Science.gov

Sample records for pore structure characterization

  1. Pore structure characterization of catalyst supports via low field NMR

    SciTech Connect

    Smith, D.M.; Glaves, C.L.; Gallegos, D.P.; Brinker, C.J.

    1988-01-01

    In this paper, the application of low-field NMR to both surface area and pore structure analysis of catalyst supports will be presented. Low-field (20 MHz) spin-lattice relaxation (T/sub 1/) experiments are performed on fluids contained in alumina and silica catalyst supports. Pore size distributions (PSD) calculated from these NMR experiments are compared to those obtained from mercury porosimetry and nitrogen condensation. 18 refs., 4 figs., 2 tabs.

  2. Pore structure characterization of catalyst supports via low field NMR

    SciTech Connect

    Smith, D.M.; Glaves, C.L.; Gallegos, D.P. )

    1988-09-01

    The pore structures of two types of catalyst support material were studied: {gamma}-alumina and silica aerogel. The alumina samples were commercial catalyst supports made in 1/8 inch diameter pellet form by Harshaw Chemical. Aerogels were prepared by forming a gel in a two-step, base-catalyzed process using TEOS, followed by supercritical drying to form the aerogel. Two different aerogels were made, one undergoing the drying process immediately after gel formation (non-aged), and the other being aged in the gel state for two weeks in a basic solution of 0.1 molar NH{sub 4}OH at 323 K before being supercritically dried (aged). The aging process is believed to alter the aerogel pore structure. The pore size distribution of the alumina material was determined via NMR and compared to results obtained by mercury intrusion and nitrogen adsorption/condensation techniques. The pore size distributions of the two aerogel samples were measured via NMR and nitrogen adsorption/condensation; the material was too compressible for porosimetry.

  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. Characterization of pore structure of polymer blended films used for controlled drug release.

    PubMed

    Häbel, Henrike; Andersson, Helene; Olsson, Anna; Olsson, Eva; Larsson, Anette; Särkkä, Aila

    2016-01-28

    The characterization of the pore structure in pharmaceutical coatings is crucial for understanding and controlling mass transport properties and function in controlled drug release. Since the drug release rate can be associated with the film permeability, the effect of the pore structure on the permeability is important to study. In this paper, a new approach for characterizing the pore structure in polymer blended films was developed based on an image processing procedure for given two-dimensional scanning electron microscopy images of film cross-sections. The focus was on different measures for characterizing the complexity of the shape of a pore. The pore characterization developed was applied to ethyl cellulose (EC) and hydroxypropyl cellulose (HPC) blended films, often used as pharmaceutical coatings, where HPC acts as the pore former. It was studied how two different HPC viscosity grades influence the pore structure and, hence, mass transport through the respective films. The film with higher HPC viscosity grade had been observed to be more permeable than the other in a previous study; however, experiments had failed to show a difference between their pore structures. By instead characterizing the pore structures using tools from image analysis, statistically significant differences in pore area fraction and pore shape were identified. More specifically, it was found that the more permeable film with higher HPC viscosity grade seemed to have more extended and complex pore shapes than the film with lower HPC viscosity grade. This result indicates a greater degree of connectivity in the film with higher permeability and statistically confirms hypotheses on permeability from related experimental studies. PMID:26686080

  5. Image-based characterization of cement pore structure using Wood`s metal intrusion

    SciTech Connect

    Willis, K.L.; Abell, A.B.; Lange, D.A.

    1998-12-01

    Mercury intrusion porosimetry is a widely used technique for characterization of the pore size distribution of cement-based materials. However, the technique has several limitations, among which are the ink bottle effect and a cylindrical pore geometry assumption that lead to inaccurate pore size distribution curves. By substituting Wood`s metal for mercury as the intruding liquid, scanning electron microscopy and imaging techniques can be applied to the sample after intrusion. The molten Wood`s metal solidifies within the pore structure of the sample, which allows it to be sectioned and observed in the scanning electron microscopy. From here, the sample can be analyzed both qualitatively, by observing the changes in the appearance of the sample as the intrusion process progresses, and quantitatively, by applying image analysis techniques. This study provides insight for better interpretation of mercury intrusion porosimetry results and the possibility for quantitative characterization of the spatial geometry of pores in cement-based materials.

  6. 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.

  7. 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.

  8. 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.

  9. Using X-ray computed tomography in pore structure characterization for a Berea sandstone: Resolution effect

    NASA Astrophysics Data System (ADS)

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

    2012-11-01

    SummaryX-ray computed tomography (XCT) is a powerful tool for detecting the micro-scale pore structure 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 pore structure. Several key pore structure 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.

  10. 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

  11. Characterization of pore structure of a strong anion-exchange membrane adsorbent under different buffer and salt concentration conditions.

    PubMed

    Tatárová, Ivana; Fáber, René; Denoyel, Renaud; Polakovic, Milan

    2009-02-01

    The quantitative characterization of pore structure of Sartobind Q, a strongly basic membrane anion exchanger that is formed by cross-linked cellulose support and a hydrogel layer on its pore surface, was made combining the results obtained by several experimental techniques: liquid impregnation, batch size-exclusion, inverse size-exclusion chromatography, and permeability. Mercury intrusion and nitrogen sorption porosimetry were carried out for a dry cellulose support membrane in order to get additional information for building a model of the bimodal pore structure. The model incorporated the distribution of the total pore volume between transport and gel-layer pores and the partitioning of solutes of different molecular weights was expressed through the cylindrical pore model for the transport pores and random plane model for the gel layer. The effect of composition of liquid phase on the pore structure was investigated in redistilled water, phosphate and Tris-HCl buffers containing up to 1M NaCl. Evident differences in the bimodal pore structure were observed here when both the specific volume and size of the hydrogel layer pores significantly decreased with the ionic strength of liquid phase. PMID:19117574

  12. Synthesis and characterization of magnetically active carbon nanofiber/iron oxide composites with hierarchical pore structures

    NASA Astrophysics Data System (ADS)

    Panels, Jeanne E.; Lee, Jinwoo; Park, Kang Yeol; Kang, Seung Yeon; Marquez, Manuel; Wiesner, Ulrich; Lak Joo, Yong

    2008-11-01

    Polyacrylonitrile (PAN) solution containing the iron oxide precursor iron (III) acetylacetonate (AAI) was electrospun and thermally treated to produce electrically conducting, magnetic carbon nanofiber mats with hierarchical pore structures. The morphology and material properties of the resulting multifunctional nanofiber mats including the surface area and the electric and magnetic properties were examined using various characterization techniques. Scanning electron microscopy images show that uniform fibers were produced with a fiber diameter of ~600 nm, and this uniform fiber morphology is maintained after graphitization with a fiber diameter of ~330 nm. X-ray diffraction (XRD) and Raman studies reveal that both graphite and Fe3O4 crystals are formed after thermal treatment, and graphitization can be enhanced by the presence of iron. A combination of XRD and transmission electron microscopy experiments reveals the formation of pores with graphitic nanoparticles in the walls as well as the formation of magnetite nanoparticles distributed throughout the fibers. Physisorption experiments show that the multifunctional fiber mats exhibit a high surface area (200-400 m2 g-1) and their pore size is dependent on the amount of iron added and graphitization conditions. Finally, we have demonstrated that the fibers are electrically conducting as well as magnetically active.

  13. Multiple Approaches to Characterizing Nano-Pore Structure of Barnett Shale

    NASA Astrophysics Data System (ADS)

    Hu, Q.; Gao, Z.; Ewing, R. P.; Dultz, S.; Kaufmann, J.; Hamamoto, S.; Webber, B.; Ding, M.

    2013-12-01

    Microscopic characteristics of porous media - pore shape, pore-size distribution, and pore connectivity - control fluid flow and mass transport. This presentation discusses various approaches to investigating nano-pore structure of Barnett shale, with its implications in gas production behavior. The innovative approaches include imbibition, tracer diffusion, edge-accessible porosity, porosimetry (mercury intrusion porosimetry, nitrogen and water vapor sorption isotherms, and nuclear magnetic resonance cyroporometry), and imaging (Wood's metal impregnation followed with laser ablation-inductively coupled plasma-mass spectrometry, focused ion beam/scanning electron microscopy, and small angle neutron scattering). Results show that the shale pores are predominantly in the nm size range, with measured median pore-throat diameters about 5 nm. But small pore size is not the major contributor to low gas recovery; rather, the low mass diffusivity appears to be caused by low pore connectivity of Barnett shale. Chemical diffusion in sparsely-connected pore spaces is not well described by classical Fickian behavior; anomalous behavior is suggested by percolation theory, and confirmed by results of imbibition and diffusion tests. Our evolving complementary approaches, with their several advantages and disadvantages, provide a rich toolbox for tackling the nano-pore structure characteristics of shales and other natural rocks.

  14. 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. PMID:15792584

  15. 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

  16. 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.

  17. 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, Y.; Hall, S.; Baud, P.; Wong, T.

    2013-12-01

    X-ray Computed Tomography (CT) and Digital Image Correlation (DIC) have been widely used for characterizing the pore structure and damage evolution in porous clastic rocks. In comparison, these 3D imaging techniques have not been used as widely in carbonate rocks. This paucity of 3D imaging arises primarily because carbonates have pore geometry that is significantly more complex than siliciclastics and consequently microCT imaging of the pore space is not straightforward. Hence most investigations of the pore structure and damage development in porous carbonate rocks have been done on 2D thin-sections, synthesizing observations on different scales using the optical microscope and SEM. In this study, we used two techniques for characterizing the pore structure and development of strain localization in Majella limestone of 31% porosity. The first technique allows us to extract 3D information from microCT data on the partitioning of porosity and pore size statistics in this limestone. Specifically the microCT image was partitioned into three distinct domains separated by two thresholds in the global histogram: macropores, solid grains and an intermediate domain (made up of voxels of solid embedded with micropores). Our morphological analysis of the microCT images shows that both the solid and intermediate domains are basically interconnected. Our new data underscore some of the 3D complexities of the macropores and implies that a dual porosity model is necessary for analyzing the mechanical behavior of porous carbonate rock. The second technique undertaken in this study is DIC analysis of the failure mode in relation to the brittle-ductile transition. With decrease in confinement, the failure mode of a porous rock undergoes a transition from delocalized compaction to brittle faulting. The damage associated with strain localization in Majella limestone is subtle and not easily resolvable under optical microscope or SEM. Our first application of 3D-volumetric DIC to a

  18. Characterization and structural investigation of fractal porous-silica over an extremely wide scale range of pore size.

    PubMed

    Ono, Yusuke; Mayama, Hiroyuki; Furó, István; Sagidullin, Alexander I; Matsushima, Keiichiro; Ura, Haruo; Uchiyama, Tomoyuki; Tsujii, Kaoru

    2009-08-01

    We have succeeded in creating Menger sponge-like fractal body, i.e., porous-silica samples with Menger sponge-like fractal geometries, by a novel template method utilizing template particles of alkylketene dimer (AKD) and a sol-gel synthesis of tetramethyl orthosilicate (TMOS). We report here the first experimental results on characterization and structural investigations of the fractal porous-silica samples prepared with various conditions such as calcination temperature and packing condition of the template particles. In order to characterize the fractal porous-silica samples, pore volume distribution, porosity and specific surface area were measured over an extremely wide scale from 1 nm to 100 microm by means of mercury porosimetry, (1)H NMR cryoporometry, nitrogen gas adsorption experiments together with direct evaluations of cross-sectional fractal dimension D(cs), and size limits of D(cs). We have found that the pore volume distribution and specific surface area of the fractal porous-silica samples can be discussed in terms of different fractal porous structures at different scale regions. PMID:19406424

  19. 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.

  20. Characterization of pore structure in cement-based materials using pressurization-depressurization cycling mercury intrusion porosimetry (PDC-MIP)

    SciTech Connect

    Zhou Jian; Ye Guang; Breugel, Klaas van

    2010-07-15

    Numerous mercury intrusion porosimetry (MIP) studies have been carried out to investigate the pore structure in cement-based materials. However, the standard MIP often results in an underestimation of large pores and an overestimation of small pores because of its intrinsic limitation. In this paper, an innovative MIP method is developed in order to provide a more accurate estimation of pore size distribution. The new MIP measurements are conducted following a unique mercury intrusion procedure, in which the applied pressure is increased from the minimum to the maximum by repeating pressurization-depressurization cycles instead of a continuous pressurization followed by a continuous depressurization. Accordingly, this method is called pressurization-depressurization cycling MIP (PDC-MIP). By following the PDC-MIP testing sequence, the volumes of the throat pores and the corresponding ink-bottle pores can be determined at every pore size. These values are used to calculate pore size distribution by using the newly developed analysis method. This paper presents an application of PDC-MIP on the investigation of the pore size distribution in cement-based materials. The experimental results of PDC-MIP are compared with those measured by standard MIP. The PDC-MIP is further validated with the other experimental methods and numerical tool, including nitrogen sorption, backscanning electron (BSE) image analysis, Wood's metal intrusion porosimetry (WMIP) and the numerical simulation by the cement hydration model HYMOSTRUC3D.

  1. USING A NEW FINITE SLIT PORE MODEL FOR NLDFT ANALYSIS OF CARBON PORE STRUCTURE

    SciTech Connect

    Jagiello, Jacek; Kenvin, Jeffrey; Oliver, James P; Lupini, Andrew R; Contescu, Cristian I

    2011-01-01

    In this work, we present a model for analyzing activated carbon micropore structures based on graphene sheet walls of finite thickness and extent. This is a two-dimensional modification of the widely used infinite slit pore model that assumes graphite-like infinitely extended pore walls. The proposed model has two versions: (1) a strip pore constructed with graphene strip walls that have finite length L in the x direction and are infinite in the y direction. Strip pores are open on both sides in the x direction. (2) A channel pore is a strip pore partially closed along one edge by a perpendicularly oriented graphene wall. This more realistic model allows pore termination via both physical pore entrances and pore blockage. The model consequently introduces heterogeneity of the adsorption potential that is reduced near pore entrances and enhanced near corners of pore walls. These energetically heterogeneous structures fill with adsorbate more gradually than homogeneous pores of the same width. As a result, the calculated adsorption isotherms are smoother and less steep for the finite versus the infinite pore model. In the application of this model for carbon characterization it is necessary to make an assumption about the pore length. In this work we made this assumption based on the high resolution scanning transmission electron microscopy (STEM) results. We find the agreement between the experiment and the model significantly better for the finite than for the infinite pore model.

  2. PORE STRUCTURE MODEL OF CEMENT HYDRATES CONSIDERING PORE WATER CONTENT AND REACTION PROCESS UNDER ARBITRARY HUMIDITY

    NASA Astrophysics Data System (ADS)

    Fujikura, Yusuke; Oshita, Hideki

    A simulation model to estimate the pore structure of cement hydrates by curing in arbitrary relative humidity is presented. This paper describes procedures for predicting phase compositions based on the classical hydration model of Portland cement, calculating the particle size distribution of constituent phases and evaluating the pore size distribution by stereological and statistical considerations. And to estimate the water content in pore structure under any relative humidity, we proposed the simulation model of adsorption isotherm model based on the pore structure. To evaluate the effectiveness of this model, simulation results were compared with experimental results of the pore size distribution measured by mercury porosimetry. As a result, it was found that the experimental and simulated results were in close agreement, and the simulated results indicated characterization of the po re structure of cement hydrates.

  3. Synthesis and characterization of high-surface-area millimeter-sized silica beads with hierarchical multi-modal pore structure by the addition of agar

    SciTech Connect

    Han, Yosep; Choi, Junhyun; Tong, Meiping; Kim, Hyunjung

    2014-04-01

    Millimeter-sized spherical silica foams (SSFs) with hierarchical multi-modal pore structure featuring high specific surface area and ordered mesoporous frameworks were successfully prepared using aqueous agar addition, foaming and drop-in-oil processes. The pore-related properties of the prepared spherical silica (SSs) and SSFs were systematically characterized by field emission-scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), small-angle X-ray diffraction (SAXRD), Hg intrusion porosimetry, and N{sub 2} adsorption–desorption isotherm measurements. Improvements in the BET surface area and total pore volume were observed at 504 m{sup 2} g{sup −1} and 5.45 cm{sup 3} g{sup −1}, respectively, after an agar addition and foaming process. Despite the increase in the BET surface area, the mesopore wall thickness and the pore size of the mesopores generated from the block copolymer with agar addition were unchanged based on the SAXRD, TEM, and BJH methods. The SSFs prepared in the present study were confirmed to have improved BET surface area and micropore volume through the agar loading, and to exhibit interconnected 3-dimensional network macropore structure leading to the enhancement of total porosity and BET surface area via the foaming process. - Highlights: • Millimeter-sized spherical silica foams (SSFs) are successfully prepared. • SSFs exhibit high BET surface area and ordered hierarchical pore structure. • Agar addition improves BET surface area and micropore volume of SSFs. • Foaming process generates interconnected 3-D network macropore structure of SSFs.

  4. Morphological Characterization of the Polyflux 210H Hemodialysis Filter Pores

    PubMed Central

    Hedayat, A.; Szpunar, J.; Kumar, N. A. P. Kiran; Peace, R.; Elmoselhi, H.; Shoker, A.

    2012-01-01

    Background. Morphological characterization of hemodialysis membranes is necessary to improve pore design. Aim. To delineate membrane pore structure of a high flux filter, Polyflux 210H. Methods. We used a Joel JSM-6010LV scanning electron microscope (SEM) and a SU6600 Hitachi field emission scanning electron microscope (FESEM) to characterize the pore and fiber morphology. The maximal diameters of selected uremic toxins were calculated using the macromolecular modeling Crystallographic Object-Oriented Toolkit (COOT) software. Results. The mean pore densities on the outermost and innermost surfaces of the membrane were 36.81% and 5.45%, respectively. The membrane exhibited a tortuous structure with poor connection between the inner and outer pores. The aperture's width in the inner surface ranged between 34 and 45 nm, which is 8.76–11.60 times larger than the estimated maximum diameter of β2-microglobulin (3.88 nm). Conclusion. The results suggest that the diameter size of inner pore apertures is not a limiting factor to middle molecules clearance, the extremely diminished density is. Increasing inner pore density and improving channel structure are strategies to improve clearance of middle molecules. PMID:23209902

  5. Measuring kinetic drivers of pneumolysin pore structure.

    PubMed

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

    2016-05-01

    Most membrane attack complex-perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins are thought to form pores in target membranes by assembling into pre-pore oligomers before undergoing a pre-pore to pore transition. Assembly during pore formation is into both full rings of subunits and incomplete rings (arcs). The balance between arcs and full rings is determined by a mechanism dependent on protein concentration in which arc pores arise due to kinetic trapping of the pre-pore forms by the depletion of free protein subunits during oligomerization. Here we describe the use of a kinetic assay to study pore formation in red blood cells by the MACPF/CDC pneumolysin from Streptococcus pneumoniae. We show that cell lysis displays two kinds of dependence on protein concentration. At lower concentrations, it is dependent on the pre-pore to pore transition of arc oligomers, which we show to be a cooperative process. At higher concentrations, it is dependent on the amount of pneumolysin bound to the membrane and reflects the affinity of the protein for its receptor, cholesterol. A lag occurs before cell lysis begins; this is dependent on oligomerization of pneumolysin. Kinetic dissection of cell lysis by pneumolysin demonstrates the capacity of MACPF/CDCs to generate pore-forming oligomeric structures of variable size with, most likely, different functional roles in biology. PMID:26906727

  6. Atomic Structure of Graphene Subnanometer Pores.

    PubMed

    Robertson, Alex W; Lee, Gun-Do; He, Kuang; Gong, Chuncheng; Chen, Qu; Yoon, Euijoon; Kirkland, Angus I; Warner, Jamie H

    2015-12-22

    The atomic structure of subnanometer pores in graphene, of interest due to graphene's potential as a desalination and gas filtration membrane, is demonstrated by atomic resolution aberration corrected transmission electron microscopy. High temperatures of 500 °C and over are used to prevent self-healing of the pores, permitting the successful imaging of open pore geometries consisting of between -4 to -13 atoms, all exhibiting subnanometer diameters. Picometer resolution bond length measurements are used to confirm reconstruction of five-membered ring projections that often decorate the pore perimeter, knowledge which is used to explore the viability of completely self-passivated subnanometer pore structures; bonding configurations where the pore would not require external passivation by, for example, hydrogen to be chemically inert. PMID:26524121

  7. 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.

