Atwell, Shane; Thompson, Devon A.; Emtage, J. Spencer; Wasserman, Stephen R.; Rout, Michael P.; Sauder, J. Michael; Burley, Stephen K.

    2012-04-30

    Nuclear pore complexes (NPCs) are large, octagonally symmetric dynamic macromolecular assemblies responsible for exchange of proteins and RNAs between the nucleus and cytoplasm. NPCs are made up of at least 456 polypeptides from {approx}30 distinct nucleoporins. Several of these components, sharing similar structural motifs, form stable subcomplexes that form a coaxial structure containing two outer rings (the nuclear and cytoplasmic rings), two inner rings, and a membrane ring. The yeast (Saccharomyces cerevisiae) Nup145 and its human counterpart are unique among the nucleoporins, in that they undergo autoproteolysis to generate functionally distinct proteins. The human counterpart of Nup145 is expressed as two alternatively spliced mRNA transcripts. The larger 190 kDa precursor undergoes post-translational autoproteolysis at the Phe863-Ser864 peptide bond yielding the 92 kDa Nup98 and the 96 kDa Nup96. The smaller 98 kDa precursor is also autoproteolysed at an analogous site giving 92 kDa Nup98-N and a 6 kDa C-terminal fragment, which may form a noncovalent complex. The yeast Nup145 precursor [Fig. 1(A)] contains twelve repeats of a 'GLFG' peptide motif (FG repeats) at its N-terminus, an internal autoproteolytic domain (a region of high conservation with the homologous yeast nucleoporins Nup110 and Nup116, neither of which undergo autoproteolysis), followed by the C-terminal domain. Various forms of the FG repeats are present in nearly half of all nucleoporins; they form intrinsically disordered regions implicated in gating mechanisms that control passage of macromolecules through NPCs. Nup145 undergoes autoproteolysis at the Phe605-Ser606 peptide bond to generate two functionally distinct proteins, Nup145N and Nup145C. Subsequently, Nup145C associates with six other proteins to form the heptameric Y-complex, a component of the outer rings of the NPC. Nup145N, on the other hand, can shuttle between the NPC and the nuclear interior. It has been suggested that Nup

  12. The Structure and Organization within the Membrane of the Helices Composing the Pore-Forming Domain of Bacillus thuringiensis δ -Endotoxin are Consistent with an ``Umbrella-Like'' Structure of the Pore

    NASA Astrophysics Data System (ADS)

    Gazit, Ehud; La Rocca, Paolo; Sansom, Mark S. P.; Shai, Yechiel

    1998-10-01

    The aim of this study was to elucidate the mechanism of membrane insertion and the structural organization of pores formed by Bacillus thuringiensis δ -endotoxin. We determined the relative affinities for membranes of peptides corresponding to the seven helices that compose the toxin pore-forming domain, their modes of membrane interaction, their structures within membranes, and their orientations relative to the membrane normal. In addition, we used resonance energy transfer measurements of all possible combinatorial pairs of membrane-bound helices to map the network of interactions between helices in their membrane-bound state. The interaction of the helices with the bilayer membrane was also probed by a Monte Carlo simulation protocol to determine lowest-energy orientations. Our results are consistent with a situation in which helices α 4 and α 5 insert into the membrane as a helical hairpin in an antiparallel manner, while the other helices lie on the membrane surface like the ribs of an umbrella (the ``umbrella model''). Our results also support the suggestion that α 7 may serve as a binding sensor to initiate the structural rearrangement of the pore-forming domain.

  13. NMR cryoporometry characterisation studies of the relation between drug release profile and pore structural evolution of polymeric nanoparticles

    PubMed Central

    Gopinathan, Navin; Yang, Bin; Lowe, John P.; Edler, Karen J.; Rigby, Sean P.

    2014-01-01

    PLGA/PLA polymeric nanoparticles could potentially enhance the effectiveness of convective delivery of drugs, such as carboplatin, to the brain, by enabling a more sustained dosage over a longer time than otherwise possible. However, the link between the controlled release nanoparticle synthesis route, and the subsequent drug release profile obtained, is not well-understood, which hinders design of synthesis routes and availability of suitable nanoparticles. In particular, despite pore structure evolution often forming a key aspect of past theories of the physical mechanism by which a particular drug release profile is obtained, these theories have not been independently tested and validated against pore structural information. Such validation is required for intelligent synthesis design, and NMR cryoporometry can supply the requisite information. Unlike conventional pore characterisation techniques, NMR cryoporometry permits the investigation of porous particles in the wet state. NMR cryoporometry has thus enabled the detailed study of the evolving, nanoscale structure of nanoparticles during drug release, and thus related pore structure to drug release profile in a way not done previously for nanoparticles. Nanoparticles with different types of carboplatin drug release profiles were compared, including burst release, and various forms of delayed release. ESEM and TEM images of these nanoparticles also provided supporting data showing the rapid initial evolution of some nanoparticles. Different stages, within a complex, varying drug release profile, were found to be associated with particular types of changes in the nanostructure which could be distinguished by NMR. For a core-coat nanoparticle formulation, the development of smaller nanopores, following an extended induction period with no structural change, was associated with the onset of substantial drug release. This information could be used to independently validate the rationale for a particular synthesis

  14. Crucial Role of Perfringolysin O D1 Domain in Orchestrating Structural Transitions Leading to Membrane-perforating Pores

    PubMed Central

    Kacprzyk-Stokowiec, Aleksandra; Kulma, Magdalena; Traczyk, Gabriela; Kwiatkowska, Katarzyna; Sobota, Andrzej; Dadlez, Michał

    2014-01-01

    Perfringolysin O (PFO) is a toxic protein that binds to cholesterol-containing membranes, oligomerizes, and forms a β-barrel transmembrane pore, leading to cell lysis. Previous studies have uncovered the sequence of events in this multistage structural transition to a considerable detail, but the underlying molecular mechanisms are not yet fully understood. By measuring hydrogen-deuterium exchange patterns of peptide bond amide protons monitored by mass spectrometry (MS), we have mapped structural changes in PFO and its variant bearing a point mutation during incorporation to the lipid environment. We have defined all regions that undergo structural changes caused by the interaction with the lipid environment both in wild-type PFO, thus providing new experimental constraints for molecular modeling of the pore formation process, and in a point mutant, W165T, for which the pore formation process is known to be inefficient. We have demonstrated that point mutation W165T causes destabilization of protein solution structure, strongest for domain D1, which interrupts the pathway of structural transitions in other domains necessary for proper oligomerization in the membrane. In PFO, the strongest changes accompanying binding to the membrane focus in D1; the C-terminal part of D4; and strands β1, β4, and β5 of D3. These changes were much weaker for PFOW165Tlipo where substantial stabilization was observed only in D4 domain. In this study, the application of hydrogen-deuterium exchange analysis monitored by MS provided new insight into conformational changes of PFO associated with the membrane binding, oligomerization, and lytic pore formation. PMID:25164812

  15. Atomic constraints between the voltage sensor and the pore domain in a voltage-gated K+ channel of known structure.

    PubMed

    Lewis, Anthony; Jogini, Vishwanath; Blachowicz, Lydia; Lainé, Muriel; Roux, Benoît

    2008-06-01

    In voltage-gated K(+) channels (Kv), membrane depolarization promotes a structural reorganization of each of the four voltage sensor domains surrounding the conducting pore, inducing its opening. Although the crystal structure of Kv1.2 provided the first atomic resolution view of a eukaryotic Kv channel, several components of the voltage sensors remain poorly resolved. In particular, the position and orientation of the charged arginine side chains in the S4 transmembrane segments remain controversial. Here we investigate the proximity of S4 and the pore domain in functional Kv1.2 channels in a native membrane environment using electrophysiological analysis of intersubunit histidine metallic bridges formed between the first arginine of S4 (R294) and residues A351 or D352 of the pore domain. We show that histidine pairs are able to bind Zn(2+) or Cd(2+) with high affinity, demonstrating their close physical proximity. The results of molecular dynamics simulations, consistent with electrophysiological data, indicate that the position of the S4 helix in the functional open-activated state could be shifted by approximately 7-8 A and rotated counterclockwise by 37 degrees along its main axis relative to its position observed in the Kv1.2 x-ray structure. A structural model is provided for this conformation. The results further highlight the dynamic and flexible nature of the voltage sensor.

  16. Characterization of nuclear pore complex components in fission yeast Schizosaccharomyces pombe.

    PubMed

    Asakawa, Haruhiko; Yang, Hui-Ju; Yamamoto, Takaharu G; Ohtsuki, Chizuru; Chikashige, Yuji; Sakata-Sogawa, Kumiko; Tokunaga, Makio; Iwamoto, Masaaki; Hiraoka, Yasushi; Haraguchi, Tokuko

    2014-01-01

    The nuclear pore complex (NPC) is an enormous proteinaceous complex composed of multiple copies of about 30 different proteins called nucleoporins. In this study, we analyzed the composition of the NPC in the model organism Schizosaccharomyces pombe using strains in which individual nucleoporins were tagged with GFP. We identified 31 proteins as nucleoporins by their localization to the nuclear periphery. Gene disruption analysis in previous studies coupled with gene disruption analysis in the present study indicates that 15 of these nucleoporins are essential for vegetative cell growth and the other 16 nucleoporins are non-essential. Among the 16 non-essential nucleoporins, 11 are required for normal progression through meiosis and their disruption caused abnormal spore formation or poor spore viability. Based on fluorescence measurements of GFP-fused nucleoporins, we estimated the composition of the NPC in S. pombe and found that the organization of the S. pombe NPC is largely similar to that of other organisms; a single NPC was estimated as being 45.8-47.8 MDa in size. We also used fluorescence measurements of single NPCs and quantitative western blotting to analyze the composition of the Nup107-Nup160 subcomplex, which plays an indispensable role in NPC organization and function. Our analysis revealed low amounts of Nup107 and Nup131 and high amounts of Nup132 in the Nup107-Nup160 subcomplex, suggesting that the composition of this complex in S. pombe may differ from that in S. cerevisiae and humans. Comparative analysis of NPCs in various organisms will lead to a comprehensive understanding of the functional architecture of the NPC.

  17. Characterization of the respiration-induced yeast mitochondrial permeability transition pore.

    PubMed

    Bradshaw, Patrick C; Pfeiffer, Douglas R

    2013-12-01

    When isolated mitochondria from the yeast Saccharomyces cerevisiae oxidize respiratory substrates in the absence of phosphate and ADP, the yeast mitochondrial unselective channel, also called the yeast permeability transition pore (yPTP), opens in the inner membrane, dissipating the electrochemical gradient. ATP also induces yPTP opening. yPTP opening allows mannitol transport into isolated mitochondria of laboratory yeast strains, but mannitol is not readily permeable through the yPTP in an industrial yeast strain, Yeast Foam. The presence of oligomycin, an inhibitor of ATP synthase, allowed for respiration-induced mannitol permeability in mitochondria from this strain. Potassium (K+) had varied effects on the respiration-induced yPTP, depending on the concentration of the respiratory substrate added. At low respiratory substrate concentrations K+ inhibited respiration-induced yPTP opening, while at high substrate concentrations this effect diminished. However, at the high respiratory substrate concentrations, the presence of K+ partially prevented phosphate inhibition of yPTP opening. Phosphate was found to inhibit respiration-induced yPTP opening by binding a site on the matrix space side of the inner membrane in addition to its known inhibitory effect of donating protons to the matrix space to prevent the pH change necessary for yPTP opening. The respiration-induced yPTP was also inhibited by NAD, Mg2+, NH4 + or the oxyanion vanadate polymerized to decavanadate. The results demonstrate similar effectors of the respiration-induced yPTP as those previously described for the ATP-induced yPTP and reconcile previous strain-dependent differences in yPTP solute selectivity.

  18. Mathematical model relating uniaxial compressive behavior of manufactured sand mortar to MIP-derived pore structure parameters.

    PubMed

    Tian, Zhenghong; Bu, Jingwu

    2014-01-01

    The uniaxial compression response of manufactured sand mortars proportioned using different water-cement ratio and sand-cement ratio is examined. Pore structure parameters such as porosity, threshold diameter, mean diameter, and total amounts of macropores, as well as shape and size of micropores are quantified by using mercury intrusion porosimetry (MIP) technique. Test results indicate that strains at peak stress and compressive strength decreased with the increasing sand-cement ratio due to insufficient binders to wrap up entire sand. A compression stress-strain model of normal concrete extending to predict the stress-strain relationships of manufactured sand mortar is verified and agreed well with experimental data. Furthermore, the stress-strain model constant is found to be influenced by threshold diameter, mean diameter, shape, and size of micropores. A mathematical model relating stress-strain model constants to the relevant pore structure parameters of manufactured sand mortar is developed.

  19. Mathematical Model Relating Uniaxial Compressive Behavior of Manufactured Sand Mortar to MIP-Derived Pore Structure Parameters

    PubMed Central

    Tian, Zhenghong; Bu, Jingwu

    2014-01-01

    The uniaxial compression response of manufactured sand mortars proportioned using different water-cement ratio and sand-cement ratio is examined. Pore structure parameters such as porosity, threshold diameter, mean diameter, and total amounts of macropores, as well as shape and size of micropores are quantified by using mercury intrusion porosimetry (MIP) technique. Test results indicate that strains at peak stress and compressive strength decreased with the increasing sand-cement ratio due to insufficient binders to wrap up entire sand. A compression stress-strain model of normal concrete extending to predict the stress-strain relationships of manufactured sand mortar is verified and agreed well with experimental data. Furthermore, the stress-strain model constant is found to be influenced by threshold diameter, mean diameter, shape, and size of micropores. A mathematical model relating stress-strain model constants to the relevant pore structure parameters of manufactured sand mortar is developed. PMID:25133257

  20. Pore structure and reactivity changes in hot coal gas desulfurization sorbents. Final report, September 1987--January 1991

    SciTech Connect

    Sotirchos, S.V.

    1991-05-01

    The primary objective of the project was the investigation of the pore structure and reactivity changes occurring in metal/metal oxide sorbents used for desulfurization of hot coal gas during sulfidation and regeneration, with particular emphasis placed on the effects of these changes on the sorptive capacity and efficiency of the sorbents. Commercially available zinc oxide sorbents were used as model solids in our experimental investigation of the sulfidation and regeneration processes.

  1. Optimization and Characterization of Self-assembled Triblock Polymer Membranes with Chemically-Tunable Pore Walls for Nanofiltration Applications

    NASA Astrophysics Data System (ADS)

    Sargent, Jessica; Mulvenna, Ryan; Prato, Rafael; Weidman, Jacob; Phillip, William; Boudouris, Bryan

    2015-03-01

    The field of block polymer-based membranes for separation applications has grown considerably in the past several years. However, decreasing the domain sizes of these membranes to below 5 nm has proven to be a challenge in many instances. Here, we demonstrate that a triblock polymer, polyisoprene- b-polystyrene- b-poly(tert-butyl methacrylate) (PI-PS-PtBMA), can be utilized to form nanoporous membranes capable of high flux and high selectivity based on both size and chemical composition. By controlling the synthesis, solution self-assembly, and non-solvent induced phase separation of these polymers, a scalable fabrication process can produce thin-film membranes that feature monodisperse pores approaching 1 nm in diameter, tunable pore-wall chemistry, good mechanical stability, and chlorine degradation resistance. The PtBMA functionality can further be converted to a number of side chain functionalities through simple coupling chemistry to produce membranes with specific chemical and structural characteristics tailored to meet the needs of various applications. In particular, these membranes provide a promising, inexpensive platform for chlorine degradation and fouling-resistant membranes for water purification that can be produced on an industrial scale.

  2. Sandwich-like heat-resistance composite separators with tunable pore structure for high power high safety lithium ion batteries

    NASA Astrophysics Data System (ADS)

    Shi, Junli; Shen, Tao; Hu, Huasheng; Xia, Yonggao; Liu, Zhaoping

    2014-12-01

    We demonstrate a new kind of composite separators. A unique feature of the separators is the three-tier structure, i.e. the crosslinked polyethylene glycol (PEG) skin layer being formed on both sides of the nonwoven separators by in-situ polymerization and the large pores in the interior of the nonwoven separators being remained. The surface pore structure and the thickness of the skin layer could be adjusted by controlling the concentration of the coating solution. The skin layer is proved to be able to provide internal short circuit protection, to contribute a more stable interfacial resistance and to alleviate liquid electrolyte leakage effectively, yielding an excellent cyclability. The remained large pores in the interior of the composite separators could provide an access for the fast transportation of lithium ions, giving rise to a very high ion conductivity. The polyimide (PI) nonwoven is employed to ensure enhanced thermal stability of the composite separators. More notably, the composite separators fabricated from the coating solution with a composition ratio of 20 wt% provide superior cell performances owing to the well-tailored microporous structure, comparing with the commercialized polypropylene (PP) separator, which show great promise for the application in the high power lithium ion batteries.

  3. Reading the primary structure of a protein with 0.07 nm3 resolution using a subnanometre-diameter pore

    NASA Astrophysics Data System (ADS)

    Kennedy, Eamonn; Dong, Zhuxin; Tennant, Clare; Timp, Gregory

    2016-11-01

    The primary structure of a protein consists of a sequence of amino acids and is a key factor in determining how a protein folds and functions. However, conventional methods for sequencing proteins, such as mass spectrometry and Edman degradation, suffer from short reads and lack sensitivity, so alternative approaches are sought. Here, we show that a subnanometre-diameter pore, sputtered through a thin silicon nitride membrane, can be used to detect the primary structure of a denatured protein molecule. When a denatured protein immersed in electrolyte is driven through the pore by an electric field, measurements of a blockade in the current reveal nearly regular fluctuations, the number of which coincides with the number of residues in the protein. Furthermore, the amplitudes of the fluctuations are highly correlated with the volumes that are occluded by quadromers (four residues) in the primary structure. Each fluctuation, therefore, represents a read of a quadromer. Scrutiny of the fluctuations reveals that the subnanometre pore is sensitive enough to read the occluded volume that is related to post-translational modifications of a single residue, measuring volume differences of ∼0.07 nm3, but it is not sensitive enough to discriminate between the volumes of all twenty amino acids.

  4. The diverse roles of the Nup93/Nic96 complex proteins - structural scaffolds of the nuclear pore complex with additional cellular functions.

    PubMed

    Vollmer, Benjamin; Antonin, Wolfram

    2014-05-01

    Nuclear pore complexes mediate the transport between the cell nucleoplasm and cytoplasm. These 125 MDa structures are among the largest assemblies found in eukaryotes, built from proteins organized in distinct subcomplexes that act as building blocks during nuclear pore complex biogenesis. In this review, we focus on one of these subcomplexes, the Nup93 complex in metazoa and its yeast counterpart, the Nic96 complex. We discuss its essential function in nuclear pore complex assembly as a linker between the nuclear membrane and the central part of the pore and its various roles in nuclear transport processes and beyond.

  5. In situ 3-D mapping of pore structures and hollow grains of interplanetary dust particles with phase contrast X-ray nanotomography

    NASA Astrophysics Data System (ADS)

    Hu, Z. W.; Winarski, R. P.

    2016-09-01

    Unlocking the 3-D structure and properties of intact chondritic porous interplanetary dust particles (IDPs) in nanoscale detail is challenging, which is also complicated by atmospheric entry heating, but is important for advancing our understanding of the formation and origins of IDPs and planetary bodies as well as dust and ice agglomeration in the outer protoplanetary disk. Here, we show that indigenous pores, pristine grains, and thermal alteration products throughout intact particles can be noninvasively visualized and distinguished morphologically and microstructurally in 3-D detail down to ~10 nm by exploiting phase contrast X-ray nanotomography. We have uncovered the surprisingly intricate, submicron, and nanoscale pore structures of a ~10-μm-long porous IDP, consisting of two types of voids that are interconnected in 3-D space. One is morphologically primitive and mostly submicron-sized intergranular voids that are ubiquitous; the other is morphologically advanced and well-defined intragranular nanoholes that run through the approximate centers of ~0.3 μm or lower submicron hollow grains. The distinct hollow grains exhibit complex 3-D morphologies but in 2-D projections resemble typical organic hollow globules observed by transmission electron microscopy. The particle, with its outer region characterized by rough vesicular structures due to thermal alteration, has turned out to be an inherently fragile and intricately submicron- and nanoporous aggregate of the sub-μm grains or grain clumps that are delicately bound together frequently with little grain-to-grain contact in 3-D space.

  6. 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

    conditions. A series of instantaneous two-dimensional flow fields in a simple pore space has been reconstructed permitting quantification of the mean flow. A not symmetric flow structure has been highlighted showing the strong dependence of flow on the bed geometry and presence of the free surface. Preliminary results will be discussed here in order to highlight the critical aspects of the technique. Illumination from the laser endoscope must be optimized in terms of angle of divergence, uniformity and stability, with any source of irregular illumination causing strong reflections from the surface of the spheres resulting in saturation of huge image areas. The preliminary results obtained demonstrate the utility of the fully endoscopic PIV technique for investigation of flow structure in pore spaces. Further developments of the technique will include improving light uniformity, removing reflections from images and increasing the illuminated portion of the pore space area.

  7. Structural Characterization of Bacterioferritin from Blastochloris viridis

    PubMed Central

    Wahlgren, Weixiao Y.; Omran, Hadil; von Stetten, David; Royant, Antoine; van der Post, Sjoerd; Katona, Gergely

    2012-01-01

    Iron storage and elimination of toxic ferrous iron are the responsibility of bacterioferritins in bacterial species. Bacterioferritins are capable of oxidizing iron using molecular oxygen and import iron ions into the large central cavity of the protein, where they are stored in a mineralized form. We isolated, crystallized bacterioferritin from the microaerophilic/anaerobic, purple non-sulfur bacterium Blastochloris viridis and determined its amino acid sequence and X-ray structure. The structure and sequence revealed similarity to other purple bacterial species with substantial differences in the pore regions. Static 3- and 4-fold pores do not allow the passage of iron ions even though structural dynamics may assist the iron gating. On the other hand the B-pore is open to water and larger ions in its native state. In order to study the mechanism of iron import, multiple soaking experiments were performed. Upon Fe(II) and urea treatment the ferroxidase site undergoes reorganization as seen in bacterioferritin from Escherichia coli and Pseudomonas aeruginosa. When soaking with Fe(II) only, a closely bound small molecular ligand is observed close to Fe1 and the coordination of Glu94 to Fe2 changes from bidentate to monodentate. DFT calculations indicate that the bound ligand is most likely a water or a hydroxide molecule representing a product complex. On the other hand the different soaking treatments did not modify the conformation of other pore regions. PMID:23056552

  8. Precise small-angle X-ray scattering evaluation of the pore structures in track-etched membranes: Comparison with other convenient evaluation methods

    NASA Astrophysics Data System (ADS)

    Miyazaki, Tsukasa; Takenaka, Mikihito

    2017-03-01

    Poly(ethylene terephthalate) (PET)-based track-etched membranes (TMs) with pore sizes ranging from few nanometers to approximately 1 μm are used in various applications in the biological field, and their pore structures are determined by small-angle X-ray scattering (SAXS). These TMs with the nanometer-sized cylindrical pores aligned parallel to the film thickness direction are produced by chemical etching of the track in the PET films irradiated by heavy ions with the sodium hydroxide aqueous solution. It is well known that SAXS allows us to precisely and statistically estimate the pore size and the pore size distribution in the TMs by using the form factor of a cylinder with the extremely long pore length relative to the pore diameter. The results obtained were compared with those estimated with scanning electron microscopy and gas permeability measurements. The result showed that the gas permeability measurement is convenient to evaluate the pore size of TMs within a wide length scale, and the SEM observation is also suited to estimate the pore size, although SEM observation is usually limited above approximately 30 nm.

  9. Structural characterization of solid foams

    NASA Astrophysics Data System (ADS)

    Maire, Éric; Adrien, Jérôme; Petit, Clémence

    2014-10-01

    For being a useful contribution to the understanding of the properties of solid foams, the characterization of the structure of solid foams has to be performed at different scales. The microstructure of the solid part of the foams has to be analyzed. For this, standard SEM observations are often used. The most important aspect (and the most problematic) remains the characterization of the porous architecture of these materials. The methods introduced in this paper concern both scales and the article discusses the specificity of the experiments in the case of porous materials. X-ray tomography is described in more details because it becomes widely used for this purpose. The paper also shows how the obtained 3D images (sometimes obtained during deformation) can be processed to yield important morphological parameters describing the foams. xml:lang="fr"

  10. Thermal Investigations of Periodically Nanoporous Si Films -- The Impact of Structure Sizes and Pore-Edge Amorphization

    NASA Astrophysics Data System (ADS)

    Xu, Dongchao; Zhao, Hongbo; Hao, Qing

    In recent years, nanoporous Si films have been intensively studied as promising thermoelectric materials, which mainly benefits from their dramatically reduced lattice thermal conductivity kL and bulk-like electrical properties.1,2 Despite many encouraging results, challenges still exist in the theoretical explanation of the observed low kL.3 Existing studies mainly attribute the low kL to 1) phonon bandstructure modification by coherent phonon processes in a periodic structure (phononic effects), and/or 2) pore-edge defects. In this work, temperature-dependent kL is measured for nanoporous Si films with different pore sizes and spacing to compare with model predictions. For systematic studies, two fabrication techniques are used to drill the nanopores: 1) reactive ion etching, and 2) a focus ion beam to introduce more pore-edge defects. The results from this work will provide guidance for phonon engineering in general materials with periodic interfaces or boundaries. References: 1. Tang et al., Nano Letters 10, 4279-4283 (2010). 2. Yu et al., Nature Nanotechnology 5, 718-721 (2010). 3. Cahill et al., Applied Physics Reviews 1, 011305/1-45 (2014) Nanoscale thermal transport. II. 2003-2012.

  11. Structure, thermodynamic properties, and phase diagrams of few colloids confined in a spherical pore.

    PubMed

    Paganini, Iván E; Pastorino, Claudio; Urrutia, Ignacio

    2015-06-28

    We study a system of few colloids confined in a small spherical cavity with event driven molecular dynamics simulations in the canonical ensemble. The colloidal particles interact through a short range square-well potential that takes into account the basic elements of attraction and excluded-volume repulsion of the interaction among colloids. We analyze the structural and thermodynamic properties of this few-body confined system in the framework of inhomogeneous fluids theory. Pair correlation function and density profile are used to determine the structure and the spatial characteristics of the system. Pressure on the walls, internal energy, and surface quantities such as surface tension and adsorption are also analyzed for a wide range of densities and temperatures. We have characterized systems from 2 to 6 confined particles, identifying distinctive qualitative behavior over the thermodynamic plane T - ρ, in a few-particle equivalent to phase diagrams of macroscopic systems. Applying the extended law of corresponding states, the square well interaction is mapped to the Asakura-Oosawa model for colloid-polymer mixtures. We link explicitly the temperature of the confined square-well fluid to the equivalent packing fraction of polymers in the Asakura-Oosawa model. Using this approach, we study the confined system of few colloids in a colloid-polymer mixture.

