Science.gov

Sample records for pore structure characterization

  1. Microstructural characterization and pore structure analysis of nuclear graphite

    NASA Astrophysics Data System (ADS)

    Kane, J.; Karthik, C.; Butt, D. P.; Windes, W. E.; Ubic, R.

    2011-08-01

    Graphite will be used as a structural and moderator material in next-generation nuclear reactors. While the overall nature of the production of nuclear graphite is well understood, the historic nuclear grades of graphite are no longer available. This paper reports the virgin microstructural characteristics of filler particles and macro-scale porosity in virgin nuclear graphite grades of interest to the Next Generation Nuclear Plant program. Optical microscopy was used to characterize filler particle size and shape as well as the arrangement of shrinkage cracks. Computer aided image analysis was applied to optical images to quantitatively determine the variation of pore structure, area, eccentricity, and orientation within and between grades. The overall porosity ranged between ˜14% and 21%. A few large pores constitute the majority of the overall porosity. The distribution of pore area in all grades was roughly logarithmic in nature. The average pore was best fit by an ellipse with aspect ratio of ˜2. An estimated 0.6-0.9% of observed porosity was attributed to shrinkage cracks in the filler particles. Finally, a preferred orientation of the porosity was observed in all grades.

  2. Microstructural Characterization and Pore Structure Analysis of Nuclear Graphite

    SciTech Connect

    J. Kane; C. Karthik; D. P. Butt; W. E. Windes; R. Ubic

    2011-08-01

    Graphite will be used as a structural and moderator material in next-generation nuclear reactors. While the overall nature of the production of nuclear graphite is well understood, the historic nuclear grades of graphite are no longer available. This paper reports the virgin microstructural characteristics of filler particles and macro-scale porosity in virgin nuclear graphite grades of interest to the Next Generation Nuclear Plant program. Optical microscopy was used to characterize filler particle size and shape as well as the arrangement of shrinkage cracks. Computer aided image analysis was applied to optical images to quantitatively determine the variation of pore structure, area, eccentricity, and orientation within and between grades. The overall porosity ranged between {approx}14% and 21%. A few large pores constitute the majority of the overall porosity. The distribution of pore area in all grades was roughly logarithmic in nature. The average pore was best fit by an ellipse with aspect ratio of {approx}2. An estimated 0.6-0.9% of observed porosity was attributed to shrinkage cracks in the filler particles. Finally, a preferred orientation of the porosity was observed in all grades.

  3. Pore 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.

  4. 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.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Abou Najm, M. R.; Atallah, N. M.; Selker, J. S.; Roques, C.; Stewart, R. D.; Rupp, D. E.; Saad, G.; El-Fadel, M.

    2015-12-01

    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 while still representing the functional hydraulic behavior of real porous media. We present a new method for experimentally estimating the pore structure of porous media using a combination of Newtonian and non-Newtonian fluids. The proposed method 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). This method allows for estimating the soil retention curve using only saturated experiments. Experimental and numerical validation comparing the functional flow behavior of different soils to their modeled flow with N representative radii revealed the ability of the proposed method to represent the water retention and 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 that the use of different non-Newtonian fluids enables the definition of the radii and corresponding percent contribution to flow of multiple representative pores, thus improving the ability of pore-scale models to mimic the functional behavior of real porous media in terms of flow and porosity. 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

  8. 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.

  9. 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.

  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. 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.

  13. Improved pore space structure characterization by fusion of relaxation tomography maps.

    PubMed

    Borgia, G C; Bortolotti, V; Fantazzini, P; Gombia, M; Zaniboni, M

    2003-01-01

    Quantitative Relaxation Tomography in porous media furnishes maps of internal sections where each pixel represents T1 or T2 of water 1H in the corresponding voxel, so that quantitative information on the pore space structure can be obtained. The porosity can be determined at different length scales by correcting pixel by pixel the signal intensity for T2 decay. Moreover, on the basis of the distribution of T1, the microporosity fraction can be computed, as well as several voxel-average porosities. Since T1 and T2 encode different pieces of information, fusion image techniques can improve the characterization of the pore space, showing simultaneously, on the same image, maps of the two parameters. Examples are given of application to a water-saturated travertine core and to a pig femur. Different kinds of look-up tables were tried by varying two of the three dimensions of the HSV color space in such a way as to optimize both the T1 and T2 contrasts simultaneously. PMID:12850742

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. Characterization of atomic structure of oxide films on carbon steel in simulated concrete pore solutions using EELS

    NASA Astrophysics Data System (ADS)

    Gunay, H. Burak; Ghods, Pouria; Isgor, O. Burkan; Carpenter, Graham J. C.; Wu, Xiaohua

    2013-06-01

    The atomic structure of oxide films formed on carbon steel that are exposed to highly alkaline simulated concrete pore solutions was investigated using Electron Energy Loss Spectroscopy (EELS). In particular, the effect of chloride exposure on film structure was studied in two types of simulated pore solutions: saturated calcium hydroxide (CH) and a solution prepared to represent typical concrete pore solutions (CP). It was shown that the films that form on carbon steel in simulated concrete pore solutions contained three indistinct layers. The inner oxide film had a structure similar to that of FeIIO, which is known to be unstable in the presence of chlorides. The outer oxide film mainly resembled Fe3O4 (FeIIO·Fe2IIIO3) in the CH solution and α-Fe2IIIO3/Fe3O4 in the CP solution. The composition of the transition layer between the inner and outer layers of the oxide film was mainly composed of Fe3O4 (FeIIO·Fe2IIIO3). In the presence of chloride, the relative amount of the FeIII/FeII increased, confirming that chlorides induce valence state transformation of oxides from FeII to FeIII, and the difference between the atomic structures of oxide film layers diminished.