  8. 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).

  9. 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.

  10. 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.

  11. Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex*

    PubMed Central

    Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P.; Chait, Brian T.

    2014-01-01

    Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. PMID:25161197

  12. Soil pore structure and substrate C mineralization

    NASA Astrophysics Data System (ADS)

    Sleutel, Steven; Maenhout, Peter; Vanhoorebeke, Luc; Cnudde, Veerle; De Neve, Stefaan

    2014-05-01

    Our aim was to investigate the complex interactions between soil pore structure, soil biota and decomposition of added OM substrates. We report on a lab incubation experiment in which CO2 respiration from soil cores was monitored (headspace GC analysis) and an X-ray CT approach yielded soil pore size distributions. Such combined use of X-ray CT with soil incubation studies was obstructed, until now, by many practical constraints such as CT-volume quality, limited resolution, scanning time and complex soil pore network quantification, which have largely been overcome in this study. We incubated a sandy loam soil (with application of ground grass or sawdust) in 18 small aluminium rings (Ø 1 cm, h 1 cm). Bulk density was adjusted to 1.1 or 1.3 Mg m-3 (compaction) and 6 rings were filled at a coarser Coarse Sand:Fine Sand:Silt+Clay ratio. While compaction induced a strong reduction in the cumulative C mineralization for both grass and sawdust substrates, artificial change to a coarser soil texture only reduced net C mineralization from the added sawdust. There thus appears to be a strong interaction effect between soil pore structure and substrate type on substrate decomposition. Correlation coefficients between the C mineralization rates and volumes of 7 pore size classes (from the X-ray CT data) also showed an increasing positive correlation with increasing pore size. Since any particulate organic matter initially present in the soil was removed prior to the experiment (sieving, ashing the >53µm fraction and recombining with the <53µm fraction), the added OM can be localized by means of X-ray CT. Through on-going image analysis the surrounding porosity of the added grass or sawdust particles is being quantified to further study the interaction between the soil pore structure and substrate decomposition.

  13. Pore structure analysis of American coals

    SciTech Connect

    Gallegos, D.P.; Smith, D.M.; Stermer, D.L.

    1987-01-01

    The pore structure of 19 American coals, representing a wide range of rank and geographic origin, has been studied via gas adsorption, mercury porosimetry, helium displacement and NMR spin-lattice relaxation measurements. Nitrogen adsorption at 77 K was used to determine surface area in the pore range of r/sub p/ > approx. = 1nm and carbon dioxide adsorption at 273 K was used to obtain the total surface area. Porosimetry results were complicated by inter-particle void filling, surface roughness/porosity and sample compression. By employing a range of particle sizes, information concerning the relative magnitude of these mechanisms was ascertained as a function of pressure. Spin-lattice relaxation measurements of water contained in saturated coal were used to find pore size distributions over a broad range of T/sub 1/, the spin-lattice relaxation time. Good qualitative agreement was obtained between these measurements and gas adsorption/condensation results. 13 refs., 3 figs., 1 tab.

  14. SCAM analysis of Panx1 suggests a peculiar pore structure.

    PubMed

    Wang, Junjie; Dahl, Gerhard

    2010-11-01

    Vertebrates express two families of gap junction proteins: the well-characterized connexins and the pannexins. In contrast to connexins, pannexins do not appear to form gap junction channels but instead function as unpaired membrane channels. Pannexins have no sequence homology to connexins but are distantly related to the invertebrate gap junction proteins, innexins. Despite the sequence diversity, pannexins and connexins form channels with similar permeability properties and exhibit similar membrane topology, with two extracellular loops, four transmembrane (TM) segments, and cytoplasmic localization of amino and carboxy termini. To test whether the similarities extend to the pore structure of the channels, pannexin 1 (Panx1) was subjected to analysis with the substituted cysteine accessibility method (SCAM). The thiol reagents maleimidobutyryl-biocytin and 2-trimethylammonioethyl-methanethiosulfonate reacted with several cysteines positioned in the external portion of the first TM segment (TM1) and the first extracellular loop. These data suggest that portions of TM1 and the first extracellular loop line the outer part of the pore of Panx1 channels. In this aspect, the pore structures of Panx1 and connexin channels are similar. However, although the inner part of the pore is lined by amino-terminal amino acids in connexin channels, thiol modification was detected in carboxyterminal amino acids in Panx1 channels by SCAM analysis. Thus, it appears that the inner portion of the pores of Panx1 and connexin channels may be distinct. PMID:20937692

  15. A characterization of the coupled evolution of grain fabric and pore space using complex networks: Pore connectivity and optimized flows in the presence of shear bands

    NASA Astrophysics Data System (ADS)

    Russell, Scott; Walker, David M.; Tordesillas, Antoinette

    2016-03-01

    A framework for the multiscale characterization of the coupled evolution of the solid grain fabric and its associated pore space in dense granular media is developed. In this framework, a pseudo-dual graph transformation of the grain contact network produces a graph of pores which can be readily interpreted as a pore space network. Survivability, a new metric succinctly summarizing the connectivity of the solid grain and pore space networks, measures material robustness. The size distribution and the connectivity of pores can be characterized quantitatively through various network properties. Assortativity characterizes the pore space with respect to the parity of the number of particles enclosing the pore. Multiscale clusters of odd parity versus even parity contact cycles alternate spatially along the shear band: these represent, respectively, local jamming and unjamming regions that continually switch positions in time throughout the failure regime. Optimal paths, established using network shortest paths in favor of large pores, provide clues on preferential paths for interstitial matter transport. In systems with higher rolling resistance at contacts, less tortuous shortest paths thread through larger pores in shear bands. Notably the structural patterns uncovered in the pore space suggest that more robust models of interstitial pore flow through deforming granular systems require a proper consideration of the evolution of in situ shear band and fracture patterns - not just globally, but also inside these localized failure zones.

  16. 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.

  17. Effect of addition of pore expanding agent on changes of structure characteristics of ordered mesoporous silicas

    NASA Astrophysics Data System (ADS)

    Derylo-Marczewska, A.; Marczewski, A. W.; Skrzypek, I.; Pikus, S.; Kozak, M.

    2008-12-01

    A series of mesoporous silica materials were synthesized by applying two types of Pluronic copolymers as pore creating agents. Differentiation of pore structure of the obtained sorbents was attained by changing the amount of trimethylbenzene as pore expander introduced to a reacting mixture. The parameters characterizing porous structure were estimated from nitrogen adsorption/desorption isotherms. The changes of pore arrangement in the synthesized materials were investigated by using X-ray diffraction. The structural transformations were found at the TMB/polymer ratio of 0.8 and 1. Correlations between the values of structure parameters and the content of TMB were found.

  18. 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

  19. 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 ([Formula: see text]), 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

  20. Nondestructive technique for the characterization of the pore size distribution of soft porous constructs for tissue engineering.

    PubMed

    Safinia, Laleh; Mantalaris, Athanasios; Bismarck, Alexander

    2006-03-28

    Polymer scaffolds tailored for tissue engineering applications possessing the desired pore structure require reproducible fabrication techniques. Nondestructive, quantitative methods for pore characterization are required to determine the pore size and its distribution. In this study, a promising alternative to traditional pore size characterization techniques is presented. We introduce a quantitative, nondestructive and inexpensive method to determine the pore size distribution of large soft porous solids based on the on the displacement of a liquid, that spreads without limits though a porous medium, by nitrogen. The capillary pressure is measured and related to the pore sizes as well as the pore size distribution of the narrowest bottlenecks of the largest interconnected pores in a porous medium. The measured pore diameters correspond to the narrowest bottleneck of the largest pores connecting the bottom with the top surface of a given porous solid. The applicability and reproducibility of the breakthrough technique is demonstrated on two polyurethane foams, manufactured using the thermally induced phase separation (TIPS) process, with almost identical overall porosity (60-70%) but very different pore morphology. By selecting different quenching temperatures to induce polymer phase separation, the pore structure could be regulated while maintaining the overall porosity. Depending on the quenching temperature, the foams exhibited either longitudinally oriented tubular macropores interconnected with micropores or independent macropores connected to adjacent pores via openings in the pore walls. The pore size and its distribution obtained by the breakthrough test were in excellent agreement to conventional characterization techniques, such as scanning electron microscopy combined with image analysis, BET technique, and mercury intrusion porosimetry. This technique is suitable for the characterization of the micro- and macropore structure of soft porous solids

  1. Desymmetrized Vertex Design for the Synthesis of Covalent Organic Frameworks with Periodically Heterogeneous Pore Structures.

    PubMed

    Zhu, Youlong; Wan, Shun; Jin, Yinghua; Zhang, Wei

    2015-11-01

    Two novel porous 2D covalent organic frameworks (COFs) with periodically heterogeneous pore structures were successfully synthesized through desymmetrized vertex design strategy. Condensation of C(2v) symmetric 5-(4-formylphenyl)isophthalaldehyde or 5-((4-formylphenyl)ethylene)isophthalaldehyde with linear hydrazine linker under the solvothermal or microwave heating conditions yields crystalline 2D COFs, HP-COF-1 and HP-COF-2, with high specific surface areas and dual pore structures. PXRD patterns and computer modeling study, together with pore size distribution analysis confirm that each of the resulting COFs exhibits two distinctively different hexagonal pores. The structures were characterized by FT-IR, solid state (13)C NMR, gas adsorption, SEM, TEM, and theoretical simulations. Such rational design and synthetic strategy provide new possibilities for preparing highly ordered porous polymers with heterogeneous pore structures. PMID:26478274

  2. 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

  3. 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. PMID:25961729

  4. The structure of a melittin-stabilized pore.

    PubMed

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

    2015-05-19

    Melittin has been reported to form toroidal pores under certain conditions, but the atomic-resolution structure of these pores is unknown. A 9-μs all-atom molecular-dynamics simulation starting from a closely packed transmembrane melittin tetramer in DMPC shows formation of a toroidal pore after 1 μs. The pore remains stable with a roughly constant radius for the rest of the simulation. Surprisingly, one or two melittin monomers frequently transition between transmembrane and surface states. All four peptides are largely helical. A simulation in a DMPC/DMPG membrane did not lead to a stable pore, consistent with the experimentally observed lower activity of melittin on anionic membranes. The picture that emerges from this work is rather close to the classical toroidal pore, but more dynamic with respect to the configuration of the peptides. PMID:25992720

  5. Influence of pore structure on compressive strength of cement mortar.

    PubMed

    Zhao, Haitao; Xiao, Qi; Huang, Donghui; Zhang, Shiping

    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

  6. 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.

  7. Gaseous Diffusion and Pore Structure in Nuclear Graphites.

    NASA Astrophysics Data System (ADS)

    Mays, Timothy John

    Available from UMI in association with The British Library. With the incentive of providing more information for oxidation and safety studies of graphite components in thermal nuclear reactors, a new method has been developed to determine the gas transport pore structure in nuclear graphites. It involves an analysis of the dependence on pressure of the isobaric, isothermal (room temperature) diffusivity ratios of components in a binary gas mixture flowing through annular graphite samples. A Wicke-Kallenbach apparatus was specially built to measure He-Ar diffusivity ratios at pressures below 100 Torr. The new apparatus incorporates capacitance manometers and servovalves for pressure measurement and control, hot wire meters for flow rate measurements, and a mass spectrometer for gas analysis. As pressure decreased, the diffusivity ratios were observed to decrease non-linearly, indicating that the mechanism of flow in the materials was in the transition region between molecular and Knudsen diffusion. A mathematical model was derived to relate the pressure dependence of the transition diffusivity ratio to gas transport pore structure, and a statistical analysis based on Tikhonov regularisation was developed which gave a good fit of the model to the data, and optimal estimates of the number of model capillary pores, and the distribution of pore sizes. In comparison, the established methods of molecular diffusion and permeation (flow of pure gases) only give mean data on the pore size distribution. Pore structure data from the new method accurately predicted CO_2-Ar molecular diffusivity ratios, but overestimated N_2 permeability coefficients, due, it was assumed, to differences between diffusion and permeation pore structure. The cumulative volume distributions for transport pores from the transition diffusion data were similar in shape to those for open pores from mercury porosimetry, but shifted towards higher pore radii, indicating that diffusion is not so influenced

  8. 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.

  9. 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.

  10. 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. PMID:25778700

  11. Atomic structure of anthrax PA pore elucidates toxin translocation

    PubMed Central

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

    2015-01-01

    Summary Anthrax toxin, comprising protective antigen (PA), lethal factor (LF) and edema factor (EF), is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in human and animals. PA forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes LF and EF into the cytosol of target cells1. PA 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. Based on biochemical and electrophysiological results, researchers have proposed that a Φ-clamp composed of Phe427 residues of PA catalyzes protein translocation via a charge-state dependent Brownian ratchet2–9. Although atomic structures of PA prepores are available10–14, how PA senses low pH, converts to active pore and translocates LF and EF are not well defined without an atomic model of the PA pore. Here, by cryo electron microscopy (cryoEM) with direct electron counting, we have determined the PA 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. PMID:25778700

  12. Structural characterization of water and ice in mesoporous SBA-15 silicas: II. The 'almost-filled' case for 86 Å pore diameter.

    PubMed

    Seyed-Yazdi, J; Farman, H; Dore, John C; Webber, J Beau W; Findenegg, G H; Hansen, T

    2008-05-21

    Neutron diffraction measurements for D(2)O in SBA-15 silica of pore diameter 86 Å have been made in a temperature range from 300 to 100 K. The pore-filling factor for the liquid phase is 0.95, resulting in an 'almost-filled' sample. The nucleation and transformation of the ice phase were determined for cooling and warming cycles at two different rates. The primary nucleation event at 258 K leads to a defective form of ice-I with predominantly cubic ice features. For temperatures below the main nucleation event, the data indicate the formation of an interfacial layer of disordered water/ice that varies with temperature and is reversible. The main diffraction peak for the water phase shows similar features to those observed in earlier studies, indicating enhanced hydrogen bonding and network correlations for the confined phase as the temperature is decreased. A detailed profile analysis of the triplet peak is presented in the accompanying paper (Seyed-Yazdi et al 2008 J. Phys.: Condens. Matter 20 205108). PMID:21694288

  13. 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.

  14. 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.

  15. On the application of focused ion beam nanotomography in characterizing the 3D pore space geometry of Opalinus clay

    NASA Astrophysics Data System (ADS)

    Keller, Lukas M.; Holzer, Lorenz; Wepf, Roger; Gasser, Philippe; Münch, Beat; Marschall, Paul

    The evaluation and optimization of radioactive disposal systems requires a comprehensive understanding of mass transport processes. Among others, mass transport in porous geomaterials depends crucially on the topology and geometry of the pore space. Thus, understanding the mechanism of mass transport processes ultimately requires a 3D characterization of the pore structure. Here, we demonstrate the potential of focused ion beam nanotomography (FIB-nT) in characterizing the 3D geometry of pore space in clay rocks, i.e. Opalinus clay. In order to preserve the microstructure and to reduce sample preparation artefacts we used high pressure freezing and subsequent freeze drying to prepare the samples. Resolution limitations placed the lower limit in pore radii that can be analyzed by FIB-nT to about 10-15 nm. Image analysis and the calculation of pore size distribution revealed that pores with radii larger than 15 nm are related to a porosity of about 3 vol.%. To validate the method, we compared the pores size distribution obtained by FIB-nT with the one obtained by N 2 adsorption analysis. The latter yielded a porosity of about 13 vol.%. This means that FIB-nT can describe around 20-30% of the total pore space. For pore radii larger than 15 nm the pore size distribution obtained by FIB-nT and N 2 adsorption analysis were in good agreement. This suggests that FIB-nT can provide representative data on the spatial distribution of pores for pore sizes in the range of about 10-100 nm. Based on the spatial analysis of 3D data we extracted information on the spatial distribution of pore space geometrical properties.

  16. Pore-forming protein toxins: from structure to function.

    PubMed

    Parker, Michael W; Feil, Susanne C

    2005-05-01

    Pore-forming protein toxins (PFTs) are one of Nature's most potent biological weapons. An essential feature of their toxicity is the remarkable property that PFTs can exist either in a stable water-soluble state or as an integral membrane pore. In order to convert from the water-soluble to the membrane state, the toxin must undergo large conformational changes. There are now more than a dozen PFTs for which crystal structures have been determined and the nature of the conformational changes they must undergo is beginning to be understood. Although they differ markedly in their primary, secondary, tertiary and quaternary structures, nearly all can be classified into one of two families based on the types of pores they are thought to form: alpha-PFTs or beta-PFTs. Recent work suggests a number of common features in the mechanism of membrane insertion may exist for each class. PMID:15561302

  17. 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).

  18. 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

  19. Advanced NMR-based techniques for pore structure analysis of coal

    SciTech Connect

    Smith, D.M.

    1992-01-01

    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 closed 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. We believe that measurement of the NMR parameters of various gas phase and adsorbed phase NMR active probes can provide the resolution to this problem. 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 and the pore surfaces in coals. These molecules have been selected for their chemical and physical properties. A special NMR probe will be constructed which will allow the concurrent measurement of NMR properties and adsorption uptake at a variety of temperatures. All samples will be subjected to a suite of conventional'' pore structure analyses. These include nitrogen adsorption at 77 K with BET analysis, CO[sub 2] and CH[sub 4] adsorption at 273 K with D-R (Dubinin-Radushkevich) analysis, helium pycnometry, and small angle X-ray scattering as well as gas diffusion measurements.