  12. Structure, thermodynamic properties, and phase diagrams of few colloids confined in a spherical pore

    SciTech Connect

    Paganini, Iván E.; Pastorino, Claudio Urrutia, Ignacio

    2015-06-28

    We study a system of few colloids confined in a small spherical cavity with event driven molecular dynamics simulations in the canonical ensemble. The colloidal particles interact through a short range square-well potential that takes into account the basic elements of attraction and excluded-volume repulsion of the interaction among colloids. We analyze the structural and thermodynamic properties of this few-body confined system in the framework of inhomogeneous fluids theory. Pair correlation function and density profile are used to determine the structure and the spatial characteristics of the system. Pressure on the walls, internal energy, and surface quantities such as surface tension and adsorption are also analyzed for a wide range of densities and temperatures. We have characterized systems from 2 to 6 confined particles, identifying distinctive qualitative behavior over the thermodynamic plane T − ρ, in a few-particle equivalent to phase diagrams of macroscopic systems. Applying the extended law of corresponding states, the square well interaction is mapped to the Asakura-Oosawa model for colloid-polymer mixtures. We link explicitly the temperature of the confined square-well fluid to the equivalent packing fraction of polymers in the Asakura-Oosawa model. Using this approach, we study the confined system of few colloids in a colloid-polymer mixture.

  13. The pore structure and fractal characteristics of shales with low thermal maturity from the Yuqia Coalfield, northern Qaidam Basin, northwestern China

    NASA Astrophysics Data System (ADS)

    Hou, Haihai; Shao, Longyi; Li, Yonghong; Li, Zhen; Zhang, Wenlong; Wen, Huaijun

    2016-12-01

    The continental shales from the Middle Jurassic Shimengou Formation of the northern Qaidam Basin, northwestern China, have been investigated in recent years because of their shale gas potential. In this study, a total of twenty-two shale samples were collected from the YQ-1 borehole in the Yuqia Coalfield, northern Qaidam Basin. The total organic carbon (TOC) contents, pore structure parameters, and fractal characteristics of the samples were investigated using TOC analysis, low-temperature nitrogen adsorption experiments, and fractal analysis. The results show that the average pore size of the Shimengou shales varied from 8.149 nm to 20.635 nm with a mean value of 10.74 nm, which is considered mesopore-sized. The pores of the shales are mainly inkbottle- and slit-shaped. The sedimentary environment plays an essential role in controlling the TOC contents of the low maturity shales, with the TOC values of shales from deep to semi-deep lake facies (mean: 5.23%) being notably higher than those of the shore-shallow lake facies (mean: 0.65%). The fractal dimensions range from 2.4639 to 2.6857 with a mean of 2.6122, higher than those of marine shales, which indicates that the pore surface was rougher and the pore structure more complex in these continental shales. The fractal dimensions increase with increasing total pore volume and total specific surface area, and with decreasing average pore size. With increasing TOC contents in shales, the fractal dimensions increase first and then decrease, with the highest value occurring at 2% of TOC content, which is in accordance with the trends between the TOC and both total specific surface area and total pore volume. The pore structure complexity and pore surface roughness of these low-maturity shales would be controlled by the combined effects of both sedimentary environments and the TOC contents.

  14. EFFECTS OF PORE STRUCTURE CHANGE AND MULTI-SCALE HETEROGENEITY ON CONTAMINANT TRANSPORT AND REACTION RATE UPSCALING

    SciTech Connect

    Lindquist, W. Brent; Jones, Keith W.; Um, Wooyong; Rockhold, mark; Peters, Catherine A.; Celia, Michael A.

    2013-02-15

    This project addressed the scaling of geochemical reactions to core and field scales, and the interrelationship between reaction rates and flow in porous media. We targeted reactive transport problems relevant to the Hanford site - specifically the reaction of highly caustic, radioactive waste solutions with subsurface sediments, and the immobilization of 90Sr and 129I through mineral incorporation and passive flow blockage, respectively. We addressed the correlation of results for pore-scale fluid-soil interaction with field-scale fluid flow, with the specific goals of (i) predicting attenuation of radionuclide concentration; (ii) estimating changes in flow rates through changes of soil permeabilities; and (iii) estimating effective reaction rates. In supplemental work, we also simulated reactive transport systems relevant to geologic carbon sequestration. As a whole, this research generated a better understanding of reactive transport in porous media, and resulted in more accurate methods for reaction rate upscaling and improved prediction of permeability evolution. These scientific advancements will ultimately lead to better tools for management and remediation of DOE’s legacy waste problems. We established three key issues of reactive flow upscaling, and organized this project in three corresponding thrust areas. 1) Reactive flow experiments. The combination of mineral dissolution and precipitation alters pore network structure and the subsequent flow velocities, thereby creating a complex interaction between reaction and transport. To examine this phenomenon, we conducted controlled laboratory experimentation using reactive flow-through columns. Results and Key Findings: Four reactive column experiments (S1, S3, S4, S5) have been completed in which simulated tank waste leachage (STWL) was reacted with pure quartz sand, with and without Aluminum. The STWL is a caustic solution that dissolves quartz. Because Al is a necessary element in the formation of

  15. Wnt Signaling Prevents the Aβ Oligomer-Induced Mitochondrial Permeability Transition Pore Opening Preserving Mitochondrial Structure in Hippocampal Neurons

    PubMed Central

    Arrázola, Macarena S.; Ramos-Fernández, Eva; Cisternas, Pedro; Ordenes, Daniela; Inestrosa, Nibaldo C.

    2017-01-01

    Alzheimer’s disease (AD) is a neurodegenerative disorder mainly known for synaptic impairment and neuronal cell loss, affecting memory processes. Beside these damages, mitochondria have been implicated in the pathogenesis of AD through the induction of the mitochondrial permeability transition pore (mPTP). The mPTP is a non-selective pore that is formed under apoptotic conditions, disturbing mitochondrial structure and thus, neuronal viability. In AD, Aβ oligomers (Aβos) favor the opening of the pore, activating mitochondria-dependent neuronal cell death cascades. The Wnt signaling activated through the ligand Wnt3a has been described as a neuroprotective signaling pathway against amyloid-β (Aβ) peptide toxicity in AD. However, the mechanisms by which Wnt signaling prevents Aβos-induced neuronal cell death are unclear. We proposed here to study whether Wnt signaling protects neurons earlier than the late damages in the progression of the disease, through the preservation of the mitochondrial structure by the mPTP inhibition. To study specific events related to mitochondrial permeabilization we performed live-cell imaging from primary rat hippocampal neurons, and electron microscopy to analyze the mitochondrial morphology and structure. We report here that Wnt3a prevents an Aβos-induced cascade of mitochondrial events that leads to neuronal cell death. This cascade involves (a) mPTP opening, (b) mitochondrial swelling, (c) mitochondrial membrane potential loss and (d) cytochrome c release, thus leading to neuronal cell death. Furthermore, our results suggest that the activation of the Wnt signaling prevents mPTP opening by two possible mechanisms, which involve the inhibition of mitochondrial GSK-3β and/or the modulation of mitochondrial hexokinase II levels and activity. This study suggests a possible new approach for the treatment of AD from a mitochondrial perspective, and will also open new lines of study in the field of Wnt signaling in neuroprotection

  16. Wnt Signaling Prevents the Aβ Oligomer-Induced Mitochondrial Permeability Transition Pore Opening Preserving Mitochondrial Structure in Hippocampal Neurons.

    PubMed

    Arrázola, Macarena S; Ramos-Fernández, Eva; Cisternas, Pedro; Ordenes, Daniela; Inestrosa, Nibaldo C

    2017-01-01

    Alzheimer's disease (AD) is a neurodegenerative disorder mainly known for synaptic impairment and neuronal cell loss, affecting memory processes. Beside these damages, mitochondria have been implicated in the pathogenesis of AD through the induction of the mitochondrial permeability transition pore (mPTP). The mPTP is a non-selective pore that is formed under apoptotic conditions, disturbing mitochondrial structure and thus, neuronal viability. In AD, Aβ oligomers (Aβos) favor the opening of the pore, activating mitochondria-dependent neuronal cell death cascades. The Wnt signaling activated through the ligand Wnt3a has been described as a neuroprotective signaling pathway against amyloid-β (Aβ) peptide toxicity in AD. However, the mechanisms by which Wnt signaling prevents Aβos-induced neuronal cell death are unclear. We proposed here to study whether Wnt signaling protects neurons earlier than the late damages in the progression of the disease, through the preservation of the mitochondrial structure by the mPTP inhibition. To study specific events related to mitochondrial permeabilization we performed live-cell imaging from primary rat hippocampal neurons, and electron microscopy to analyze the mitochondrial morphology and structure. We report here that Wnt3a prevents an Aβos-induced cascade of mitochondrial events that leads to neuronal cell death. This cascade involves (a) mPTP opening, (b) mitochondrial swelling, (c) mitochondrial membrane potential loss and (d) cytochrome c release, thus leading to neuronal cell death. Furthermore, our results suggest that the activation of the Wnt signaling prevents mPTP opening by two possible mechanisms, which involve the inhibition of mitochondrial GSK-3β and/or the modulation of mitochondrial hexokinase II levels and activity. This study suggests a possible new approach for the treatment of AD from a mitochondrial perspective, and will also open new lines of study in the field of Wnt signaling in neuroprotection.

  17. Simulations of the pore structures for a M2G1yR derived channel forming peptide in membrane

    NASA Astrophysics Data System (ADS)

    Al-Rawi, Ahlam N.; Al-Rawi, Asma; Chen, Jianhan; Herrera, Alvaro; Tomich, John; Rahman, Talat S.

    2008-03-01

    In an effort to develop a peptide-based compound suitable for clinical use as a channel replacement therapeutic for treating channelopathies such as cystic fibrosis, we present a reductionist model that appears to capture many of the biophysical properties of an intact ion channel using short channel-forming peptides. We have developed two anion selective channel-forming peptides with near native and altered properties from the peptides derived from the glycine receptor: NK4-M2GlyR-p22 WT (KKKKPAR-VGLGITTVLTMTTQS) and NK4-M2GlyR-p22 S22W (KKKKPARVGLGITTVLTMTTQW), respectively. Starting with the two structures determined by solution multidimensional NMR (800 MHz) in SDS, we used CHARMM and NAMD to perform molecular dynamics simulations on the monomers. Using the existing experimental data, we then built an initial 5- helix assembly by altering the tilted angle, rotational angle and pore radius. We investigated the impact of the single mutation at position 22 on the structure and dynamics of the pore formed in a membrane build in a hydrated POPC lipid bilayer. Probable structures for both assemblies are presented.

  18. Model inspired by nuclear pore complex suggests possible roles for nuclear transport receptors in determining its structure.

    PubMed

    Osmanović, Dino; Ford, Ian J; Hoogenboom, Bart W

    2013-12-17

    Nuclear transport receptors (NTRs) mediate nucleocytoplasmic transport via their affinity for unstructured proteins (polymers) in the nuclear pore complex (NPC). Here, we have modeled the effect of NTRs on polymeric structure in the nanopore confinement of the NPC central conduit. The model explicitly takes into account inter- and intramolecular interactions, as well as the finite size of the NTRs (∼20% of the NPC channel diameter). It reproduces various proposed scenarios for the channel structure, ranging from a central polymer condensate (selective phase) to brushlike polymer arrangements localized at the channel wall (virtual gate, reduction of dimensionality), with the transport receptors lining the polymer surface. In addition, it predicts a new structure in which NTRs become an integral part of the transport barrier by forming a cross-linked network with the unstructured proteins stretching across the pore. The model provides specific and distinctive predictions for the equilibrium spatial distributions of NTRs for these different scenarios that can be experimentally verified by, e.g., superresolution fluorescence microscopy. Moreover, it suggests mechanisms by which globular macromolecules (colloidal particles) can cause polymer-coated nanopores to switch between open and closed configurations, a possible explanation of the biological function of the NPC, and suggests potential technological applications for filtration and single-molecule sensing.

  19. Discrete Slip, Amorphous Silica and Pore Structure of Slickensided Gouge Layers in 2004-2006 Mt. St. Helens Lava Domes

    NASA Astrophysics Data System (ADS)

    White, J. C.; Kennedy, L. A.; Russell, J. K.; Friedlander, B.

    2012-12-01

    Spines of dacite lava formed during the 2004-2006 Mt. St. Helens (MSH) effusion event are enveloped by extrusion gouges created during upward movement of crystallized magma. Multiple slickenside sets form one of the most distinctive feature types within this gouge carapace. Macroscopically, slickenside surfaces are seen to be composite features composed of discrete slip surfaces in Y- and R-shear orientations. In general, the spacing between the slip surfaces decreases toward the outer, exposed slickensided surface until they appear to coalesce. Slickensides are formed in association with all MSH spines, unlike some other fault rock fabrics within the gouge; therefore, their morphology can be inferred to be independent of syn-faulting residence time. As a significant record of the extrusion process, the MSH slickensides have been characterized by analytical scanning/transmission electron microscopy (STEM) to elucidate the mechanisms of energy dissipation and material transport. At the scale of these observations, the individual surfaces within a slickenside set comprise comminution bands (10-20 μm wide), each bounded by a discrete slip surface. The internal structure of these shear bands consists of a consistent sense of decreasing grain size toward the slip surface away and away from the spire core; grain size is routinely less than 100nm within the bands. The 1-5 μm wide slip layers that bound comminution bands are variously composed of amorphous silica or polycrystalline aggregates of sub-100nm grain size plagioclase, k-feldspar and quartz. Grain aggregates in the slip layer form an extended fabric parallel to the displacement direction, creating a "flow" foliation at edges of the shears. Specific to the slip bands are nano-scale pores, often silica-filled, whose circular cross-sections indicate the presence of fluids throughout slickenside formation. It is contended that the development of discrete slip surfaces is consistent with formation of the gouge by

  20. Structural flyby characterization of nanoporosity

    NASA Astrophysics Data System (ADS)

    Rosa, R. R.; Ferreira da Silva, A.; Brito, R. C.; Roman, L. S.; Baroni, M. P. M. A.; Ramos, F. M.; Ahuja, R.; Persson, C.

    2004-08-01

    Recently, Ferreira da Silva et al. [3] have performed a gradient pattern analysis of a canonical sample set (CSS) of scanning force microscopy (SFM) images of p-Si. They applied the so-called Gradient Pattern Analysis to images of three typical p-Si samples distinguished by different absorption energy levels and aspect ratios. Taking into account the measures of spatial asymmetric fluctuations they interpreted the global porosity not only in terms of the amount of roughness, but rather in terms of the structural complexity (e.g., walls and fine structures as slots). This analysis has been adapted in order to operate in a OpenGL flyby environment (the StrFB code), whose application give the numerical characterization of the structure during the flyby real time. Using this analysis we compare the levels of asymmetric fragmentation of active porosity related to different materials as p-Si and "porous diamond-like" carbon. In summary we have shown that the gradient pattern analysis technique in a flyby environment is a reliable sensitive method to investigate, qualitatively and quantitatively, the complex morphology of active nanostructures.

  1. Nuclear Pore Complexes and Nucleocytoplasmic Transport: From Structure to Function to Disease.

    PubMed

    Dickmanns, Achim; Kehlenbach, Ralph H; Fahrenkrog, Birthe

    2015-01-01

    Nucleocytoplasmic transport is an essential cellular activity and occurs via nuclear pore complexes (NPCs) that reside in the double membrane of the nuclear envelope. Significant progress has been made during the past few years in unravelling the ultrastructural organization of NPCs and their constituents, the nucleoporins, by cryo-electron tomography and X-ray crystallography. Mass spectrometry and genomic approaches have provided deeper insight into the specific regulation and fine tuning of individual nuclear transport pathways. Recent research has also focused on the roles nucleoporins play in health and disease, some of which go beyond nucleocytoplasmic transport. Here we review emerging results aimed at understanding NPC architecture and nucleocytoplasmic transport at the atomic level, elucidating the specific function individual nucleoporins play in nuclear trafficking, and finally lighting up the contribution of nucleoporins and nuclear transport receptors in human diseases, such as cancer and certain genetic disorders.

  2. Imaging the assembly, structure, and function of the nuclear pore inside cells.

    PubMed

    Otsuka, Shotaro; Szymborska, Anna; Ellenberg, Jan

    2014-01-01

    The nuclear pore complex (NPC) mediates selective transport across the nuclear envelope (NE) and plays crucial roles in several additional cellular functions. In higher eukaryotes, the NPC and the NE disassemble and reassemble during cell division and live-cell imaging has been a powerful tool to analyze these dynamic processes. Here, we present a method for the kinetic analysis of postmitotic NPC assembly and reestablishment of transport competence in intact cells by multicolor 4D imaging and photoswitching. By applying the methods we have established previously using normal rat kidney to HeLa cells, we demonstrate the conservation of NPC assembly in different mammalian cells. We recently showed that the molecular organization of the NPC can be studied by combining stochastic super-resolution microscopy with single-particle averaging and present this method here in detail.

  3. 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

  4. Cloning, functional characterization, and mode of action of a novel insecticidal pore-forming toxin, sphaericolysin, produced by Bacillus sphaericus.

    PubMed

    Nishiwaki, Hisashi; Nakashima, Kenta; Ishida, Chiharu; Kawamura, Tadayuki; Matsuda, Kazuhiko

    2007-05-01

    An insecticidal protein produced by Bacillus sphaericus A3-2 was purified to elucidate its structure and mode of action. The active principle purified from the culture broth of A3-2 was a protein with a molecular mass of 53 kDa that rapidly intoxicated German cockroaches (Blattela germanica) at a dose of about 100 ng when injected. The insecticidal protein sphaericolysin possessed the undecapeptide motif of cholesterol-dependent cytolysins and had a unique N-terminal sequence. The recombinant protein expressed in Escherichia coli was equally as potent as the native protein. Sphaericolysin-induced hemolysis resulted from the protein's pore-forming action. This activity as well as the insecticidal activity was markedly reduced by a Y159A mutation. Also, coapplication of sphaericolysin with cholesterol abolished the insecticidal action, suggesting that cholesterol binding plays an important role in insecticidal activity. Sphaericolysin-lysed neurons dissociated from the thoracic ganglia of the German cockroaches. In addition, sphaericolysin's activity in ganglia was suppressed by the Y159A mutation. The sphaericolysin-induced damage to the cockroach ganglia was greater than the damage to the ganglia of common cutworms (Spodoptera litura), which accounts, at least in part, for the higher sensitivity to sphaericolysin displayed by the cockroaches than that displayed by cutworms.

  5. Crystal structure of Cry6Aa: A novel nematicidal ClyA-type α-pore-forming toxin from Bacillus thuringiensis.

    PubMed

    Huang, Jinbo; Guan, Zeyuan; Wan, Liting; Zou, Tingting; Sun, Ming

    2016-09-09

    Crystal (Cry) proteins from Bacillus thuringiensis (Bt) are globally used in agriculture as proteinaceous insecticides. Numerous crystal structures have been determined, and most exhibit conserved three-dimensional architectures. Recently, we have identified a novel nematicidal mechanism by which Cry6Aa triggers cell death through a necrosis-signaling pathway via an interaction with the host protease ASP-1. However, we found little sequence conservation of Cry6Aa in our functional study. Here, we report the 1.90 angstrom (Å) resolution structure of the proteolytic form of Cry6Aa (1-396), determined by X-ray crystallography. The structure of Cry6Aa is highly similar to those of the pathogenic toxin family of ClyA-type α-pore-forming toxins (α-PFTs), which are characterized by a bipartite structure comprising a head domain and a tail domain, thus suggesting that Cry6Aa exhibits a previously undescribed nematicidal mode of action. This structure also provides a framework for the functional study of other nematicidal toxins.

  6. Structure of a Yeast Dyn2-Nup159 Complex and Molecular Basis for Dynein Light Chain-Nuclear Pore Interaction*

    PubMed Central

    Romes, Erin M.; Tripathy, Ashutosh; Slep, Kevin C.

    2012-01-01

    The nuclear pore complex gates nucleocytoplasmic transport through a massive, eight-fold symmetric channel capped by a nucleoplasmic basket and structurally unique, cytoplasmic fibrils whose tentacles bind and regulate asymmetric traffic. The conserved Nup82 complex, composed of Nsp1, Nup82, and Nup159, forms the unique cytoplasmic fibrils that regulate mRNA nuclear export. Although the nuclear pore complex plays a fundamental, conserved role in nuclear trafficking, structural information about the cytoplasmic fibrils is limited. Here, we investigate the structural and biochemical interactions between Saccharomyces cerevisiae Nup159 and the nucleoporin, Dyn2. We find that Dyn2 is predominantly a homodimer and binds arrayed sites on Nup159, promoting the Nup159 parallel homodimerization. We present the first structure of Dyn2, determined at 1.85 Å resolution, complexed with a Nup159 target peptide. Dyn2 resembles homologous metazoan dynein light chains, forming homodimeric composite substrate binding sites that engage two independent 10-residue target motifs, imparting a β-strand structure to each peptide via antiparallel extension of the Dyn2 core β-sandwich. Dyn2 recognizes a highly conserved QT motif while allowing sequence plasticity in the flanking residues of the peptide. Isothermal titration calorimetric analysis of the comparative binding of Dyn2 to two Nup159 target sites shows similar affinities (18 and 13 μm), but divergent thermal binding modes. Dyn2 homodimers are arrayed in the crystal lattice, likely mimicking the arrayed architecture of Dyn2 on the Nup159 multivalent binding sites. Crystallographic interdimer interactions potentially reflect a cooperative basis for Dyn2-Nup159 complex formation. Our data highlight the determinants that mediate oligomerization of the Nup82 complex and promote a directed, elongated cytoplasmic fibril architecture. PMID:22411995

  7. The Structures of Coiled-Coil Domains from Type III Secretion System Translocators Reveal Homology to Pore-Forming Toxins

    SciTech Connect

    Barta, Michael L.; Dickenson, Nicholas E.; Patil, Mrinalini; Keightley, Andrew; Wyckoff, Gerald J.; Picking, William D.; Picking, Wendy L.; Geisbrecht, Brian V.

    2012-03-26

    Many pathogenic Gram-negative bacteria utilize type III secretion systems (T3SSs) to alter the normal functions of target cells. Shigella flexneri uses its T3SS to invade human intestinal cells to cause bacillary dysentery (shigellosis) that is responsible for over one million deaths per year. The Shigella type III secretion apparatus is composed of a basal body spanning both bacterial membranes and an exposed oligomeric needle. Host altering effectors are secreted through this energized unidirectional conduit to promote bacterial invasion. The active needle tip complex of S. flexneri is composed of a tip protein, IpaD, and two pore-forming translocators, IpaB and IpaC. While the atomic structure of IpaD has been elucidated and studied, structural data on the hydrophobic translocators from the T3SS family remain elusive. We present here the crystal structures of a protease-stable fragment identified within the N-terminal regions of IpaB from S. flexneri and SipB from Salmonella enterica serovar Typhimurium determined at 2.1 {angstrom} and 2.8 {angstrom} limiting resolution, respectively. These newly identified domains are composed of extended-length (114 {angstrom} in IpaB and 71 {angstrom} in SipB) coiled-coil motifs that display a high degree of structural homology to one another despite the fact that they share only 21% sequence identity. Further structural comparisons also reveal substantial similarity to the coiled-coil regions of pore-forming proteins from other Gram-negative pathogens, notably, colicin Ia. This suggests that these mechanistically separate and functionally distinct membrane-targeting proteins may have diverged from a common ancestor during the course of pathogen-specific evolutionary events.

  8. Structure of a yeast Dyn2-Nup159 complex and molecular basis for dynein light chain-nuclear pore interaction.

    PubMed

    Romes, Erin M; Tripathy, Ashutosh; Slep, Kevin C

    2012-05-04

    The nuclear pore complex gates nucleocytoplasmic transport through a massive, eight-fold symmetric channel capped by a nucleoplasmic basket and structurally unique, cytoplasmic fibrils whose tentacles bind and regulate asymmetric traffic. The conserved Nup82 complex, composed of Nsp1, Nup82, and Nup159, forms the unique cytoplasmic fibrils that regulate mRNA nuclear export. Although the nuclear pore complex plays a fundamental, conserved role in nuclear trafficking, structural information about the cytoplasmic fibrils is limited. Here, we investigate the structural and biochemical interactions between Saccharomyces cerevisiae Nup159 and the nucleoporin, Dyn2. We find that Dyn2 is predominantly a homodimer and binds arrayed sites on Nup159, promoting the Nup159 parallel homodimerization. We present the first structure of Dyn2, determined at 1.85 Å resolution, complexed with a Nup159 target peptide. Dyn2 resembles homologous metazoan dynein light chains, forming homodimeric composite substrate binding sites that engage two independent 10-residue target motifs, imparting a β-strand structure to each peptide via antiparallel extension of the Dyn2 core β-sandwich. Dyn2 recognizes a highly conserved QT motif while allowing sequence plasticity in the flanking residues of the peptide. Isothermal titration calorimetric analysis of the comparative binding of Dyn2 to two Nup159 target sites shows similar affinities (18 and 13 μM), but divergent thermal binding modes. Dyn2 homodimers are arrayed in the crystal lattice, likely mimicking the arrayed architecture of Dyn2 on the Nup159 multivalent binding sites. Crystallographic interdimer interactions potentially reflect a cooperative basis for Dyn2-Nup159 complex formation. Our data highlight the determinants that mediate oligomerization of the Nup82 complex and promote a directed, elongated cytoplasmic fibril architecture.

  9. Characterization of Pore Defects and Fatigue Cracks in Die Cast AM60 Using 3D X-ray Computed Tomography

    NASA Astrophysics Data System (ADS)

    Yang, Zhuofei; Kang, Jidong; Wilkinson, David S.

    2015-08-01

    AM60 high pressure die castings have been used in automobile applications to reduce the weight of vehicles. However, the pore defects that are inherent in die casting may negatively affect mechanical properties, especially the fatigue properties. Here we have studied damage ( e.g., pore defects, fatigue cracks) during strained-controlled fatigue using 3-dimensional X-ray computed tomography (XCT). The fatigue test was interrupted every 2000 cycles and the specimen was removed to be scanned using a desktop micro-CT system. XCT reveals pore defects, cracks, and fracture surfaces. The results show that pores can be accurately measured and modeled in 3D. Defect bands are found to be made of pores under 50 µm (based on volume-equivalent sphere diameter). Larger pores are randomly distributed in the region between the defect bands. Observation of fatigue cracks by XCT is performed in three ways such that the 3D model gives the best illustration of crack-porosity interaction while the other two methods, with the cracks being viewed on transverse or longitudinal cross sections, have better detectability on crack initiation and crack tip observation. XCT is also of value in failure analysis on fracture surfaces. By assessing XCT data during fatigue testing and observing fracture surfaces on a 3D model, a better understanding on the crack initiation, crack-porosity interaction, and the morphology of fracture surface is achieved.

  10. Pore structure modified diatomite-supported PEG composites for thermal energy storage

    NASA Astrophysics Data System (ADS)

    Qian, Tingting; Li, Jinhong; Deng, Yong

    2016-09-01

    A series of novel composite phase change materials (PCMs) were tailored by blending PEG and five kinds of diatomite via a vacuum impregnation method. To enlarge its pore size and specific surface area, different modification approaches including calcination, acid treatment, alkali leaching and nano-silica decoration on the microstructure of diatomite were outlined. Among them, 8 min of 5 wt% NaOH dissolution at 70 °C has been proven to be the most effective and facile. While PEG melted during phase transformation, the maximum load of PEG could reach 70 wt.%, which was 46% higher than that of the raw diatomite. The apparent activation energy of PEG in the composite was 1031.85 kJ·mol‑1, which was twice higher than that of the pristine PEG. Moreover, using the nano-silica decorated diatomite as carrier, the maximum PEG load was 66 wt%. The composite PCM was stable in terms of thermal and chemical manners even after 200 cycles of melting and freezing. All results indicated that the obtained composite PCMs were promising candidate materials for building applications due to its large latent heat, suitable phase change temperature, excellent chemical compatibility, improved supercooling extent, high thermal stability and long-term reliability.

  11. Pore structure modified diatomite-supported PEG composites for thermal energy storage.

    PubMed

    Qian, Tingting; Li, Jinhong; Deng, Yong

    2016-09-01

    A series of novel composite phase change materials (PCMs) were tailored by blending PEG and five kinds of diatomite via a vacuum impregnation method. To enlarge its pore size and specific surface area, different modification approaches including calcination, acid treatment, alkali leaching and nano-silica decoration on the microstructure of diatomite were outlined. Among them, 8 min of 5 wt% NaOH dissolution at 70 °C has been proven to be the most effective and facile. While PEG melted during phase transformation, the maximum load of PEG could reach 70 wt.%, which was 46% higher than that of the raw diatomite. The apparent activation energy of PEG in the composite was 1031.85 kJ·mol(-1), which was twice higher than that of the pristine PEG. Moreover, using the nano-silica decorated diatomite as carrier, the maximum PEG load was 66 wt%. The composite PCM was stable in terms of thermal and chemical manners even after 200 cycles of melting and freezing. All results indicated that the obtained composite PCMs were promising candidate materials for building applications due to its large latent heat, suitable phase change temperature, excellent chemical compatibility, improved supercooling extent, high thermal stability and long-term reliability.

  12. Pore structure modified diatomite-supported PEG composites for thermal energy storage

    PubMed Central

    Qian, Tingting; Li, Jinhong; Deng, Yong

    2016-01-01

    A series of novel composite phase change materials (PCMs) were tailored by blending PEG and five kinds of diatomite via a vacuum impregnation method. To enlarge its pore size and specific surface area, different modification approaches including calcination, acid treatment, alkali leaching and nano-silica decoration on the microstructure of diatomite were outlined. Among them, 8 min of 5 wt% NaOH dissolution at 70 °C has been proven to be the most effective and facile. While PEG melted during phase transformation, the maximum load of PEG could reach 70 wt.%, which was 46% higher than that of the raw diatomite. The apparent activation energy of PEG in the composite was 1031.85 kJ·mol−1, which was twice higher than that of the pristine PEG. Moreover, using the nano-silica decorated diatomite as carrier, the maximum PEG load was 66 wt%. The composite PCM was stable in terms of thermal and chemical manners even after 200 cycles of melting and freezing. All results indicated that the obtained composite PCMs were promising candidate materials for building applications due to its large latent heat, suitable phase change temperature, excellent chemical compatibility, improved supercooling extent, high thermal stability and long-term reliability. PMID:27580677

  13. Comparative study of the structure and interaction of the pore helices of the hERG and Kv1.5 potassium channels in model membranes.

    PubMed

    Beaugrand, Maïwenn; Arnold, Alexandre A; Bourgault, Steve; Williamson, Philip T F; Marcotte, Isabelle

    2017-03-17

    The hERG channel is a voltage-gated potassium channel found in cardiomyocytes that contributes to the repolarization of the cell membrane following the cardiac action potential, an important step in the regulation of the cardiac cycle. The lipids surrounding K(+) channels have been shown to play a key role in their regulation, with anionic lipids shown to alter gating properties. In this study, we investigate how anionic lipids interact with the pore helix of hERG and compare the results with those from Kv1.5, which possesses a pore helix more typical of K(+) channels. Circular dichroism studies of the pore helix secondary structure reveal that the presence of the anionic lipid DMPS within the bilayer results in a slight unfolding of the pore helices from both hERG and Kv1.5, albeit to a lesser extent for Kv1.5. In the presence of anionic lipids, the two pore helices exhibit significantly different interactions with the lipid bilayer. We demonstrate that the pore helix from hERG causes significant perturbation to the order in lipid bicelles, which contrasts with only small changes observed for Kv1.5. These observations suggest that the atypical sequence of the pore helix of hERG may play a key role in determining how anionic lipids influence its gating.

  14. 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

  15. 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.

  16. 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.

  17. Influence of Pore Structure on the Effectiveness of a Biogenic Carbonate Surface Treatment for Limestone Conservation ▿

    PubMed Central

    De Muynck, Willem; Leuridan, Stijn; Van Loo, Denis; Verbeken, Kim; Cnudde, Veerle; De Belie, Nele; Verstraete, Willy

    2011-01-01

    A ureolytic biodeposition treatment was applied to five types of limestone in order to investigate the effect of pore structure on the protective performance of a biogenic carbonate surface treatment. Protective performance was assessed by means of transport and degradation processes, and the penetration depth of the treatment was visualized by microtomography. Pore size governs bacterial adsorption and hence the location and amount of carbonate precipitated. This study indicated that in macroporous stone, biogenic carbonate formation occurred to a larger extent and at greater depths than in microporous stone. As a consequence, the biodeposition treatment exhibited the greatest protective performance on macroporous stone. While precipitation was limited to the outer surface of microporous stone, biogenic carbonate formation occurred at depths of greater than 2 mm for Savonnières and Euville. For Savonnières, the presence of biogenic carbonate resulted in a 20-fold decreased rate of water absorption, which resulted in increased resistance to sodium sulfate attack and to freezing and thawing. While untreated samples were completely degraded after 15 cycles of salt attack, no damage was observed in biodeposition-treated Savonnières. From this study, it is clear that biodeposition is very effective and more feasible for macroporous stones than for microporous stones. PMID:21821746

  18. Damping characterization in large structures

    NASA Technical Reports Server (NTRS)

    Eke, Fidelis O.; Eke, Estelle M.

    1991-01-01

    This research project has as its main goal the development of methods for selecting the damping characteristics of components of a large structure or multibody system, in such a way as to produce some desired system damping characteristics. The main need for such an analytical device is in the simulation of the dynamics of multibody systems consisting, at least partially, of flexible components. The reason for this need is that all existing simulation codes for multibody systems require component-by-component characterization of complex systems, whereas requirements (including damping) often appear at the overall system level. The main goal was met in large part by the development of a method that will in fact synthesize component damping matrices from a given system damping matrix. The restrictions to the method are that the desired system damping matrix must be diagonal (which is almost always the case) and that interbody connections must be by simple hinges. In addition to the technical outcome, this project contributed positively to the educational and research infrastructure of Tuskegee University - a Historically Black Institution.

  19. Metallic cobalt and iron particles in large and medium pore zeolites. Methods of generation and ferromagnetic resonance characterization

    SciTech Connect

    Iton, L.E.; Beal, R.B.; Hamot, P.J.

    1983-01-01

    Spectroscopic studies utilizing photoacoustic electronic spectroscopy, electron paramagnetic resonance, and ferromagnetic resonance have been made on the formation of (1) Co metal particles from CO(NH/sub 3/)/sub 6//sup 3 +/ exchanged into Y zeolite and (2) Fe metal particles from nonframework Fe/sup 3 +/ ions in an aluminoferrisilicate analogue of ZSM-5 zeolite. Decomposition of the Co(NH/sub 3/)/sub 6//sup 3 +/ complex is accompanied by autoreduction to the Co/sup 2 +/ state, observed by EPR at 7/sup 0/K, but no Co metal is formed. The Co/sup 2 +/ ions migrate from the supercage locations of the parent complexes into the hexagonal prisms and are subsequently very difficult to reduce, even with H/sub 2/ at 823/sup 0/K. High-temperature FMR data suggest that the small amount of Co metal particles which are formed exist with the fcc crystal structure yielding g = 2.17 at 508/sup 0/K, consistent with an empirically calculated value for fcc Co. Hexagonal close packed Co particles are expected to exhibit much larger magnetic anisotropy than was observed. The Fe/sup 3 +/ ions in the medium pore pentasil aluminoferrisilicate zeolite can be reduced to the metallic state following either (a) precipitation of the inclusion compound, Fe/sup III/(Fe/sup II/(CN)/sub 5/(NO)), in the zeolite, or (b) generation of superparamagnetic oxidic ferric ion clusters. High-temperature FMR data establish that smaller Fe particles can be obtained by the latter method.

  20. 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.

  1. Preparation and characterization of a hierarchical porous char from sewage sludge with superior adsorption capacity for toluene by a new two-step pore-fabricating process.

    PubMed

    Kong, Lingjun; Xiong, Ya; Tian, Shuanghong; Luo, Rongshu; He, Chun; Huang, Haibao

    2013-10-01

    A kind of hierarchical porous char (SCCA/Zn) was prepared from sewage sludge by a new two-step pore-fabricating process coupling citric acid (CA) with ZnCl2 in a pyrolysis process. The char was characterized by element analysis, N2-adsorption and mercury intrusion measurement etc. It is found that coupling CA and ZnCl2 can synergistically fabricate pores in the pyrolysis process, resulting in a hierarchical porous char, SCCA/Zn, with the largest SBET of 867.6 m(2) g(-1) due to the fact that the former contributes to the fabrication of macro-pores, which provides more space for fabricating meso- and micro-pores by ZnCl2 activation. Although the SBET of SCCA/Zn was 15% less than that of activated carbon fiber (ACF, SBET=999.5 m(2) g(-1)), SCCA/Zn had a higher toluene adsorption capacity (0.83 g g(-1)) than ACF. The inconsistence between their SBET and adsorption capacity can be ascribed to the strong hydrophobic property of SCCA/Zn.

  2. Adsorption of 4,6-dimethyldibenzothiophene and collidine over MoO3/γ-Al2O3 catalysts with different pore structures.

    PubMed

    Zhang, Di; Xue, Lijun; Xu, Yongqiang; Song, Lijuan; Liu, Xinmei

    2017-05-01

    Mesoporous γ-Al2O3 supports with different pore structures were prepared by the cation-anion double hydrolysis method. Based on these samples, MoO3/γ-Al2O3 catalysts were made via impregnation. The adsorptions of 4,6-dimethyldibenzothiophene (4,6-DMDBT) and collidine over the supports and catalysts were studied by FT-IR. The supports or catalysts with larger pores can adsorb more 4,6-DMDBT. The methyl groups on adsorbate molecules are very close to the sulfur atom, resulting in apparent steric hindrance. Increasing the pore size can promote the interaction between the adsorbates and supports or catalysts, enhancing the CC bond and weakening the CS bond of 4,6-DMDBT. 4,6-DMDBT molecules were coordinated with the unsaturated Mo atoms over the catalysts to form π-complexation adsorption. There was much difference between thiophene and 4,6-DMDBT adsorption. The adsorption of collidine over the catalysts also illustrated that there existed steric hindrance. Significantly, the catalyst with hierarchical mesopores was beneficial for the adsorbates with larger molecular dynamics diameter. Compared with the pore size, the specific surface area was not the key factor to affect the adsorptions of 4,6-DMDBT and collidine. The hydrodesulfurization reaction of 4,6-DMDBT illustrated that the catalysts with larger pore size or hierarchical pore structure presented higher desulfurization efficiency (above than 80%).

  3. Investigation of the pore structure and morphology of cellulose acetate membranes using small-angle neutron scattering. 2: Ultrafiltration and reverse-osmosis membranes

    SciTech Connect

    Kulkarni, S.; Krause, S. ); Wignall, G.D. . Solid State Div.)

    1994-11-07

    Pore structure in cellulose acetate ultrafiltration (UF) and reverse-osmosis (RO) membranes has been studied using small-angle neutron scattering. Scattering experiments were carried out on dry membranes as well as on membranes swollen with deuterated solvents (D[sub 2]O and CD[sub 3]OD). In addition, the RO membranes were studied both before and after annealing (a process of heating a membrane in a water bath at [approximately]75 C to improve its separation properties). The pore surface in UF membranes was found to be smooth and nonfractal, as evidenced by the fourth power law behavior at high Q. Values of average pore sizes obtained for dry and solvent swollen membranes agree well with pore sizes obtained by other methods. For cellulose acetate RO membranes in their dry state, the unannealed membrane appears to consist of two discrete pore size distributions in the intermediate and high Q region while the annealed membrane contains a much wider distribution of pore sizes. These results give a good account of the changes occurring in the structure of RO membranes as a result of annealing, and agree well with the prediction of other authors.

  4. Preparation, characterization, and condensation of copper tellurolate clusters in the pores of periodic mesoporous silica MCM-41.

    PubMed

    Kowalchuk, Collin M; Schmid, Günter; Meyer-Zaika, Wolfgang; Huang, Yining; Corrigan, John F

    2004-01-12

    The copper-tellurolate cluster [(Cu(6)(TePh)(6)(PPh(2)Et)(5)] has been loaded into the pores of MCM-41 by solid-state impregnation techniques. It was found that the best loading conditions are 110 degrees C and 10(-)(3) Torr static vacuum. The resulting material was analyzed by powder X-ray diffraction (PXRD), nitrogen adsorption isotherms, thermogravimetric analysis (TGA), (31)P CP MAS NMR spectroscopy, and TEM. It was observed that loading is accompanied by loss of the phosphine shell, with retention of the copper-tellurium core. Condensation of the impregnated material may proceed thermally or photochemically. Thermal condensation results in the formation of Cu(2)Te nanoparticles as demonstrated by PXRD, and TEM data suggests that the process has taken place inside the pores of MCM-41. Photochemical condensation yields larger metal-chalcogen clusters in the pores as suggested by the result of UV-vis diffuse reflectance spectroscopy and TEM measurements.

  5. Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex

    SciTech Connect

    Sampathkumar, Parthasarathy; Gheyi, Tarun; Miller, Stacy A.; Bain, Kevin T.; Dickey, Mark; Bonanno, Jeffrey B.; Kim, Seung Joong; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D.; Martel, Anne; Tsuruta, Hiro; Atwell, Shane; Thompson, Devon A.; Emtage, J. Spencer; Wasserman, Stephen R.; Rout, Michael P.; Sali, Andrej; Sauder, J. Michael; Burley, Stephen K.

    2012-10-23

    Nuclear pore complexes (NPCs), responsible for the nucleo-cytoplasmic exchange of proteins and nucleic acids, are dynamic macromolecular assemblies forming an eight-fold symmetric co-axial ring structure. Yeast (Saccharomyces cerevisiae) NPCs are made up of at least 456 polypeptide chains of {approx}30 distinct sequences. Many of these components (nucleoporins, Nups) share similar structural motifs and form stable subcomplexes. We have determined a high-resolution crystal structure of the C-terminal domain of yeast Nup133 (ScNup133), a component of the heptameric Nup84 subcomplex. Expression tests yielded ScNup133(944-1157) that produced crystals diffracting to 1.9{angstrom} resolution. ScNup133(944-1157) adopts essentially an all {alpha}-helical fold, with a short two stranded {beta}-sheet at the C-terminus. The 11 {alpha}-helices of ScNup133(944-1157) form a compact fold. In contrast, the previously determined structure of human Nup133(934-1156) bound to a fragment of human Nup107 has its constituent {alpha}-helices are arranged in two globular blocks. These differences may reflect structural divergence among homologous nucleoporins.

  6. Nitrogen-mediated effects of elevated CO2 on intra-aggregate soil pore structure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    While previous elevated atmospheric CO2 research has addressed changes in belowground processes, its effects on soil structure remain virtually undescribed. This study examined the long-term effects of elevated CO2 and N fertilization on soil structural changes in a bahiagrass pasture grown on a san...

  7. Modeling the construction of polymeric adsorbent media: effects of counter-ions on ligand immobilization and pore structure.

    PubMed

    Riccardi, Enrico; Wang, Jee-Ching; Liapis, Athanasios I

    2014-02-28

    Molecular dynamics modeling and simulations are employed to study the effects of counter-ions on the dynamic spatial density distribution and total loading of immobilized ligands as well as on the pore structure of the resultant ion exchange chromatography adsorbent media. The results show that the porous adsorbent media formed by polymeric chain molecules involve transport mechanisms and steric resistances which cause the charged ligands and counter-ions not to follow stoichiometric distributions so that (i) a gradient in the local nonelectroneutrality occurs, (ii) non-uniform spatial density distributions of immobilized ligands and counter-ions are formed, and (iii) clouds of counter-ions outside the porous structure could be formed. The magnitude of these counter-ion effects depends on several characteristics associated with the size, structure, and valence of the counter-ions. Small spherical counter-ions with large valence encounter the least resistance to enter a porous structure and their effects result in the formation of small gradients in the local nonelectroneutrality, higher ligand loadings, and more uniform spatial density distributions of immobilized ligands, while the formation of exterior counter-ion clouds by these types of counter-ions is minimized. Counter-ions with lower valence charges, significantly larger sizes, and elongated shapes, encounter substantially greater steric resistances in entering a porous structure and lead to the formation of larger gradients in the local nonelectroneutrality, lower ligand loadings, and less uniform spatial density distributions of immobilized ligands, as well as substantial in size exterior counter-ion clouds. The effects of lower counter-ion valence on pore structure, local nonelectroneutrality, spatial ligand density distribution, and exterior counter-ion cloud formation are further enhanced by the increased size and structure of the counter-ion. Thus, the design, construction, and functionality of

  8. Importance of open pore structures with mechanical integrity in designing the cathode electrode for lithium-sulfur batteries

    NASA Astrophysics Data System (ADS)

    Kim, C.-S.; Guerfi, A.; Hovington, P.; Trottier, J.; Gagnon, C.; Barray, F.; Vijh, A.; Armand, M.; Zaghib, K.

    2013-11-01

    The robustness of conductive networks and the accessibility of electrolyte into the network are important factors in designing the cathode electrode for lithium/sulfur (Li/S) batteries containing liquid electrolytes that involve liquid phase electrochemical reactions. We show that the performance of Li/S cells can be significantly improved by simply optimizing the electrode processing conditions to have open pore structures and mechanical integrity of the electrode architecture. It is demonstrated that the capacity of 1000 mAh g-1 at 0.1 C and the stable capacity retention of >700 mAh g-1 after 200 cycles at 0.5 C can be achieved with relatively high sulfur content of 68%. 417 Wh kg-1 in specific energy and 623 Wh l-1 in energy density are achievable with this new technology.

  9. Finite-size effects in the microscopic structure of a hard-sphere fluid in a narrow cylindrical pore.

    PubMed

    Román, F L; White, J A; González, A; Velasco, S

    2006-04-21

    We examine the microscopic structure of a hard-sphere fluid confined to a small cylindrical pore by means of Monte Carlo simulation. In order to analyze finite-size effects, the simulations are carried out in the framework of different statistical mechanics ensembles. We find that the size effects are specially relevant in the canonical ensemble where noticeable differences are found with the results in the grand canonical ensemble (GCE) and the isothermal isobaric ensemble (IIE) which, in most situations, remain very close to the infinite system results. A customary series expansion in terms of fluctuations of either the number of particles (GCE) or the inverse volume (IIE) allows us to connect with the results of the canonical ensemble.

  10. Optimization of Pore Structure of Cathodic Carbon Supports for Solvate Ionic Liquid Electrolytes Based Lithium-Sulfur Batteries.

    PubMed

    Zhang, Shiguo; Ikoma, Ai; Li, Zhe; Ueno, Kazuhide; Ma, Xiaofeng; Dokko, Kaoru; Watanabe, Masayoshi

    2016-10-04

    Lithium-sulfur (Li-S) batteries are a promising energy-storage technology owing to their high theoretical capacity and energy density. However, their practical application remains a challenge because of the serve shuttle effect caused by the dissolution of polysulfides in common organic electrolytes. Polysulfide-insoluble electrolytes, such as solvate ionic liquids (ILs), have recently emerged as alternative candidates and shown great potential in suppressing the shuttle effect and improving the cycle stability of Li-S batteries. Redox electrochemical reactions in polysulfide-insoluble electrolytes occur via a solid-state process at the interphase between the electrolyte and the composite cathode; therefore, creating an appropriate interface between sulfur and a carbon support is of great importance. Nevertheless, the porous carbon supports established for conventional organic electrolytes may not be suitable for polysulfide-insoluble electrolytes. In this work, we investigated the effect of the porous structure of carbon materials on the Li-S battery performance in polysulfide-insoluble electrolytes using solvate ILs as a model electrolyte. We determined that the pore volume (rather than the surface area) exerts a major influence on the discharge capacity of S composite cathodes. In particular, inverse opal carbons with three-dimensionally ordered interconnected macropores and a large pore volume deliver the highest discharge capacity. The battery performance in both polysulfide-soluble electrolytes and solvate ILs was used to study the effect of electrolytes. We propose a plausible mechanism to explain the different porous structure requirements in polysulfide-soluble and polysulfide-insoluble electrolytes.

  11. Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata

    SciTech Connect

    Sampathkumar, Parthasarathy; Kim, Seung Joong; Manglicmot, Danalyn; Bain, Kevin T.; Gilmore, Jeremiah; Gheyi, Tarun; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D.; Matsui, Tsutomu; Tsuruta, Hiro; Atwell, Shane; Thompson, Devon A.; Emtage, J. Spencer; Wasserman, Stephen R.; Rout, Michael P.; Sali, Andrej; Sauder, J. Michael; Almo, Steven C.; Burley, Stephen K.

    2012-10-23

    The nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and the cytoplasm. The yeast NPC is an eightfold symmetric annular structure composed of {approx}456 polypeptide chains contributed by {approx}30 distinct proteins termed nucleoporins. Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N-terminal 'FG' repeats containing a Gle2p-binding sequence motif and a NPC targeting domain at its C-terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882-1034 [CgNup116(882-1034)], at 1.94 {angstrom} resolution. The X-ray structure of CgNup116(882-1034) is consistent with the molecular envelope determined in solution by small-angle X-ray scattering. Structural similarities of CgNup116(882-1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiae Nup145N, and human Nup98 are discussed.

  12. Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata.

    PubMed

    Sampathkumar, Parthasarathy; Kim, Seung Joong; Manglicmot, Danalyn; Bain, Kevin T; Gilmore, Jeremiah; Gheyi, Tarun; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D; Matsui, Tsutomu; Tsuruta, Hiro; Atwell, Shane; Thompson, Devon A; Emtage, J Spencer; Wasserman, Stephen R; Rout, Michael P; Sali, Andrej; Sauder, J Michael; Almo, Steven C; Burley, Stephen K

    2012-08-01

    The nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and the cytoplasm. The yeast NPC is an eightfold symmetric annular structure composed of ~456 polypeptide chains contributed by ~30 distinct proteins termed nucleoporins. Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N-terminal "FG" repeats containing a Gle2p-binding sequence motif and a NPC targeting domain at its C-terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882-1034 [CgNup116(882-1034)], at 1.94 Å resolution. The X-ray structure of CgNup116(882-1034) is consistent with the molecular envelope determined in solution by small-angle X-ray scattering. Structural similarities of CgNup116(882-1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiae Nup145N, and human Nup98 are discussed.

  13. Application of Neutron imaging in pore structure of hydrated wellbore cement: comparison of hydration of H20 with D2O based Portland cements

    NASA Astrophysics Data System (ADS)

    Dussenova, D.; Bilheux, H.; Radonjic, M.

    2012-12-01

    Wellbore Cement studies have been ongoing for decades. The studies vary from efforts to reduce permeability and resistance to corrosive environment to issues with gas migration also known as Sustained Casing Pressure (SCP). These practical issues often lead to health and safety problems as well as huge economic loss in oil and gas industry. Several techniques have been employed to reduce the impact of gas leakage. In this study we purely focus on expandable liners, which are introduced as part of oil well reconstruction and work-overs and as well abandonment procedures that help in prevention of SCP. Expandable liner is a tube that after application of a certain tool can increase its diameter. The increase in diameter creates extra force on hydrated cement that results in reducing width of interface fractures and cement-tube de-bonding. Moreover, this also causes cement to change its microstructure and other porous medium properties, primarily hydraulic conductivity. In order to examine changes before and after operations, cement pore structure must be well characterized and correlated to cement slurry design as well as chemical and physical environmental conditions. As modern oil well pipes and tubes contain iron, it is difficult to perform X-ray tomography of a bulk measurement of the cement in its wellbore conditions, which are tube wall-cement-tube wall. Neutron imaging is a complementary technique to x-ray imaging and is well suited for detection of light elements imbedded in metallic containers. Thus, Neutron Imaging (NI) is investigated as a tool for the detection of pore structure of hydrated wellbore cement. Recent measurements were conducted at the Oak Ridge National Laboratory (ORNL) High Flux Isotope Reactor (HFIR) neutron imaging facility. NI is is highly sensitive to light elements such as Hydrogen (H). Oil well cements that have undergone a full hydration contain on average 30%-40% of free water in its pore structure. The unreacted water is the main

  14. Pore structure of raw and purified HiPco single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Cinke, Martin; Li, Jing; Chen, Bin; Cassell, Alan; Delzeit, Lance; Han, Jie; Meyyappan, M.

    2002-10-01

    Very high purity single-walled carbon nanotubes (SWNTs) were obtained from HiPco SWNT samples containing Fe particles by a two-step purification process. The raw and purified samples were characterized using high resolution transmission electron microscopy (HRTEM), Raman spectroscopy and thermogravimetric analysis (TGA). The purified sample consists of ˜0.4% Fe and the process does not seem to introduce any additional defects. The N 2 adsorption isotherm studies at 77 K reveal that the total surface area of the purified sample increases to 1587 m 2/g from 567 m 2/g for the raw material, which is the highest value reported for SWNTs.

  15. Automated Characterization Of Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

    Bayard, David S.; Yam, Yeung; Mettler, Edward; Hadaegh, Fred Y.; Milman, Mark H.; Scheid, Robert E.

    1992-01-01

    Automated method of characterizing dynamical properties of large flexible structure yields estimates of modal parameters used by robust control system to stabilize structure and minimize undesired motions. Based on extraction of desired modal and control-design data from responses of structure to known vibrational excitations. Applicable to terrestrial structures where vibrations are important - aircraft, buildings, bridges, cranes, and drill strings.