  20. Influence of pore shape on the structure of a nanoconfined Gay-Berne liquid crystal

    NASA Astrophysics Data System (ADS)

    Ji, Qing; Lefort, Ronan; Morineau, Denis

    2009-08-01

    We present results from molecular dynamics simulations of a Gay-Berne mesogenic system GB(4.4,20,1,1) under short scale spatial confinement in a slab, a cylinder and a sphere geometry. The structure adopted by the confined phases is characterized by the density profile and the orientational order parameter as a function of temperature, and compared to the bulk. Though confinement always induces a strong surface ordering, the topological constrain introduced by the different pore shapes results in different molecular arrangements. This first study on pore shape effect on the structure of a nanoconfined Gay-Berne system is relevant to numerous experimental studies performed with different mesoporous matrices.

  1. Characterization of geologic media using Minkowski functionals and applying pore connectivity as an extra ruling factor when estimating permeability

    NASA Astrophysics Data System (ADS)

    Rodrigues, L. M.; Anwar, S.

    2013-12-01

    Over the last two decades, several approaches to characterize porous medium were developed. One of them being the topology based Minkowski functionals, which are basic geometric measures defined for binary image of porous media. By segmenting three-dimensional (3D) pore space representations, it is possible to characterize quantitatively structural features at the pore scale such as porosity, pore mean curvature, specific surficial area, and pore connectivity using these measures. Structural features are believed to strongly control the permeability of porous media; however a rigorous mathematical validation of such relationship between structural features and the hydraulic property is missing in the literature. We hypothesize that rock permeability not only depend on the macroscopic properties such as porosity and grain size distribution but also depend on the structural features of porous media such as pore connectivity, specific surficial area, and pore mean curvature. We aim to develop a relationship between such structural features of porous media that occurs at pore scale with macroscopic properties such as hydraulic conductivity. Our hypothesis is tested by using a numerical scheme for computational fluid dynamics called Lattice Boltzmann method (LBM), which enables the estimation of hydraulic parameters such as tortuosity and permeability which are relatively difficult and time consuming when obtained from laboratory experiments. 3D pore networks with similar porosity but significantly different structural properties are numerically generated using SGeMS. A series of LBM based flow simulations in different 3D pore networks are designed to understand the correlation between the structural property of porous media and its permeability.

  2. 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.

  3. Open pore structure analysis of lithium bearing ceramics

    NASA Astrophysics Data System (ADS)

    Elbel, H.

    1988-07-01

    The analysis of the open pore structure includes mercury porosimetry, helium stereopycnometry, gas permeability and specific surface area measurements. These methods were used in the analysis of different types of Li 2SiO 3 and Li 4SiO 4 specimens whose behaviour is tested under operation conditions in various irradiation experiments. Mercury porosimetry yielded density of the specimens, size distribution of the channels and amount of the open porosity. The correlation between mercury pressure and channel diameter was approximated by the Washburn equation. Density determinations by means of helium stereopycnometry demonstrated the existence of open pore volume below the mercury porosimetry detection. Additional information about the structure of open porosity was obtained by gas permeability measurements evaluated using the Carman relation, which is a generalization of the Hagen-Poiseuille law. This approach correlates structure parameters of the open porosity with permeability coefficients. The specific surface area was determined by applying the BET theory to volumetric nitrogen gas adsorption.

  4. The role of pore structure on char reactivity

    SciTech Connect

    Sarofim, A.F.

    1992-06-01

    The Wyoming lignite raw coal was size classified to 38--45 [mu]m, first by air-classification to remove the fine panicles, and then by sieving with a standard Ro-tap sieving machine. The size-classified Wyoming lignite was then pyrolyzed in a laboratory-scale laminar flow furnace at 1650K, 100% N[sub 2]. About one gram of pyrolyzed char was collected with Millipore membrane filters (teflon/polyethylene). The char sample thus collected was carefully poured into an cylindrical mold filled with epoxy resin and thoroughly mixed with epoxy resin. In order to remove the air bubbles trapped during mixing in the mixture, the sample-filled mold was placed in a dessicator connected to a vacuum pump. By periodically evacuating the dessicator, trapped air bubbles could be removed. The mold with the char sample and epoxy resin was placed in a cool area for 24 hours until it hardened. One end of the hardened cylindrical plug was carefully polished with alumina paste so that char particles embedded could also be cross-sectioned. The polished end of the sample plug thus prepared was observed under a Wetzlar optical microscope with a built-in camera. Pictures of fifty cross-sections of char particles were taken. The magnification was in the range of [times] l00 and [times] 650. Figure 1 shows cross-sections of char particles shown in black and white images. (The carbonaceous matrix is shown in black). Characterization of the pore structure of the char was carried out by digital image processing on cross-sections of the char particles. Pictures of cross-sections were scanned in, digitized in 600 [times] 5l2-pixel, 256-grayscale images using an Apple Scanner. Grayscale images were first converted to binary black-and-white images by setting a grayscale threshold that gives the best images of pores and char. Editing, i.e., sharpening and noise reduction, was performed to the binary images using Image v 1.17, a public domain program.

  5. 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

  6. Advanced NMR-based techniques for pore structure analysis of coal

    SciTech Connect

    Smith, D.M.

    1992-01-01

    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 closed 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. We believe that measurement of the NMR parameters of various gas phase and adsorbed phase NMR active probes can provide the resolution to this problem. We now have two suites of well-characterized microporous materials including oxides (zeolites and silica gel) and activated carbons from our industrial partner, Air Products in Allentown, PA. Our current work may be divided into three areas: small-angle X-ray scattering (SAXS), adsorption, and NMR.

  7. 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

  8. Advanced NMR-based techniques for pore structure analysis of coal

    SciTech Connect

    Smith, D.M.

    1991-01-01

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. We propose to 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 2}H{sub 2}, {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 the pore surfaces in coals. These molecules have been selected for their chemical and physical properties.

  9. 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.

  10. Anisotropy of Pore Structure and Permeability in Granite: Preliminary Results

    NASA Astrophysics Data System (ADS)

    Onishi, C. T.; Shimizu, I.; Mizoguchi, K.; Uehara, S.; Shimamoto, T.

    2001-12-01

    The permeability of rocks is sensitive to pore structures. In fault zones where brittle deformation dominates, connectivity of cracks is perhaps the most important factor to control the fluid permeability. The relationship between microstructure, porosity-pore structures and permeability were investigated, using drill core samples from the Toki Granite in Gifu Prefecture, Central Japan. Core samples taken from a borehole penetrating a fault strand of the Tsukiyoshi Fault at the depth of 700 m were used for analysis and measurements. The Toki Granite shows textural variations. For example, away from the fault zone, the granite is fresh, massive biotite granite. Toward the fault the granitic texture is largely destroyed, reflecting deformation due to fault movement, with extensive fracturing and development of calcite veins. The central part of the fault zone constitutes foliated ultra-cataclasites with a fine grained matrix. Microstructural observations indicate that fragmentation of crystals is the cause of grain size reduction in the fault zone and anisotropy in micro-crack development. The effective porosity of bulk samples measured by Helium pycnometer varies from 0.54% for unaltered fresh granite to over 5.4% for foliated cataclasite from the central part of the fault zone. The pore structures of the granite samples were visualized by the Laser Scanning Microscope (LSM). The samples were impregnated with low viscosity fluorescent resin under vacuum condition, and then observed by the LSM. Quasi 3-D images of pore structures were constructed from optical slices (confocal images) of thick sections. Micro-cracks in granites were successfully filled with the fluorescent resin. Micro-cracks were mainly observed at grain boundaries, and the intra and inter granular fractures. Permeability measurements were performed by a High Pressure Temperature (HPT) gas apparatus using the pore oscillation technique. Confining pressure was increased and then decreased in the range

  11. 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.

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

    SciTech Connect

    Jiang, Y; He, Y H; Zou, J; Huang, B; Liu, C

    2008-01-01

    PorousTi Alalloys 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 porousTi Alalloys can have three crystalline phases (i.e., 2-Ti3Al, -TiAl, and TiAl3) when using different compositions. The fundamental reasons behind these phenomena have been explored.

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

    PubMed

    Belwalkar, A; Grasing, E; Van Geertruyden, W; Huang, Z; Misiolek, W Z

    2008-07-01

    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 microm. 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

  14. 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

  15. 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

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

    NASA Astrophysics Data System (ADS)

    Wang, Hsiu-Wen; Anovitz, Lawrence M.; Burg, Avihu; Cole, David R.; Allard, Lawrence F.; Jackson, Andrew J.; Stack, Andrew G.; Rother, Gernot

    2013-11-01

    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 low- and 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.

  17. 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.

  18. Finding and Characterizing Tunnels in Macromolecules with Application to Ion Channels and Pores

    PubMed Central

    Coleman, Ryan G.; Sharp, Kim A.

    2009-01-01

    Abstract We describe a new algorithm, CHUNNEL, to automatically find, characterize, and display tunnels or pores in proteins. The correctness and accuracy of the algorithm is verified on a constructed set of proteins and used to analyze large sets of real proteins. The verification set contains proteins with artificially created pores of known path and width profile. The previous benchmark algorithm, HOLE, is compared with the new algorithm. Results show that the major advantage of the new algorithm is that it can successfully find and characterize tunnels with no a priori guidance or clues about the location of the tunnel mouth, and it will successfully find multiple tunnels if present. CHUNNEL can also be used in conjunction with HOLE, with the former used to prime HOLE and the latter to track and characterize the pores. Analysis was conducted on families of membrane protein structures culled from the Protein Data Bank as well as on a set of transmembrane proteins with predicted membrane-aqueous phase interfaces, yielding the first completely automated examination of tunnels through membrane proteins, including tunnels that exit in the membrane bilayer. PMID:18849407

  19. 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).

  20. Application of controlled interfacial pore structures to kinetic studies in alumina

    SciTech Connect

    Roedel, J.; Glaeser, A.M.

    1988-04-01

    The application of controlled-geometry interfacial pore structures to fundamental kinetic studies in alumina is described. Results from studies of the morphological stability of high aspect ratio pore channels, crack healing, pore coarsening and pore elimination in sapphire are presented.

  1. 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.

  2. 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. PMID:26416747

  3. Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein.

    PubMed

    Jia, Ning; Liu, Nan; Cheng, Wang; Jiang, Yong-Liang; Sun, Hui; Chen, Lan-Lan; Peng, Junhui; Zhang, Yonghui; Ding, Yue-He; Zhang, Zhi-Hui; Wang, Xuejuan; Cai, Gang; Wang, Junfeng; Dong, Meng-Qiu; Zhang, Zhiyong; Wu, Hui; Wang, Hong-Wei; Chen, Yuxing; Zhou, Cong-Zhao

    2016-02-01

    Various aerolysin-like pore-forming proteins have been identified from bacteria to vertebrates. However, the mechanism of receptor recognition and/or pore formation of the eukaryotic members remains unknown. Here, we present the first crystal and electron microscopy structures of a vertebrate aerolysin-like protein from Danio rerio, termed Dln1, before and after pore formation. Each subunit of Dln1 dimer comprises a β-prism lectin module followed by an aerolysin module. Specific binding of the lectin module toward high-mannose glycans triggers drastic conformational changes of the aerolysin module in a pH-dependent manner, ultimately resulting in the formation of a membrane-bound octameric pore. Structural analyses combined with computational simulations and biochemical assays suggest a pore-forming process with an activation mechanism distinct from the previously characterized bacterial members. Moreover, Dln1 and its homologs are ubiquitously distributed in bony fishes and lamprey, suggesting a novel fish-specific defense molecule. PMID:26711430

  4. 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. PMID:27016207

  5. Pore structure and effective permeability of metallic filters

    NASA Astrophysics Data System (ADS)

    Hejtmánek, Vladimír; Veselý, Martin; Čapek, Pavel

    2013-02-01

    The pore structures (microstructures) of two metallic filters were reconstructed using the stochastic reconstruction method based on simulated annealing. The following microstructural descriptors were included in the description of the real microstructures: the two-point probability function, the lineal-path functions for the void or solid phases, i.e. simulated annealing was constrained by all low-order statistical measures that were accessible through the analysis of images of polished sections. An effect of the microstructural descriptors on the course of reconstruction was controlled by modifying two parameters of the reconstruction procedure [1]. Their values resulted from repeated reconstruction of two-dimensional microstructures in such a way that the reference (experimental) and calculated two-point cluster functions deviated negligibly. It was tacitly assumed that the parameters adjusted during two-dimensional reconstruction had the same influence on the formation of the three-dimensional microstructures. Since connectivity of phases is a critical property of the stochastically reconstructed media, clusters of pore and solid voxels were determined using the Hoshen-Kopelman algorithm. It was found that the solid phase formed one large cluster in accordance with the physical feasibility. The void phase created one large cluster and a few small clusters representing the isolated porosity. The percolation properties were further characterised using the local porosity theory [2]. Effective permeability of the replicas was estimated by solving the Stokes equation for creeping flow of an incompressible liquid in pore space. Calculated permeability values matched well their experimental counterparts.

  6. [Use of mercury porosimetry, assisted by nitrogen adsorption in the investigation of the pore structure of tablets].

    PubMed

    Szepes, Anikó; Kovács, József; Szabóné Revész, Piroska

    2006-01-01

    The microstructure of pharmaceutical solid dosage forms (porosity, pore volume-size distribution, specific surface area) can be investigated by different methods. Mercury porosimetry and nitrogen gas adsorption have been widely used to characterize the pore structure of tablets because these methods enable the determination of porosity and pore size distribution in one step. The two techniques are based on different physical interactions and cover specific ranges of pore size. Mercury porosimetry determines mesopores and macropores, whereas gas adsorption covers the micropore range. The aim of this study was to investigate the relationship between the compression force and the structure of tablets containing theophylline. The porosity parameters determined with mercury porosimetry and nitrogen adsorption were compared. The results indicated a good correlation between the applied compression forces and the porosity parameters of the tablets. The pore volume-size distributions, the pore size frequencies and the specific surface areas obtained with mercury porosimetry and nitrogen adsorption were not equal, which can be attributed to the different measurement ranges and to the complexity of the pore structures. Our results allow the conclusion that mercury porosimetry, assisted by nitrogen adsorption as a complementary technique, is an acceptable method to achieve a proper characterization of the internal structure of tablets. PMID:17094658

  7. 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.

  8. 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

  9. 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

  10. Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly.

    PubMed

    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

  11. 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.

  12. NMDA receptor structures reveal subunit arrangement and pore architecture

    PubMed Central

    Lee, Chia-Hsueh; Lü, Wei; Michel, Jennifer Carlisle; Goehring, April; Du, Juan; Song, Xianqiang; Gouaux, Eric

    2014-01-01

    Summary N-methyl-d-aspartate (NMDA) receptors are Hebbian-like coincidence detectors, requiring binding of glycine and glutamate in combination with the relief of voltage-dependent magnesium block to open an ion conductive pore across the membrane bilayer. Despite the importance of the NMDA receptor in the development and function of the brain, a molecular structure of an intact receptor has remained elusive. Here we present x-ray crystal structures of the GluN1/GluN2B NMDA receptor with the allosteric inhibitor, Ro25-6981, partial agonists and the ion channel blocker, MK-801. Receptor subunits are arranged in a 1-2-1-2 fashion, demonstrating extensive interactions between the amino terminal and ligand binding domains. The transmembrane domains harbor a closed-blocked ion channel, a pyramidal central vestibule lined by residues implicated in binding ion channel blockers and magnesium, and a ~2-fold symmetric arrangement of ion channel pore loops. These structures provide new insights into the architecture, allosteric coupling and ion channel function of NMDA receptors. PMID:25008524

  13. Structure and gating of the nuclear pore complex

    PubMed Central

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

    2015-01-01

    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. PMID:26112706

  14. Interfacially Controlled Synthesis of Hollow Mesoporous Silica Spheres with Radially Oriented Pore Structures

    SciTech Connect

    Li, Juan; Liu, Jun; Wang, Donghai; Guo, Ruisong; Li, Xiaolin; Qi, Wen N.

    2010-06-24

    This paper reports an alternative process to prepare hollow mesoporous silica spheres (HMS) using a single cationic surfactant with a tunable wall thickness and radially oriented pore structures. Using N,N-dimethylformide (DMF) as the intermediate solvent bridging the organic and aqueous phase, hollow mesoporous silica spheres were synthesized with interfacial hydrolysis reactions at the surface of liquid droplets. These spheres have an ordered pore structure aligned along the radial direction, and the wall thickness and sphere sizes can be tuned by adjusting the experimental conditions. Transmission electron microscopy and nitrogen absorption techniques were used to characterize HMS and its formation procedure. A hypothetic formation mechanism was proposed on the basis of a morphology transformation with the correct amount of DMF and a careful observation of the early hydrolysis stages. Au and magnetic Fe3O4 nanoparticles have been encapsulated in the HMS hollow core for potential applications.

  15. Interfacially controlled synthesis of hollow mesoporous silica spheres with radially oriented pore structures.

    PubMed

    Li, Juan; Liu, Jun; Wang, Donghai; Guo, Ruisong; Li, Xiaolin; Qi, Wen

    2010-07-20

    This paper reports an alternative process to prepare hollow mesoporous silica spheres (HMS) using a single cationic surfactant with a tunable wall thickness and radially oriented pore structures. Using N,N-dimethylformide (DMF) as the intermediate solvent bridging the organic and aqueous phase, hollow mesoporous silica spheres were synthesized with interfacial hydrolysis reactions at the surface of liquid droplets. These spheres have an ordered pore structure aligned along the radial direction, and the wall thickness and sphere sizes can be tuned by adjusting the experimental conditions. Transmission electron microscopy and nitrogen absorption techniques were used to characterize HMS and its formation procedure. A hypothetic formation mechanism was proposed on the basis of a morphology transformation with the correct amount of DMF and a careful observation of the early hydrolysis stages. Au and magnetic Fe(3)O(4) nanoparticles have been encapsulated in the HMS hollow core for potential applications. PMID:20575542

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

    PubMed Central

    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

    2016-01-01

    Summary Nuclear pore complexes (NPCs) are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Elucidating their 110 MDa structure imposes a formidable challenge and requires in situ structural biology approaches. Fifteen out of about thirty nucleoporins (Nups) 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 1. The scaffold is decorated with transport channel Nups that often contain phenylalanine (FG)-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 combined cryo electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modeling to generate the most comprehensive architectural model of the NPC to date. Our data suggest previously unknown protein interfaces across Y-complexes and to inner ring complex members. We demonstrate that the higher eukaryotic transport channel Nup358 (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, similarly to coated vesicles, multiple copies of the same structural building block - although compositionally identical - engage in different local sets of interactions and conformations. PMID:26416747

  17. Local X-ray Computed Tomography Imaging for Mineralogical and Pore Characterization

    NASA Astrophysics Data System (ADS)

    Mills, G.; Willson, C. S.

    2015-12-01

    Sample size, material properties and image resolution are all tradeoffs that must be considered when imaging porous media samples with X-ray computed tomography. In many natural and engineered samples, pore and throat sizes span several orders of magnitude and are often correlated with the material composition. Local tomography is a nondestructive technique that images a subvolume, within a larger specimen, at high resolution and uses low-resolution tomography data from the larger specimen to reduce reconstruction error. The high-resolution, subvolume data can be used to extract important fine-scale properties but, due to the additional noise associated with the truncated dataset, it makes segmentation of different materials and mineral phases a challenge. The low-resolution data of a larger specimen is typically of much higher-quality making material characterization much easier. In addition, the imaging of a larger domain, allows for mm-scale bulk properties and heterogeneities to be determined. In this research, a 7 mm diameter and ~15 mm in length sandstone core was scanned twice. The first scan was performed to cover the entire diameter and length of the specimen at an image voxel resolution of 4.1 μm. The second scan was performed on a subvolume, ~1.3 mm in length and ~2.1 mm in diameter, at an image voxel resolution of 1.08 μm. After image processing and segmentation, the pore network structure and mineralogical features were extracted from the low-resolution dataset. Due to the noise in the truncated high-resolution dataset, several image processing approaches were applied prior to image segmentation and extraction of the pore network structure and mineralogy. Results from the different truncated tomography segmented data sets are compared to each other to evaluate the potential of each approach in identifying the different solid phases from the original 16 bit data set. The truncated tomography segmented data sets were also compared to the whole

  18. Analysing pore structure dynamic at clod scales: implications for flow and transport

    NASA Astrophysics Data System (ADS)

    Boivin, Pascal

    2014-05-01

    Based on capillary theory and rigid pore flow equations, the assessment and modelling of flow and transport in soils face severe difficulties since decades. These difficulties can be related to some of the assumptions commonly required by the physical background used. In particular, the assumptions of rigidity and homogeneity were not verified in most soils. Attempts to overcome these limitations were developed along with their evidence, e.g. to take into account soil swelling in flow models, to characterize preferential flow, or to correlate the soil physical parameters to soil constituents and their associated properties to better account for spatial variability. The fundamental splitting of the soil porosity into structural and plasma pores makes a consensus in many fields of soil science. This was seldom considered, however, as a basis for soil physical behaviour modelling, so far. Nevertheless, the mathematical bases for this are deciphered in recent works. Today, the quantification and modelling of these pore systems and their dynamics according to water content, soil constituents, soil biology and chemistry, or external stress, has greatly improved. These factors show different time and space scale dynamics, which are therefore, extremely important to assess separately. The dynamic of the two pore systems appears to be large according to the different factors and time scales. Contrarily to structural pores, the plasma pores do not allow air entry in most of their water content range, which is of consequence for capillary theory and its applications. The soil shrinkage behaviour appears to be closely related to the content in colloidal constituents, though the relation is different according to the two pore system, which is of consequence to account for spatial variability. The mechanical response to stresses is different for the two pore systems as well. The role of soil organic matter variability and changes is strongly highlighted by these researches

  19. 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

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

    PubMed Central

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

    2014-01-01

    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 NPC1. Whilst the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized2-5, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins5,6, and is therefore not well understood. Here, we show that stiffness topography7 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 microscopy2-5. 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. PMID:25420031

  1. Dependence of hydrogen permeabilities of isotropic graphites on the pore structure

    NASA Astrophysics Data System (ADS)

    Yamawaki, M.; Yamaguchi, K.; Suzuki, Y.; Tanaka, S.

    1991-03-01

    The permeation behavior of molecular hydrogen through isotropic graphites is investigated. The observed dependences of the permeation rate on pressure, specimen thickness, temperature and molecular weight suggest that hydrogen permeates by molecular flow, probably through open pores. A simple pore structure model is developed and is compared with the experimental results. It is revealed that hydrogen permeation through isotropic graphites depends not only on the pore size or the porosity, but also on the pore size distribution and tortuosity.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    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 contin-ued, 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-µm 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.

  4. Highly ordered periodic mesoporous organosilica nanoparticles with controllable pore structures

    NASA Astrophysics Data System (ADS)

    Guan, Buyuan; Cui, Yan; Ren, Zhongyuan; Qiao, Zhen-An; Wang, Li; Liu, Yunling; Huo, Qisheng

    2012-09-01

    A general synthetic procedure for highly ordered and well-dispersed periodic mesoporous organosilica (PMO) nanoparticles is reported based on a single cationic surfactant cetyltrimethylammonium bromide (CTAB) and simple silica sources with organic bridging groups via an ammonia-catalyzed sol-gel reaction. By changing the bridging group in the silica sources, the pore structures of the as-made particles with three-dimensional hexagonal (P63/mmc), cubic (Pm3n), two-dimensional hexagonal (P6mm), and wormlike structure were evidenced by powder X-ray diffraction analysis (XRD) and transmission electron microscopy (TEM). The size range of the nanoparticles can be adjusted from 30 nm to 500 nm by variation of the ammonia concentration or the co-solvent content of the reaction medium. The PMO nanoparticles with high concentration of organic groups in the framework offered good thermal stability, good dispersion in low polarity solvent and high adsorption of small hydrophobic molecules. Finally, the dye functionalized PMO nanoparticles show low cytotoxicity and excellent cell permeability, which offers great potential for biomedical applications.A general synthetic procedure for highly ordered and well-dispersed periodic mesoporous organosilica (PMO) nanoparticles is reported based on a single cationic surfactant cetyltrimethylammonium bromide (CTAB) and simple silica sources with organic bridging groups via an ammonia-catalyzed sol-gel reaction. By changing the bridging group in the silica sources, the pore structures of the as-made particles with three-dimensional hexagonal (P63/mmc), cubic (Pm3n), two-dimensional hexagonal (P6mm), and wormlike structure were evidenced by powder X-ray diffraction analysis (XRD) and transmission electron microscopy (TEM). The size range of the nanoparticles can be adjusted from 30 nm to 500 nm by variation of the ammonia concentration or the co-solvent content of the reaction medium. The PMO nanoparticles with high concentration of organic

  5. Diagenetic facies controls on pore structure and rock electrical parameters in tight gas sandstone

    NASA Astrophysics Data System (ADS)

    Liu, Hongping; Zhao, Yanchao; Luo, Yang; Chen, Zhaoyou; He, Sheng

    2015-08-01

    Rock electrical parameters of tight gas sandstone show large variations in the T2 member in Dingbei Block, Ordos Basin, China. Applying the same rock electrical parameters in water saturation calculations would lead to large errors. Based on casting thin sections, x-ray diffraction, scanning electron microscopy (SEM), cathode luminescence, porosity and permeability, image analysis, and high-pressure mercury intrusion/withdrawal method, identification of the diagenetic facies are first conducted, and then their pore structure and their relationship with rock electrical parameters are investigated. Five diagenetic facies (A-E), which are identified based mainly on pore types and authigenic minerals, have different pore structure and rock electrical parameters. Conceptual models that incorporate the rock properties of each diagenetic facies have been built, before applying the electrical efficiency theory to explain the values of cementation exponent (m) and saturation exponent (n). A conventional network model, a shunt pore model, a netted pore model, and a dotted line model are utilized to mimic the intergranular pores, authigenic kaolinite intercrystal pores, carbonate-cement dissolution pores, and clay-matrix intercrystal pores, respectively. A decrease of the contents of large pores increases electrical efficiency and therefore reduces m. The saturation exponent, which depends on the distribution of water and gas, can be better understood by applying the different pore models. In the shunt and netted pore models, gas displacement starts from the larger pores and smaller pores provide alternative conduction pathways, hence sustaining electrical efficiency and decreasing n. Clay-matrix intercrystal pores are mainly micropores, since the brine in the rocks are isolated after gas displacement, reducing overall electrical efficiency and dramatically increasing the value of n in the diagenetic facies, which is dominated by clay-matrix intercrystal pores.

  6. 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

  7. Crystal Structure of a Voltage-gated K+ Channel Pore Module in a Closed State in Lipid Membranes*

    PubMed Central

    Santos, Jose S.; Asmar-Rovira, Guillermo A.; Han, Gye Won; Liu, Wei; Syeda, Ruhma; Cherezov, Vadim; Baker, Kent A.; Stevens, Raymond C.; Montal, Mauricio

    2012-01-01

    Voltage-gated K+ channels underlie the electrical excitability of cells. Each subunit of the functional tetramer consists of the tandem fusion of two modules, an N-terminal voltage-sensor and a C-terminal pore. To investigate how sensor coupling to the pore generates voltage-dependent channel opening, we solved the crystal structure and characterized the function of a voltage-gated K+ channel pore in a lipid membrane. The structure of a functional channel in a membrane environment at 3.1 Å resolution establishes an unprecedented connection between channel structure and function. The structure is unique in delineating an ion-occupied ready to conduct selectivity filter, a confined aqueous cavity, and a closed activation gate, embodying a dynamic entity trapped in an unstable closed state. PMID:23095758

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

    PubMed Central

    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

    2015-01-01

    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. PMID:26191088

  9. 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.

  10. 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

  11. Solubilization and characterization of the anthrax toxin pore in detergent micelles

    PubMed Central

    Vernier, Gregory; Wang, Jie; Jennings, Laura D; Sun, Jianjun; Fischer, Audrey; Song, Likai; Collier, R John

    2009-01-01

    Proteolytically activated Protective Antigen (PA) moiety of anthrax toxin self-associates to form a heptameric ring-shaped oligomer (the prepore). Acidic pH within the endosome converts the prepore to a pore that serves as a passageway for the toxin's enzymatic moieties to cross the endosomal membrane. Prepore is stable in solution under mildly basic conditions, and lowering the pH promotes a conformational transition to an insoluble pore-like state. N-tetradecylphosphocholine (FOS14) was the only detergent among 110 tested that prevented aggregation without dissociating the multimer into its constituent subunits. FOS14 maintained the heptamers as monodisperse, insertion-competent 440-kDa particles, which formed channels in planar phospholipid bilayers with the same unitary conductance and ability to translocate a model substrate protein as channels formed in the absence of detergent. Electron paramagnetic resonance analysis detected pore-like conformational changes within PA on solubilization with FOS14, and electron micrograph images of FOS14-solubilized pore showed an extended, mushroom-shaped structure. Circular dichroïsm measurements revealed an increase in α helix and a decrease in β structure in pore formation. Spectral changes caused by a deletion mutation support the hypothesis that the 2β2-2β3 loop transforms into the transmembrane segment of the β-barrel stem of the pore. Changes caused by selected point mutations indicate that the transition to α structure is dependent on residues of the luminal 2β11-2β12 loop that are known to affect pore formation. Stabilizing the PA pore in solution with FOS14 may facilitate further structural analysis and a more detailed understanding of the folding pathway by which the pore is formed. PMID:19609933

  12. Porous spherical carbon/sulfur nanocomposites by aerosol-assisted synthesis: the effect of pore structure and morphology on their electrochemical performance as lithium/sulfur battery cathodes.

    PubMed

    Sohn, Hiesang; Gordin, Mikhail L; Xu, Terrence; Chen, Shuru; Lv, Dongping; Song, Jiangxuan; Manivannan, Ayyakkannu; Wang, Donghai

    2014-05-28

    Porous spherical carbons (PSCs) with tunable pore structure (pore volume, pore size, and surface area) were prepared by an aerosol-assisted process. PSC/sulfur composites (PSC/S, S: ca.59 wt %) were then made and characterized as cathodes in lithium/sulfur batteries. The relationships between the electrochemical performance of PSC/S composites and their pore structure and particle morphology were systematically investigated. PSC/S composite cathodes with large pore volume (>2.81 cm(3)/g) and pore size (>5.10 nm) were found to exhibit superior electrochemical performance, likely due to better mass transport in the cathode. In addition, compared with irregularly shaped carbon/sulfur composite, the spherical shaped PSC/S composite showed better performance due to better electrical contact among the particles. PMID:24758613

  13. Topology sorting and characterization of folded polymers using nano-pores

    NASA Astrophysics Data System (ADS)

    Nikoofard, Narges; Mashaghi, Alireza

    2016-02-01

    Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied: one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the molecule passes through the nano-pore. The topology of a folded polymer chain is defined as the arrangement of the intramolecular contacts, known as circuit topology. In the case where intramolecular contacts remain intact, we show that the dynamics of passage through a nano-pore varies for molecules with differing topologies: a phenomenon that can be exploited to enrich certain topologies in mixtures. We find that the nano-pore allows reading of the topology for short chains. Moreover, when the passage is coupled with unfolding, the nano-pore enables discrimination between pure states, i.e., states in which the majority of contacts are arranged identically. In this case, as we show here, it is also possible to read the positions of the contact sites along a chain. Our results demonstrate the applicability of nano-pore technology to characterize and sort molecules based on their topology.Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied: one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the molecule passes through the nano-pore. The topology of a folded polymer chain is defined as the arrangement of the intramolecular contacts, known as circuit topology. In the case where intramolecular contacts remain intact, we show that the dynamics of passage through a nano-pore varies for molecules with differing topologies: a phenomenon that can be exploited to enrich certain topologies in mixtures. We find that the nano-pore allows reading of the topology for short chains. Moreover, when the passage is coupled with unfolding, the nano-pore enables discrimination between pure states, i.e., states in which the

  14. 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.

  15. Characterization of Pores in Dense Nanopapers and Nanofibrillated Cellulose Membranes: A Critical Assessment of Established Methods.

    PubMed

    Orsolini, Paola; Michen, Benjamin; Huch, Anja; Tingaut, Philippe; Caseri, Walter R; Zimmermann, Tanja

    2015-11-25

    Nanofibrillated cellulose (NFC) is a natural fibrous material that can be readily processed into membranes. NFC membranes for fluid separation work in aqueous medium, thus in their swollen state. The present study is devoted to a critical investigation of porosity, pore volume, specific surface area, and pore size distribution of dry and wet NFC nanopapers, also known as membranes, with various established techniques, such as electron microscopy, helium pycnometry, mercury intrusion, gas adsorption (N2 and Kr), and thermoporometry. Although these techniques can be successfully applied to inorganic materials (e.g., mesoporous silica), it is necessary to appraise them for organic and hydrophilic products such as NFC membranes. This is due to different phenomena occurring at the materials interfaces with the probing fluids. Mercury intrusion and gas adsorption are often used for the characterization of porosity-related properties; nevertheless, both techniques characterize materials in the dry state. In parallel, thermoporometry was employed to monitor the structure changes upon swelling, and a water permeance test was run to show the accessibility of the membranes to fluids. For the first time, the methods were systematically screened, and we highlighted the need of uniform sample treatments prior to the measurements (i.e., sample cutting and outgassing protocols) in order to harmonize results from the literature. The need for revising the applicability range of mercury intrusion and the inappropriateness of nitrogen adsorption were pointed out. We finally present a table for selecting the most appropriate method to determine a desired property and propose guidelines for results interpretation from which future users could profit. PMID:26516781

  16. The role of pore structure on char reactivity. Quarterly progress report, April 1995--June 1995

    SciTech Connect

    Sarofim, A.F.

    1995-07-01

    In order to examine the role of pore structure, studies will be conducted on coal chars in the electrodynamic balance. Larger particles will also be examined using a fluidized bed to examine diffusion control reactions, and soots will also be investigated to examine the role of meso-and micro-pores without macro-pore interference. These studies will allow a full range of particles sizes and temperatures to be investigated and eventually modelled.

  17. Characterization of horizontal flows around solar pores from high-resolution time series of images

    NASA Astrophysics Data System (ADS)

    Vargas Domínguez, S.; de Vicente, A.; Bonet, J. A.; Martínez Pillet, V.

    2010-06-01

    Context. Though there is increasing evidence linking the moat flow and the Evershed flow along the penumbral filaments, there is not a clear consensus regarding the existence of a moat flow around umbral cores and pores, and the debate is still open. Solar pores appear to be a suitable scenario to test the moat-penumbra relation as they correspond to a direct interaction between the umbra and the convective plasma in the surrounding photosphere without any intermediate structure in between. Aims: We study solar pores based on high-resolution ground-based and satellite observations. Methods: Local correlation tracking techniques were applied to different-duration time series to analyze the horizontal flows around several solar pores. Results: Our results establish that the flows calculated from different solar pore observations are coherent among each other and show the determining and overall influence of exploding events in the granulation around the pores. We do not find any sign of moat-like flows surrounding solar pores, but a clearly defined region of inflows surrounding them. Conclusions: The connection between moat flows and flows associated to penumbral filaments is hereby reinforced.

  18. Structural Characterization of Nanoporous Pmssq Thin Films

    NASA Astrophysics Data System (ADS)

    Briber, R. M.; Yang, G. Y.; Huang, E.; Kim, H. C.; Rice, P. M.; Volksen, W.; Miller, R. D.; Shin, K.

    2002-03-01

    The semiconductor industry roadmap requires the next generation of interlayer dielectric materials to have a dielectric constant k below 2.0 and thermal stability to 500 ^oC. Porous Dielectrics are an attractive route to obtain such materials. One potential system is polymethylsilsesquioxane (PMSSQ) with nanometer sized pores templated by the incorporation of a thermally degradable polymer. Film were prepared by dissolving the matrix precursor materials (MSSQ oligomer mixture) and porogen (PMMA-co-DMAEMA) as a template for creating the pores in a common solvent (propylene glycol methyl ether) and spin casting onto a silicon single crystal substrate. The film is subjected to an initial heat treatment in nitrogen at 225^oC to cure the matrix (i.e. polymerize and cross-link) and then a second heat treatment to 375 450^oC to degrade the porogen to form the pores. The pore evolution and characterization are performed using small angle neutron scattering (SANS), transmission electron microscopy (TEM) and neutron reflectivity (NR). In-situ SANS experiments revealed that the pores evolution follows a process of phase separation and burnout of the porogen copolymer. TEM observation shows that pore size, morphology and spatial distribution depend on the concentration of porogen in the original hybrid material. Average pore size increases as a function of porogen concentration. Porous morphology changes from isolated pores at low porogen concentration (<10 wt. %) to fully interconnected pores at higher porogen concentration (>40 wt. %). Percolation threshold is located at 30 wt. % porogen content. Neutron reflectivity is used to study the pore structure and distribution normal to the film thickness.

  19. Effect of pore structure on seismic rock-physics characteristics of dense carbonates

    NASA Astrophysics Data System (ADS)

    Pan, Jian-Guo; Wang, Hong-Bin; Li, Chuang; Zhao, Jian-Guo

    2015-03-01

    The Ordovician carbonate rocks of the Yingshan formation in the Tarim Basin have a complex pore structure owing to diagenetic and secondary structures. Seismic elastic parameters (e.g., wave velocity) depend on porosity and pore structure. We estimated the average specific surface, average pore-throat radius, pore roundness, and average aspect ratio of carbonate rocks from the Tazhong area. High P-wave velocity samples have small average specific surface, small average pore-throat radius, and large average aspect ratio. Differences in the pore structure of dense carbonate samples lead to fluid-related velocity variability. However, the relation between velocity dispersion and average specific surface, or the average aspect ratio, is not linear. For large or small average specific surface, the pore structure of the rock samples becomes uniform, which weakens squirt flow and minimizes the residuals of ultrasonic data and predictions with the Gassmann equation. When rigid dissolved (casting mold) pores coexist with less rigid microcracks, there are significant P-wave velocity differences between measurements and predictions.