  16. Photonic band structures of periodic arrays of pores in a metallic host: tight-binding beyond the quasistatic approximation

    NASA Astrophysics Data System (ADS)

    Kim, Kwangmoo; Stroud, David

    2014-03-01

    We have calculated the photonic band structures of metallic inverse opals and of periodic linear chains of spherical pores in a metallic host, below a plasma frequency ωp. In both cases, we use a tight-binding approximation, assuming a Drude dielectric function for the metallic component, but without making the quasistatic approximation. The tight-binding modes are linear combinations of the single-cavity transverse magnetic (TM) modes. For the inverse-opal structures, the lowest modes are analogous to those constructed from the three degenerate atomic p-states in fcc crystals. For the linear chains, in the limit of small spheres compared to a wavelength, the results bear some qualitative resemblance to the dispersion relation for metal spheres in an insulating host, as calculated by Brongersma et al. [Phys. Rev. B 62, R16356 (2000)]. Because the electromagnetic fields of these modes decay exponentially in the metal, there are no radiative losses, in contrast to the case of arrays of metallic spheres in air. We suggest that this tight-binding approach to photonic band structures of such metallic inverse materials may be a useful approach for studying photonic crystals containing metallic components. This work was supported by KIAS, by NSF-MRSEC at OSU (DMR-0820414), and by DOE Grant No. DE-FG02-07ER46424. Computing resources were provided by OSC and by Abacus at KIAS.

  17. Photonic band structures of periodic arrays of pores in a metallic host: tight-binding beyond the quasistatic approximation.

    PubMed

    Kim, Kwangmoo; Stroud, D

    2013-08-26

    We have calculated the photonic band structures of metallic inverse opals and of periodic linear chains of spherical pores in a metallic host, below a plasma frequency ωp. In both cases, we use a tight-binding approximation, assuming a Drude dielectric function for the metallic component, but without making the quasistatic approximation. The tight-binding modes are linear combinations of the single-cavity transverse magnetic (TM) modes. For the inverse-opal structures, the lowest modes are analogous to those constructed from the three degenerate atomic p-states in fcc crystals. For the linear chains, in the limit of small spheres compared to a wavelength, the results bear some qualitative resemblance to the dispersion relation for metal spheres in an insulating host, as calculated by Brongersma et al. [Phys. Rev. B 62, R16356 (2000)]. Because the electromagnetic fields of these modes decay exponentially in the metal, there are no radiative losses, in contrast to the case of arrays of metallic spheres in air. We suggest that this tight-binding approach to photonic band structures of such metallic inverse materials may be a useful approach for studying photonic crystals containing metallic components, even beyond the quasistatic approximation.

  18. Electro-Spun Poly(vinylidene fluoride) Nanofiber Web as Separator for Lithium Ion Batteries: Effect of Pore Structure and Thickness.

    PubMed

    Lim, Seung-Gyu; Jo, Hye-Dam; Kim, Chan; Kim, Hee-Tak; Chang, Duck-Rye

    2016-01-01

    Electro-spun nanofiber web is highly attractive as a separator for lithium ion batteries because of its high electrical properties. In moving toward wider battery applications of the nanofiber separators, a deeper understanding on the structure and property relationship is highly meaningful. In this regard, we prepared electro-spun poly(vinylidene fluoride) (PVdF) webs with various thicknesses (10.5~100 µm) and investigated their structures and electrochemical performances. As the thickness of the web is decreased, a decrease of porosity and an increase of pore size are resulted in. For the 10.5 µm-thick separator, a minor short-circuit was detected, stressing the importance of reducing pore-size on prevention of short-circuit. However, above the thickness of 21 µm, well-connected, submicron-sized pores are generated, and, with lowering the separator thickness, discharge capacity and rate capability are enhanced owing to the lowered area-specific resistance.

  19. Process Developed for Fabricating Engineered Pore Structures for High- Fuel-Utilization Solid Oxide Fuel Cells

    NASA Technical Reports Server (NTRS)

    Sofie, Stephen W.; Cable, Thomas L.; Salamone, Sam M.

    2005-01-01

    Solid oxide fuel cells (SOFCs) have tremendous commercial potential because of their high efficiency, high energy density, and flexible fuel capability (ability to use fossil fuels). The drive for high-power-utilizing, ultrathin electrolytes (less than 10 microns), has placed an increased demand on the anode to provide structural support, yet allow sufficient fuel entry for sustained power generation. Concentration polarization, a condition where the fuel demand exceeds the supply, is evident in all commercial-based anode-supported cells, and it presents a significant roadblock to SOFC commercialization.

  20. Pore-Scale Effects of Soil Structure And Microbial EPS Production On Soil Water Retention

    NASA Astrophysics Data System (ADS)

    Orner, E.; Anderson, E.; Rubinstein, R. L.; Chau, J. F.; Shor, L. M.; Gage, D. J.

    2013-12-01

    Climate-induced changes to the hydrological cycle will increase the frequency of extreme weather events including powerful storms and prolonged droughts. Moving forward, one of the major factors limiting primary productivity in terrestrial ecosystems will be sub-optimal soil moisture. We focus here on the ability of soils to retain moisture under drying conditions. A soil's ability to retain moisture is influenced by many factors including its texture, its structure, and the activities of soil microbes. In soil microcosms, the addition of small amounts of microbially-produced extracellular polymeric substances (EPS) can dramatically shift moisture retention curves. The objective of this research is to better understand how soil structure and EPS may act together to retain moisture in unsaturated soils. Replicate micromodels with exactly-conserved 2-D physical geometry were initially filled with aqueous suspensions of one of two types of bacteria: one mutant was ultra- muccoid and the other was non-muccoid. Replicate micromodels were held at a fixed, external, relative humidity, and the position of the air-water interface was imaged over time as water evaporates. There was no forced convection of air or water inside the micromodels: drying was achieved by water evaporation and diffusion alone. We used a fully automated, inverted microscope to image replicate drying lanes each with dimensions of 1 mm x 10 mm. A complete set of images was collected every 30 minutes for 30 hours. The results show devices loaded with the highly muccoid strain remained >40% hydrated for 13 h, while devices loaded with the non-muccoid remained >40% hydrated for only 6 h, and were completely dry by 13 h. Current work is comparing interfacial water fluxes in structured and unstructured settings, and is attempting to model the synergistic effects of soil structure and EPS content on moisture retention in real soils. This research may allow more accurate description of naturally

  1. The estimation of permeability of a porous medium with a generalized pore structure by geometry identification

    NASA Astrophysics Data System (ADS)

    Rezaei Niya, S. M.; Selvadurai, A. P. S.

    2017-03-01

    The paper presents an approach for estimating the permeability of a porous medium that is based on the characteristics of the porous structure. The pressure drop in different fluid flow passages is estimated and these are combined to evaluate the overall reduction. The theory employed is presented and the level of accuracy for different cases is discussed. The successive steps in the solution algorithm are described. The accuracy and computational efficiency of the approach are compared with results obtained from a finite-element-based multiphysics formulation. It is shown that for a comparable accuracy, the computational efficiency of the approach can be two orders of magnitude faster. Finally, the model predictions are examined with conventional relationships that have been reported in the literature and are based on permeability-porosity relationships. It is shown that estimating the permeability of a porous medium using porosity can lead to an order of magnitude error and the expected permeability range in different porosities is presented using 10 000 random structures.

  2. Pore-scale Modeling on the Characterization of Kyeongsang Basin, South Korea for the Geological CO2 Sequestration

    NASA Astrophysics Data System (ADS)

    Han, J.; Keehm, Y.

    2011-12-01

    Carbon dioxide is a green-house gas and is believed to be responsible for global warming and climate change. Many countries are looking for various techniques for effective storage of CO2 and the geological sequestration is regarded as the most economical and efficient option. For successful geological sequestration, accurate evaluation of physical properties of the target formation and their changes when CO2 is injected, is essential. Since physical property changes during CO2 injection are strongly dependent on the pore-scale details of the target formation, we used a series of pore-scale simulation techniques including CO2 injection simulation to estimate physical properties of CO2 bearing formations. The study area, Kyeongsang basin is located in southeastern part of Korea, which has many industrial complexes including power plants. We first obtained high-resolution 3D microstructures from core samples of the prospective formation. We performed a set of pore-scale simulation and estimated physical properties, such as porosity, permeability, electrical conductivity and velocity. Then we used lattice-Boltzmann two-phase flow simulation to mimic CO2 injection into the formation. During this simulation, a variety of microstructures with different CO2 saturation were obtained and we again performed pore-scale simulation to estimate the changes of physical properties as CO2 saturation increases. These quantitative interrelations between physical properties and CO2 saturation would be a valuable piece of information to evaluate the performance of the target formation. Acknowledgement: This work was supported by the Energy Resources R&D program of the Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government Ministry of Knowledge Economy (No. 2010201020001A)

  3. 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.

  4. Design of novel 3D gene activated PEG scaffolds with ordered pore structure.

    PubMed

    Orsi, Silvia; Guarnieri, Daniela; Netti, Paolo A

    2010-03-01

    The ability to genetically modify cells seeded inside synthetic hydrogel scaffolds offers a suitable approach to induce and control tissue repair and regeneration guiding cell fate. In fact the transfected cells can act as local in vivo bioreactor, secreting plasmid encoded proteins that augment tissue regeneration processes. We have realized a DNA bioactivated high porous poly(ethylene glycol) (PEG) matrix by polyethyleneimine (PEI)/DNA complexes adsorption. As the design of the microarchitectural features of a scaffold also contributes to promote and influence cell fate, we appropriately designed the inner structure of gene activated PEG hydrogels by gelatine microparticles templating. Microarchitectural properties of the scaffold were analysed by scanning electron microscopy. 3D cell migration and transfection were monitored through time-lapse videomicroscopy and confocal laser scanning microscopy.

  5. On the complex structural diffusion of proton holes in nanoconfined alkaline solutions within slit pores

    PubMed Central

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-01-01

    The hydroxide anion OH−(aq) in homogeneous bulk water, that is, the solvated proton hole, is known to feature peculiar properties compared with excess protons solvated therein. In this work, it is disclosed that nanoconfinement of such alkaline aqueous solutions strongly affects the key structural and dynamical properties of OH−(aq) compared with the bulk limit. The combined effect of the preferred hypercoordinated solvation pattern of OH−(aq), its preferred perpendicular orientation relative to the confining surfaces, the pronounced layering of nanoconfined water and the topology of the hydrogen bond network required for proton hole transfer lead to major changes of the charge transport mechanism, in such a way that the proton hole migration mechanism depends exquisitely on the width of the confined space that hosts the water film. Moreover, the anionic Zundel complex, which is of transient nature in homogeneous bulk solutions, can be dynamically trapped as a shallow intermediate species by suitable nanoconfinement conditions. PMID:27550616

  6. Hemolytic lectin CEL-III heptamerizes via a large structural transition from α-helices to a β-barrel during the transmembrane pore formation process.

    PubMed

    Unno, Hideaki; Goda, Shuichiro; Hatakeyama, Tomomitsu

    2014-05-02

    CEL-III is a hemolytic lectin isolated from the sea cucumber Cucumaria echinata. This lectin is composed of two carbohydrate-binding domains (domains 1 and 2) and one oligomerization domain (domain 3). After binding to the cell surface carbohydrate chains through domains 1 and 2, domain 3 self-associates to form transmembrane pores, leading to cell lysis or death, which resembles other pore-forming toxins of diverse organisms. To elucidate the pore formation mechanism of CEL-III, the crystal structure of the CEL-III oligomer was determined. The CEL-III oligomer has a heptameric structure with a long β-barrel as a transmembrane pore. This β-barrel is composed of 14 β-strands resulting from a large structural transition of α-helices accommodated in the interface between domains 1 and 2 and domain 3 in the monomeric structure, suggesting that the dissociation of these α-helices triggered their structural transition into a β-barrel. After heptamerization, domains 1 and 2 form a flat ring, in which all carbohydrate-binding sites remain bound to cell surface carbohydrate chains, stabilizing the transmembrane β-barrel in a position perpendicular to the plane of the lipid bilayer.

  7. 3D bioprinting matrices with controlled pore structure and release function guide in vitro self-organization of sweat gland.

    PubMed

    Liu, Nanbo; Huang, Sha; Yao, Bin; Xie, Jiangfan; Wu, Xu; Fu, Xiaobing

    2016-10-03

    3D bioprinting matrices are novel platforms for tissue regeneration. Tissue self-organization is a critical process during regeneration that implies the features of organogenesis. However, it is not clear from the current evidences whether 3D printed construct plays a role in guiding tissue self-organization in vitro. Based on our previous study, we bioprinted a 3D matrix as the restrictive niche for direct sweat gland differentiation of epidermal progenitors by different pore structure (300-μm or 400-μm nozzle diameters printed) and reported a long-term gradual transition of differentiated cells into glandular morphogenesis occurs within the 3D construct in vitro. At the initial 14-day culture, an accelerated cell differentiation was achieved with inductive cues released along with gelatin reduction. After protein release completed, the 3D construct guide the self-organized formation of sweat gland tissues, which is similar to that of the natural developmental process. However, glandular morphogenesis was only observed in 300-μm-printed constructs. In the absence of 3D architectural support, glandular morphogenesis was not occurred. This striking finding made us to identify a previously unknown role of the 3D-printed structure in glandular tissue regeneration, and this self-organizing strategy can be applied to forming other tissues in vitro.

  8. 3D bioprinting matrices with controlled pore structure and release function guide in vitro self-organization of sweat gland

    PubMed Central

    Liu, Nanbo; Huang, Sha; Yao, Bin; Xie, Jiangfan; Wu, Xu; Fu, Xiaobing

    2016-01-01

    3D bioprinting matrices are novel platforms for tissue regeneration. Tissue self-organization is a critical process during regeneration that implies the features of organogenesis. However, it is not clear from the current evidences whether 3D printed construct plays a role in guiding tissue self-organization in vitro. Based on our previous study, we bioprinted a 3D matrix as the restrictive niche for direct sweat gland differentiation of epidermal progenitors by different pore structure (300-μm or 400-μm nozzle diameters printed) and reported a long-term gradual transition of differentiated cells into glandular morphogenesis occurs within the 3D construct in vitro. At the initial 14-day culture, an accelerated cell differentiation was achieved with inductive cues released along with gelatin reduction. After protein release completed, the 3D construct guide the self-organized formation of sweat gland tissues, which is similar to that of the natural developmental process. However, glandular morphogenesis was only observed in 300-μm–printed constructs. In the absence of 3D architectural support, glandular morphogenesis was not occurred. This striking finding made us to identify a previously unknown role of the 3D-printed structure in glandular tissue regeneration, and this self-organizing strategy can be applied to forming other tissues in vitro. PMID:27694985

  9. Structural basis for binding the TREX2 complex to nuclear pores, GAL1 localisation and mRNA export.

    PubMed

    Jani, Divyang; Valkov, Eugene; Stewart, Murray

    2014-06-01

    The conserved Sac3:Thp1:Sem1:Sus1:Cdc31 (TREX2) complex binds to nuclear pore complexes (NPCs) and, in addition to integrating mRNA nuclear export with preceding steps in the gene expression pathway, facilitates re-positioning of highly regulated actively transcribing genes (such as GAL1) to NPCs. Although TREX2 is thought to bind NPC protein Nup1, defining the precise role of this interaction has been frustrated by the complex pleiotropic phenotype exhibited by nup1Δ strains. To provide a structural framework for understanding the binding of TREX2 to NPCs and its function in the gene expression pathway, we have determined the structure of the Nup1:TREX2 interaction interface and used this information to engineer a Sac3 variant that impairs NPC binding while not compromising TREX2 assembly. This variant inhibited the NPC association of both de-repressed and activated GAL1 and also produced mRNA export and growth defects. These results indicate that the TREX2:Nup1 interaction facilitates the efficient nuclear export of bulk mRNA together with the re-positioning of GAL1 to NPCs that is required for transcriptional control that is mediated by removal of SUMO from repressors by NPC-bound Ulp1.

  10. cDNA cloning and characterization of Npap60: a novel rat nuclear pore-associated protein with an unusual subcellular localization during male germ cell differentiation.

    PubMed

    Fan, F; Liu, C P; Korobova, O; Heyting, C; Offenberg, H H; Trump, G; Arnheim, N

    1997-03-15

    We have cloned and characterized a cDNA, Npap60, encoding a rat nuclear pore-associated protein. The 3-kb cDNA was obtained by antibody screening of a rat testis expression library. The predicted NPAP60 contains 381 amino acids with a composition of 25.6% charged residues and is highly hydrophilic. The Npap60 gene appears to be conserved in mouse, rat, and human. Immunofluorescence studies with anti-NPAP60 fusion protein antibody show that the NPAP60 protein colocalizes with nuclear pore complexes in RAT1A cells. The expression of Npap60 is about 10-20 times higher in rat testis than in somatic tissues. The subcellular localization of NPAP60 protein changes dramatically during male germ cell differentiation, from nuclear pore complex-like staining in spermatocytes to whole nucleus staining in spermatids and finally to a nuclear surface staining in mature spermatozoa. These changes are temporally and spatially related to nuclear reorganization during male germ cell differentiation.

  11. Facile one-pot approach to the synthesis of spherical mesoporous silica nanoflowers with hierarchical pore structure

    NASA Astrophysics Data System (ADS)

    Yang, Hui; Liao, Shijun; Huang, Chao; Du, Li; Chen, Peng; Huang, Peiyan; Fu, Zhiyong; Li, Yingwei

    2014-09-01

    Hierarchically structured spherical mesoporous nanoflowers (HSMNF) with well-defined morphology and uniform size were synthesized by a hydrothermal method, in which a mixture of cyclohexane and water was used as the solvent, with cetylpyridinium bromide (CPB) as the template, tetraethyl orthosilicate as the source of inorganic silica, and urea as the hydrolysis additive. The flower size ranged from 200 nm to 500 nm, and the thickness of a “petal” was about 10 nm. We investigated the effects of solvent composition (Vcyclohexane/Vwater), hydrothermal temperature, and molar ratio of Si to CPB on morphology and structure. The presence of cyclohexane was found to be crucial for the nanoflowers to form, and a solvent with high cyclohexane content was beneficial for the formation of smaller and more uniform nanoflowers, whereas low cyclohexane content resulted in the collapse of the nanoflower structure. The optimal ratio of cyclohexane to water was 1:1 by volume. The hydrothermal temperature and molar ratio of Si to CPB strongly affected nanoflower size and structure, as well as petal thickness. The optimal hydrothermal temperature was 120 °C, and the optimal molar ratio of Si to CPB was 4.37. The sample synthesized under optimal conditions exhibited well-defined morphology and uniform flower size. Its BET surface area reached 502 m2/g. The nanoflowers were under 200 nm in diameter, and their average mesopore size was ca. 4 nm, as measured by N2 adsorption-desorption. Using synthesized nanoflowers as the support, we prepared a supported PdAu bimetallic catalyst for the hydrogenation of phenol. This catalyst exhibited high activity (with a conversion rate of up to 90%) and high selectivity for cyclohexanone (up to 92%). This nanoflower's morphology, high surface area, and large pore size may make it a valuable and promising material for applications in the catalysis, adsorption and controlled release of drugs fields.

  12. Impact of selected solvent systems on the pore and solid structure of cellulose aerogels.

    PubMed

    Pircher, Nicole; Carbajal, Leticia; Schimper, Christian; Bacher, Markus; Rennhofer, Harald; Nedelec, Jean-Marie; Lichtenegger, Helga C; Rosenau, Thomas; Liebner, Falk

    The impact of selected cellulose solvent systems based on the principal constituents tetrabutylammonium fluoride (TBAF), 1-ethyl-3-methyl-1H-imidazolium-acetate, N-methylmorpholine-N-oxide, or calcium thiocyanate octahydrate (CTO) on the properties of cellulose II aerogels prepared from these solvent systems has been investigated as a means towards tailoring cellulose aerogel properties with respect to specific applications. Cotton linters were used as representative plant cellulose. Cellulose was coagulated from solutions with comparable cellulose content, and dried with supercritical carbon dioxide after solvent exchange. The resulting bulk aerogels were comprehensively morphologically and mechanically tested to relate structure and mechanical properties. Different solvent systems caused considerable differences in the properties of the bulk samples, such as internal surface area (nitrogen sorption), morphology, porosity (He pycnometry, thermoporosimetry), and mechanical stability (compression testing). The results of SAXS, WAXS, and solid-state (13)C NMR spectroscopy suggest that this is due to different mechanisms of cellulose self-assembling on the supramolecular and nanostructural level, respectively, as reflected by the broad ranges of cellulose crystallinity, fibril diameter, fractal dimension and skeletal density. Both solid state NMR and WAXS experiments confirmed the sole existence of the cellulose II allomorph for all aerogels, with crystallinity reaching a maximum of 46-50 % for CTO-derived aerogels. Generally, higher fibril diameter, degree of crystallinity, hence increased skeletal density were associated with good preservation of shape and dimension throughout conversion of lyogels to aerogels, and enhanced mechanical stability, but somewhat reduced specific surface area. Amorphous, yet highly rigid aerogels derived from TBAF/DMSO mixtures deviated from this trend, most likely due to their particular homogeneous and nanostructured morphology.

  13. Restricted primitive model for electrolyte solutions in slit-like pores with grafted chains: microscopic structure, thermodynamics of adsorption, and electric properties from a density functional approach.

    PubMed

    Pizio, Orest; Sokołowski, Stefan

    2013-05-28

    We apply a density functional theory to describe properties of a restricted primitive model of an ionic fluid in slit-like pores. The pore walls are modified by grafted chains. The chains are built of uncharged or charged segments. We study the influence of modification of the pore walls on the structure, adsorption, ion selectivity, and the electric double layer capacitance of ionic fluid under confinement. The brush built of uncharged segments acts as a collection of obstacles in the walls vicinity. Consequently, separation of charges requires higher voltages, in comparison to the models without brushes. At high grafting densities the formation of crowding-type structure is inhibited. The double layer structure becomes more complex in various aspects, if the brushes are built of charged segments. In particular, the evolution of the brush height with the bulk fluid density and with the charge on the walls depends on the length of the blocks of charged spheres as well as on the distribution of charged species along chains. We also investigated how the dependence of the double layer capacitance on the electrostatic potential (or on the charge on the walls) changes with grafting density, the chain length, distribution of charges along the chain, the bulk fluid density, and, finally, with the pore width. The shape of the electric double layer capacitance vs. voltage changes from a camel-like to bell-like shape, if the bulk fluid density changes from low to moderate and high. If the bulk density is appropriately chosen, it is possible to alter the shape of this curve from the double hump to single hump by changing the grafting density. Moreover, in narrow pores one can observe the capacitance curve with even three humps for a certain set of parameters describing brush. This behavior illustrates how strong the influence of brushes on the electric double layer properties can be, particularly for ionic fluids in narrow pores.

  14. Characterisation of the Pore Structure of Functionalised Calcium Carbonate Tablets by Terahertz Time-Domain Spectroscopy and X-ray Computed Microtomography.

    PubMed

    Markl, Daniel; Wang, Parry; Ridgway, Cathy; Karttunen, Anssi-Pekka; Chakraborty, Mousumi; Bawuah, Prince; Pääkkönen, Pertti; Gane, Patrick; Ketolainen, Jarkko; Peiponen, Kai; Zeitler, J Axel

    2017-03-03

    Novel excipients are entering the market to enhance the bioavailability of drug particles by having a high porosity and thus providing a rapid liquid uptake and disintegration to accelerate subsequent drug dissolution. One example of such a novel excipient is functionalised calcium carbonate (FCC), which enables the manufacture of compacts with a bimodal pore size distribution consisting of larger inter-particle and fine intra-particle pores. Five sets of FCC tablets with a target porosity of 45% to 65% were prepared in 5% steps and characterised using terahertz time-domain spectroscopy (THz-TDS) and X- ray computed microtomography (XμCT). THz-TDS was employed to derive the porosity using effective medium approximations (EMAs), i.e., the traditional and an anisotropic Bruggeman model. The anisotropic Bruggeman model yields the better correlation with the nominal porosity (R(2) = 0.995) and it provided additional information about the shape and orientation of the pores within the powder compact. The spheroidal (ellipsoids of revolution) shaped pores have a preferred orientation perpendicular to the compaction direction causing an anisotropic behaviour of the dielectric porous medium. The results from XμCT confirmed the non-spherical shape as well as the orientation of the pores and it further revealed that the anisotropic behaviour is mainly caused by the inter-particle pores. The information from both techniques provide a detailed insight into the pore structure of pharmaceutical tablets. This is of great interest to study the impact of tablet microstructure on the disintegration and dissolution performance.

  15. Crystal structure of Cry51Aa1: A potential novel insecticidal aerolysin-type β-pore-forming toxin from Bacillus thuringiensis.

    PubMed

    Xu, Chengchen; Chinte, Unmesh; Chen, Lirong; Yao, Qingqing; Meng, Ying; Zhou, Dayong; Bi, Li-Jun; Rose, John; Adang, Michael J; Wang, Bi-Cheng; Yu, Ziniu; Sun, Ming

    2015-07-03

    The structures of several Bacillus thuringiensis (Bt) insecticidal crystal proteins have been determined by crystallographic methods and a close relationship has been explicated between specific toxicities and conserved three-dimensional architectures. In this study, as a representative of the coleopteran- and hemipteran-specific Cry51A group, the complete structure of Cry51Aa1 protoxin has been determined by X-ray crystallography at 1.65 Å resolution. This is the first report of a coleopteran-active Bt insecticidal toxin with high structural similarity to the aerolysin-type β-pore forming toxins (β-PFTs). Moreover, study of featured residues and structural elements reveal their possible roles in receptor binding and pore formation events. This study provides new insights into the action of aerolysin-type β-PFTs from a structural perspective, and could be useful for the control of coleopteran and hemipteran insect pests in agricultures.

  16. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola

    PubMed Central

    Dhakshnamoorthy, Balasundaresan; Rohaim, Ahmed; Rui, Huan; Blachowicz, Lydia; Roux, Benoît

    2016-01-01

    The selectivity filter is an essential functional element of K+ channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca2+ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca2+ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca2+ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel. PMID:27678077

  17. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola

    NASA Astrophysics Data System (ADS)

    Dhakshnamoorthy, Balasundaresan; Rohaim, Ahmed; Rui, Huan; Blachowicz, Lydia; Roux, Benoît

    2016-09-01

    The selectivity filter is an essential functional element of K+ channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca2+ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca2+ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca2+ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel.

  18. Low-temperature adsorption/storage of hydrogen on FAU, MFI, and MOR zeolites with various Si/Al ratios: effect of electrostatic fields and pore structures.

    PubMed

    Jhung, Sung Hwa; Yoon, Ji Woong; Lee, Ji Sun; Chang, Jong-San

    2007-01-01

    Several zeolites, such as faujasite, mordenite, and ZSM-5, with various aluminum contents have been used to analyze the effect of aluminum or cation concentration (strength of electrostatic field) on hydrogen adsorption at low temperature. Irrespective of the zeolite structure, the adsorption capacity, isosteric heat of adsorption (-DeltaHads), surface coverage, and micropore occupancy increase with increasing aluminum content of a zeolite. Zeolites with a higher amount of aluminum favorably adsorb hydrogen at relatively low pressures. For zeolites with similar aluminum contents, the adsorption capacity, isosteric heat of adsorption, surface coverage, and micropore occupancy are in the order of mordenite>ZSM-5>faujasite, probably due to differing pore sizes and the presence or absence of pore intersections. This work demonstrates that zeolites with strong electrostatic fields and narrow pores without intersections are beneficial for high hydrogen uptake.