  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. Surface fractal analysis of pore structure of high-volume fly-ash cement pastes

    NASA Astrophysics Data System (ADS)

    Zeng, Qiang; Li, Kefei; Fen-Chong, Teddy; Dangla, Patrick

    2010-11-01

    The surface fractal dimensions of high-volume fly-ash cement pastes are evaluated for their hardening processes on the basis of mercury intrusion porosimetry (MIP) data. Two surface fractal models are retained: Neimark's model with cylindrical pore hypothesis and Zhang's model without pore geometry assumption. From both models, the logarithm plots exhibit the scale-dependent fractal properties and three distinct fractal regions (I, II, III) are identified for the pore structures. For regions I and III, corresponding to the large (capillary) and small (C-S-H inter-granular) pore ranges respectively, the pore structure shows strong fractal property and the fractal dimensions are evaluated as 2.592-2.965 by Neimark's model and 2.487-2.695 by Zhang's model. The fractal dimension of region I increases with w/ b ratio and hardening age but decreases with fly-ash content by its physical filling effect; the fractal dimension of region III does not evolve much with these factors. The region II of pore size range, corresponding to small capillary pores, turns out to be a transition region and show no clear fractal properties. The range of this region is much influenced by fly-ash content in the pastes. Finally, the correlation between the obtained fractal dimensions and pore structure evolution is discussed in depth.

  2. 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

  3. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 7, April 1, 1993--June 31, 1993

    SciTech Connect

    Smith, D.M.

    1993-09-01

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultramicro 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 closed 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 2}H{sub 2},{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 the pore surfaces in coals.

  4. 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.

  5. Advanced NMR-based techniques for pore structure analysis of coal. Quarter report {number_sign}8, 7/1/93--9/30/93

    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/ultramicro 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 closed 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. 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 is investigated. In particular, 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 is studied.

  6. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 6, January 1, 1993--March 31, 1993

    SciTech Connect

    Smith, D.M.

    1993-08-01

    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 closed 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 2}H{sub 2}, {sup 14}N{sub 2},{sup 14}NH{sub 3}, {sup 15}N{sup 2}, {sup 13}CH{sub 4}, {sup 13}CO{sub 2}) and the pore surfaces in coals.

  7. Large-Pore Mesoporous Silica with Three-Dimensional Wormhole Framework Structures.

    PubMed

    Park, In; Pinnavaia, Thomas J

    2009-02-01

    Large-pore mesoporous silica with 3D wormhole framework structures (denoted MSU-J) are prepared through a supramolecular hydrogen-bonding assembly pathway from low-cost sodium silicate as the silica source and commercially available mono- and triamine Jeffamine and Surfonamine surfactants as structure-directing porogens. The calcined mesostructures exhibit large pore sizes (up to 8.2 nm), surface areas (632-1030 m(2)/g) and pore volumes (0.5-2.0 cm(3)/g), depending on the surfactant chain length and synthesis temperature (25-65 °C). The textural properties of these new wormhole mesostructures are comparable to those of hexagonal SBA-15 derivatives and large pore MCM-48. However, unlike the SBA-15 structure type, wherein the 3D pore network is formed by connecting 1D cylindrical mesopores through micropores, MSU-J mesophases have wormhole framework structures containing fully interconnected 3D mesopores that can minimize the diffusion limitations often encountered in adsorption and chemical catalysis. Also, unlike large pore MCM-48, which requires cost-intensive tetraethylorthosilicate as a silica source and the use of a co-surfactant as a pore expander under strong acid conditions, MSU-J mesostructures are assembled from low cost sodium silicate in the presence of a single Jeffamine or Surfonamine porogen at near-neutral pH. PMID:20126285

  8. 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

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

    PubMed

    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

  10. Pore-scale dispersion: Bridging the gap between microscopic pore structure and the emerging macroscopic transport behavior

    NASA Astrophysics Data System (ADS)

    Meyer, Daniel W.; Bijeljic, Branko

    2016-07-01

    We devise an efficient methodology to provide a universal statistical description of advection-dominated dispersion (Péclet→∞ ) in natural porous media including carbonates. First, we investigate the dispersion of tracer particles by direct numerical simulation (DNS). The transverse dispersion is found to be essentially determined by the tortuosity and it approaches a Fickian limit within a dozen characteristic scales. Longitudinal dispersion was found to be Fickian in the limit for bead packs and superdiffusive for all other natural media inspected. We demonstrate that the Lagrangian velocity correlation length is a quantity that characterizes the spatial variability for transport. Finally, a statistical transport model is presented that sheds light on the connection between pore-scale characteristics and the resulting macroscopic transport behavior. Our computationally efficient model accurately reproduces the transport behavior in longitudinal direction and approaches the Fickian limit in transverse direction.

  11. Pore-scale dispersion: Bridging the gap between microscopic pore structure and the emerging macroscopic transport behavior.

    PubMed

    Meyer, Daniel W; Bijeljic, Branko

    2016-07-01

    We devise an efficient methodology to provide a universal statistical description of advection-dominated dispersion (Péclet→∞) in natural porous media including carbonates. First, we investigate the dispersion of tracer particles by direct numerical simulation (DNS). The transverse dispersion is found to be essentially determined by the tortuosity and it approaches a Fickian limit within a dozen characteristic scales. Longitudinal dispersion was found to be Fickian in the limit for bead packs and superdiffusive for all other natural media inspected. We demonstrate that the Lagrangian velocity correlation length is a quantity that characterizes the spatial variability for transport. Finally, a statistical transport model is presented that sheds light on the connection between pore-scale characteristics and the resulting macroscopic transport behavior. Our computationally efficient model accurately reproduces the transport behavior in longitudinal direction and approaches the Fickian limit in transverse direction. PMID:27575217

  12. Representing geometric structures in 3D tomography soil images: Application to pore-space modeling

    NASA Astrophysics Data System (ADS)

    Monga, Olivier; Ndeye Ngom, Fatou; François Delerue, Jean

    2007-09-01

    Only in the last decade have geoscientists started to use 3D computed tomography (CT) images of soil for better understanding and modeling of soil properties. In this paper, we propose one of the first approaches to allow the definition and computation of stable (intrinsic) geometric representations of structures in 3D CT soil images. This addresses the open problem set by the description of volume shapes from discrete traces without any a priori information. The basic concept involves representing the volume shape by a piecewise approximation using simple volume primitives (bowls, cylinders, cones, etc.). This typical representation is assumed to optimize a criterion ensuring its stability. This criterion includes the representation scale, which characterizes the trade-off between the fitting error and the number of patches. We also take into account the preservation of topological properties of the initial shape: the number of connected components, adjacency relationships, etc. We propose an efficient computation method for this piecewise approximation using cylinders or bowls. For cylinders, we use optimal region growing in a valuated adjacency graph that represents the primitives and their adjacency relationships. For bowls, we compute a minimal set of Delaunay spheres recovering the skeleton. Our method is applied to modeling of a coarse pore space extracted from 3D CT soil images. The piecewise bowls approximation gives a geometric formalism corresponding to the intuitive notion of pores and also an efficient way to compute it. This geometric and topological representation of coarse pore space can be used, for instance, to simulate biological activity in soil.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Hyman, Jeffrey D.; Winter, C. Larrabee

    2014-11-01

    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.

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

    PubMed

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

    2015-01-01

    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. PMID:25716479

  16. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25716479

  18. 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)

  19. Can intra-aggregate pore structures affect the aggregate's effectiveness in protecting carbon?

    SciTech Connect

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

    2012-11-15

    Aggregates are known to provide physical protection to soil organic matter shielding it from rapid decomposition. Spatial arrangement and size distribution of intra-aggregate pores play an important role in this process. This study examined relationships between intra-aggregate pores measured using X-ray computed micro-tomography images and concentrations of total C in 4–6 mm macro-aggregates from two contrasting land use and management practices, namely, conventionally tilled and managed row crop agricultural system (CT) and native succession vegetation converted from tilled agricultural land in 1989 (NS). Previous analyses of these aggregates indicated that small (<15 μm) and large (>100 μm) pores prevail in NS aggregates while medium (30–90 μm) pores are more abundant in CT aggregates (Kravchenko et al., 2011; Wang et al., 2012). We hypothesized that these differences in pore size distributions affect the ability of macro-aggregates to protect C. The results of this study supported this hypothesis. Consistent with greater heterogeneity of pore distributions within NS aggregates we observed higher total C and greater intra-aggregate C variability in NS as compared with CT aggregates. Total C concentrations and intra-aggregate C standard deviations were negatively correlated with fractions of medium sized pores, indicating that presence of such pores was associated with lower but more homogeneously distributed total C. While total C was positively correlated with presence of small and large pores. The results suggest that because of their pore structure NS macro-aggregates provide more effective physical protection to C than CT aggregates.

  20. The interactions of astrocytes and fibroblasts with defined pore structures in static and perfusion cultures

    PubMed Central

    Sun, Tao; Donoghue, Peter S.; Higginson, Jennifer R.; Gadegaard, Nikolaj; Barnett, Susan C.; Riehle, Mathis O.

    2011-01-01

    Open pores to maintain nutrient diffusion and waste removal after cell colonization are crucial for the successful application of constructs based on assembled membranes, in our case tubular scaffolds made of ɛ-polycaprolactone (PCL), for use in tissue engineering. Due to the complex three-dimensional structure and large size of such scaffolds needed for transplantable tissues, it is difficult to investigate the cell–pore interactions in situ. Therefore miniaturized bioreactors inside Petri dishes (30 mm in diameter), containing porous PCL or poly-dimethylsiloxane (PDMS) membranes, were developed to allow the interactions of different cells with defined pores to be investigated in situ during both static and perfusion cultures. Investigation of two different cell types (fibroblasts and cortical astrocytes) and how they interact with a range of pores (100–350 μm in diameter) for up to 50 days indicated that the cells either ‘covered’ or ‘bridged’ the pores. Three distinct behaviors were observed in the way cortical astrocytes interacted with pores, while fibroblasts were able to quickly bridge the pores based on consistent “joint efforts”. Our studies demonstrate that the distinct pore sealing behaviors of both cell types were influenced by pore size, initial cell density and culture period, but not by medium perfusion within the range of shear forces investigated. These findings form important basic data about the usability of pores within scaffolds that could inform the design and fabrication of suitable scaffolds for various applications in tissue engineering. PMID:21163522

  1. Structural insights into the oligomerization and architecture of eukaryotic membrane pore-forming toxins.

    PubMed

    Mechaly, Ariel E; Bellomio, Augusto; Gil-Cartón, David; Morante, Koldo; Valle, Mikel; González-Mañas, Juan Manuel; Guérin, Diego M A

    2011-02-01

    Pore-forming toxins (PFTs) are proteins that are secreted as soluble molecules and are inserted into membranes to form oligomeric transmembrane pores. In this paper, we report the crystal structure of Fragaceatoxin C (FraC), a PFT isolated from the sea anemone Actinia fragacea, at 1.8 Å resolution. It consists of a crown-shaped nonamer with an external diameter of about 11.0 nm and an internal diameter of approximately 5.0 nm. Cryoelectron microscopy studies of FraC in lipid bilayers reveal the pore structure that traverses the membrane. The shape and dimensions of the crystallographic oligomer are fully consistent with the membrane pore. The FraC structure provides insight into the interactions governing the assembly process and suggests the structural changes that allow for membrane insertion. We propose a nonameric pore model that spans the membrane by forming a lipid-free α-helical bundle pore. PMID:21300287

  2. Pore-scale intermittent velocity structure underpinning anomalous transport through 3-D porous media

    NASA Astrophysics Data System (ADS)

    Kang, Peter K.; Anna, Pietro; Nunes, Joao P.; Bijeljic, Branko; Blunt, Martin J.; Juanes, Ruben

    2014-09-01

    We study the nature of non-Fickian particle transport in 3-D porous media by simulating fluid flow in the intricate pore space of real rock. We solve the full Navier-Stokes equations at the same resolution as the 3-D micro-CT (computed tomography) image of the rock sample and simulate particle transport along the streamlines of the velocity field. We find that transport at the pore scale is markedly anomalous: longitudinal spreading is superdiffusive, while transverse spreading is subdiffusive. We demonstrate that this anomalous behavior originates from the intermittent structure of the velocity field at the pore scale, which in turn emanates from the interplay between velocity heterogeneity and velocity correlation. Finally, we propose a continuous time random walk model that honors this intermittent structure at the pore scale and captures the anomalous 3-D transport behavior at the macroscale.

  3. 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)

  4. Investigation of the problems with using gas adsorption to probe catalyst pore structure evolution during coking.

    PubMed

    Gopinathan, Navin; Greaves, Malcolm; Wood, Joseph; Rigby, Sean P

    2013-03-01

    A common approach to try to understand the mechanism of coking in heterogeneous catalysts is to monitor the evolution of the pore structure using gas adsorption analysis of discharged pellets. However, the standard methods of analysis of gas adsorption data, to obtain pore-size distributions, make the key assumption of thermodynamically-independent pores. This assumption neglects the possibility of co-operative adsorption phenomena, which will shown to be a critical problem when looking at coking catalysts. In this work the serial adsorption technique has been used to detect and assess the extent of co-operative effects in adsorption within coking catalysts. The reaction of decane over a hydroprocessing catalyst was used as a case study. It has been shown that the conventional analysis method would lead to a flawed picture of the pore structure changes during the coking process. For the case-study considered in this work, it was found that co-operative adsorption effects meant that 26% of the measured adsorption was occurring in pores up to three times larger than the size conventional analysis would presume. The serial adsorption technique was thus shown to provide important additional information on pore structure evolution during coking. A study of the kinetics of adsorption has been used to infer information about the general spatial location of the coking process within a pellet. PMID:23141698

  5. The effects of pore structure on the behavior of water in lignite coal and activated carbon.

    PubMed

    Nwaka, Daniel; Tahmasebi, Arash; Tian, Lu; Yu, Jianglong

    2016-09-01

    The effects of physical structure (pore structure) on behavior of water in lignite coal and activated carbon (AC) samples were investigated by using Differential Scanning Calorimetry (DSC) and low-temperature X-ray diffraction (XRD) techniques. AC samples with different pore structures were prepared at 800°C in steam and the results were compared with that of parent lignite coal. The DSC results confirmed the presence of two types of freezable water that freeze at -8°C (free water) and -42°C (freezable bound water). A shift in peak position of free water (FW) towards lower temperature was observed in AC samples compared to the lignite coal with decreasing water loading. The amount of free water (FW) increased with increasing gasification conversion. The amounts of free and freezable bound water (FBW) in AC samples were calculated and correlated to pore volume and average pore size. The amount of FW in AC samples is well correlated to the pore volume and average pore size of the samples, while an opposite trend was observed for FBW. The low-temperature XRD analysis confirmed the existence of non-freezable water (NFW) in coal and AC with the boundary between the freezable and non-freezable water (NFW) determined. PMID:27254256

  6. 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. PMID:22360994

  7. 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).

  8. 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.

  9. Adsorptive capacity and evolution of the pore structure of alumina on reaction with gaseous hydrogen fluoride.

    PubMed

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

    2015-05-19

    Brunauer-Emmet-Teller (BET) specific surface areas are generally used to gauge the propensity of uptake on adsorbents, with less attention paid to kinetic considerations. We explore the importance of such parameters by modeling the pore size distributions of smelter grade aluminas following HF adsorption, an industrially important process in gas cleaning at aluminum smelters. The pore size distributions of industrially fluorinated aluminas, and those contacted with HF in controlled laboratory trials, are reconstructed from the pore structure of the untreated materials when filtered through different models of adsorption. These studies demonstrate the presence of three distinct families of pores: those with uninhibited HF uptake, kinetically limited porosity, and pores that are surface blocked after negligible scrubbing. The surface areas of the inaccessible and blocked pores will overinflate estimates of the adsorption capacity of the adsorbate. We also demonstrate, contrary to conventional understanding, that porosity changes are attributed not to monolayer uptake but more reasonably to pore length attenuation. The model assumes nothing specific regarding the Al2O3-HF system and is therefore likely general to adsorbate/adsorbent phenomena. PMID:25913681

  10. 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.

  11. 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. PMID:26342334

  12. Effects of carbonation on the pore structure of non-hydraulic lime mortars

    SciTech Connect

    Lawrence, Robert M. . E-mail: mike@cc-w.co.uk; Mays, Timothy J.; Rigby, Sean P.; Walker, Peter; D'Ayala, Dina

    2007-07-15

    The pore structures of carbonated non-hydraulic lime mortars made with a range of different aggregates and concentrations of lime have been determined using mercury intrusion porosimetry (MIP). MIP data have been correlated with scanning electron microscopy images and other porosity data. During carbonation there is an increase in pore volume in the {approx} 0.1 {mu}m pore diameter range across all mortar types which is attributed to the transformation of portlandite to calcite. Also there is a monotonic increase in the volumes of pores with diameters below 0.03 {mu}m. A model is proposed for the changes in pore structure caused by carbonation. This attributes the increase in the volume of sub 0.03 {mu}m pores to the attachment of calcite crystals to the surface of aggregate particles, and in some cases to the surface of portlandite crystals. This phenomenon may explain the continuing presence of portlandite in mortars that, apparently, have fully carbonated.

  13. Effect of pore structure on surface characteristics of zirconium phosphate-modified silica.

    PubMed

    El Shafei, Gamal M S

    2002-06-15

    Three samples of silica of different pore structure-predominantly microporous, S1; mesoporous, S2; and nonporous, S3-were modified with zirconium phosphate and examined. Pore structure analysis showed that modification had taken place in wider pores of S1 leaving a totally microporous sample, and in large pores of S2 giving a mesoporous sample of narrower pore size distribution. The modification of the nonporous sample decreased the surface area and pore volume to a lower extent than in the other two samples, but resulted in a surface of lower energy toward N2. The different distribution of surface silanol groups on the surfaces of different porosity may result in variable pictures on the modified surfaces as reflected in the differences observed in Brønsted acidity of modified surfaces. The use of these modified silica samples for amino acid adsorption (L-glutamic acid and L-alanine) indicated that both the isoelectric point of the amino acid and the distribution of surface groups on modified solids are controlling the adsorption process. PMID:16290676

  14. Integrating mercury injection and nitrogen adsorption data to characterize marine sediment pore systems: An example from the Nankai Trough

    NASA Astrophysics Data System (ADS)

    Daigle, H.; Thomas, B.