  19. Characterization of reactive flow-induced evolution of carbonate rocks using digital core analysis- part 1: Assessment of pore-scale mineral dissolution and deposition

    NASA Astrophysics Data System (ADS)

    Qajar, Jafar; Arns, Christoph H.

    2016-09-01

    The application of X-ray micro-computed tomography (μ-CT) for quantitatively characterizing reactive-flow induced pore structure evolution including local particle detachment, displacement and deposition in carbonate rocks is investigated. In the studies conducted in this field of research, the experimental procedure has involved alternating steps of imaging and ex-situ core sample alteration. Practically, it is impossible to return the sample, with micron precision, to the same position and orientation. Furthermore, successive images of a sample in pre- and post-alteration states are usually taken at different conditions such as different scales, resolutions and signal-to-noise ratios. These conditions accompanying with subresolution features in the images make voxel-by-voxel comparisons of successive images problematic. In this paper, we first address the respective challenges in voxel-wise interpretation of successive images of carbonate rocks subject to reactive flow. Reactive coreflood in two carbonate cores with different rock types are considered. For the first rock, we used the experimental and imaging results published by Qajar et al. (2013) which showed a quasi-uniform dissolution regime. A similar reactive core flood was conducted in the second rock which resulted in wormhole-like dissolution regime. We particularly examine the major image processing operations such as transformation of images to the same grey-scale, noise filtering and segmentation thresholding and propose quantitative methods to evaluate the effectiveness of these operations in voxel-wise analysis of successive images of a sample. In the second part, we generalize the methodology based on the three-phase segmentation of normalized images, microporosity assignment and 2D histogram of image intensities to estimate grey-scale changes of individual image voxels for a general case where the greyscale images are segmented into arbitrary number of phases. The results show that local (voxel

  20. Characterization of reactive flow-induced evolution of carbonate rocks using digital core analysis- part 1: Assessment of pore-scale mineral dissolution and deposition.

    PubMed

    Qajar, Jafar; Arns, Christoph H

    2016-09-01

    The application of X-ray micro-computed tomography (μ-CT) for quantitatively characterizing reactive-flow induced pore structure evolution including local particle detachment, displacement and deposition in carbonate rocks is investigated. In the studies conducted in this field of research, the experimental procedure has involved alternating steps of imaging and ex-situ core sample alteration. Practically, it is impossible to return the sample, with micron precision, to the same position and orientation. Furthermore, successive images of a sample in pre- and post-alteration states are usually taken at different conditions such as different scales, resolutions and signal-to-noise ratios. These conditions accompanying with subresolution features in the images make voxel-by-voxel comparisons of successive images problematic. In this paper, we first address the respective challenges in voxel-wise interpretation of successive images of carbonate rocks subject to reactive flow. Reactive coreflood in two carbonate cores with different rock types are considered. For the first rock, we used the experimental and imaging results published by Qajar et al. (2013) which showed a quasi-uniform dissolution regime. A similar reactive core flood was conducted in the second rock which resulted in wormhole-like dissolution regime. We particularly examine the major image processing operations such as transformation of images to the same grey-scale, noise filtering and segmentation thresholding and propose quantitative methods to evaluate the effectiveness of these operations in voxel-wise analysis of successive images of a sample. In the second part, we generalize the methodology based on the three-phase segmentation of normalized images, microporosity assignment and 2D histogram of image intensities to estimate grey-scale changes of individual image voxels for a general case where the greyscale images are segmented into arbitrary number of phases. The results show that local (voxel

  1. Prediction of CO/sub 2/ flood performance: Interaction of phase behavior with microscopic pore structure heterogeneity

    SciTech Connect

    Dui, K.K.; Orr, F.M.

    1984-09-01

    This paper examines the effects of microscopic heterogeneity, present in rock pore structures or resulting from high water saturations, on the performance of one-dimensional CO/sub 2/ floods. A one-dimensional simulator, shown previously to model slim tube displacements quantitatively, was modified to include effects of an isolated or trapped fraction, unavailable for mixing with injected fluids, and a dendritic fraction, which exchanges material with the flowing fraction by mass transfer. Model formulation, numerical solution and validation tests are described. Results of simulations with no water present indicate that performance of a one-dimensional CO/sub 2/ flood is sensitive to restrictions to local mixing. Calculated oil recovery decreases as the flowing fraction, Peclet number and Damkohler number decrease. Comparisons of calculated and measured residual oil saturations in CO/sub 2/ core floods support this observation. Comparison of secondary and tertiary displacements by continuous CO/sub 2/ injection and alternate and simultaneous injection of CO/sub 2/ and water indicates that performance of secondary displacements is not strongly affected by restricted local mixing. In tertiary displacements, however, total oil recovery and the rate of recovery are reduced if effects of trapped and dendritic saturations are included.

  2. Effects of Temperature and Pore Structure on High Surface Area-Activated Carbon Obtained from Peanut Shells.

    PubMed

    Kalpana, D; Lee, Y S

    2016-03-01

    Activated carbon was synthesized from peanut shells by treating with H3PO4 with an intention to enhance the surface area and to find its electrochemical performance in EDLC as electrode material. The powdered peanut shells were pyrolyzed at three different temperatures namely 300 degrees C, 600 degrees C and 800 degrees C respectively. The structural and surface properties of the pyrolyzed carbon materials were studied using N2 adsorption/desorption, Raman, TEM and SEM analysis. There has been remarkable increase in the surface area of the carbon pyrolyzed at 600 degrees C due to the effect of pore generations. The surface area of the 600 degrees C pyrolyzed sample was found to be 1629 m2/g. The electrochemical properties of all the samples were evaluated by cyclic voltammetry, impedance spectroscopy, and galvanostatic charge-discharge tests. The system showed excellent cycleability and a maximum specific capacitance of 291 Fg(-1) was obtained in a 0.1 M H2SO4 electrolyte solution. The effects of the various properties of the activated carbon on the EDLC performance are discussed.

  3. Boosted Supercapacitive Energy with High Rate Capability of aCarbon Framework with Hierarchical Pore Structure in an Ionic Liquid.

    PubMed

    Wang, Xuehang; Zhou, Haitao; Lou, Fengliu; Li, Yahao; Buan, Marthe E M; Duan, Xuezhi; Walmsley, John C; Sheridan, Edel; Chen, De

    2016-11-09

    The specific energy of a supercapacitor (SC) with an ionic liquid (IL)-based electrolyte is larger than that using an aqueous electrolyte owing to the wide operating voltage window provided by the IL. However, the wide-scale application of high-energy SCs using ILs is limited owing to a serious reduction of the energy with increasing power. The introduction of macropores to the porous material can mitigate the reduction in the gravimetric capacitance at high rates, but this lowers the volumetric capacitance. Synthetic polymers can be used to obtain macroporous frameworks with high apparent densities, but the preservation of the frameworks during activation is challenging. To simultaneously achieve high gravimetric capacitance, volumetric capacitance, and rate capability, a systematic strategy was used to synthesize a densely knitted carbon framework with a hierarchical pore structure by using a polymer. The energy of the SC using the hierarchically porous carbon was 160 Wh kg(-1) and 85 Wh L(-1) on an active material base at a power of 100 W kg(-1) in an IL electrolyte, and 60 % of the energy was still retained at a power larger than 5000 W kg(-1) . To illustrate, a full-packaged SC with the material could store/release energy comparable to a Ni-metal hydride battery (gravimetrically) and one order of magnitude higher than a commercial carbon-based SC (volumetrically), within one minute.

  4. Relevance of Pore Structure and Diffusion-Accessible Porosity for Calcium-Bromide Diffusion in Na-Montmorillonite

    NASA Astrophysics Data System (ADS)

    Tinnacher, R. M.; Davis, J. A.

    2013-12-01

    Bentonite is an important hydraulic barrier material in many geotechnical applications, such as geosynthetic clay liners at solid waste landfills, or as proposed backfill material in engineered barrier systems at nuclear waste repositories. The limited permeability of bentonite is at least partially the result of its low porosity and the swelling of Na-montmorillonite, its major mineralogical component, in water. Due to these characteristics, the transport of contaminants through bentonite layers is expected to be limited and dominated by diffusion processes. In bentonite, the majority of the connected porosity is associated with montmorillonite particles, which consist of stacks of negatively-charged smectite layers. As a result, compacted smectite has two types of porosities: (1) large pores between clay particles, where diffusion is less affected by electric-double-layer forces, and (2) very thin interlayer spaces within individual clay particles, where diffusion is strongly impacted by surface charge and ionic strength. As diffusion is expected to take place differently in these two volumes, this essentially creates two 'small-scale diffusion pathways', where each may become dominant under different system conditions. Furthermore, for surface-reactive solutes, these two porous regimes differ with regards to surface complexation reactions. Electrostatic and hydration forces only are thought to govern interlayer binding, whereas chemical bonding with surface ligands is dominant for reactions at edge sites of layered clay particles and for iron oxide nanoparticles on outer basal planes. In this presentation, we will demonstrate the relevance of clay pore structure and diffusion-accessible porosity for solute diffusion rates, and hence, contaminant mobility in bentonites. First, we will discuss the effects of chemical solution conditions on montmorillonite properties, such as clay surface charge, diffusion-accessible porosity, clay tortuosity and constrictivity

  5. An Estimation Method of Pore Structure and Mineral Moduli Based on Kuster-Toksöz (KT) Model and Biot's Coefficient

    NASA Astrophysics Data System (ADS)

    Peng, Da; Yin, Cheng; Zhao, Hu; Liu, Wei

    2016-12-01

    Pore structure and mineral matrix elastic moduli are indispensable in rock physics models. We propose an estimation method of pore structure and mineral moduli based on Kuster-Toksöz model and Biot's coefficient. In this technique, pore aspect ratios of five different scales from 100 to 10-4 are considered, Biot's coefficient is used to determine bounds of mineral moduli, and an estimation procedure combined with simulated annealing (SA) algorithm to handle real logs or laboratory measurements is developed. The proposed method is applied to parameter estimations on 28 sandstone samples, the properties of which have been measured in lab. The water saturated data are used for estimating pore structure and mineral moduli, and the oil saturated data are used for testing these estimated parameters through fluid substitution in Kuster-Toksöz model. We then compare fluid substitution results with lab measurements and find that relative errors of P-wave and S-wave velocities are all less than 5%, which indicates that the estimation results are accurate.

  6. Structural Characterization of Schladitz Whiskers.

    DTIC Science & Technology

    1982-05-01

    and Eicke, 9 ,14 Lashmore ,16 and Newkirk and Wilsdorf. 1 7 7 I The ultimate tensile strength (UTS) of polycrystalline steel whiskers has been reported...have * Private communication by D. S. Lashmore , L. J. Swartzendruber and L. H. Bennett. 17 a combined with Fe to Fe 3 C. It was calculated that 18 + 2...by Lashmore (1977), and Schladitz (1968) reported values approach- ing 8 GPa. The structural details described in the previous chapter do not fit into

  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. Metal-organic frameworks: structure, properties, methods of synthesis and characterization

    NASA Astrophysics Data System (ADS)

    Butova, V. V.; Soldatov, M. A.; Guda, A. A.; Lomachenko, K. A.; Lamberti, C.

    2016-03-01

    This review deals with key methods of synthesis and characterization of metal-organic frameworks (MOFs). The modular structure affords a wide variety of MOFs with different active metal sites and organic linkers. These compounds represent a new stage of development of porous materials in which the pore size and the active site structure can be modified within wide limits. The set of experimental methods considered in this review is sufficient for studying the short-range and long-range order of the MOF crystal structure, determining the morphology of samples and elucidating the processes that occur at the active metal site in the course of chemical reactions. The interest in metal-organic frameworks results, first of all, from their numerous possible applications, ranging from gas separation and storage to chemical reactions within the pores. The bibliography includes 362 references.

  9. A physicochemical characterization of fully acetylated chitin structure isolated from two spider species: with new surface morphology.

    PubMed

    Kaya, Murat; Seyyar, Osman; Baran, Talat; Erdoğan, Sevil; Kar, Musa

    2014-04-01

    Spiders are a huge group which includes more than 44,000 species. But there has been no study of the chitin structure of spiders. In this study we physicochemically characterized chitin structure of two common spider species (Geolycosa vultuosa and Hogna radiata). Chitin content was determined as 8-8.5% for G. vultuosa and 6.5-7% for H. radiata. FTIR, TGA and XRD results showed that the chitin structures are in α-form. Environmental scanning electron microscopy (ESEM) revealed that the surface morphology of each species is different. Chitin yielded from G. vultuosa has two different pore structures. The type one pore is rarely sequenced and its size ranges between 190 and 240 nm, while the type two pore is tightly sequenced and its size ranges between 11 and 32 nm. There is no information in previous studies about the chitin structure with two different pore morphologies. A new chitin surface morphology has been determined in G. vultuosa. The chitin isolated from H. radiata, has classic morphology: nanofibre structures (10-17 nm) and 195-260 nm sized pores. Acetylation degree of the chitin samples was calculated as 97% for G. vultuosa and 99% for H. radiata in accordance with elemental analysis results.

  10. Health Monitoring for Airframe Structural Characterization

    NASA Technical Reports Server (NTRS)

    Munns, Thomas E.; Kent, Renee M.; Bartolini, Antony; Gause, Charles B.; Borinski, Jason W.; Dietz, Jason; Elster, Jennifer L.; Boyd, Clark; Vicari, Larry; Ray, Asok; Cooper, E. G. (Technical Monitor)

    2002-01-01

    This study established requirements for structural health monitoring systems, identified and characterized a prototype structural sensor system, developed sensor interpretation algorithms, and demonstrated the sensor systems on operationally realistic test articles. Fiber-optic corrosion sensors (i.e., moisture and metal ion sensors) and low-cycle fatigue sensors (i.e., strain and acoustic emission sensors) were evaluated to validate their suitability for monitoring aging degradation; characterize the sensor performance in aircraft environments; and demonstrate placement processes and multiplexing schemes. In addition, a unique micromachined multimeasure and sensor concept was developed and demonstrated. The results show that structural degradation of aircraft materials could be effectively detected and characterized using available and emerging sensors. A key component of the structural health monitoring capability is the ability to interpret the information provided by sensor system in order to characterize the structural condition. Novel deterministic and stochastic fatigue damage development and growth models were developed for this program. These models enable real time characterization and assessment of structural fatigue damage.

  11. X-ray and Cryo-electron Microscopy Structures of Monalysin Pore-forming Toxin Reveal Multimerization of the Pro-form.

    PubMed

    Leone, Philippe; Bebeacua, Cecilia; Opota, Onya; Kellenberger, Christine; Klaholz, Bruno; Orlov, Igor; Cambillau, Christian; Lemaitre, Bruno; Roussel, Alain

    2015-05-22

    β-Barrel pore-forming toxins (β-PFT), a large family of bacterial toxins, are generally secreted as water-soluble monomers and can form oligomeric pores in membranes following proteolytic cleavage and interaction with cell surface receptors. Monalysin has been recently identified as a β-PFT that contributes to the virulence of Pseudomonas entomophila against Drosophila. It is secreted as a pro-protein that becomes active upon cleavage. Here we report the crystal and cryo-electron microscopy structure of the pro-form of Monalysin as well as the crystal structures of the cleaved form and of an inactive mutant lacking the membrane-spanning region. The overall structure of Monalysin displays an elongated shape, which resembles those of β-pore-forming toxins, such as Aerolysin, but is devoid of a receptor-binding domain. X-ray crystallography, cryo-electron microscopy, and light-scattering studies show that pro-Monalysin forms a stable doughnut-like 18-mer complex composed of two disk-shaped nonamers held together by N-terminal swapping of the pro-peptides. This observation is in contrast with the monomeric pro-form of the other β-PFTs that are receptor-dependent for membrane interaction. The membrane-spanning region of pro-Monalysin is fully buried in the center of the doughnut, suggesting that upon cleavage of pro-peptides, the two disk-shaped nonamers can, and have to, dissociate to leave the transmembrane segments free to deploy and lead to pore formation. In contrast with other toxins, the delivery of 18 subunits at once, nearby the cell surface, may be used to bypass the requirement of receptor-dependent concentration to reach the threshold for oligomerization into the pore-forming complex.

  12. Fabrication, characterization, and application of microresonators and resonant structures

    NASA Astrophysics Data System (ADS)

    Cohoon, Gregory A.

    Optical resonators are structures that allow light to circulate and store energy for a duration of time. This work primarily looks at the fabrication, characterization, and application of whispering gallery mode microresonators and the analysis of organic photonic crystal-like structures and simulation of their resonant effects. Whispering gallery mode (WGM) microresonators are a class of cylindrically symmetric optical resonator which light circulates around the equator of the structure. These resonators are named after acoustic whispering galleries, where a whisper can be heard anywhere along the perimeter of a circular room. These optical structures are known for their ultra high Q-factor and their low mode volume. Q-factor describes the photon lifetime in the cavity and is responsible for the energy buildup within the cavity and sharp spectral characteristics of WGM resonators. The energy buildup is ideal for non-linear optics and the sharp spectral features are beneficial for sensing applications. Characterization of microbubble resonators is done by coupling light from a tunable laser source via tapered optical fiber into the cavity. The fabrication of quality tapered optical fiber on the order of 1--2 microm is critical to working on WGM resonators. The measurement of Q-factors up to 2x10 8 and mode spectra are possible with these resonators and experimental techniques. This work focuses on microdisk and microbubble WGM resonators. The microdisk resonators are fabricated by femtosecond laser micromachining. The micromachined resonators are fabricated by ablating rotating optical fiber to generate the disk shape and then heated to reflow the surface to improve optical quality. These resonators have a spares mode spectrum and display a Q factor as high a 2x106. The microbubble resonators are hollow microresonators fabricated by heating a pressurized capillary tube which forms a bubble in the area exposed to heat. These have a wall thickness of 2--5 microm and

  13. Modelling the effect of pore structure and wetting angles on capillary rise in soils having different wettabilities

    NASA Astrophysics Data System (ADS)

    Czachor, Henryk

    2006-09-01

    SummaryCapillary rise in axis symmetrical sinusoidal capillary (SC) has been modelled. Analytical formula for meniscus radius, capillary pressure and meniscus rate in SC have been found. Capillary shape described by wall waviness highly influences all of them. The limit between wettability and repellency in such capillary is described by critical value of contact angle θc which is related to the pore geometry by the equation ctg( θc) = πd2, where d2 - pore wall waviness. Kinetics of capillary rise in sinusoidal capillary has been determined by numerical integration of meniscus rate equation for a wide range of pore wall waviness and several values of contact angles. Application of Washburn theory to the data obtained from simulation gives the contact angle value much higher than the true one. In contrast, the obtained pore radius value is usually well correlated with capillary neck. However, in some cases a calculated radius can be even smaller. Above conclusions have been qualitatively confirmed by experiments performed on glass beads and soils. Contact angle measured on flat glass was 27.4°. The calculations concerning the data from capillary rise experiments on 90-1000 μm fraction of glass powder and Washburn theory gave values ca. 80°. The contact angle values for peat soils and loamy sand have close values, which supports the opinion that non-cylindrical shape of soil pores highly influences both the wettability/repellency and the water flux in soils.

  14. Structure and Functional Characterization of Vibrio parahaemolyticus Thermostable Direct Hemolysin*

    PubMed Central

    Yanagihara, Itaru; Nakahira, Kumiko; Yamane, Tsutomu; Kaieda, Shuji; Mayanagi, Kouta; Hamada, Daizo; Fukui, Takashi; Ohnishi, Kiyouhisa; Kajiyama, Shin'ichiro; Shimizu, Toshiyuki; Sato, Mamoru; Ikegami, Takahisa; Ikeguchi, Mitsunori; Honda, Takeshi; Hashimoto, Hiroshi

    2010-01-01

    Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 Å resolution. The TDH tetramer forms a central pore with dimensions of 23 Å in diameter and ∼50 Å in depth. π-Cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin. PMID:20335168

  15. Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin.

    PubMed

    Yanagihara, Itaru; Nakahira, Kumiko; Yamane, Tsutomu; Kaieda, Shuji; Mayanagi, Kouta; Hamada, Daizo; Fukui, Takashi; Ohnishi, Kiyouhisa; Kajiyama, Shin'ichiro; Shimizu, Toshiyuki; Sato, Mamoru; Ikegami, Takahisa; Ikeguchi, Mitsunori; Honda, Takeshi; Hashimoto, Hiroshi

    2010-05-21

    Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 A resolution. The TDH tetramer forms a central pore with dimensions of 23 A in diameter and approximately 50 A in depth. Pi-cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin.

  16. Fabrication and Structure Characterization of Alumina-Aluminum Interpenetrating Phase Composites

    NASA Astrophysics Data System (ADS)

    Dolata, Anna J.

    2016-08-01

    Alumina-Aluminum composites with interpenetrating networks structure belong to advanced materials with potentially better properties when compared with composites reinforced by particles or fibers. The paper presents the experimental results of fabrication and structure characterization of Al matrix composites locally reinforced via Al2O3 ceramic foam. The composites were obtained using centrifugal infiltration of porous ceramics by liquid aluminum alloy. Both scanning electron microscopy (SEM + EDS) and x-ray tomography were used to determine the structure of foams and composites especially in reinforced areas. The quality of castings, degree of pore filling in ceramic foams by Al alloy, and microstructure in area of interface were assessed.

  17. Pore-size dependent effects on structure and vibrations of 1-ethyl-3-methylimidazolium tetrafluoroborate in nanoporous carbon

    NASA Astrophysics Data System (ADS)

    Thürmer, Stephan; Kobayashi, Yoshikazu; Ohba, Tomonori; Kanoh, Hirofumi

    2015-09-01

    We report XRD and IR measurements of 1-ethyl-3-methylimidazolium tetrafluoroborate (EMI-BF4) adsorbed in activated carbons, molecular sieving carbon, and single wall carbon nanohorn, where we specifically chose a wide range of pore sizes from 0.5 nm to 2.5 nm. Electron radial distribution function analysis reveals denser packing upon adsorption in two steps, for pore widths larger and comparable to the ion size. Average ion-distance was decreased by 0.05 nm in the latter case. With support of DFT calculations we identify a suppression of specific vibrational modes, which are interpreted as constrainment by the pore walls. Possible consequences for supercapacitor application are discussed.

  18. Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels.

    PubMed

    Shaya, David; Findeisen, Felix; Abderemane-Ali, Fayal; Arrigoni, Cristina; Wong, Stephanie; Nurva, Shailika Reddy; Loussouarn, Gildas; Minor, Daniel L

    2014-01-23

    Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail "neck", are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the "outer ion" site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies, shows that this site forms a previously unknown determinant of CaV high-affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily.

  19. Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels

    PubMed Central

    Shaya, David; Findeisen, Felix; Abderemane-Ali, Fayal; Arrigoni, Cristina; Wong, Stephanie; Nurva, Shailika Reddy; Loussouarn, Gildas; Minor, Daniel L.

    2013-01-01

    Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail ‘neck’, are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the ‘outer ion’ site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies shows that this site forms a previously unknown determinant of CaV high affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily. PMID:24120938

  20. Expression of DNAJB12 or DNAJB14 causes coordinate invasion of the nucleus by membranes associated with a novel nuclear pore structure.

    PubMed

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

    2014-01-01

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

  1. Development of an in-situ soil structure characterization methodology

    NASA Astrophysics Data System (ADS)

    Debos, Endre; Kriston, Sandor

    2015-04-01

    The agricultural cultivation has several direct and indirect effects on the soil properties, among which the soil structure degradation is the best known and most detectable one. Soil structure degradation leads to several water and nutrient management problems, which reduce the efficiency of agricultural production. There are several innovative technological approaches aiming to reduce these negative impacts on the soil structure. The tests, validation and optimization of these methods require an adequate technology to measure the impacts on the complex soil system. This study aims to develop an in-situ soil structure and root development testing methodology, which can be used in field experiments and which allows one to follow the real time changes in the soil structure - evolution / degradation and its quantitative characterization. The method is adapted from remote sensing image processing technology. A specifically transformed A/4 size scanner is placed into the soil into a safe depth that cannot be reached by the agrotechnical treatments. Only the scanner USB cable comes to the surface to allow the image acquisition without any soil disturbance. Several images from the same place can be taken throughout the vegetation season to follow the soil consolidation and structure development after the last tillage treatment for the seedbed preparation. The scanned image of the soil profile is classified using supervised image classification, namely the maximum likelihood classification algorithm. The resulting image has two principal classes, soil matrix and pore space and other complementary classes to cover the occurring thematic classes, like roots, stones. The calculated data is calibrated with filed sampled porosity data. As the scanner is buried under the soil with no changes in light conditions, the image processing can be automated for better temporal comparison. Besides the total porosity each pore size fractions and their distributions can be calculated for

  2. Experiments In Characterizing Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

    Yam, Yeung; Hadaegh, Fred Y.; Bayard, David S.

    1993-01-01

    Report discusses experiments conducted to test methods of identification of vibrational and coupled rotational/vibrational modes of flexible structure. Report one in series that chronicle development of integrated system of methods, sensors, actuators, analog and digital signal-processing equipment, and algorithms to suppress vibrations in large, flexible structure even when dynamics of structure partly unknown and/or changing. Two prior articles describing aspects of research, "Autonomous Frequency-Domain Indentification" (NPO-18099), and "Automated Characterization Of Vibrations Of A Structure" (NPO-18141).

  3. Integrated Pore-Water and Geophysical Investigations StreamlineCharacterization of Ground-Water Discharges to Surface Water

    EPA Science Inventory

    This issue of Technology News and Trends highlights strategies and tools for characterizing or monitoring remediation of sites with contaminated sediment. Addressing these sites often relies upon dynamic workplans that involve more efficient, cost-effective, and practical methods...

  4. Structural characterization of unusually stable polycyclic ozonides

    NASA Astrophysics Data System (ADS)

    Cusati, R. C.; Pereira, U. A.; Barbosa, L. C. A.; Maltha, C. R. A.; Carneiro, José W. M.; Corrêa, R. S.; Doriguetto, A. C.

    2015-02-01

    The single crystal structure of seven tri- and tetracyclic ozonides derived from 8-oxabicycle[3.2.1]oct-6-en-3-ones have been characterized by X-ray diffraction method. Five ozonides (4, 5, 6, 7 and 8) crystallize in the monoclinic crystal system with P21/c space group. Compound 3 crystallize in the unusual centrosymmetric space group R 3 bar m, which represents ∼0.04% of the total number of structures know. The supramolecular structure of 3 forms infinite channels in a hexagram fashion, resulting in a honeycomb-like structure. Semi-empirical (PM6) and density functional theory methods (DFT) with the B3LYP functional and the 6-31G(d) basis set were used to optimize the geometries and compute structural parameters (bond lengths, angles and dihedral angles) that could be compared to the refined crystal structure. The theoretical results show good agreements with the experimental structure.

  5. Ion and water transport in a Nafion{reg_sign} membrane pore: A statistical mechanical model with molecular structure

    SciTech Connect

    Paddison, S.J.; Zawodzinski, T.A. Jr.; Paul, R.

    1998-12-31

    With the well established importance of the coupling of water and protons through electroosmotic drag in operating PEFCs the authors present here a derivation of a mathematical model that focuses on the computation of the mobility of an hydronium ion through an arbitrary cylindrical pore of a PEM with a non-uniform charge distribution on the walls of the pore. The total Hamiltonian is derived for the hydronium ion as it moves through the hydrated pore and is effected by the net potential due to interaction with the solvent molecules and the pendant side chains. The corresponding probability density is derived through solution of the Liouville equation. This probability density is then used to compute the friction tensor for the hydronium ion. The authors find two types of contributions: (a) due to the solvent-ion interactions for which they adopt the conventional continuum model; (b) due to the interaction between the pendant charges and the hydronium ion. The latter is a new result and displays the role of the non-uniform nature of the charge distribution on the pore wall.

  6. Electrochemical characterization of InP structures

    NASA Technical Reports Server (NTRS)

    Faur, Maria; Faur, Mircea; Vargas-Aburto, Carlos; Wilt, David M.; Goradia, Manju

    1992-01-01

    Electrochemical (EC) techniques represent a simple and yet accurate method to characterize InP and related materials structures. With EC techniques, uncertainties in the measurements arising from factors such as surface effects, the composition and thickness of a front dead layer, the contacts, etc., can be significantly reduced when both a suitable electrolyte is used and the measuring conditions are carefully selected. In this work, the use of photoelectrochemical techniques with InP structures is reported. The work focuses on both the characterization and the optimization of structures grown by thermal diffusion and by epitaxial methods. Characterization of the structures is done by studying the variation in the density of surface states, number of defects, and net majority carrier concentration as a function of material removed. A step-by-step optimization process of n(sup +)p and p(sup+)n InP structures is also described. This involves the passivation and subsequent removal of damaged layers in order to extract the performance parameters of solar cells fabricated with these structures.

  7. 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.

  8. Improving bone repair of femoral and radial defects in rabbit by incorporating PRP into PLGA/CPC composite scaffold with unidirectional pore structure.

    PubMed

    He, Fupo; Chen, Yan; Li, Jiyan; Lin, Bomiao; Ouyang, Yi; Yu, Bo; Xia, Yuanyou; Yu, Bo; Ye, Jiandong

    2015-04-01

    In this study, a platelet-rich plasma poly(lactic-co-glycolic acid) (PRP-PLGA)/calcium phosphate cement (CPC) composite scaffold was prepared by incorporating PRP into PLGA/CPC scaffold with unidirectional pore structure, which was fabricated by the unidirectional freeze casting of CPC slurry and the following infiltration of PLGA. The results from in vitro cell experiments and in vivo implantation in femoral defects manifested that incorporation of PRP into PLGA/CPC scaffold improved in vitro cell response (cell attachment, proliferation, and differentiation), and markedly boosted bone formation, angiogenesis and material degradation. The incorporation of PRP into scaffold showed more outstanding improvement in osteogenesis as the scaffolds were used to repair the segmental radial defects, especially at the early stage. The new bone tissues grew along the unidirectional lamellar pores of scaffold. At 12 weeks postimplantation, the segmental radial defects treated with PRP-PLGA/CPC scaffold had almost recuperated, whereas treated with the scaffold without PRP was far from healed. Taken together, the PRP-PLGA/CPC scaffold with unidirectional pore structure is a promising candidate to repair bone defects at various sites.

  9. The dependence of phase change enthalpy on the pore structure and interfacial groups in hydrated salts/silica composites via sol-gel.

    PubMed

    Wu, Yuping; Wang, Tao

    2015-06-15

    It was found that the procedures for incorporating hydrated salts into silica, including mixing with sol in an instant (S1 procedure), mixing with sol via drop by drop (S2 procedure) and mixing until the sol forming the gel (S3 procedure), had pronounced effects on the phase change enthalpy of hydrated salts/silica composite via sol-gel process. The discrepancy of phase change enthalpies of the composites with the same content of hydrated salts can be as high as 40 kJ/kg. To unveil the mechanism behind, the pore structure of silica matrix and interfacial functional groups were investigated extensively. It was revealed that different incorporation procedures resulted in distinct pore structure of silica matrix and different intensities of interfacial Si-OH groups. The S3 procedure was beneficial to induce the silica matrix with bigger pore size and fewer Si-OH groups. Consequently, the phase change enthalpy of the hydrated salts/silica composite prepared by this procedure was the highest because of its lower size confinement effects and weaker adsorption by Si-OH groups. This study will provide insight into the preparation of shape-stabilized phase change materials for thermal energy storage applications.

  10. Pore-water chemistry from the ICDP-USGS core hole in the Chesapeake Bay impact structure-Implications for paleohydrology, microbial habitat, and water resources

    USGS Publications Warehouse

    Sanford, W.E.; Voytek, M.A.; Powars, D.S.; Jones, B.F.; Cozzarelli, I.M.; Cockell, C.S.; Eganhouse, R.P.

    2009-01-01

    We investigated the groundwater system of the Chesapeake Bay impact structure by analyzing the pore-water chemistry in cores taken from a 1766-m-deep drill hole 10 km north of Cape Charles, Virginia. Pore water was extracted using high-speed centrifuges from over 100 cores sampled from a 1300 m section of the drill hole. The pore-water samples were analyzed for major cations and anions, stable isotopes of water and sulfate, dissolved and total carbon, and bioavailable iron. The results reveal a broad transition between freshwater and saline water from 100 to 500 m depth in the postimpact sediment section, and an underlying synimpact section that is almost entirely filled with brine. The presence of brine in the lowermost postimpact section and the trend in dissolved chloride with depth suggest a transport process dominated by molecular diffusion and slow, compaction-driven, upward flow. Major ion results indicate residual effects of diagenesis from heating, and a pre-impact origin for the brine. High levels of dissolved organic carbon (6-95 mg/L) and the distribution of electron acceptors indicate an environment that may be favorable for microbial activity throughout the drilled section. The concentration and extent of the brine is much greater than had previously been observed, suggesting that its occurrence may be common in the inner crater. However, groundwater-flow conditions in the structure may reduce the saltwater-intrusion hazard associated with the brine. ?? 2009 The Geological Society of America.

  11. Pore-water chemistry from the ICDP-USGS coer hole in the Chesapeake Bay impact structure--Implications for paleohydrology, microbial habitat, and water resources

    USGS Publications Warehouse

    Sanford, Ward E.; Voytek, Mary A.; Powars, David S.; Jones, Blair F.; Cozzarelli, Isabelle M.; Eganhouse, Robert P.; Cockell, Charles S.

    2009-01-01

    We investigated the groundwater system of the Chesapeake Bay impact structure by analyzing the pore-water chemistry in cores taken from a 1766-m-deep drill hole 10 km north of Cape Charles, Virginia. Pore water was extracted using high-speed centrifuges from over 100 cores sampled from a 1300 m section of the drill hole. The pore-water samples were analyzed for major cations and anions, stable isotopes of water and sulfate, dissolved and total carbon, and bioavailable iron. The results reveal a broad transition between fresh and saline water from 100 to 500 m depth in the post-impact sediment section, and an underlying syn-impact section that is almost entirely filled with brine. The presence of brine in the lowermost post-impact section and the trend in the dissolved chloride with depth suggest a transport process dominated by molecular diffusion and slow, compaction-driven, upward flow. Major ion results indicate residual effects of diagenesis from heating, and a pre-impact origin for the brine. High levels of dissolved organic carbon (6-95 mg/L) and the distribution of electron acceptors indicate an environment that may be favorable for microbial activity throughout the drilled section. The concentration and extent of the brine is much greater than had previously been observed, suggesting its occurrence may be common in the inner crater. However, groundwater flow conditions in the structure may reduce the salt-water-intrusion hazard associated with the brine.

  12. A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels

    PubMed Central

    Napolitano, Luisa Maria Rosaria; Bisha, Ina; De March, Matteo; Marchesi, Arin; Arcangeletti, Manuel; Demitri, Nicola; Mazzolini, Monica; Rodriguez, Alex; Magistrato, Alessandra; Onesti, Silvia; Laio, Alessandro; Torre, Vincent

    2015-01-01

    Cyclic nucleotide-gated (CNG) ion channels, despite a significant homology with the highly selective K+ channels, do not discriminate among monovalent alkali cations and are permeable also to several organic cations. We combined electrophysiology, molecular dynamics (MD) simulations, and X-ray crystallography to demonstrate that the pore of CNG channels is highly flexible. When a CNG mimic is crystallized in the presence of a variety of monovalent cations, including Na+, Cs+, and dimethylammonium (DMA+), the side chain of Glu66 in the selectivity filter shows multiple conformations and the diameter of the pore changes significantly. MD simulations indicate that Glu66 and the prolines in the outer vestibule undergo large fluctuations, which are modulated by the ionic species and the voltage. This flexibility underlies the coupling between gating and permeation and the poor ionic selectivity of CNG channels. PMID:26100907

  13. A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels.

    PubMed

    Napolitano, Luisa Maria Rosaria; Bisha, Ina; De March, Matteo; Marchesi, Arin; Arcangeletti, Manuel; Demitri, Nicola; Mazzolini, Monica; Rodriguez, Alex; Magistrato, Alessandra; Onesti, Silvia; Laio, Alessandro; Torre, Vincent

    2015-07-07

    Cyclic nucleotide-gated (CNG) ion channels, despite a significant homology with the highly selective K(+) channels, do not discriminate among monovalent alkali cations and are permeable also to several organic cations. We combined electrophysiology, molecular dynamics (MD) simulations, and X-ray crystallography to demonstrate that the pore of CNG channels is highly flexible. When a CNG mimic is crystallized in the presence of a variety of monovalent cations, including Na(+), Cs(+), and dimethylammonium (DMA(+)), the side chain of Glu66 in the selectivity filter shows multiple conformations and the diameter of the pore changes significantly. MD simulations indicate that Glu66 and the prolines in the outer vestibule undergo large fluctuations, which are modulated by the ionic species and the voltage. This flexibility underlies the coupling between gating and permeation and the poor ionic selectivity of CNG channels.

  14. Pore structure and dielectric behaviour of the 3D collagen-DAC scaffolds designed for nerve tissue repair.

    PubMed

    Pietrucha, Krystyna; Marzec, Ewa; Kudzin, Marcin

    2016-11-01

    The design and selection of a suitable scaffold with well-defined pores size distribution and dielectric properties are critical features for neural tissue engineering. In this study we use mercury porosimetry and the dielectric spectroscopy in the alpha-dispersion region of the electric field to determine the microarchitecture and activation energy of collagen (Col) modified by 2,3 dialdehyde cellulose (DAC). The scaffold was synthesized in three steps: (i) preparation of DAC by oxidation of cellulose, (ii) construction of a 3D Col sponge-shape or film, (iii) cross-linkage of the Col samples using DAC. The activation energy needed to break the bonds formed by water in the Col-DAC composite is approximately 2 times lower than that in the unmodified Col. In addition, the magnitude of conductivity for modified Col at 70°C is approximately 40% lower than that recorded for the unmodified Col. The largest fraction, of which at least 70% of the total pore volume comprises the sponge, is occupied by pores ranging from 20 to 100μm in size. The knowledge on the dielectric behaviour and microstructure of the Col-DAC scaffold may prove relevant to neural tissue engineering focused on the regeneration of the nervous system.

  15. The role of the C terminus of the SNARE protein SNAP-25 in fusion pore opening and a model for fusion pore mechanics

    PubMed Central

    Fang, Qinghua; Berberian, Khajak; Gong, Liang-Wei; Hafez, Ismail; Sørensen, Jakob B.; Lindau, Manfred

    2008-01-01

    Formation of a fusion pore between a vesicle and its target membrane is thought to involve the so-called SNARE protein complex. However, there is no mechanistic model explaining how the fusion pore is opened by conformational changes in the SNARE complex. It has been suggested that C-terminal zipping triggers fusion pore opening. A SNAP-25 mutant named SNAP-25Δ9 (lacking the last nine C-terminal residues) should lead to a less-tight C-terminal zipping. Single exocytotic events in chromaffin cells expressing this mutant were characterized by carbon fiber amperometry and cell-attached patch capacitance measurements. Cells expressing SNAP-25Δ9 displayed smaller amperometric “foot-current” currents, reduced fusion pore conductances, and lower fusion pore expansion rates. We propose that SNARE/lipid complexes form proteolipid fusion pores. Fusion pores involving the SNAP-25Δ9 mutant will be less tightly zipped and may lead to a longer fusion pore structure, consistent with the observed decrease of fusion pore conductance. PMID:18829435

  16. Pre-pore oligomer formation by Vibrio cholerae cytolysin: insights from a truncated variant lacking the pore-forming pre-stem loop.

    PubMed

    Paul, Karan; Chattopadhyay, Kausik

    2014-01-03

    Vibrio cholerae cytolysin (VCC), a β-barrel pore-forming toxin (β-PFT), induces killing of the target eukaryotic cells by forming heptameric transmembrane β-barrel pores. Consistent with the β-PFT mode of action, binding of the VCC toxin monomers with the target cell membrane triggers formation of pre-pore oligomeric intermediates, followed by membrane insertion of the β-strands contributed by the pre-stem motif within the central cytolysin domain of each protomer. It has been shown previously that blocking of membrane insertion of the VCC pre-stem motif arrests conversion of the pre-pore state to the functional transmembrane pore. Consistent with the generalized β-PFT mechanism, it therefore appears that the VCC pre-stem motif plays a critical role toward forming the structural scaffold of the transmembrane β-barrel pore. It is, however, still not known whether the pre-stem motif plays any role in the membrane interaction process, and subsequent pre-pore structure formation by VCC. In this direction, we have constructed a recombinant variant of VCC deleting the pre-stem region, and have characterized the effect(s) of physical absence of the pre-stem motif on the distinct steps of the membrane pore-formation process. Our results show that the deletion of the pre-stem segment does not affect membrane binding and pre-pore oligomer formation by the toxin, but it critically abrogates the functional pore-forming activity of VCC. Present study extends our insights regarding the structure-function mechanism associated with the membrane pore formation by VCC, in the context of the β-PFT mode of action.

  17. In-situ characterization of wettability and pore-scale displacements during two- and three-phase flow in natural porous media

    NASA Astrophysics Data System (ADS)

    Khishvand, M.; Alizadeh, A. H.; Piri, M.

    2016-11-01

    We establish a unique approach to measure in-situ contact angle from micro-CT images acquired during two- and three-phase miniature core-flooding experiments in order to overcome the uncertainties associated with conventional contact angle measurement techniques. The measurements are used to quantify the wettability behavior of the rock and explain pore-level displacement events occurring in three-phase flow. Six two-phase experiments are performed on individual core samples with three pairs of fluids, i.e., oil-brine, gas-oil, and gas-brine, and under two thermodynamic conditions: (a) binary-equilibrated, when only the two respective phases are at equilibrium and (b) ternary-equilibrated, when all three phases are equilibrated and only the two desired fluids are injected into the core. A three-phase experiment set is also performed under ternary-equilibrated conditions, which includes gas injection, a waterflood, and an oilflood process. All experiments are performed on Berea miniature core samples using a nonspreading brine-oil-gas fluid system. We measure receding and advancing contact angles at arc menisci and main terminal menisci for the two-phase binary-equilibrated experiments and characterize contact angle hysteresis for each fluid pair. Contact angle hysteresis values are almost identical for all fluid pairs. The results of the two-phase binary- and ternary-equilibrated experiments show similar contact angle distributions for each fluid pair. Contact angle distributions during the three-phase flow experiment are analyzed to develop new insights into relevant complex displacement mechanisms. The results indicate that, during gas injection, the majority of displacements involving oil and water are oil-to-water events. It is observed that, during the waterflood, both oil-to-gas and gas-to-oil displacement events take place. However, the relative frequency of the former is greater. For the oilflood, gas-water interfaces only slightly hinge in pore elements

  18. Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism.

    PubMed

    Uchida, Tatsuya; Yamasaki, Takayuki; Eto, Seiichiro; Sugawara, Hajime; Kurisu, Genji; Nakagawa, Atsushi; Kusunoki, Masami; Hatakeyama, Tomomitsu

    2004-08-27

    CEL-III is a Ca(2+)-dependent and galactose-specific lectin purified from the sea cucumber, Cucumaria echinata, which exhibits hemolytic and hemagglutinating activities. Six molecules of CEL-III are assumed to oligomerize to form an ion-permeable pore in the cell membrane. We have determined the crystal structure of CELIII by using single isomorphous replacement aided by anomalous scattering in lead at 1.7 A resolution. CEL-III consists of three distinct domains as follows: the N-terminal two carbohydrate-binding domains (1 and 2), which adopt beta-trefoil folds such as the B-chain of ricin and are members of the (QXW)(3) motif family; and domain 3, which is a novel fold composed of two alpha-helices and one beta-sandwich. CEL-III is the first Ca(2+)-dependent lectin structure with two beta-trefoil folds. Despite sharing the structure of the B-chain of ricin, CEL-III binds five Ca(2+) ions at five of the six subdomains in both domains 1 and 2. Considering the relatively high similarity among the five subdomains, they are putative binding sites for galactose-related carbohydrates, although it remains to be elucidated whether bound Ca(2+) is directly involved in interaction with carbohydrates. The paucity of hydrophobic interactions in the interfaces between the domains and biochemical data suggest that these domains rearrange upon carbohydrate binding in the erythrocyte membrane. This conformational change may be responsible for oligomerization of CEL-III molecules and hemolysis in the erythrocyte membranes.

  19. 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.

  20. Structural characterization of electrospun micro/nanofibrous scaffolds by liquid extrusion porosimetry: a comparison with other techniques.

    PubMed

    Cortez Tornello, Pablo R; Caracciolo, Pablo C; Cuadrado, Teresita R; Abraham, Gustavo A

    2014-08-01

    Poly(ε-caprolactone) micro/nanofibrous scaffolds obtained by electrospinning technique from polymer solutions were characterized in terms of fiber diameter (as measured by scanning electron microscopy-SEM), pore size and its distribution (as measured by liquid extrusion porosimetry), and porosity (as determined by gravimetric measurement, liquid intrusion method, SEM image analysis and liquid extrusion porosimetry - LEP). Nonwoven micro/nanofibrous scaffolds were formed by uniform bead-free fibers with mean diameters in the range of 0.4 to 7 μm. The results indicate that pore size and pore size distribution are strongly associated to fiber diameter. Porosity results were analyzed taking into account the accuracy and limitations of each method. LEP resulted as the most suitable technique for measuring through-pore diameter and porosity. In order to compare empirical data of pore size from LEP, a theoretical multiplanar model for stochastic fiber networks was applied. The results predicted by the model were in good agreement with the experimental data provided by LEP for mean diameters higher than 1 μm. The present study shows the potential of LEP as a valuable instrumental technique for characterizing the porous structure of electrospun fibrous scaffolds.

  1. 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).

  2. Characterization and Cure Monitoring of Structural Adhesives

    DTIC Science & Technology

    1989-02-01

    OX tiLE (OP? MTL TR 89-15 AD CHARACTERIZATION AND CURE MONITORING OF STRUCTURAL ADHESIVES CD WALTER X. ZUKAS, HOWARD H. WONG, DAVID A. DUNN, and...REPORT NUMB3ER 7. AUTHOR(s) 8. CONTRACT OR GRANT NUMBERs) Walter X. Zukas, Howard H. Wong, David A. Dunn, and Stanley E. Wentworth I. PERFORING...Technology, Gaithersburg, MD 20899 1 ATTN: B. Fanconi, Polymer Standards Division 1 D. Hunston, Polymer Standards Division 1 Dr. Stanley M. Barkin , Staff

  3. 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

  4. Instrumentation for the Characterization of Inflatable Structures

    NASA Technical Reports Server (NTRS)

    Swanson, Gregory T.; Cassell, Alan M.; Johnson, R. Keith

    2012-01-01

    Current entry, descent, and landing technologies are not practical for heavy payloads due to mass and volume constraints dictated by limitations imposed by launch vehicle fairings. Therefore, new technologies are now being explored to provide a mass- and volume-efficient solution for heavy payload capabilities, including Inflatable Aerodynamic Decelerators (IAD) [1]. Consideration of IADs for space applications has prompted the development of instrumentation systems for integration with flexible structures to characterize system response to flight-like environment testing. This development opportunity faces many challenges specific to inflatable structures in extreme environments, including but not limited to physical flexibility, packaging, temperature, structural integration and data acquisition [2]. In the spring of 2012, two large scale Hypersonic Inflatable Aerodynamic Decelerators (HIAD) will be tested in the National Full-Scale Aerodynamics Complex s 40 by 80 wind tunnel at NASA Ames Research Center. The test series will characterize the performance of a 3.0 m and 6.0 m HIAD at various angles of attack and levels of inflation during flight-like loading. To analyze the performance of these inflatable test articles as they undergo aerodynamic loading, many instrumentation systems have been researched and developed. These systems will utilize new experimental sensing systems developed by the HIAD ground test campaign instrumentation team, in addition to traditional wind tunnel sensing techniques in an effort to improve test article characterization and model validation. During the 2012 test series the instrumentation systems will target inflatable aeroshell static and dynamic deformation, structural strap loading, surface pressure distribution, localized skin deflection, and torus inflation pressure. This paper will offer an overview of inflatable structure instrumentation, and provide detail into the design and implementation of the sensors systems that will

  5. 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.

  6. Characterization of multi-scale porous structure of fly ash/phosphate geopolymer hollow sphere structures: from submillimeter to nano-scale.

    PubMed

    Li, Ruifeng; Wu, Gaohui; Jiang, Longtao; Sun, Dongli

    2015-01-01

    In the present work, the porous structure of fly ash/phosphate geopolymer hollow sphere structures (FPGHSS), prepared by pre-bonding and curing technology, has been characterized by multi-resolution methods from sub-millimeter to nano-scale. Micro-CT and confocal microscopy could provide the macroscopic distribution of porous structure on sub-millimeter scale, and hollow fly ashes with sphere shape and several sub-millimeter open cells with irregular shape were identified. SEM is more suitable to illustrate the distribution of micro-sized open and closed cells, and it was found that the open cells of FPGHSS were mainly formed in the interstitial porosity between fly ashes. Mercury porosimeter measurement showed that the micro-sized open cell of FPGHSS demonstrated a normal/bimodal distribution, and the peaks of pore size distribution were mainly around 100 and 10 μm. TEM observation revealed that the phosphate geopolymer was mainly composed of the porous area with nano-pores and dense areas, which were amorphous Al-O-P phase and α-Al2O3 respectively. The pore size of nano-pores demonstrated a quasi-normal distribution from about 10 to 100 nm. Therefore, detailed information of the porous structure of FPGHSS could be revealed using multiple methods.

  7. Improvement of cell response of the poly(lactic-co-glycolic acid)/calcium phosphate cement composite scaffold with unidirectional pore structure by the surface immobilization of collagen via plasma treatment.

    PubMed

    He, Fupo; Li, Jiyan; Ye, Jiandong

    2013-03-01

    In this study, calcium phosphate cement (CPC)-based scaffold with unidirectional lamellar pore structure was fabricated by unidirectional freeze casting. Poly(lactic-co-glycolic acid) (PLGA) was infiltrated into the CPC scaffold to improve its strength and toughness, which compromised the bioactivity and osteoconductivity of CPC. Collagen (Col) was immobilized on the pore surface of the PLGA/CPC scaffold to enhance the bioactivity of the scaffold using plasma treatment under the ammonia (NH(3)) atmosphere. The immobilization of collagen was characterized by infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). Compared to the PLGA/CPC composite scaffold, the Col/PLGA/CPC composite scaffold had higher contact angle, porosity and water absorption, while the compressive strength of both scaffolds was comparable. Rat bone marrow mesenchymal stem cells (rMSCs) seeded on the Col/PLGA/CPC scaffold showed markedly improved cell seeding, attachment, proliferation and differentiation than those on the PLGA/CPC scaffold. These results suggest that the surface immobilization of collagen by plasma treatment can improve the bioactivity of the PLGA/CPC scaffold and the Col/PLGA/CPC composite scaffold is a promising candidate for bone tissue engineering.

  8. X-ray Crystallographic Structures of a Trimer, Dodecamer, and Annular Pore Formed by an Aβ17-36 β-Hairpin.

    PubMed

    Kreutzer, Adam G; Hamza, Imane L; Spencer, Ryan K; Nowick, James S

    2016-04-06

    High-resolution structures of oligomers formed by the β-amyloid peptide Aβ are needed to understand the molecular basis of Alzheimer's disease and develop therapies. This paper presents the X-ray crystallographic structures of oligomers formed by a 20-residue peptide segment derived from Aβ. The development of a peptide in which Aβ17-36 is stabilized as a β-hairpin is described, and the X-ray crystallographic structures of oligomers it forms are reported. Two covalent constraints act in tandem to stabilize the Aβ17-36 peptide in a hairpin conformation: a δ-linked ornithine turn connecting positions 17 and 36 to create a macrocycle and an intramolecular disulfide linkage between positions 24 and 29. An N-methyl group at position 33 blocks uncontrolled aggregation. The peptide readily crystallizes as a folded β-hairpin, which assembles hierarchically in the crystal lattice. Three β-hairpin monomers assemble to form a triangular trimer, four trimers assemble in a tetrahedral arrangement to form a dodecamer, and five dodecamers pack together to form an annular pore. This hierarchical assembly provides a model, in which full-length Aβ transitions from an unfolded monomer to a folded β-hairpin, which assembles to form oligomers that further pack to form an annular pore. This model may provide a better understanding of the molecular basis of Alzheimer's disease at atomic resolution.

  9. The crystal structure of the Ran-Nup153ZnF2 complex: a general Ran docking site at the nuclear pore complex.

    PubMed

    Schrader, Nils; Koerner, Carolin; Koessmeier, Katja; Bangert, Jan-Amadé; Wittinghofer, Alfred; Stoll, Raphael; Vetter, Ingrid R

    2008-07-01

    Nucleoporin (Nup) 153 is a highly mobile, multifunctional, and essential nuclear pore protein. It contains four zinc finger motifs that are thought to be crucial for the regulation of transport-receptor/cargo interactions via their binding to the small guanine nucleotide binding protein, Ran. We found this interaction to be independent of the phoshorylation state of the nucleotide. Ran binds with the highest affinity to the second zinc finger motif of Nup153 (Nup153ZnF2). Here we present the crystal structure of this complex, revealing a new type of Ran-Ran interaction partner interface together with the solution structure of Nup153ZnF2. According to our complex structure, Nup153ZnF2 binding to Ran excludes the formation of a Ran-importin-beta complex. This finding suggests a local Nup153-mediated Ran reservoir at the nucleoplasmic distal ring of the nuclear pore, where nucleotide exchange may take place in a ternary Nup153-Ran-RCC1 complex, so that import complexes are efficiently terminated.