    2013-12-01

    Fine-grained, clay-rich marine sediments typically exhibit complex pore geometries due to the presence of high-aspect-ratio clay particles, nannofossils, and diagenetically altered grain fragments. The pore systems in these sediments have a wide range of shapes and may contain significant pore volume in mesopores (1-25 nm radius) and micropores (< 1 nm radius). This renders pore size measurements difficult, even in samples with high porosity. Porosity values from mercury injection capillary pressure (MICP) measurements performed on samples from Integrated Ocean Drilling Program (IODP) Sites C0011, C0012, and C0018 in the Nankai Trough offshore Japan were compared to porosity determined by proton nuclear magnetic resonance (NMR) in the laboratory. The MICP porosities were systematically lower than the NMR porosities by up to 26% of the NMR porosity value. This porosity mismatch is due to the presence of pores with radii smaller than the effective lower limit of MICP measurements, which is 10-40 nm for this data set. Nitrogen gas adsorption offers a means to characterize pores between ~0.87 nm and ~100 nm radius, thus measuring the portion of the pore size distribution not investigated by MICP measurements. Combining MICP and nitrogen gas adsorption data yields a more complete characterization of the pore system of marine sediments. Merged MICP and nitrogen gas adsorption data obtained for the Nankai Trough samples yield porosity values that more accurately match the NMR porosity values, indicating that the entire pore space of the samples can be measured by a combination of the two techniques. These samples possess significant quantities of porosity below the resolution of MICP (>10% of pore volume), even in samples with porosity exceeding 65%. This work illustrates the complexity of marine sediment pore systems even at shallow depths of burial, and provides a new method for assessing pore sizes in scientific ocean drilling studies.

  15. Facile Synthesis, Characterization, and Catalytic Behavior of a Large-Pore Zeolite with the IWV Framework.

    PubMed

    Schmidt, Joel E; Chen, Cong-Yan; Brand, Stephen K; Zones, Stacey I; Davis, Mark E

    2016-03-14

    Large-pore microporous materials are of great interest to process bulky hydrocarbon and biomass-derived molecules. ITQ-27 (IWV) has a two-dimensional pore system bounded by 12-membered rings (MRs) that lead to internal cross-sections containing 14 MRs. Investigations into the catalytic behavior of aluminosilicate (zeolite) materials with this framework structure have been limited until now due to barriers in synthesis. The facile synthesis of aluminosilicate IWV in both hydroxide and fluoride media is reported herein using simple, diquaternary organic structure-directing agents (OSDAs) that are based on tetramethylimidazole. In hydroxide media, a zeolite product with Si/Al=14.8-23.2 is obtained, while in fluoride media an aluminosilicate product with Si/Al up to 82 is synthesized. The material produced in hydroxide media is tested for the hydroisomerization of n-hexane, and results from this test reaction suggest that the effective pore size of zeolites with the IWV framework structure is similar to but slightly larger than that of ZSM-12 (MTW), in fairly good agreement with crystallographic data. PMID:26833857

  16. 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.

  17. Adsorption of hydrogen sulfide onto activated carbon fibers: effect of pore structure and surface chemistry.

    PubMed

    Feng, Wenguo; Kwon, Seokjoon; Borguet, Eric; Vidic, Radisav

    2005-12-15

    To understand the nature of H2S adsorption onto carbon surfaces under dry and anoxic conditions, the effects of carbon pore structure and surface chemistry were studied using activated carbon fibers (ACFs) with different pore structures and surface areas. Surface pretreatments, including oxidation and heattreatment, were conducted before adsorption/desorption tests in a fixed-bed reactor. Raw ACFs with higher surface area showed greater adsorption and retention of sulfur, and heat treatment further enhanced adsorption and retention of sulfur. The retained amount of hydrogen sulfide correlated well with the amount of basic functional groups on the carbon surface, while the desorbed amount reflected the effect of pore structure. Temperature-programmed desorption (TPD) and thermal gravimetric analysis (TGA) showed that the retained sulfurous compounds were strongly bonded to the carbon surface. In addition, surface chemistry of the sorbent might determine the predominant form of adsorbate on the surface. PMID:16475362

  18. Formation of the pore structure of brown coal upon thermolysis with potassium hydroxide

    SciTech Connect

    T.G. Shendrik; Y.V. Tamarkina; T.V. Khabarova; V.A. Kucherenko; N.V. Chesnokov; B.N. Kuznetsov

    2009-07-01

    The pore-structure characteristics of active carbons prepared by the thermolysis (800{sup o}C) of brown coal impregnated with potassium hydroxide were studied. The dependence of the specific surface area, total pore volume, micropore volume, micropore fraction, and micropore size distribution on the KOH/coal weight ratio R{sub KOH}{le} 1.0 g/g was found. Condensation processes with the formation of a low-porosity material were predominant at low ratios of R{sub KOH} {le} 0.1 g/g. The development of a micropore structure was observed at R{sub KOH} {ge} 0.1 g/g, and it increased as R{sub KOH} was increased to 1.0 g/g. It was hypothesized that pore formation was due to the thermally initiated reactions of the structural fragments of coal with KOH molecules, which occurred within the framework of coal.

  19. 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.

  20. 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.

  1. 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``.

  2. 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.

  3. 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.

  4. Microfluidic synthesis of monodisperse nanoporous oxide particles and control of hierarchical pore structure.

    PubMed

    Carroll, Nick J; Crowder, Peter F; Pylypenko, Svitlana; Patterson, Wendy; Ratnaweera, Dilru R; Perahia, Dvora; Atanassov, Plamen; Petsev, Dimiter N

    2013-05-01

    Particles with hierarchical porosity can be formed by templating silica microparticles with a specially designed surfactant micelle/oil nanoemulsion mixture. The nanoemulsion oil droplet and micellar dimensions determine the pore size distribution: one set of pores with diameters of tens of nanometers coexisting with a second subset of pores with diameters of single nanometers. Further practical utility of these nanoporous particles requires precise tailoring of the hierarchical pore structure. In this synthesis study, the particle nanostructure is tuned by adjusting the oil, water, and surfactant mixture composition for the controlled design of nanoemulsion-templated features. We also demonstrate control of the size distribution and surface area of the smaller micelle-templated pores as a consequence of altering the hydrophobic chain length of the molecular surfactant template. Moreover, a microfluidic system is designed to process the low interfacial system for fabrication of monodisperse porous particles. The ability to direct the assembly of template nanoemulsion and micelle structures creates new opportunities to engineer hierarchically porous particles for utility as electrocatalysts for fuel cells, chromatography separations, drug delivery vehicles, and other applications. PMID:23387998

  5. The role of pore structure on char reactivity. Quarterly progress report, [October--December 1995

    SciTech Connect

    Sarofim, A.F.

    1996-01-01

    In order to examine the role of pore structure, studies will be conducted on coal chars in the electrodynamic balance. Larger particles will also be examined using a fluidized bed to examine diffusion control reactions, and soots will also be investigated to examine the role of meso- and micro-pores without macro-pore interference. These studies will allow a full range of particles sizes and temperatures to be investigated and eventually modelled. The project has examined the effect of the pore structure diffusivity changes on the generation of NO{sub x} and N{sub 2}O from the Fluidized Bed Combustor. Furthermore, refinement of the techniques necessary to determine micropore characteristics from TEM imaging have been further refined. The continuing focus of this research has been the examination of the evolution of model compounds such as spherocarbon during oxidation in order to simplify structural analysis. The structure of spherocarbon now has been fully analyzed at three conversions (0, 44, and 96% conversion).

  6. Sensitivity of concrete properties to the pore structure of hardened cement paste

    SciTech Connect

    Oktar, O.N.; Moral, H.; Tasdemir, M.A.

    1996-11-01

    Coefficients and degrees of sensitivity are introduced to define quantitatively the sensitivity of concrete properties to the pore structure of cement paste. Proposed parameters have been applied to experimental data obtained from 60 different concrete mixtures, measuring eight properties for each mix and the results obtained have been discussed and evaluated.

  7. 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

  8. Pore space characterization in carbonate rocks - Approach to combine nuclear magnetic resonance and elastic wave velocity measurements

    NASA Astrophysics Data System (ADS)

    Müller-Huber, Edith; Schön, Jürgen; Börner, Frank

    2016-04-01

    Pore space features influence petrophysical parameters such as porosity, permeability, elastic wave velocity or nuclear magnetic resonance (NMR). Therefore they are essential to describe the spatial distribution of petrophysical parameters in the subsurface, which is crucial for efficient reservoir characterization especially in carbonate rocks. While elastic wave velocity measurements respond to the properties of the solid rock matrix including pores or fractures, NMR measurements are sensitive to the distribution of pore-filling fluids controlled by rock properties such as the pore-surface-to-pore-volume ratio. Therefore a combination of both measurement principles helps to investigate carbonate pore space using complementary information. In this study, a workflow is presented that delivers a representative average semi-axis length of ellipsoidal pores in carbonate rocks based on the pore aspect ratio received from velocity interpretation and the pore-surface-to-pore-volume ratio Spor as input parameters combined with theoretical calculations for ellipsoidal inclusions. A novel method to calculate Spor from NMR data based on the ratio of capillary-bound to movable fluids and the thickness of the capillary-bound water film is used. To test the workflow, a comprehensive petrophysical database was compiled using micritic and oomoldic Lower Muschelkalk carbonates from Germany. The experimental data indicate that both mud-dominated and grain-dominated carbonates possess distinct ranges of petrophysical parameters. The agreement between the predicted and measured surface-to-volume ratio is satisfying for oomoldic and most micritic samples, while pyrite or significant sample heterogeneity may lead to deviations. Selected photo-micrographs and scanning electron microscope images support the validity of the estimated representative pore dimensions.

  9. Cysteine mutagenesis to study the structure of claudin-2 paracellular pores.

    PubMed

    Angelow, Susanne; Yu, Alan S L

    2009-05-01

    The structure and transport mechanism of paracellular pores are only poorly understood. Here we describe for the first time how the substituted cysteine accessibility method (SCAM), previously developed to study transmembrane transport, can be applied to analyze the pathway of paracellular ion permeation. Using stable transfected Madin Darby canine kidney type I cells, induced to express claudin-2, we show that paracellular cation transport can be blocked by sulfhydryl-specific methanethiosulfonate (MTS) and that SCAM can be used to identify residues that line paracellular pores. PMID:19538299

  10. 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.

  11. Structure of residual oil as a function of wettability using pore-network modelling

    NASA Astrophysics Data System (ADS)

    Ryazanov, A. V.; Sorbie, K. S.; van Dijke, M. I. J.

    2014-01-01

    In the water flooding of mixed-wet porous media, oil may drain down to relatively low residual oil saturations (Sor). Various studies have indicated that such low saturations can only be reached when oil layers in pore corners are included in the pore-scale modelling. These processes within a macroscopic porous medium can be modelled at the pore-scale by incorporating the fundamental physics of capillary dominated displacement within idealised pore network models. Recently, the authors have developed thermodynamic criteria for oil layer existence in pores with non-uniform wettability which takes as input geometrically and topologically representative networks, to calculate realistic Sor values for mixed-wet and oil-wet sandstones [16, 21]. This previous work is developed in this paper to include (i) the visualisation of the 3D structure of this residual oil, and (ii) a statistical analysis of this "residual/remaining" oil. Both the visualisation and the statistical analysis are done under a wide range of wettability conditions, which is reported for the first time in this paper.

  12. Advanced NMR-based techniques for pore structure analysis of coal. Quarter report No. 4, 1 October 1992--30 December 1992

    SciTech Connect

    Smith, D.M.

    1992-12-31

    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 closed 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. We believe that measurement of the NMR parameters of various gas phase and adsorbed phase NMR active probes can provide the resolution to this problem. 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 and the pore surfaces in coals. These molecules have been selected for their chemical and physical properties. A special NMR probe will be constructed which will allow the concurrent measurement of NMR properties and adsorption uptake at a variety of temperatures. All samples will be subjected to a suite of ``conventional`` pore structure analyses. These include nitrogen adsorption at 77 K with BET analysis, CO{sub 2} and CH{sub 4} adsorption at 273 K with D-R (Dubinin-Radushkevich) analysis, helium pycnometry, and small angle X-ray scattering as well as gas diffusion measurements.

  13. 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

  14. Relationship between pore structure and mechanical properties of ordinary concrete under bending fatigue

    SciTech Connect

    Zhang, B.

    1998-05-01

    Progressive macro damage of concrete under fatigue loading is caused by the change of its internal micro-meso properties such as pore structure. In this study, porosity, pore size distribution, and specific surface area of ordinary concrete at different fatigue stages were investigated using mercury intrusion, helium flow, and nitrogen adsorption (BET) methods. These properties changed with increasing loading cycles and could be taken as micro-meso damage parameters to evaluate macro fatigue damage of concrete. Test results showed that both porosity in mortar (mainly macro pores) and interface between mortar and coarse aggregates (interfacial cracks) developed at a similar rate. The corresponding residual bending fatigue strength and dynamic bending Young`s modulus were also obtained and their relationships with these micro-meso properties were established. The intrinsic bending strength and intrinsic bending Young`s modulus were predicted from these relationships.

  15. 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.

  16. Surface chemistry, reactivity, and pore structure of porous silicon oxidized by various methods.

    PubMed

    Riikonen, Joakim; Salomäki, Mikko; van Wonderen, Jessica; Kemell, Marianna; Xu, Wujun; Korhonen, Ossi; Ritala, Mikko; MacMillan, Fraser; Salonen, Jarno; Lehto, Vesa-Pekka

    2012-07-17

    Oxidation is the most commonly used method of passivating porous silicon (PSi) surfaces against unwanted reactions with guest molecules and temporal changes during storage or use. In the present study, several oxidation methods were compared in order to find optimal methods able to generate inert surfaces free of reactive hydrides but would cause minimal changes in the pore structure of PSi. The studied methods included thermal oxidations, liquid-phase oxidations, annealings, and their combinations. The surface-oxidized samples were studied by Fourier transform infrared spectroscopy, isothermal titration microcalorimetry, nitrogen sorption, ellipsometry, X-ray diffraction, electron paramagnetic resonance spectroscopy, and scanning electron microscopy imaging. Treatment at high temperature was found to have two advantages. First, it enables the generation of surfaces free of hydrides, which is not possible at low temperatures in a liquid or a gas phase. Second, it allows the silicon framework to partially accommodate a volume expansion because of oxidation, whereas at low temperature the volume expansion significantly consumes the free pore volume. The most promising methods were further optimized to minimize the negative effects on the pore structure. Simple thermal oxidation at 700 °C was found to be an effective oxidation method although it causes a large decrease in the pore volume. A novel combination of thermal oxidation, annealing, and liquid-phase oxidation was also effective and caused a smaller decrease in the pore volume with no significant change in the pore diameter but was more complicated to perform. Both methods produced surfaces that were not found to react with a model drug cinnarizine in isothermal titration microcalorimetry experiments. The study enables a reasonable choice of oxidation method for PSi applications. PMID:22671967

  17. Polyaniline nanofibers with a high specific surface area and an improved pore structure for supercapacitors

    NASA Astrophysics Data System (ADS)

    Xu, Hailing; Li, Xingwei; Wang, Gengchao

    2015-10-01

    Polyaniline (PANI) with a high specific surface area and an improved pore structure (HSSA-PANI) has been prepared by using a facile method, treating PANI nanofibers with chloroform (CHCl3), and its structure, morphology and pore structure are investigated. The specific surface area and pore volume of HSSA-PANI are 817.3 m2 g-1 and 0.6 cm3 g-1, and those of PANI are 33.6 m2 g-1 and 0.2 cm3 g-1. As electrode materials, a large specific surface area and pore volume can provide high electroactive regions, accelerate the diffusion of ions, and mitigate the electrochemical degradation of active materials. Compared with PANI, the capacity retention rate of HSSA-PANI is 90% with a growth of current density from 5.0 to 30 A g-1, and that of PANI is 29%. At a current density of 30 A g-1, the specific capacitance of HSSA-PANI still reaches 278.3 F g-1, and that of PANI is 86.7 F g-1. At a current density of 5.0 A g-1, the capacitance retention of HSSA-PANI is 53.1% after 2000 cycles, and that of PANI electrode is only 28.1%.

  18. A novel synthesis and characterization of ordered meso/macroporous alumina with hierarchical and adjustable pore size.

    PubMed

    Meng, Xiuhong; Duan, Linhai; Qin, Huibo; Xie, Xiaohua; Umar, Ahmad; Wang, Haiyan; Wang, Qiang

    2014-09-01

    The sub-micron polystyrene (PS) microspheres with adjustable size were firstly synthesized using emulsion polymerization method by adding only a small amount of emulsifier. Then, three dimensionally ordered macroporous alumina with mesoporous walls and adjustable macropore size was facilely prepared by the colloidal template method. The alumina and PS spheres were characterized by nanoparticle size analyzer, SEM, XRD and N2 adsorption. The results show that the polystyrene microsphere has adjustable single-sized pore with diameter in the range of 100-350 nm and the yield is higher than that prepared by soap free emulsion polymerization. The alumina materials as prepared using the PS colloidal crystals as the template, had ordered meso-macroporous structures and adjustable apertures. The mesopores (about 3.6 nm) in γ-alumina were formed by controlling the heat treatment of alumina precursor. BET surface area and pore volume of the hierarchical alumina as obtained can reach to 241.3 m2/g and 0.33 cm3/g, respectively. PMID:25924412

  19. 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

  20. 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.

  1. Characterization of a pore-forming cytotoxin expressed by Salmonella enterica serovars typhi and paratyphi A.

    PubMed

    Oscarsson, Jan; Westermark, Marie; Löfdahl, Sven; Olsen, Björn; Palmgren, Helena; Mizunoe, Yoshimitsu; Wai, Sun Nyunt; Uhlin, Bernt Eric

    2002-10-01

    Cytolysin A (ClyA) is a pore-forming cytotoxic protein encoded by the clyA gene that has been characterized so far only in Escherichia coli. Using DNA sequence analysis and PCR, we established that clyA is conserved in the human-specific typhoid Salmonella enterica serovars Typhi and Paratyphi A and that the entire clyA gene locus is absent in many other S. enterica serovars, including Typhimurium. The gene products, designated ClyA(STy) and ClyA(SPa), show >/=90% amino acid identity to E. coli cytolysin A, ClyA(EC), and they are immunogenically related. The Salmonella proteins showed a pore-forming activity and are hence functional homologues to ClyA(EC). The chromosomal clyA(STy) gene locus was expressed at detectable levels in the serovar Typhi strains S2369/96 and S1112/97. Furthermore, in the serovar Typhi vaccine strain Ty21a, expression of clyA(STy) reached phenotypic levels, as detected on blood agar plates. The hemolytic phenotype was abolished by the introduction of an in-frame deletion in the clyA(STy) chromosomal locus of Ty21a. Transcomplementation of the mutant with a cloned clyA(STy) gene restored the hemolytic phenotype. To our knowledge, Ty21a is the first reported phenotypically hemolytic Salmonella strain in which the genetic determinant has been identified. PMID:12228306

  2. Addition of cement to lime-based mortars: Effect on pore structure and vapor transport

    SciTech Connect

    Mosquera, M.J. . E-mail: mariajesus.mosquera@uca.es; Silva, B.; Prieto, B.; Ruiz-Herrera, E.

    2006-09-15

    The main focus of this work is to determine the effect of cement addition, a common practice in many restorations, on the pore structure of lime-based mortars. A second target is to establish correlations between microstructure and water vapor transport across the mortar, which is a key characteristic of building decay. In order to achieve these objectives, we prepared a set of mortars consisting of air-hardening lime with a progressively increasing cement content, as well as a mortar containing hydraulic lime. Several different techniques, most notably mercury intrusion porosimetry and scanning electron microscopy in the backscatter mode, were used to investigate the pore structure. The results from these procedures led to the conclusion that porosity and pore size are progressively reduced as cement content increases. Moreover, an excellent correlation between pore radius parameter and the vapor diffusion coefficient was established. Hydraulic lime mortar exhibited textural parameters and diffusivity values halfway between those of the different lime/cement mixes studied.

  3. Crystal structure of the octameric pore of staphylococcal γ-hemolysin reveals the β-barrel pore formation mechanism by two components

    PubMed Central

    Yamashita, Keitaro; Kawai, Yuka; Tanaka, Yoshikazu; Hirano, Nagisa; Kaneko, Jun; Tomita, Noriko; Ohta, Makoto; Kamio, Yoshiyuki; Yao, Min; Tanaka, Isao

    2011-01-01

    Staphylococcal γ-hemolysin is a bicomponent pore-forming toxin composed of LukF and Hlg2. These proteins are expressed as water-soluble monomers and then assemble into the oligomeric pore form on the target cell. Here, we report the crystal structure of the octameric pore form of γ-hemolysin at 2.5 Å resolution, which is the first high-resolution structure of a β-barrel transmembrane protein composed of two proteins reported to date. The octameric assembly consists of four molecules of LukF and Hlg2 located alternately in a circular pattern, which explains the biochemical data accumulated over the past two decades. The structure, in combination with the monomeric forms, demonstrates the elaborate molecular machinery involved in pore formation by two different molecules, in which interprotomer electrostatic interactions using loops connecting β2 and β3 (loop A: Asp43-Lys48 of LukF and Lys37-Lys43 of Hlg2) play pivotal roles as the structural determinants for assembly through unwinding of the N-terminal β-strands (amino-latch) of the adjacent protomer, releasing the transmembrane stem domain folded into a β-sheet in the monomer (prestem), and interaction with the adjacent protomer. PMID:21969538

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. The role of pore structure on char reactivity. Quarterly progress report

    SciTech Connect

    Sarofim, A.F.

    1992-06-01

    The Wyoming lignite raw coal was size classified to 38--45 {mu}m, first by air-classification to remove the fine panicles, and then by sieving with a standard Ro-tap sieving machine. The size-classified Wyoming lignite was then pyrolyzed in a laboratory-scale laminar flow furnace at 1650K, 100% N{sub 2}. About one gram of pyrolyzed char was collected with Millipore membrane filters (teflon/polyethylene). The char sample thus collected was carefully poured into an cylindrical mold filled with epoxy resin and thoroughly mixed with epoxy resin. In order to remove the air bubbles trapped during mixing in the mixture, the sample-filled mold was placed in a dessicator connected to a vacuum pump. By periodically evacuating the dessicator, trapped air bubbles could be removed. The mold with the char sample and epoxy resin was placed in a cool area for 24 hours until it hardened. One end of the hardened cylindrical plug was carefully polished with alumina paste so that char particles embedded could also be cross-sectioned. The polished end of the sample plug thus prepared was observed under a Wetzlar optical microscope with a built-in camera. Pictures of fifty cross-sections of char particles were taken. The magnification was in the range of {times} l00 and {times} 650. Figure 1 shows cross-sections of char particles shown in black and white images. (The carbonaceous matrix is shown in black). Characterization of the pore structure of the char was carried out by digital image processing on cross-sections of the char particles. Pictures of cross-sections were scanned in, digitized in 600 {times} 5l2-pixel, 256-grayscale images using an Apple Scanner. Grayscale images were first converted to binary black-and-white images by setting a grayscale threshold that gives the best images of pores and char. Editing, i.e., sharpening and noise reduction, was performed to the binary images using Image v 1.17, a public domain program.

  9. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 3, July 1, 1992--September 30, 1992

    SciTech Connect

    Smith, D.M.

    1992-12-31

    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 closed 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. We believe that measurement of the NMR parameters of various gas phase and adsorbed phase NMR active probes can provide the resolution to this problem. We now have two suites of well-characterized microporous materials including oxides (zeolites and silica gel) and activated carbons from our industrial partner, Air Products in Allentown, PA. Our current work may be divided into three areas: small-angle X-ray scattering (SAXS), adsorption, and NMR.

  10. 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

    2013-01-01

    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

  11. 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.

  12. Molecular Characterization and Functional Analysis of Annulate Lamellae Pore Complexes in Nuclear Transport in Mammalian Cells

    PubMed Central

    Raghunayakula, Sarita; Subramonian, Divya; Dasso, Mary; Kumar, Rita; Zhang, Xiang-Dong

    2015-01-01

    Annulate lamellae are cytoplasmic organelles containing stacked sheets of membranes embedded with pore complexes. These cytoplasmic pore complexes at annulate lamellae are morphologically similar to nuclear pore complexes at the nuclear envelope. Although annulate lamellae has been observed in nearly all types of cells, their biological functions are still largely unknown. Here we show that SUMO1-modification of the Ran GTPase-activating protein RanGAP1 not only target RanGAP1 to its known sites at nuclear pore complexes but also to annulate lamellae pore complexes through interactions with the Ran-binding protein RanBP2 and the SUMO-conjugating enzyme Ubc9 in mammalian cells. Furthermore, upregulation of annulate lamellae, which decreases the number of nuclear pore complexes and concurrently increases that of annulate lamellae pore complexes, causes a redistribution of nuclear transport receptors including importin α/β and the exportin CRM1 from nuclear pore complexes to annulate lamellae pore complexes and also reduces the rates of nuclear import and export. Moreover, our results reveal that importin α/β-mediated import complexes initially accumulate at annulate lamellae pore complexes upon the activation of nuclear import and subsequently disassociate for nuclear import through nuclear pore complexes in cells with upregulation of annulate lamellae. Lastly, CRM1-mediated export complexes are concentrated at both nuclear pore complexes and annulate lamellae pore complexes when the disassembly of these export complexes is inhibited by transient expression of a Ran GTPase mutant arrested in its GTP-bound form, suggesting that RanGAP1/RanBP2-activated RanGTP hydrolysis at these pore complexes is required for the dissociation of the export complexes. Hence, our findings provide a foundation for further investigation of how upregulation of annulate lamellae decreases the rates of nuclear transport and also for elucidation of the biological significance of the

  13. 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

  14. 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.

  15. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 1, September 1, 1991--November 30, 1991

    SciTech Connect

    Smith, D.M.

    1991-12-31

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. We propose to 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 2}H{sub 2}, {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 the pore surfaces in coals. These molecules have been selected for their chemical and physical properties.

  16. 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. PMID:26046137

  17. Anisotropic rock physics models for interpreting pore structures in carbonate reservoirs

    NASA Astrophysics Data System (ADS)

    Li, Sheng-Jie; Shao, Yu; Chen, Xu-Qiang

    2016-03-01

    We developed an anisotropic effective theoretical model for modeling the elastic behavior of anisotropic carbonate reservoirs by combining the anisotropic self-consistent approximation and differential effective medium models. By analyzing the measured data from carbonate samples in the TL area, a carbonate pore-structure model for estimating the elastic parameters of carbonate rocks is proposed, which is a prerequisite in the analysis of carbonate reservoirs. A workflow for determining elastic properties of carbonate reservoirs is established in terms of the anisotropic effective theoretical model and the pore-structure model. We performed numerical experiments and compared the theoretical prediction and measured data. The result of the comparison suggests that the proposed anisotropic effective theoretical model can account for the relation between velocity and porosity in carbonate reservoirs. The model forms the basis for developing new tools for predicting and evaluating the properties of carbonate reservoirs.

  18. Strength and pore structure of ternary blended cement mortars containing blast furnace slag and silica fume

    SciTech Connect

    Bagel, L.

    1998-07-01

    Blended cement mortars with fixed workability and incorporating blast furnace slag and silica fume, were tested for compressive strength and mercury intrusion, with a view to comparing their performance with that of plain Portland cement mortar and/or slag-cement mortar. The obtained results showed that with high portions of slag and silica fume in the binding system, the mortars reached relatively satisfactory level of compressive strength and contributed to the significantly denser pore structure.

  19. Two-pore Channels Enter the Atomic Era: Structure of Plant TPC Revealed.

    PubMed

    Patel, Sandip; Penny, Christopher J; Rahman, Taufiq

    2016-06-01

    Two-pore channels (TPCs) are intracellular Ca(2+)-permeable ion channels that are expressed on acidic Ca(2+) stores. They are co-regulated by voltage and Ca(2+) in plant vacuoles and by the second messenger NAADP in animal endo-lysosomes. Two new studies of plant TPC structures reveal essential features of their architecture and provide mechanistic insight into their workings. PMID:27156118

  20. 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.

  1. 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...

  2. Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana.

    PubMed

    Kintzer, Alexander F; Stroud, Robert M

    2016-03-10

    Two-pore channels (TPCs) comprise a subfamily (TPC1-3) of eukaryotic voltage- and ligand-gated cation channels with two non-equivalent tandem pore-forming subunits that dimerize to form quasi-tetramers. Found in vacuolar or endolysosomal membranes, they regulate the conductance of sodium and calcium ions, intravesicular pH, trafficking and excitability. TPCs are activated by a decrease in transmembrane potential and an increase in cytosolic calcium concentrations, are inhibited by low luminal pH and calcium, and are regulated by phosphorylation. Here we report the crystal structure of TPC1 from Arabidopsis thaliana at 2.87 Å resolution as a basis for understanding ion permeation, channel activation, the location of voltage-sensing domains and regulatory ion-binding sites. We determined sites of phosphorylation in the amino-terminal and carboxy-terminal domains that are positioned to allosterically modulate cytoplasmic Ca(2+) activation. One of the two voltage-sensing domains (VSD2) encodes voltage sensitivity and inhibition by luminal Ca(2+) and adopts a conformation distinct from the activated state observed in structures of other voltage-gated ion channels. The structure shows that potent pharmacophore trans-Ned-19 (ref. 17) acts allosterically by clamping the pore domains to VSD2. In animals, Ned-19 prevents infection by Ebola virus and other filoviruses, presumably by altering their fusion with the endolysosome and delivery of their contents into the cytoplasm. PMID:26961658

  3. Structure of Voltage-gated Two-pore Channel TPC1 from Arabidopsis thaliana

    PubMed Central

    Guo, Jiangtao; Zeng, Weizhong; Chen, Qingfeng; Lee, Changkeun; Chen, Liping; Yang, Yi; Cang, Chunlei; Ren, Dejian; Jiang, Youxing

    2015-01-01

    Two-pore channels (TPCs) contain two copies of a Shaker-like six-transmembrane (6-TM) domain in each subunit and are ubiquitously expressed in both animals and plants as organellar cation channels. Here, we present the first crystal structure of a vacuolar two-pore channel from Arabidopsis thaliana, AtTPC1, which functions as a homodimer. AtTPC1 activation requires both voltage and cytosolic Ca2+. Ca2+ binding to the cytosolic EF-hand domain triggers conformational changes coupled to the pair of pore-lining inner helices (IS6 helices) from the first 6-TM domains, whereas membrane potential only activates the second voltage-sensing domain (VSD2) whose conformational changes are coupled to the pair of inner helices (IIS6 helices) from the second 6-TM domains. Luminal Ca2+ or Ba2+ can modulate voltage activation by stabilizing VSD2 in the resting state and shifts voltage activation towards more positive potentials. Our Ba2+ bound AtTPC1 structure reveals a voltage sensor in the resting state, providing hitherto unseen structural insight into the general voltage-gating mechanism among voltage-gated channels. PMID:26689363

  4. Structure of the voltage-gated two-pore channel TPC1 from Arabidopsis thaliana.

    PubMed

    Guo, Jiangtao; Zeng, Weizhong; Chen, Qingfeng; Lee, Changkeun; Chen, Liping; Yang, Yi; Cang, Chunlei; Ren, Dejian; Jiang, Youxing

    2016-03-10

    Two-pore channels (TPCs) contain two copies of a Shaker-like six-transmembrane (6-TM) domain in each subunit and are ubiquitously expressed in both animals and plants as organellar cation channels. Here we present the crystal structure of a vacuolar two-pore channel from Arabidopsis thaliana, AtTPC1, which functions as a homodimer. AtTPC1 activation requires both voltage and cytosolic Ca(2+). Ca(2+) binding to the cytosolic EF-hand domain triggers conformational changes coupled to the pair of pore-lining inner helices from the first 6-TM domains, whereas membrane potential only activates the second voltage-sensing domain, the conformational changes of which are coupled to the pair of inner helices from the second 6-TM domains. Luminal Ca(2+) or Ba(2+) can modulate voltage activation by stabilizing the second voltage-sensing domain in the resting state and shift voltage activation towards more positive potentials. Our Ba(2+)-bound AtTPC1 structure reveals a voltage sensor in the resting state, providing hitherto unseen structural insight into the general voltage-gating mechanism among voltage-gated channels. PMID:26689363

  5. 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

  6. 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

  7. Pore structure modification of diatomite as sulfuric acid catalyst support by high energy electron beam irradiation and hydrothermal treatment

    NASA Astrophysics Data System (ADS)

    Li, Chong; Zhang, Guilong; Wang, Min; Chen, Jianfeng; Cai, Dongqing; Wu, Zhengyan

    2014-08-01

    High energy electron beam (HEEB) irradiation and hydrothermal treatment (HT), were applied in order to remove the impurities and enlarge the pore size of diatomite, making diatomite more suitable to be a catalyst support. The results demonstrated that, through thermal, charge, impact and etching effects, HEEB irradiation could make the impurities in the pores of diatomite loose and remove some of them. Then HT could remove rest of them from the pores and contribute significantly to the modification of the pore size distribution of diatomite due to thermal expansion, water swelling and thermolysis effects. Moreover, the pore structure modification improved the properties (BET (Brunauer-Emmett-Teller) specific surface area, bulk density and pore volume) of diatomite and the catalytic efficiency of the catalyst prepared from the treated diatomite.

  8. Single-Molecule Imaging to Characterize the Transport Mechanism of the Nuclear Pore Complex.

    PubMed

    Jeremy, Grace; Stevens, James; Lowe, Alan R

    2016-01-01

    In the eukaryotic cell, a large macromolecular channel, known as the Nuclear Pore Complex (NPC), mediates all molecular transport between the nucleus and cytoplasm. In recent years, single-molecule fluorescence (SMF) imaging has emerged as a powerful tool to study the molecular mechanism of transport through the NPC. More recently, techniques such as single-molecule localization microscopy (SMLM) have enabled the spatial and temporal distribution of cargos, transport receptors and even structural components of the NPC to be determined with nanometre accuracy. In this protocol, we describe a method to study the position and/or motion of individual molecules transiting through the NPC with high spatial and temporal precision. PMID:27283299

  9. 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.

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

    PubMed

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

    2016-01-01

    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. PMID:27405240

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

    PubMed Central

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

    2016-01-01

    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. PMID:27405240

  12. Formation of an ink-bottle-like pore structure in SBA-15 by MOCVD.

    PubMed

    Zhang, Ying; Lam, Frank Leung-Yuk; Hu, Xijun; Yan, Zifeng

    2008-11-01

    Metallorganic chemical vapor deposition is used as a simple pore-modifying method to fine tune the pore-opening size of SBA-15 materials without significant loss in pore volume and surface area. PMID:18956045

  13. PARTICLE SIZE SEGREGATION DURING HAND PACKING OF COARSE GRANULAR MATERIALS AND IMPACTS ON LOCAL PORE-SCALE STRUCTURE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soils and sediments consist of granular particles with an intricate network of pores in between. The structure and orientation of these pores will determine how the material transports fluids and contaminants. A common practice in soil science to simplify experiments and to achieve a homogeneous med...

  14. Buckling in 2D periodic, soft and porous structures: effect of pore shape and lattice pattern

    NASA Astrophysics Data System (ADS)

    Shan, Sicong; Bertoldi, Katia; Shim, Jongmin; Overvelde, Johannes T. B.; Kang, Sung Hoon

    2013-03-01

    Adaptive structures allowing dramatic shape changes offer unique opportunities for the design of responsive and reconfigurable devices. Traditional morphing and foldable structures with stiff structural members and mechanical joints remains a challenge in manufacturing at small length scales. Soft structures where the folding mechanisms are induced by a mechanical instability represent a new class of novel adaptive materials which can be easily manufactured over a wide range of length scales. More specifically, soft porous structures with deliberately designed patterns can significantly change their architecture in response to diverse stimuli, opening avenues for reconfigurable devices that change their shapes to respond to their environment. While so far only two-dimensional periodic porous structures with circular holes arranged on a square or triangular lattice have been investigated, here we investigate both numerically and experimentally the effects of pore shape and lattice pattern on the macroscopic properties of the structures. Our results show that both the pore shape and lattice pattern can be used to effectively design desired materials and pave the way for the development of a new class of soft, active and reconfigurable devices over a wide range of length scales.

  15. Pore Velocity Estimation Uncertainties

    NASA Astrophysics Data System (ADS)

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

    1982-08-01

    Geostatistical data analysis techniques were used to stochastically model the spatial variability of groundwater pore velocity in a potential waste repository site. Kriging algorithms were applied to Hanford Reservation data to estimate hydraulic conductivities, hydraulic head gradients, and pore velocities. A first-order Taylor series expansion for pore velocity was used to statistically combine hydraulic conductivity, hydraulic head gradient, and effective porosity surfaces and uncertainties to characterize the pore velocity uncertainty. Use of these techniques permits the estimation of pore velocity uncertainties when pore velocity measurements do not exist. Large pore velocity estimation uncertainties were found to be located in the region where the hydraulic head gradient relative uncertainty was maximal.