  10. 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.

  11. 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.

  12. Analysis of the Lotus japonicus nuclear pore NUP107-160 subcomplex reveals pronounced structural plasticity and functional redundancy

    PubMed Central

    Binder, Andreas; Parniske, Martin

    2013-01-01

    Mutations in the Lotus japonicus nucleoporin genes, NUP85, NUP133, and NENA (SEH1), lead to defects in plant-microbe symbiotic signaling. The homologous proteins in yeast and vertebrates are part of the conserved NUP84/NUP107-160 subcomplex, which is an essential component of the nuclear pore scaffold and has a pivotal role in nuclear pore complex (NPC) assembly. Loss and down-regulation of NUP84/NUP107-160 members has previously been correlated with a variety of growth and molecular defects, however, in L. japonicus only surprisingly specific phenotypes have been reported. We investigated whether Lotus nup85, nup133, and nena mutants exhibit general defects in NPC composition and distribution. Whole mount immunolocalization confirmed a typical nucleoporin-like localization for NUP133, which was unchanged in the nup85-1 mutant. Severe NPC clustering and aberrations in the nuclear envelope have been reported for Saccharomyces cerevisiae nup85 and nup133 mutants. However, upon transmission electron microscopy analysis of L. japonicus nup85, nup133 and nena, we detected only a slight reduction in the average distances between neighboring NPCs in nup133. Using quantitative immunodetection on protein-blots we observed that loss of individual nucleoporins affected the protein levels of other NUP107–160 complex members. Unlike the single mutants, nup85/nup133 double mutants exhibited severe temperature dependent growth and developmental defects, suggesting that the loss of more than one NUP107–160 member affects basal functions of the NPC. PMID:24478780

  13. Structural characterization of dimeric murine aminoacylase III.

    PubMed

    Ryazantsev, Sergey; Abuladze, Natalia; Newman, Debra; Bondar, Galyna; Kurtz, Ira; Pushkin, Alexander

    2007-05-01

    Aminoacylase III (AAIII) plays an important role in deacetylation of acetylated amino acids and N-acetylated S-cysteine conjugates of halogenated alkenes and alkanes. AAIII, recently cloned from mouse kidney and partially characterized, is a mixture of tetramers and dimers. In the present work, AAIII dimers were purified and shown to be enzymatically active. Limited trypsinolysis showed two domains of approximately 9 and 25 kDa. The three-dimensional structure of the dimer was studied by electron microscopy of negative stained samples and by single-particle reconstruction. A 16A resolution model of the AAIII dimer was created. It has an unusual, cage-like, structure. A realistic AAIII tetramer model was built from two dimers.

  14. Influence of zeolite pore structure on product selectivities for protolysis and hydride transfer reactions in the cracking of n-pentane.

    PubMed

    Miyaji, Akimitsu; Iwase, Yasuyoshi; Nishitoba, Toshiki; Long, Nguyen Quang; Motokura, Ken; Baba, Toshihide

    2015-02-21

    The conversion of n-pentane was carried out to examine the effects of reaction conditions on changes in product selectivities at 823 K, using zeolites with 10- and 12-membered rings. We also investigated the influence of the pore structure of these zeolites on their catalytic activities for both protolysis and hydride transfer reactions. In the first half of this work, we examined the influence of acidic proton concentration and n-pentane pressure on the reaction rates for protolysis and hydride transfer reactions using ZSM-5 zeolites. The rates of hydride transfer reactions were more influenced by pentane pressure compared to protolysis reactions, and were proportional to the square of n-pentane pressure and the concentration of acidic protons. In the second half of this work, the influence of the zeolite pore structure on changes in product selectivities with n-pentane conversion and that on the rates of protolysis and the hydride transfer reactions were revealed using various zeolites with 10- and 12-membered rings. The catalytic activities of zeolites for the protolysis and hydride transfer reactions were influenced more by the spatial volume of the zeolite cavity than the acid strength of protons on the zeolite.

  15. Diffractaic acid: Crystalline structure and physicochemical characterization

    NASA Astrophysics Data System (ADS)

    de Castro Fonseca, Jéssica; de Oliveira, Yara Santiago; Bezerra, Beatriz P.; Ellena, Javier; Honda, Neli Kika; Silva, Camilla V. N. S.; da Silva Santos, Noemia Pereira; Santos-Magalhães, Nereide Stela; Ayala, Alejandro Pedro

    2016-08-01

    Diffractaic acid (DA) is a secondary metabolite of lichens that belongs to the chemical class of depsides, and some relevant pharmacological properties are associated with this natural product, such as antioxidant, antiulcerogenic and gastroprotective effects. Considering the relevant biological activities and taking into account that the activities are intrinsically related to the structure, the main goal of this study was to elucidate the structure of diffractaic acid by single crystal X-ray diffraction as well to characterize its physicochemical properties by powder X-ray diffraction, thermal analysis and vibrational spectroscopy. It was observed that DA belongs to the monoclinic crystal system, crystallizing in the space group P21/c with the following cell parameters: a = 18.535(7) Å, b = 4.0439(18) Å, c = 23.964(6) Å, β = 91.55(3)°. The crystal packing is characterized by difractaic acid dimers, which are reflected in the vibrational spectrum. These observations were supported by quantum mechanical calculations.

  16. Thermomechanical characterization and modeling for TSV structures

    SciTech Connect

    Jiang, Tengfei; Zhao, Qiu; Im, Jay; Ho, Paul S.; Ryu, Suk-Kyu; Huang, Rui

    2014-06-19

    Continual scaling of devices and on-chip wiring has brought significant challenges for materials and processes beyond the 32-nm technology node in microelectronics. Recently, three-dimensional (3-D) integration with through-silicon vias (TSVs) has emerged as an effective solution to meet the future technology requirements. Among others, thermo-mechanical reliability is a key concern for the development of TSV structures used in die stacking as 3-D interconnects. This paper presents experimental measurements of the thermal stresses in TSV structures and analyses of interfacial reliability. The micro-Raman measurements were made to characterize the local distribution of the near-surface stresses in Si around TSVs. On the other hand, the precision wafer curvature technique was employed to measure the average stress and deformation in the TSV structures subject to thermal cycling. To understand the elastic and plastic behavior of TSVs, the microstructural evolution of the Cu vias was analyzed using focused ion beam (FIB) and electron backscattering diffraction (EBSD) techniques. Furthermore, the impact of thermal stresses on interfacial reliability of TSV structures was investigated by a shear-lag cohesive zone model that predicts the critical temperatures and critical via diameters.

  17. Structural characterization of thioether-bridged bacteriocins.

    PubMed

    Lohans, Christopher T; Vederas, John C

    2014-01-01

    Bacteriocins are a group of ribosomally synthesized antimicrobial peptides produced by bacteria, some of which are extensively post-translationally modified. Some bacteriocins, namely the lantibiotics and sactibiotics, contain one or more thioether bridges. However, these modifications complicate the structural elucidation of these bacteriocins using conventional techniques. This review will discuss the techniques and strategies that have been applied to determine the primary structures of lantibiotics and sactibiotics. A major challenge is to identify the topology of thioether bridges in these peptides (i.e., which amino-acid residues are involved in which bridges). Edman degradation, NMR spectroscopy and tandem MS have all been commonly applied to characterize these bacteriocins, but can be incompatible with the post-translational modifications present. Chemical modifications to the modified residues, such as desulfurization and reduction, make the treated bacteriocins more compatible to analysis by these standard peptide analytical techniques. Despite their differences in structure, similar strategies have proved useful to study the structures of both lantibiotics and sactibiotics.

  18. Macroscale and Microscale Structural Characterization of Cephalopod Chromatophores

    DTIC Science & Technology

    2011-04-01

    Macroscale and Microscale Structural Characterization of Cephalopod Chromatophores by Keith M. Kirkwood, Eric D. Wetzel, George Bell, Alan M...21005 ARL-RP-0318 April 2011 Macroscale and Microscale Structural Characterization of Cephalopod Chromatophores Keith M. Kirkwood and...Structural Characterization of Cephalopod Chromatophores 5a. CONTRACT NUMBER ORISE Contract 120-1120-99 (GHIORSE) 5b. GRANT NUMBER 5c. PROGRAM

  19. Effect of non-solvent additives on the morphology, pore structure, and direct contact membrane distillation performance of PVDF-CTFE hydrophobic membranes.

    PubMed

    Zheng, Libing; Wu, Zhenjun; Zhang, Yong; Wei, Yuansong; Wang, Jun

    2016-07-01

    Four common types of additives for polymer membrane preparation including organic macromolecule and micromolecule additives, inorganic salts and acids, and the strong non-solvent H2O were used to prepare poly (vinylidene fluoride-co-chlorotrifluoroethylene) (PVDF-CTFE) hydrophobic flat-sheet membranes. Membrane properties including morphology, porosity, hydrophobicity, pore size and pore distribution were investigated, and the permeability was evaluated via direct contact membrane distillation (DCMD) of 3.5g/L NaCl solution in a DCMD configuration. Both inorganic and organic micromolecule additives were found to slightly influence membrane hydrophobicity. Polyethylene glycol (PEG), organic acids, LiCl, MgCl2, and LiCl/H2O mixtures were proved to be effective additives to PVDF-CTFE membranes due to their pore-controlling effects and the capacity to improve the properties and performance of the resultant membranes. The occurrence of a pre-gelation process showed that when organic and inorganic micromolecules were added to PVDF-CTFE solution, the resultant membranes presented a high interconnectivity structure. The membrane prepared with dibutyl phthalate (DBP) showed a nonporous surface and symmetrical cross-section. When H2O and LiCl/H2O mixtures were also used as additives, they were beneficial for solid-liquid demixing, especially when LiCl/H2O mixed additives were used. The membrane prepared with 5% LiCl+2% H2O achieved a flux of 24.53kg/(m(2)·hr) with 99.98% salt rejection. This study is expected to offer a reference not only for PVDF-CTFE membrane preparation but also for other polymer membranes.

  20. Application of toxicity-based fractionation techniques and structure-activity relationship models for the identification of phototoxic polycyclic aromatic hydrocarbons in sediment pore water

    SciTech Connect

    Kosian, P.A.; Makynen, E.A.; Monson, P.D.; Mount, D.R.; Ankley, G.T.; Spacie, A.; Mekenyan, O.G.

    1998-06-01

    Recent studies conducted at their laboratory have shown that sediments contaminated with complex mixtures of polycyclic aromatic hydrocarbons (PAHs) can exhibit enhanced toxicity (lethality) to a variety of aquatic species when the samples are tested under ultraviolet (UV) light designed to mimic the wavelengths present in sunlight. However, because these contaminated sediments can contain literally thousands of chemicals, it is difficult to use conventional analytical techniques to identify those compounds responsible for photo-induced toxicity. The purpose of this study was to adapt existing toxicity identification evaluation methods to attempt to identify those compounds contributing to the phototoxicity observed in their sediment samples. Pore water obtained from sediments collected near an oil refinery discharge was toxic to Lumbriculus variegatus following exposure to UV light, while organisms exposed to the same pore water, but without subsequent UV treatment, showed no toxic effect. Solid-phase extraction disks and high-performance liquid chromatography were used, in conjunction with toxicity tests with L. variegatus, to extract and fractionate phototoxic chemicals from the pore water. Phototoxic fractions analyzed by gas chromatography-mass spectrometry revealed the presence of a number of aliphatic hydrocarbons, substituted PAHs, and PAHs containing heteroatoms. Chemicals were screened for their phototoxic potential based on empirical data and predictive models. A refined list of PAHs was then evaluated on the basis of their phototoxic potency as defined by a recently developed quantitative structure-activity relationship model and estimates of their bioaccumulation potential. Based on the model predictions of potency and bioaccumulation, nine likely phototoxic chemicals were identified.

  1. 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

  2. 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.

  3. 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.

  4. Structural studies of ion permeation and Ca2+ blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore

    PubMed Central

    Derebe, Mehabaw G.; Zeng, Weizhong; Li, Yang; Alam, Amer; Jiang, Youxing

    2011-01-01

    Cyclic nucleotide-gated (CNG) channels play an essential role in the visual and olfactory sensory systems and are ubiquitous in eukaryotes. Details of their underlying ion selectivity properties are still not fully understood and are a matter of debate in the absence of high-resolution structures. To reveal the structural mechanism of ion selectivity in CNG channels, particularly their Ca2+ blockage property, we engineered a set of mimics of CNG channel pores for both structural and functional analysis. The mimics faithfully represent the CNG channels they are modeled after, permeate Na+ and K+ equally well, and exhibit the same Ca2+ blockage and permeation properties. Their high-resolution structures reveal a hitherto unseen selectivity filter architecture comprising three contiguous ion binding sites in which Na+ and K+ bind with different ion-ligand geometries. Our structural analysis reveals that the conserved acidic residue in the filter is essential for Ca2+ binding but not through direct ion chelation as in the currently accepted view. Furthermore, structural insight from our CNG mimics allows us to pinpoint equivalent interactions in CNG channels through structure-based mutagenesis that have previously not been predicted using NaK or K+ channel models. PMID:21187429

  5. Thermophysical property and pore structure evolution in stressed and non-stressed neutron irradiated IG-110 nuclear graphite

    NASA Astrophysics Data System (ADS)

    Snead, L. L.; Contescu, C. I.; Byun, T. S.; Porter, W.

    2016-08-01

    The nuclear graphite, IG-110, was irradiated with and without a compressive load of 5 MPa at ∼400 °C up to 9.3 × 1025 n/m2 (E > 0.1 MeV). Following irradiation physical properties were studied to compare the effect of graphite irradiation on microstructure developed under compression and in stress-free conditions. Properties included: dimensional change, thermal conductivity, dynamic modulus, and CTE. The effect of stress on open internal porosity was determined through nitrogen adsorption. The IG-110 graphite experienced irradiation-induced creep that is differentiated from irradiation-induced swelling. Irradiation under stress resulted in somewhat greater thermal conductivity and coefficient of thermal expansion. While a significant increase in dynamic modulus occurs, no differentiation between materials irradiated with and without compressive stress was observed. Nitrogen adsorption analysis suggests a difference in pore evolution in the 0.3-40 nm range for graphite irradiated with and without stress, but this evolution is seen to be a small contributor to the overall dimensional change.

  6. Thermophysical property and pore structure evolution in stressed and non-stressed neutron irradiated IG-110 nuclear graphite

    SciTech Connect

    Snead, Lance; Contescu, Christian I.; Byun, Thak Sang; Porter, Wallace D.

    2016-08-01

    The nuclear graphite, IG-110, was irradiated with and without a compressive load of 5 MPa at ~400 *C up to 9.3E25 n/m2 (E > 0.1 MeV). Following irradiation physical properties were studied to compare the effect of graphite irradiation on microstructure developed under compression and in stress-free conditions. Properties included: dimensional change, thermal conductivity, dynamic modulus, and CTE. The effect of stress on open internal porosity was determined through nitrogen adsorption. The IG-110 graphite experienced irradiation-induced creep that is differentiated from irradiation-induced swelling. Irradiation under stress resulted in somewhat greater thermal conductivity and coefficient of thermal expansion. While a significant increase in dynamic modulus occurs, no differentiation between materials irradiated with and without compressive stress was observed. Nitrogen adsorption analysis suggests a difference in pore evolution in the 0.3e40 nm range for graphite irradiated with and without stress, but this evolution is seen to be a small contributor to the overall dimensional change.

  7. EFFECTS OF PORE STRUCTURE CHANGE AND MULTI-SCALE HETEROGENEITY ON CONTAMINANT TRANSPORT AND REACTION RATE UPSCALING

    SciTech Connect

    Peters, Catherine A

    2013-05-15

    This project addressed the scaling of geochemical reactions to core and field scales, and the interrelationship between reaction rates and flow in porous media. We targeted reactive transport problems relevant to the Hanford site specifically the reaction of highly caustic, radioactive waste solutions with subsurface sediments, and the immobilization of 90Sr and 129I through mineral incorporation and passive flow blockage, respectively. We addressed the correlation of results for pore-scale fluid-soil interaction with field-scale fluid flow, with the specific goals of (i) predicting attenuation of radionuclide concentration; (ii) estimating changes in flow rates through changes of soil permeabilities; and (iii) estimating effective reaction rates. In supplemental work, we also simulated reactive transport systems relevant to geologic carbon sequestration. As a whole, this research generated a better understanding of reactive transport in porous media, and resulted in more accurate methods for reaction rate upscaling and improved prediction of permeability evolution. These scientific advancements will ultimately lead to better tools for management and remediation of DOE legacy waste problems.

  8. Thermophysical property and pore structure evolution in stressed and non-stressed neutron irradiated IG-110 nuclear graphite

    DOE PAGES

    Snead, Lance L.; Contescu, C. I.; Byun, T. S.; ...

    2016-04-23

    The nuclear graphite, IG-110, was irradiated with and without a compressive load of 5 MPa at ~400 C up to 9.3x1025 n/m2 (E>0.1 MeV.) Following irradiation physical properties were studied to compare the effect of graphite irradiation on microstructure developed under compression and in stress-free condition. Properties included: dimensional change, thermal conductivity, dynamic modulus, and CTE. The effect of stress on open internal porosity was determined through nitrogen adsorption. The IG-110 graphite experienced irradiation-induced creep that is differentiated from irradiation-induced swelling. Irradiation under stress resulted in somewhat greater thermal conductivity and coefficient of thermal expansion. While a significant increase inmore » dynamic modulus occurs, no differentiation between materials irradiated with and without compressive stress was observed. Nitrogen adsorption analysis suggests a difference in pore evolution in the 0.3-40 nm range for graphite irradiated with and without stress, but this evolution is seen to be a small contributor to the overall dimensional change.« less

  9. Thermophysical property and pore structure evolution in stressed and non-stressed neutron irradiated IG-110 nuclear graphite

    SciTech Connect

    Snead, Lance L.; Contescu, C. I.; Byun, T. S.; Porter, W.

    2016-04-23

    The nuclear graphite, IG-110, was irradiated with and without a compressive load of 5 MPa at ~400 C up to 9.3x1025 n/m2 (E>0.1 MeV.) Following irradiation physical properties were studied to compare the effect of graphite irradiation on microstructure developed under compression and in stress-free condition. Properties included: dimensional change, thermal conductivity, dynamic modulus, and CTE. The effect of stress on open internal porosity was determined through nitrogen adsorption. The IG-110 graphite experienced irradiation-induced creep that is differentiated from irradiation-induced swelling. Irradiation under stress resulted in somewhat greater thermal conductivity and coefficient of thermal expansion. While a significant increase in dynamic modulus occurs, no differentiation between materials irradiated with and without compressive stress was observed. Nitrogen adsorption analysis suggests a difference in pore evolution in the 0.3-40 nm range for graphite irradiated with and without stress, but this evolution is seen to be a small contributor to the overall dimensional change.

  10. Beta environmental fine structure characterization of defects

    NASA Astrophysics Data System (ADS)

    Benedek, G.; Fiorini, E.; Giuliani, A.; Milani, P.; Monfardini, A.; Nucciotti, A.; Prandoni, M. L.; Sancrotti, M.

    1999-04-01

    The fine structure of beta emission (BEFS) due to the interference with the scattered waves from neighboring atoms, analogous to EXAFS, is known to produce oscillations in the Kurie plot. Here we suggest the use of BEFS for characterizing the lattice environment of β-emitting defects located at a distance from the crystal surface not exceeding the mean free path of β-electrons. Examples of defective structures in semiconductors whose atomic arrangement could be conveniently studied with BEFS are tritium-passivated dangling bonds, β-radioactive ions implanted in the crystal lattice or segregated at extended defects such as dislocations, grain boundaries or radiation damage. Also 14C-doped diamond-like materials and other exotic carbon forms, as well as the atomic environment of ions in metal alloys could be good candidate for BEFS. In this work we have calculated the fractional BEFS modulation for 187Re in its ordinary hcp crystal lattice for which experimental data by Cosulich et al. are available. The good correspondence between theory and experiment permits to conclude that BEFS experiments at low temperature are accessible to the present bolometric detection techniques and can provide an expedient method, as compared to EXAFS, for an accurate structural assessment of extended defects in solids.

  11. Structural characterization of rotor blades through photogrammetry

    NASA Astrophysics Data System (ADS)

    Bernardini, Giovanni; Serafini, Jacopo; Enei, Claudio; Mattioni, Luca; Ficuciello, Corrado; Vezzari, Valerio

    2016-06-01

    This paper deals with the use of photogrammetry for the experimental identification of structural and inertial properties of helicopter rotor blades4. The identification procedure is based upon theoretical/numerical algorithms for the evaluation of mass and flexural stiffness distributions which are an extension of those proposed in the past by Larsen, whereas the torsional properties (stiffness and shear center position) are determined through the Euler-Bernoulli beam theory. The identification algorithms require the knowledge of the blade displacement field produced by known steady loads. These data are experimentally obtained through photogrammetric detection technique, which allows the identification of 3D coordinates of labeled points (markers) on the structure through the correlation of 2D digital photos. Indeed, the displacement field is simply evaluated by comparing the markers positions on the loaded configuration with those on the reference one. The proposed identification procedure, numerically and experimentally validated in the past by the authors, has been here applied to the structural characterization of two main rotor blades, designed for ultra-light helicopters. Strain gauges measurements have been used to assess the accuracy of the identified properties through natural frequencies comparison as well as to evaluate the blades damping characteristics.

  12. Characterization of Imposed Ordered Structures in MDPX

    NASA Astrophysics Data System (ADS)

    Hall, Taylor; Thomas, Edward; Konopka, Uwe; Merlino, Robert; Rosenberg, Marlene

    2016-10-01

    It is well understood that the microparticles in complex, or dusty, plasmas will form self-consistent crystalline patterns at the proper plasma parameters. In the Magnetized Dusty Plasma Experiment (MDPX) device, studies have been made of imposed, ordered structuring of the dust particles to a two dimensional grid. At high magnetic field (B >1 Tesla), the dust particles are shown to become spatially oriented to the structure of a wire mesh embedded in an electrically floating, upper electrode while the particles are suspended in a plasma that is generated by the powered, lower electrode in the experiment. With even higher magnetic field (B >2 Tesla), the particles become strongly confined to the mesh pattern with the particles constrained to a quasi-discreet motion that closely follows the mesh pattern. This presentation characterizes the structure of the potential energy well in which the dust particles are trapped through observation of particle motion and measurement of the thermal properties of the particles. This work is supported by funding from the U. S. Department of Energy Grant Number DE - SC0010485 and the NASA/Jet Propulsion Laboratory, JPL-1543114.

  13. Structural characterization of copolymer embedded magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Nedelcu, G. G.; Nastro, A.; Filippelli, L.; Cazacu, M.; Iacob, M.; Rossi, C. Oliviero; Popa, A.; Toloman, D.; Dobromir, M.; Iacomi, F.

    2015-10-01

    Small magnetic nanoparticles (Fe3O4) were synthesized by co-precipitation and coated by emulsion polymerization with poly(methyl methacrylate-co-acrylic acid) (PMMA-co-AAc) to create surface functional groups that can attach drug molecules and other biomolecules. The coated and uncoated magnetite nanoparticles were stored for two years in normal closed ships and than characterized by Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, vibrating sample magnetometry, and electron paramagnetic resonance spectroscopy. The solid phase transformation of magnetite to maghemite, as well as an increase in particle size were evidenced for the uncoated nanoparticles. The coated nanoparticles preserved their magnetite structure and magnetic properties. The influences of monomers and surfactant layers on interactions between the magnetic nanoparticles evidenced that the thickness of the polymer has a significant effect on magnetic properties.

  14. Investigation of the pore structure and morphology of cellulose acetate membranes using small-angle neutron scattering. 1: Cellulose acetate active layer membranes

    SciTech Connect

    Kulkarni, S.; Krause, S. ); Wignall, G.D. . Solid State Div.); Hammouda, B. . Center for High Resolution Neutron Scattering)

    1994-11-07

    The structure of ultrathin cellulose acetate membranes, known as active layer membranes, has been investigated using small-angle neutron scattering. These membranes are known to have structural and functional similarity to the surface or skin layer in commercial reverse-osmosis (RO) membranes and hence are useful model systems for understanding the structure of the RO membrane skin layer. Active layer membranes were studied after swelling them with either D[sub 2]O or CD[sub 3]OD. The results in both cases clearly indicated the presence of very small (10--20 [angstrom]) porous structures in the membrane. The presence of such pores has been a subject of long-standing controversy in this area. The data were analyzed using a modified Debye-Bueche analysis and the resultant membrane structure was seen to agree well with structural information from electron microscopic studies. Finally, a possible explanation for the differences in scattering observed between the D[sub 2]O swollen membranes and the CD[sub 3]OD swollen membranes has been presented.

  15. Electro-mechanical characterization of structural supercapacitors

    NASA Astrophysics Data System (ADS)

    Gallagher, T.; LaMaster, D.; Ciocanel, C.; Browder, C.

    2012-04-01

    The paper presents electrical and mechanical properties of structural supercapacitors and discusses limitations associated with the approach taken for the electrical properties evaluation. The structural supercapacitors characterized in this work had the electrodes made of carbon fiber weave, separator made of several cellulose based products, and the solid electrolyte made as PEGDGE based polymer blend. The reported electrical properties include capacitance and leakage resistance; the former was measured using cyclic voltammetry. Mechanical properties have been evaluated thorough tensile and three point bending tests performed on structural supercapacitor coupons. The results indicate that the separator material plays an important role on the electrical as well as mechanical properties of the structural capacitor, and that Celgard 3501 used as separator leads to most benefits for both mechanical and electrical properties. Specific capacitance and leakage resistance as high as 1.4kF/m3 and 380kΩ, respectively, were achieved. Two types of solid polymer electrolytes were used in fabrication, with one leading to higher and more consistent leakage resistance values at the expense of a slight decrease in specific capacitance when compared to the other SPE formulation. The ultimate tensile strength and modulus of elasticity of the developed power storage composite were evaluated at 466MPa and 18.9MPa, respectively. These values are 58% and 69% of the tensile strength and modulus of elasticity values measured for a single layer composite material made with the same type of carbon fiber and with a West System 105 epoxy instead of solid polymer electrolyte.

  16. 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

  17. Pore Characterization of Shale Rock and Shale Interaction with Fluids at Reservoir Pressure-Temperature Conditions Using Small-Angle Neutron Scattering

    NASA Astrophysics Data System (ADS)

    Ding, M.; Hjelm, R.; Watkins, E.; Xu, H.; Pawar, R.