  16. Pore-forming activity and structural autoinhibition of the gasdermin family.

    PubMed

    Ding, Jingjin; Wang, Kun; Liu, Wang; She, Yang; Sun, Qi; Shi, Jianjin; Sun, Hanzi; Wang, Da-Cheng; Shao, Feng

    2016-07-01

    Inflammatory caspases cleave the gasdermin D (GSDMD) protein to trigger pyroptosis, a lytic form of cell death that is crucial for immune defences and diseases. GSDMD contains a functionally important gasdermin-N domain that is shared in the gasdermin family. The functional mechanism of action of gasdermin proteins is unknown. Here we show that the gasdermin-N domains of the gasdermin proteins GSDMD, GSDMA3 and GSDMA can bind membrane lipids, phosphoinositides and cardiolipin, and exhibit membrane-disrupting cytotoxicity in mammalian cells and artificially transformed bacteria. Gasdermin-N moved to the plasma membrane during pyroptosis. Purified gasdermin-N efficiently lysed phosphoinositide/cardiolipin-containing liposomes and formed pores on membranes made of artificial or natural phospholipid mixtures. Most gasdermin pores had an inner diameter of 10–14 nm and contained 16 symmetric protomers. The crystal structure of GSDMA3 showed an autoinhibited two-domain architecture that is conserved in the gasdermin family. Structure-guided mutagenesis demonstrated that the liposome-leakage and pore-forming activities of the gasdermin-N domain are required for pyroptosis. These findings reveal the mechanism for pyroptosis and provide insights into the roles of the gasdermin family in necrosis, immunity and diseases. PMID:27281216

  17. 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. PMID:26650856

  18. 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. PMID:27273515

  19. Protein-lipid interactions and non-lamellar lipidic structures in membrane pore formation and membrane fusion.

    PubMed

    Gilbert, Robert J C

    2016-03-01

    Pore-forming proteins and peptides act on their targeted lipid bilayer membranes to increase permeability. This approach to the modulation of biological function is relevant to a great number of living processes, including; infection, parasitism, immunity, apoptosis, development and neurodegeneration. While some pore-forming proteins/peptides assemble into rings of subunits to generate discrete, well-defined pore-forming structures, an increasing number is recognised to form pores via mechanisms which co-opt membrane lipids themselves. Among these, membrane attack complex-perforin/cholesterol-dependent cytolysin (MACPF/CDC) family proteins, Bax/colicin family proteins and actinoporins are especially prominent and among the mechanisms believed to apply are the formation of non-lamellar (semi-toroidal or toroidal) lipidic structures. In this review I focus on the ways in which lipids contribute to pore formation and contrast this with the ways in which lipids are co-opted also in membrane fusion and fission events. A variety of mechanisms for pore formation that involve lipids exists, but they consistently result in stable hybrid proteolipidic structures. These structures are stabilised by mechanisms in which pore-forming proteins modify the innate capacity of lipid membranes to respond to their environment, changing shape and/or phase and binding individual lipid molecules directly. In contrast, and despite the diversity in fusion protein types, mechanisms for membrane fusion are rather similar to each other, mapping out a pathway from pairs of separated compartments to fully confluent fused membranes. Fusion proteins generate metastable structures along the way which, like long-lived proteolipidic pore-forming complexes, rely on the basic physical properties of lipid bilayers. Membrane fission involves similar intermediates, in the reverse order. I conclude by considering the possibility that at least some pore-forming and fusion proteins are evolutionarily related

  20. 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. PMID:25222267

  1. 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. PMID:26791760

  2. Geometrical Properties of Pore Structure in Berea Sandstone under Pressurization with Micro Focus X-Ray CT

    NASA Astrophysics Data System (ADS)

    Takahashi, M.; Urushimatsu, Y.

    2008-12-01

    Three dimensional geometry and connectivity of pore space play a fundamental role in governing fluid transport properties of porous media. Total porosity and pore size distribution have been obtained through mercury intrusion porosimetry and gas absorption method, but the spatial and three dimensional information of pore geometry were difficult to obtain. To visualize in detail the manner of deformation in sedimentary rocks under various confining pressure and pore pressure, we used a micro focus X-ray CT system to obtain three dimensional images with high resolution of 5 micron. A new pressure vessel was developed to simultaneously supply both confining pressure and pore pressure to cylindrical rock specimen. Berea sandstone specimen of 10mm diameter and 20mm length was deformed hydrostatically. The diameters at every 15 degree angle were measured under the various conditions of confining pressure and pore pressures. The average diameter decreased monotonically with increasing effective confining pressure. Sensitive orientation around the specimen diameter with large deformation was recognized under pressurization. In addition, to quantify the flow-relevant geometrical properties of the pore structure, we utilized three dimensional data of Berea sandstone obtained with micro focus X-ray CT. We present measured distributions of pore size, throat size, channel length, coordination number, and of correlations between pore and throat geometry.

  3. 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. PMID:26952448

  4. 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. PMID:22525817

  5. Resistive pulse sensing of magnetic beads and supraparticle structures using tunable pores

    PubMed Central

    Willmott, Geoff R.; Platt, Mark; Lee, Gil U.

    2012-01-01

    Tunable pores (TPs) have been used for resistive pulse sensing of 1 μm superparamagnetic beads, both dispersed and within a magnetic field. Upon application of this field, magnetic supraparticle structures (SPSs) were observed. Onset of aggregation was most effectively indicated by an increase in the mean event magnitude, with data collected using an automated thresholding method. Simulations enabled discrimination between resistive pulses caused by dimers and individual particles. Distinct but time-correlated peaks were often observed, suggesting that SPSs became separated in pressure-driven flow focused at the pore constriction. The distinct properties of magnetophoretic and pressure-driven transport mechanisms can explain variations in the event rate when particles move through an asymmetric pore in either direction, with or without a magnetic field applied. Use of TPs for resistive pulse sensing holds potential for efficient, versatile analysis and measurement of nano- and microparticles, while magnetic beads and particle aggregation play important roles in many prospective biosensing applications. PMID:22662090

  6. On the structural possibility of pore-forming mitochondrial FoF1 ATP synthase.

    PubMed

    Gerle, Christoph

    2016-08-01

    The mitochondrial permeability transition is an inner mitochondrial membrane event involving the opening of the permeability transition pore concomitant with a sudden efflux of matrix solutes and breakdown of membrane potential. The mitochondrial F(o)F(1) ATP synthase has been proposed as the molecular identity of the permeability transition pore. The likeliness of potential pore-forming sites in the mitochondrial F(o)F(1) ATP synthase is discussed and a new model, the death finger model, is described. In this model, movement of a p-side density that connects the lipid-plug of the c-ring with the distal membrane bending Fo domain allows reversible opening of the c-ring and structural cross-talk with OSCP and the catalytic (αβ)(3) hexamer. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi. PMID:26968896

  7. 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'. PMID:27597792

  8. New insights into the pore structure of poly(d,l-lactide-co-glycolide) microspheres.

    PubMed

    Vay, Kerstin; Scheler, Stefan; Friess, Wolfgang

    2010-12-15

    The objective of this work was to develop a fast and significant method for the determination of the intraparticulate pore size distribution of microspheres. Poly(lactide-co-glycolide) (PLGA) microspheres prepared with a solvent extraction/evaporation process were studied. From the envelope and the skeletal volume of the microspheres the porosity was calculated. The skeletal volume was determined with nitrogen and helium pycnometry and mercury intrusion porosimetry. Based on single particle optical sensing (SPOS) a novel method was developed by which the envelope volume is calculated from the particle size distribution (PSD), provided that all particles have a spherical shape. The penetration capacity of the applied intrusion media is limited by their atomic or molecular diameter or by the surface tension and the pressure in case of mercury. A classification of the pore structure was obtained by comparing these different skeletal values with the values for the envelope volume. Two well separated pore fractions were found, a nanoporous fraction smaller than 0.36nm and a macroporous fraction larger than 3.9μm. The total porosity and the ratio between both fractions is controlled by the preparation process and was shown to depend on the solvent extraction temperature. PMID:20883760

  9. GLE2, a Saccharomyces cerevisiae homologue of the Schizosaccharomyces pombe export factor RAE1, is required for nuclear pore complex structure and function.

    PubMed Central

    Murphy, R; Watkins, J L; Wente, S R

    1996-01-01

    To identify and characterize novel factors required for nuclear transport, a genetic screen was conducted in the yeast Saccharomyces cerevisiae. Mutations that were lethal in combination with a null allele of the gene encoding the nucleoporin Nup100p were isolated using a colony-sectoring assay. Three complementation groups of gle (for GLFG lethal) mutants were identified. In this report, the characterization of GLE2 is detailed. GLE2 encodes a 40.5-kDa polypeptide with striking similarity to that of Schizosaccharomyces pombe RAE1. In indirect immunofluorescence and nuclear pore complex fractionation experiments, Gle2p was associated with nuclear pore complexes. Mutated alleles of GLE2 displayed blockage of polyadenylated RNA export; however, nuclear protein import was not apparently diminished. Immunofluorescence and thin-section electron microscopic analysis revealed that the nuclear pore complex and nuclear envelope structure was grossly perturbed in gle2 mutants. Because the clusters of herniated pore complexes appeared subsequent to the export block, the structural perturbations were likely indirect consequences of the export phenotype. Interestingly, a two-hybrid interaction was detected between Gle2p and Srp1p, the nuclear localization signal receptor, as well as Rip1p, a nuclear export signal-interacting protein. We propose that Gle2p has a novel role in mediating nuclear transport. Images PMID:8970155

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

    SciTech Connect

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

    2013-06-11

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

  11. Characterization of Two-Pore Channel 2 by Nuclear Membrane Electrophysiology.

    PubMed

    Lee, Claire Shuk-Kwan; Tong, Benjamin Chun-Kit; Cheng, Cecily Wing-Hei; Hung, Harry Chun-Hin; Cheung, King-Ho

    2016-01-01

    Lysosomal calcium (Ca(2+)) release mediated by NAADP triggers signalling cascades that regulate many cellular processes. The identification of two-pore channel 2 (TPC2) as the NAADP receptor advances our understanding of lysosomal Ca(2+) signalling, yet the lysosome is not amenable to traditional patch-clamp electrophysiology. Previous attempts to record TPC2 single-channel activity put TPC2 outside its native environment, which not reflect TPC2's true physiological properties. To test the feasibility of using nuclear membrane electrophysiology for TPC2 channel characterization, we constructed a stable human TPC2-expressing DT40TKO cell line that lacks endogenous InsP3R and RyR (DT40TKO-hTPC2). Immunostaining revealed hTPC2 expression on the ER and nuclear envelope. Intracellular dialysis of NAADP into Fura-2-loaded DT40TKO-hTPC2 cells elicited cytosolic Ca(2+) transients, suggesting that hTPC2 was functionally active. Using nuclear membrane electrophysiology, we detected a ~220 pS single-channel current activated by NAADP with K(+) as the permeant ion. The detected single-channel recordings displayed a linear current-voltage relationship, were sensitive to Ned-19 inhibition, were biphasically regulated by NAADP concentration, and regulated by PKA phosphorylation. In summary, we developed a cell model for the characterization of the TPC2 channel and the nuclear membrane patch-clamp technique provided an alternative approach to rigorously investigate the electrophysiological properties of TPC2 with minimal manipulation. PMID:26838264

  12. Characterization of Two-Pore Channel 2 by Nuclear Membrane Electrophysiology

    PubMed Central

    Lee, Claire Shuk-Kwan; Tong, Benjamin Chun-Kit; Cheng, Cecily Wing-Hei; Hung, Harry Chun-Hin; Cheung, King-Ho

    2016-01-01

    Lysosomal calcium (Ca2+) release mediated by NAADP triggers signalling cascades that regulate many cellular processes. The identification of two-pore channel 2 (TPC2) as the NAADP receptor advances our understanding of lysosomal Ca2+ signalling, yet the lysosome is not amenable to traditional patch-clamp electrophysiology. Previous attempts to record TPC2 single-channel activity put TPC2 outside its native environment, which not reflect TPC2’s true physiological properties. To test the feasibility of using nuclear membrane electrophysiology for TPC2 channel characterization, we constructed a stable human TPC2-expressing DT40TKO cell line that lacks endogenous InsP3R and RyR (DT40TKO-hTPC2). Immunostaining revealed hTPC2 expression on the ER and nuclear envelope. Intracellular dialysis of NAADP into Fura-2-loaded DT40TKO-hTPC2 cells elicited cytosolic Ca2+ transients, suggesting that hTPC2 was functionally active. Using nuclear membrane electrophysiology, we detected a ~220 pS single-channel current activated by NAADP with K+ as the permeant ion. The detected single-channel recordings displayed a linear current-voltage relationship, were sensitive to Ned-19 inhibition, were biphasically regulated by NAADP concentration, and regulated by PKA phosphorylation. In summary, we developed a cell model for the characterization of the TPC2 channel and the nuclear membrane patch-clamp technique provided an alternative approach to rigorously investigate the electrophysiological properties of TPC2 with minimal manipulation. PMID:26838264

  13. In-depth correlation of separator pore structure and electrochemical performance in lithium-ion batteries

    NASA Astrophysics Data System (ADS)

    Lee, Yunju; Park, Joonam; Jeon, Hyunkyu; Yeon, Daeyong; Kim, Byung-Hyun; Cho, Kuk Young; Ryou, Myung-Hyun; Lee, Yong Min

    2016-09-01

    To establish an accurate correlation between a separator's pore structure and the electrochemical performance of a lithium-ion battery (LIB), we fabricate well defined polyethylene (PE) separators on the same production line while maintaining most processing variables, except for composition. Four PE separators having different thicknesses and porosities (16 μm/37%, 16 μm/40%, 16 μm/47%, 22 μm/47%, respectively) are physically and electrochemically evaluated in detail. Although thickness and porosity remain good parameters by which to represent the separators' characteristics, both the normalized Gurley number and ionic conductance are found to have much stronger relationships with the rate capability.

  14. Pore-space characterization of an altered tonalite by X-ray computed microtomography and the 14C-labeled-polymethylmethacrylate method

    NASA Astrophysics Data System (ADS)

    Voutilainen, M.; Siitari-Kauppi, M.; Sardini, P.; Lindberg, A.; Timonen, J.

    2012-01-01

    The structure of geological materials strongly affects migration processes that take place in them and are also important in their weathering and alteration processes. Further information of that structure will also be important for many applications that involve geological materials. The emphasis of this study was thus to characterize the pore structure and porosity of altered tonalite by combining different measuring techniques: X-ray tomography, the14C-polymethylmethacrylate method, electron microscopy, and argon pycnometry. Intragranular porosities were determined using chemical staining of rock surfaces. Three-dimensional distributions of minerals and porosities were evaluated with consistent values for the total porosity. Porosity and pore size distributions together with pore connectivities were also determined. Combining the results of different methods, a 3-D porosity map was outlined for one sample. This porosity map enabled us to model, for example, diffusion in a more realistic environment. Scanning electron microscopy was used to identify the minerals and to obtain information on mineral texture and alteration state. The methods introduced here can be applied to many porous materials.

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

    PubMed

    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

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. Structural Evidence for Common Ancestry of the Nuclear Pore Complex and Vesicle Coats

    SciTech Connect

    Brohawn, S.; Leksa, N; Spear, E; Rajashankar, K; Schwartz, T

    2008-01-01

    Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eightfold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the nucleoporin 85 (Nup85)bulletSeh1 structure, a module in the heptameric Nup84 complex, at 3.5 angstroms resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identified interactions that define the organization of the Nup84 complex on the basis of comparison with vesicle coats and confirmed the sites by mutagenesis. We propose that the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice that provides docking sites for additional nucleoporins.

  2. 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.

  3. Three-dimensional structure of Bax-mediated pores in membrane bilayers

    PubMed Central

    Xu, X-P; Zhai, D; Kim, E; Swift, M; Reed, J C; Volkmann, N; Hanein, D

    2013-01-01

    B-cell lymphoma 2 (Bcl-2)-associated X protein (Bax) is a member of the Bcl-2 protein family having a pivotal role in triggering cell commitment to apoptosis. Bax is latent and monomeric in the cytosol but transforms into its lethal, mitochondria-embedded oligomeric form in response to cell stress, leading to the release of apoptogenic factors such as cytochrome C. Here, we dissected the structural correlates of Bax membrane insertion while oligomerization is halted. This strategy was enabled through the use of nanometer-scale phospholipid bilayer islands (nanodiscs) the size of which restricts the reconstituted system to single Bax-molecule activity. Using this minimal reconstituted system, we captured structural correlates that precede Bax homo-oligomerization elucidating previously inaccessible steps of the core molecular mechanism by which Bcl-2 family proteins regulate membrane permeabilization. We observe that, in the presence of BH3 interacting domain death agonist (Bid) BH3 peptide, Bax monomers induce the formation of ∼3.5-nm diameter pores and significantly distort the phospholipid bilayer. These pores are compatible with promoting release of ions as well as proteinaceous components, suggesting that membrane-integrated Bax monomers in the presence of Bid BH3 peptides are key functional units for the activation of the cell demolition machinery. PMID:23788040

  4. 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.

  5. Three-dimensional structure of Bax-mediated pores in membrane bilayers.

    PubMed

    Xu, X-P; Zhai, D; Kim, E; Swift, M; Reed, J C; Volkmann, N; Hanein, D

    2013-01-01

    B-cell lymphoma 2 (Bcl-2)-associated X protein (Bax) is a member of the Bcl-2 protein family having a pivotal role in triggering cell commitment to apoptosis. Bax is latent and monomeric in the cytosol but transforms into its lethal, mitochondria-embedded oligomeric form in response to cell stress, leading to the release of apoptogenic factors such as cytochrome C. Here, we dissected the structural correlates of Bax membrane insertion while oligomerization is halted. This strategy was enabled through the use of nanometer-scale phospholipid bilayer islands (nanodiscs) the size of which restricts the reconstituted system to single Bax-molecule activity. Using this minimal reconstituted system, we captured structural correlates that precede Bax homo-oligomerization elucidating previously inaccessible steps of the core molecular mechanism by which Bcl-2 family proteins regulate membrane permeabilization. We observe that, in the presence of BH3 interacting domain death agonist (Bid) BH3 peptide, Bax monomers induce the formation of ~3.5-nm diameter pores and significantly distort the phospholipid bilayer. These pores are compatible with promoting release of ions as well as proteinaceous components, suggesting that membrane-integrated Bax monomers in the presence of Bid BH3 peptides are key functional units for the activation of the cell demolition machinery. PMID:23788040

  6. 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

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

    SciTech Connect

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

    2011-10-29

    Although 'intragranular' pore space within grain aggregates, grain fractures, and mineral 24 surface coatings may contain a relatively small fraction of the total porosity within a porous 25 medium, it often contains a significant fraction of the reactive surface area, and can thus strongly 26 affect the transport of sorbing solutes. In this work, we demonstrate a batch experiment 27 procedure using tritium and bromide as high-resolution diffusive tracers to characterize the 28 intragranular pore space. The method was tested using uranium-contaminated sediments from 29 the vadose and capillary fringe zones beneath the former 300A process ponds at the Hanford site 30 (Washington State, USA). Sediments were contacted with tracers in artificial groundwater, 31 followed by replacement of bulk solution with tracer-free groundwater and monitoring of tracer 32 release. From these data, intragranular pore volumes were calculated and mass transfer rates 33 were quantified using a multirate first-order mass transfer model. Tritium-hydrogen exchange 34 on surface hydroxyls was accounted for by conducting additional tracer experiments on sediment 35 that was vacuum dried after reaction. The complementary ('wet' and 'dry') techniques allowed 36 for the simultaneous determination of intragranular porosity and surface area using tritium. The 37 Hanford 300A samples exhibited intragranular pore volumes of {approx}1% of the solid volume and 38 intragranular surface areas of {approx}20-30% of the total surface area. Comparison with N2 gas 39 adsorption suggests that this pore space includes both 'micropores' (< 2 nm diameter) and 40 'mesopores' (> 2 nm). Intragranular porosity estimates obtained using bromide were 41 significantly smaller, likely due to anion exclusion of Br- from pores with negatively charged 42 surfaces.

  8. Structures of Lysenin Reveal a Shared Evolutionary Origin for Pore-Forming Proteins And Its Mode of Sphingomyelin Recognition

    PubMed Central

    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.

    2012-01-01

    Summary 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. PMID:22819216

  9. 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

  10. 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