    2015-12-01

    Oil/gas produced from unconventional reservoirs has become strategically important for the US domestic energy independence. In unconventional realm, hydrocarbons are generated and stored in nanopores media ranging from a few to hundreds of nanometers. Fundamental knowledge of coupled thermo-hydro-mechanical-chemical (THMC) processes that control fluid flow and propagation within nano-pore confinement is critical for maximizing unconventional oil/gas production. The size and confinement of the nanometer pores creates many complex rock-fluid interface interactions. It is imperative to promote innovative experimental studies to decipher physical and chemical processes at the nanopore scale that govern hydrocarbon generation and mass transport of hydrocarbon mixtures in tight shale and other low permeability formations at reservoir pressure-temperature conditions. We have carried out laboratory investigations exploring quantitative relationship between pore characteristics of the Wolfcamp shale from Western Texas and the shale interaction with fluids at reservoir P-T conditions using small-angle neutron scattering (SANS). We have performed SANS measurements of the shale rock in single fluid (e.g., H2O and D2O) and multifluid (CH4/(30% H2O+70% D2O)) systems at various pressures up to 20000 psi and temperature up to 150 oF. Figure 1 shows our SANS data at different pressures with H2O as the pressure medium. Our data analysis using IRENA software suggests that the principal changes of pore volume in the shale occurred on smaller than 50 nm pores and pressure at 5000 psi (Figure 2). Our results also suggest that with increasing P, more water flows into pores; with decreasing P, water is retained in the pores.

  18. Structural Characterization of Bimetallic Nanocrystal Electrocatalysts

    SciTech Connect

    Cullen, David A

    2016-01-01

    Late transition metal nanocrystals find applications in heterogeneous catalysis such as plasmon-enhanced catalysis and as electrode materials for fuel cells, a zero-emission and sustainable energy technology. Their commercial viability for automotive transportation has steadily increased in recent years, almost exclusively due to the discovery of more efficient bimetallic nanocatalysts for the oxygen reduction reaction (ORR) at the cathode. Despite improvements to catalyst design, achieving high activity while maintaining durability is essential to further enhance their performance for this and other important applications in catalysis. Electronic effects arising from the generation of metal-metal interfaces, from plasmonic metals, and from lattice distortions, can vastly improve sorption properties at catalytic surfaces, while increasing durability.[1] Multimetallic lattice-strained nanoparticles are thus an interesting opportunity for fundamental research.[2,3] A colloidal synthesis approach is demonstrated to produce AuPd alloy and Pd@Au core-shell nanoicosahedra as catalysts for electro-oxidations. The nanoparticles are characterized using aberration-corrected scanning transmission electron microscopy (ac-STEM) and large solid angle energy dispersive X-ray spectroscopy (EDS) on an FEI Talos 4-detector STEM/EDS system. Figure 1 shows bright-field (BF) and high-angle annular dark-field (HAADF) ac-STEM images of the alloy and core-shell nanoicosahedra together with EDS line-scans and elemental maps. These structures are unique in that the presence of twin boundaries, alloying, and core-shell morphology could create highly strained surfaces and interfaces. The shell thickness of the core-shell structures observed in HAADF-STEM images is tuned by adjusting the ratio between metal precursors (Figure 2a-f) to produce shells ranging from a few to several monolayers. Specific activity was measured in ethanol electro-oxidation to examine the effect of shell thickness on

  19. Detection and Characterization of R Loop Structures.

    PubMed

    Boque-Sastre, Raquel; Soler, Marta; Guil, Sonia

    2017-01-01

    R loops are special three stranded nucleic acid structures that comprise a nascent RNA hybridized with the DNA template strand, leaving a non-template DNA single-stranded. More specifically, R loops form in vivo as G-rich RNA transcripts invade the DNA duplex and anneal to the template strand to generate an RNA:DNA hybrid, leaving the non-template, G-rich DNA strand in a largely single-stranded conformation (Aguilera and Garcia-Muse, Mol Cell 46:115-124, 2012).DNA-RNA hybrids are a natural occurrence within eukaryotic cells, with levels of these hybrids increasing at sites with high transcriptional activity, such as during transcription initiation, repression, and elongation. RNA-DNA hybrids influence genomic instability, and growing evidence points to an important role for R loops in active gene expression regulation (Ginno et al., Mol Cell 45, 814-825, 2012; Sun et al., Science 340: 619-621, 2013; Bhatia et al., Nature 511, 362-365, 2014). Analysis of the occurrence of such structures is therefore of increasing relevance and herein we describe methods for the in vivo and in vitro identification and characterization of R loops in mammalian systems.R loops (DNA:RNA hybrids and the associated single-stranded DNA) have been traditionally associated with threats to genome integrity, making some regions of the genome more prone to DNA-damaging and mutagenic agents. Initially considered to be rare byproducts of transcription, over the last decade accumulating evidence has pointed to a new view in which R loops form more frequently than previously thought. The R loop field has become an increasingly expanded area of research, placing these structures as a major threat to genome stability but also as potential regulators of gene expression. Special interest has arisen as they have also been linked to a variety of diseases, including neurological disorders and cancer, positioning them as potential therapeutic targets [5].

  20. Structural Characterization of Crystalline Ice Nanoclusters

    NASA Technical Reports Server (NTRS)

    Blake, David

    2000-01-01

    Water ice nanoclusters are useful analogs for studying a variety of processes that occur within icy grains in the extraterrestrial environment. The surface of ice nanoclusters prepared in the laboratory is similar to the surface of interstellar ice grains. In cold molecular clouds, the silicate cores of interstellar grains are typically approx. 100 nm in diameter and have a coating of impure amorphous water ice. Depositional, thermal and radiolytic processes leave the surface and subsurface molecules in a disordered state. In this state, structural defects become mobile and reactions of trapped gases and small molecules can occur. The large surface area of nanocluster deposits relative to their bulk allows for routine observation of such surface-mediated processes. Furthermore, the disordered surface and subsurface layers in nanocluster deposits mimic the structure of amorphous ice rinds found on interstellar dust grains. Transmission Electron Microscopy (TEM has been used tn characterize the crystallinity, growth mechanism, and size distribution of nanoclusters formed from a mixture of water vapor with an inert carrier gas that has been rapidly cooled to 77K. E M imaging reveals a Gaussian size distribution around a modal diameter that increases from approx. 15 to 30 nm as the percentage of water vapor within the mixture increases from 0.5 to 2.007, respectively . TEM bright and dark field imaging also reveals the crystalline nature of the clusters. h4any of the clusters show a mosaic structure in which crystalline domains originate at the center Other images show mirror planes that are separated by approx. 10 nm. Electron diffraction patterns of these clusters show that the clusters are composed of cubic ice with only a small hexagonal component. Further, the crystalline domain size is approximately the same as the modal diameter suggesting that the clusters are single crystals.

  1. Modeling and Analysis of Granite Matrix Pore Structure and Hydraulic Characteristics in 2D and 3D Networks

    NASA Astrophysics Data System (ADS)

    Gvozdik, L.; Polak, M.; Zaruba, J.; Vanecek, M.

    2010-12-01

    A geological environment labeled as a Granite massif represents in terms of groundwater flow and transport a distinct hydrogeological environment from that of sedimentary basins, the characterisation of which is generally more complex and uncertain. Massifs are composed of hard crystalline rocks with the very low effective porosity. Due to their rheological properties such rocks are predisposed to brittle deformation resulting from changes in stress conditions. Our specific research project (Research on the influence of intergrangular porosity on deep geological disposal: geological formations, methodology and the development of measurement apparatus) is focussed on the problem of permeable zones within apparently undisturbed granitic rock matrix. The project including the both laboratory and in-situ tracer tests study migration along and through mineral grains in fresh and altered granite. The objective of the project is to assess whether intergranular porosity is a general characteristic of the granitic rock matrix or subject to significant evolution resulting from geochemical and/or hydrogeochemical processes, geotechnical and/or mechanical processes. Moreover, the research is focussed on evaluating methods quantifying intergranular porosity by both physical testing and mathematical modelling using verified standard hydrological software tools. Groundwater flow in microfractures and intergranular pores in granite rock matrix were simulated in three standard hydrogeological modeling programs with completely different conceptual approaches: MODFLOW (Equivalent Continuum concept), FEFLOW (Discrete Fracture and Equivalent Continuum concepts) and NAPSAC (Discrete Fracture Network concept). Specialized random fracture generators were used for creation of several 2D and 3D models in each of the chosen program. Percolation characteristics of these models were tested and analyzed. Several scenarios of laboratory tests of the rock samples permeability made in triaxial

  2. Pore forming activity of the potent RTX-toxin produced by pediatric pathogen Kingella kingae: characterization and comparison to other RTX-family members*

    PubMed Central

    Bárcena-Uribarri, Iván; Benz, Roland; Winterhalter, Mathias; Zakharian, Eleonora; Balashova, Nataliya

    2015-01-01

    Pediatric septic arthritis in patients under age of four is frequently caused by the oral Gram-negative bacterium Kingella kingae. This organism may be responsible for a severe form of infective endocarditis in otherwise healthy children and adults. A major virulence factor of K. kingae is RtxA, a toxin that belongs to the RTX (Repeats-in-ToXin) group of secreted pore forming toxins. To understand the RtxA effects on host cell membranes, the toxin activity was studied using planar lipid bilayers. K. kingae strain PYKK081 and its isogenic RtxA-deficient strain, KKNB100, were tested for their ability to form pores in artificial membranes of asolectin/n-decane. RtxA, purified from PYKK081, was able to rapidly form pores with an apparent diameter of 1.9 nm as measured by the partition of nonelectrolytes in the pores. The RtxA channels are cation-selective and showed strong voltage-dependent gating. In contrast to supernatants of PYKK081, those of KKNB100 did not show any pore forming activity. We concluded that RtxA toxin is the only secreted protein from K. kingae forming large channels in host cell membranes where it induces cation flux leading to programmed cell death. Furthermore, our findings suggested that the planar lipid bilayer technique can effectively be used to test possible inhibitors of RTX toxin activity and to investigate the mechanism of the toxin binding to the membrane. PMID:25858109

  3. Pore forming activity of the potent RTX-toxin produced by pediatric pathogen Kingella kingae: Characterization and comparison to other RTX-family members.

    PubMed

    Bárcena-Uribarri, Iván; Benz, Roland; Winterhalter, Mathias; Zakharian, Eleonora; Balashova, Nataliya

    2015-07-01

    Pediatric septic arthritis in patients under age of four is frequently caused by the oral Gram-negative bacterium Kingella kingae. This organism may be responsible for a severe form of infective endocarditis in otherwise healthy children and adults. A major virulence factor of K. kingae is RtxA, a toxin that belongs to the RTX (Repeats-in-ToXin) group of secreted pore forming toxins. To understand the RtxA effects on host cell membranes, the toxin activity was studied using planar lipid bilayers. K. kingae strain PYKK081 and its isogenic RtxA-deficient strain, KKNB100, were tested for their ability to form pores in artificial membranes of asolectin/n-decane. RtxA, purified from PYKK081, was able to rapidly form pores with an apparent diameter of 1.9nm as measured by the partition of nonelectrolytes in the pores. The RtxA channels are cation-selective and showed strong voltage-dependent gating. In contrast to supernatants of PYKK081, those of KKNB100 did not show any pore forming activity. We concluded that RtxA toxin is the only secreted protein from K. kingae forming large channels in host cell membranes where it induces cation flux leading to programmed cell death. Furthermore, our findings suggested that the planar lipid bilayer technique can effectively be used to test possible inhibitors of RTX toxin activity and to investigate the mechanism of the toxin binding to the membrane.

  4. 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.

  5. 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.

  6. Fabrication of structured porous films by breath figures and phase separation processes: tuning the chemistry and morphology inside the pores using click chemistry.

    PubMed

    S de León, Alberto; Del Campo, Adolfo; Fernández-García, Marta; Rodríguez-Hernández, Juan; Muñoz-Bonilla, Alexandra

    2013-05-01

    Herein, a facile water-assisted templating technique, the so-called breath figures method, in combination with phase separation process, was employed to prepare multifunctional micropatterned films. Tetrahydrofuran solutions of incompatible ternary blends consisting of high-molecular-weight polystyrene, an amphiphilic block copolymer, polystyrene-b-poly[poly(ethylene glycol) methyl ether methacrylate] (PS40-b-P(PEGMA300)48), and a fluorinated homopolymer, poly(2,3,4,5,6-pentafluorostyrene) (P5FS21) were casted under humid atmosphere varying the proportion of the components. Two simultaneously occurring processes, i.e., the breath figures mechanism and the phase separation process, lead to unprecedented morphologies that could be tuned by simply varying the relative humidity or the composition of the blend. Confocal micro-Raman spectroscopy served to provide information about the location and distribution of the different functionalities in the films. As a result, both the amphiphilic block copolymer and the fluorinated polymer were mainly located in the cavities. Above a certain percentage of relative humidity, honeycomb structured films were obtained in which the block copolymer is distributed on the edge of the pore as a result of the affinity by the condensing water droplet and the coffee stain effect. The homopolymer is also preferentially situated at the pore edge, but forming spherical domains with narrow polydisperse sizes. Moreover, thiolated glucose molecules were specifically attached to the P5FS21 domains via thiol-para fluorine "click" reaction. Subsequently, the specific lectin (Concanavalin A, Canavalia ensiformis) was attached to the surface by conjugation with the glucose moieties. The successful binding of the Con A was demonstrated by the fluorescence, observed exclusively at the areas where P5FS21 domains are located. This nonlithographic method opens a new route to fabricate a huge variety of microstructured polymer films in terms of morphology

  7. Statistical characterization of phenolic-novolak structures

    NASA Technical Reports Server (NTRS)

    Parker, J. A.; Winkler, E. L.

    1971-01-01

    Three statistical methods of general validity are valuable for characterizing any polymer which results from chain polymerization of multifunctional branching monomers linked through bifunctional monomers.

  8. Structural characterization of soy protein nanoparticles from high shear microfluidization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soy protein nanoparticles were produced with a microfluidizer and characterized in terms of particle size, size distribution, morphology, rheological properties, and aggregate structure. Three stages of structure breakdown were observed when the soy protein dispersion was passed through the microflu...

  9. Super-paramagnetic responsive silk fibroin/chitosan/magnetite scaffolds with tunable pore structures for bone tissue engineering applications.

    PubMed

    Aliramaji, Shamsa; Zamanian, Ali; Mozafari, Masoud

    2017-01-01

    Tissue engineering is a promising approach in repairing damaged tissues. During the last few years, magnetic nanoparticles have been of great interest in this field of study due to their controlled responsive characteristics in specific external magnetic fields. In this study, after synthesizing iron oxide (magnetite) nanoparticles through a reverse coprecipitation method, silk fibroin/chitosan-based magnetic scaffolds were prepared using different amounts of magnetite nanoparticles (0, 0.5, 1 and 2%) by freeze-casting method. The physicochemical activity of the scaffolds was monitored in phosphate-buffered saline (PBS) solution to determine the biodegradation and swelling behaviors. The stability of the magnetite nanoparticles in the fabricated scaffolds was determined by atomic absorption spectroscopy (AAS). Moreover, the cellular activity of the magnetic scaffolds was examined under a static magnetic field. The results showed that the lamellar structured scaffolds having MNPs in the walls could not affect the final structure and deteriorate the biological characteristics of the scaffolds, while the ability of magnetic responsivity was added to the scaffolds. This study warrants further pre-clinical and clinical evaluations.

  10. Structural and fractal characterization of tungstophosphoric acid modified titanium dioxide photocatalyst

    NASA Astrophysics Data System (ADS)

    Petrović, S.; Rožić, Lj; Vuković, Z.; Grbić, B.; Radić, N.; Stojadinović, S.; Vasilić, R.

    2017-04-01

    This article presents the comparison of structural and fractal properties of nanocrystalline titanium dioxide (TiO2) and TiO2 modified with tungstophosphoric acid (TiO2/HPW) and their impact on the photocatalytic degradation of hazardous water pollutants. TiO2 and TiO2/HPW samples were synthesized by a combined sol-gel and hydrothermal processing. The XRD analysis of pure TiO2 samples revealed that phase composition was mainly dependent on the calcination temperature, changing from amorphous TiO2 to crystalline anatase and rutile by increasing the temperature. On the other hand, the XRD of TiO2/HPW samples calcined at temperatures above 600 °C showed crystalline peaks associated to formation of WO3 and WO2.92 crystalline domains. The N2 adsorption-desorption isotherm and pore size distribution of TiO2/HPW samples detected the existence of mesoporous characteristic with very narrow bimodal pores in the mesoporous region. The structural heterogeneity of samples was analyzed by means of pore size distribution functions, while the variation in fractal dimension were determined from the nitrogen adsorption isotherms, using the modified Frenkel-Halsey-Hill method. The results demonstrate that the approach is capable of characterizing complex textures such as those present in the TiO2 and TiO2/HPW photocatalysts. Besides, the effect of calcinations condition on photocatalytic properties of the samples was also investigated. The highest efficiency with respect to methyl orange photodecomposition was observed for TiO2/HPW photocatalysts calcined at 700 °C.

  11. The early stages of amyloid formation: biophysical and structural characterization of human calcitonin pre-fibrillar assemblies.

    PubMed

    Avidan-Shpalter, Carmit; Gazit, Ehud

    2006-12-01

    Amyloid fibril formation is a nucleation dependent process characterized by a lag-phase prior to the appearance of detectable amyloid fibrils. While the three-dimensional structure of amyloid fibrils at atomic resolution is just beginning to be elucidated, the early process of monomers assembly into oligomers is less understood. Understanding the dynamic processes that lead to the formation of these intermediates is highly important as these assemblies might be the most pathological ones. Here, we investigated the biophysical and structural features characterizing the early stage assemblies formed by the human hormone calcitonin. We calculated the initial nucleus size by experimentally determining the dependence between the lag-time length and the hCT concentrations. We used size exclusion chromatography and dynamic light scattering in order to characterize the dynamic growth process of preliminary intermediates transformed into larger structures. The early structures were visualized using high-resolution transmission electron microscopy. Annular pore-like structures were observed along with protofibrilar structures. This observed morphology is similar to structures revealed during the fibrillization processes of beta-amyloid, alpha-synuclein, and islet amyloid polypeptide, suggesting that these intermediates represent a generic early structure conformation. The results introduced here imply that a variety of intermediate assemblies are formed during the early stages of amyloid fibril formation. The characterizing of their structural features and assembly kinetics will contribute to the rational design of inhibitors directed towards early structure assemblies.

  12. Secondary structure and orientation of the pore-forming toxin lysenin in a sphingomyelin-containing membrane.

    PubMed

    Hereć, Monika; Gagoś, Mariusz; Kulma, Magdalena; Kwiatkowska, Katarzyna; Sobota, Andrzej; Gruszecki, Wiesław I

    2008-04-01

    Lysenin is a sphingomyelin-recognizing toxin which forms stable oligomers upon membrane binding and causes cell lysis. To get insight into the mechanism of the transition of lysenin from a soluble to a membrane-bound form, surface activity of the protein and its binding to lipid membranes were studied using tensiometric measurements, Fourier-transform infrared spectroscopy (FTIR) and FTIR-linear dichroism. The results showed cooperative adsorption of recombinant lysenin-His at the argon-water interface from the water subphase which suggested self-association of lysenin-His in solution. An assembly of premature oligomers by lysenin-His in solution was confirmed by blue native gel electrophoresis. When a monolayer composed of sphingomyelin and cholesterol was present at the interface, the rate of insertion of lysenin-His into the monolayer was considerably enhanced. Analysis of FTIR spectra of soluble lysenin-His demonstrated that the protein contained 27% beta-sheet, 28% aggregated beta-strands, 10% alpha-helix, 23% turns and loops and 12% different kinds of aggregated forms. In membrane-bound lysenin-His the total content of alpha-helices, turns and loops, and beta-structures did not change, however, the 1636cm(-1) beta-sheet band increased from 18% to 31% at the expense of the 1680cm(-1) beta-sheet structure. Spectral analysis of the amide I band showed that the alpha-helical component was oriented with at 41 degrees to the normal to the membrane, indicating that this protein segment could be anchored in the hydrophobic core of the membrane.

  13. Quantitative analysis of nano-pore geomaterials and representative sampling for digital rock physics

    NASA Astrophysics Data System (ADS)

    Yoon, H.; Dewers, T. A.

    2014-12-01

    Geomaterials containing nano-pores (e.g., shales and carbonate rocks) have become increasingly important for emerging problems such as unconventional gas and oil resources, enhanced oil recovery, and geologic storage of CO2. Accurate prediction of coupled geophysical and chemical processes at the pore scale requires realistic representation of pore structure and topology. This is especially true for chalk materials, where pore networks are small and complex, and require characterization at sub-micron scale. In this work, we apply laser scanning confocal microscopy to characterize pore structures and microlithofacies at micron- and greater scales and dual focused ion beam-scanning electron microscopy (FIB-SEM) for 3D imaging of nanometer-to-micron scale microcracks and pore distributions. With imaging techniques advanced for nano-pore characterization, a problem of scale with FIB-SEM images is how to take nanometer scale information and apply it to the thin-section or larger scale. In this work, several texture characterization techniques including graph-based spectral segmentation, support vector machine, and principal component analysis are applied for segmentation clusters represented by 1-2 FIB-SEM samples per each cluster. Geometric and topological properties are analyzed and lattice-Boltzmann method (LBM) is used to obtain permeability at several different scales. Upscaling of permeability to the Darcy scale (e.g., the thin-section scale) with image dataset will be discussed with emphasis on understanding microfracture-matrix interaction, representative volume for FIB-SEM sampling, and multiphase flow and reactive transport. Funding from the DOE Basic Energy Sciences Geosciences Program is gratefully acknowledged. 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

  14. Characterization of a chiral nematic mesoporous organosilica using NMR

    NASA Astrophysics Data System (ADS)

    Manning, Alan; Shopsowitz, Kevin; Giese, Michael; MacLachlan, Mark; Dong, Ronald; Michal, Carl

    2012-10-01

    Using templation with nanocrystalline cellulose, a mesoporous organosilica film with a chiral nematic pore structure has recently been developed. [1] We have used a variety of Nuclear Magnetic Resonance (NMR) techniques to characterize the pore structure. The pore size distribution has been found by analyzing the freezing point depression of absorbed water via NMR cryoporometry. The effective longitudinal and transverse pore diameters for diffusing water were investigated with Pulsed-Field Gradient (PFG) NMR and compared to a 1-D connected-pore model. Preliminary data on testing imposed chiral ordering in absorbed liquid crystals is also presented. [4pt] [1] K.E. Shopsowitz et al. JACS 134(2), 867 (2012)

  15. Structural characterization of human Uch37

    SciTech Connect

    Burgie, E. Sethe; Bingman, Craig A.; Soni, Ameet B.; Phillips, Jr., George N.

    2012-06-28

    Uch37 is a deubiquitylating enzyme (DUB) that is functionally linked with multiple protein complexes and signal transduction pathways. Uch37 associates with the 26S proteasome through Rpn13 where it serves to remove distal ubiquitin moeities from polyubiquitylated proteins. Uch37's proteasome associated activity was shown to liberate proteins from destruction. However, Uch37 may also specifically facilitate the destruction of inducible nitric oxide synthase and I{kappa}B-{alpha} at the proteasome. Wicks et al. established Uch37's potential to modulate the transforming growth factor-{beta}(TGF-{beta}) signaling cascade, through tis interaction with SMAD7. Yao et al. demonstrated that Uch37 also associates with the Ino80 chromatin-remodeling complex (Ino80 complex), which is involved in DNA repair and transcriptional regulation. Uch37's importance in metazoan development was underscored recently as Uch37 knockouts in mice result in prenatal lethality, where mutant embryos had severe defects in brain development. Protein ubiquitylation is an ATP-dependent post-translational modification that serves to signal a wide variety of cellular processes in eukaryotes. A protein cascade, generally comprising three enzymes, functions to activate, transport and specifically transfer ubiquitin to the targeted protein, culminating in an isopeptide linkage between the {epsilon}-amino group of a target protein's lysysl residue and the ubiquitin's terminal carboxylate. Monoubiquitination plays an important role in histone regulation, endocytosis, and viral budding. Further processing of the target protein may be accomplished by ubiquitylation of the protein on a different lysine, or through the formation of polyubiquitin chains, where the best-characterized outcome is destruction of the polyubiquitin-labeled protein in the proteasome. DUBs catalyze the removal of ubiquitin from proteins. This activity serves to reverse the effects of ubiquitination, permit ubiquitin recycling, or

  16. Structure-based characterization of multiprotein complexes.

    PubMed

    Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

    2014-07-08

    Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies.

  17. The "GEOMODEL" at Kiel University: A Hydrogeophysical full scale model to study pore water, contamination and structure of vadose soils

    NASA Astrophysics Data System (ADS)

    Hagrey, S. A.; Rabbel, W.; Working Group Of Wateruse

    2003-04-01

    Erecting new improved GeoModel at Kiel University is based on our experiences with the pilot model for studying preferential flow processes and takes into account objectives of the EU - project "wateruse" for developing new high resolving techniques for hydro- and bio-geophysical studies. The GeoModel consists of a soil model (3x5x2m), computer room and monitoring chamber. A special irrigation device is installed above the model to simulate irrigations of different rates, intensities and contaminations (tracers). At the base a filter pebble layer divided into different segments for monitoring lateral distribution of discharge indicating for flowpaths and processes. A self developed vacuum aperture is installed to overcome effects of the hydraulic capillary barrier which is related to the abrupt jump in grain size at the soil sand-filter pebble interface. The concept of the GeoModel is to carry out controlled experiment with predefined boundary conditions (as in laboratory) on a full scale soil model (as in the field, i.e., no scale problems). The GeoModel, currently filled with silty sand is equipped with diverse fine electrode grids, radar hardware, TDR-, Tensiometer probes for measuring electrical resistivity, electromagnetic wave velocity and amplitude, water content and potential, respectively. The (infiltration) experiments aim at developing high resolution integrative spatiotemporal 3D techniques for monitoring flow processes of fluids and contaminants, mapping fine structure as preferential flow paths, root networks and trunk rings (which opens new applications in biogeophysics and geobiology), quantification of soil water content. The GeoModel serve for calibration of new instruments and techniques and is applied for special geotechnical and environmental experiments (e.g. anti-person mines, tracer experiments) as well as for technical courses for specialists. Also laboratory study of petrophysical parameters of soil material is carried out to establish

  18. Unlocking the Physiochemical Controls on Organic Carbon Dynamics from the Soil Pore- to Core-Scale

    NASA Astrophysics Data System (ADS)

    Smith, A. P.; Tfaily, M. M.; Bond-Lamberty, B. P.; Todd-Brown, K. E.; Bailey, V. L.

    2015-12-01

    The physical organization of soil includes pore networks of varying size and connectivity. These networks control microbial access to soil organic carbon (C) by spatially separating microorganisms and C by both distance and size exclusion. The extent to which this spatially isolated C is vulnerable to microbial transformation under hydrologically dynamic conditions is unknown, and limits our ability to predict the source and sink capacity of soils. We investigated the effects of shifting hydrologic connectivity and soil structure on greenhouse gas C emissions from surface soils collected from the Disney Wilderness Preserve (Florida, USA). We subjected intact soil cores and re-packed homogenized soil cores to simulated groundwater rise or precipitation, monitoring their CO2 and CH4 emissions over 24 hours. Soil pore water was then extracted from each core usin