  19. Fine structures at pore boundary

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  20. 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.

  1. Structural characterization of water and ice in mesoporous SBA-15 silicas IV: partially filled cases for 86 Å pore diameter

    NASA Astrophysics Data System (ADS)

    Seyed-Yazdi, J.; Dore, John C.; Webber, J. Beau W.; Farman, H.

    2013-11-01

    Previous papers in this series have involved the study of water/ice in a sample of a mesoporous SBA-15 silica with a pore size of 86 Å, filling-factors f of 1.15 and 0.95. The present paper extends the study to partially filled samples with f = 0.6 and 0.4. It is found that the ice formed in the pores has characteristics that differ markedly from those seen in the previous measurements. For f = 0.6, there is a significant amount of hexagonal ice, as seen by the presence of the normal ice triplet. For f = 0.4, the triplet peaks are not seen, indicating the predominant formation of cubic ice superimposed on a broad diffuse scattering peak that is attributed to a defective form of low-density amorphous ice. A parameter-fitting routine has been used (as previously) to extract the variation of the peak intensities and shapes with temperature. A separate component analysis procedure confirms these conclusions and emphasizes the role of plastic ice in the phase conversion process for the 260-200 K temperature region. A comparison of the liquid phase data for filling-factors of 0.4 and 0.95 indicates that the structural characteristics of the water vary according to the thickness of the layer, as suggested by computer predictions.

  2. Metal structures with parallel pores

    NASA Technical Reports Server (NTRS)

    Sherfey, J. M.

    1976-01-01

    Four methods of fabricating metal plates having uniformly sized parallel pores are studied: elongate bundle, wind and sinter, extrude and sinter, and corrugate stack. Such plates are suitable for electrodes for electrochemical and fuel cells.

  3. 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

  4. 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.

  5. Fabrication and electrical characterization of a pore-cavity-pore device

    NASA Astrophysics Data System (ADS)

    Pedone, D.; Langecker, M.; Münzer, A. M.; Wei, R.; Nagel, R. D.; Rant, U.

    2010-11-01

    We present a solid state nanopore device structure comprising two nanopores which are stacked above each other and connected via a pyramidal cavity of 10 fl volume. The process of fabrication of the pore-cavity-pore device (PCP) relies on the formation of one pore in a Si3N4 membrane by electron beam lithography, while the other pore is chemically etched into the Si carrier by a feedback controlled process. The dimensions of the two nanopores as well as the cavity can be adjusted independently, which is confirmed by transmission electron microscopy. The PCP device is characterized with respect to its electrical properties, including noise analysis and impedance spectroscopy. An equivalent circuit model is identified and resistance, capacitance, and dielectric loss factors are obtained. Potential and electric field distributions inside the electrically biased device are simulated by finite element methods. The low noise characteristics of the PCP device (comparable to a single solid state nanopore) make it suitable for the stochastic sensing of single molecules; moreover, the pore-cavity-pore architecture allows for novel kinds of experiments including the trapping of single nano-objects and single molecule time-of-flight measurements.

  6. 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.

  7. 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).

  8. 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.

  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. [Characterizing Structural Composition of Dissolved and Particulate Organic Matter from Sediment Pore Water in a Urban River Using Excitation-Emission Matrix Fluorescence with Self-Organizing Map].

    PubMed

    Yu, Hui-bin; Song, Yong-hui; Yang, Nan; Du, Er-deng; Peng, Jian-feng; Zhi, Er-quan

    2015-04-01

    Excitation-emission matrix (EEM) fluorescence with self-organizing map was applied to characterize structural composition and spatial distribution of dissolved (DOM) and particulate (POM) organic matter from sediment pore water in a typical urban river. Ten sediment pore water samples were collected from the mainstream of Baitabuhe River in Shenyang City of northeast China, along a human impact gradient, i. e. river source, rural and urban regions. DOM and POM were extracted from the pore water, and their EEM fluorescence spectra were measured. ƒ450/500 of DOM ranged from 1.82 to 1.91, indicating that DOM is mainly from microbial source; ƒ450/500 of POM ranged from 1.42 to 1.68, suggesting that POM derived from land. Four components were identified from DOM and POM fractions by self-organizing map, which included tyrosine-like, tryptophan-like, fulvic-like and humic-like matters. Tyrosine-like originated from fresh and less-degraded material with a high potential for oxida- tion, which was considered as representative components of DOM and POM. Tryptophan-like was associated with microbial byproduct-like material, and can indicate microbial activities. The abundance sum of all components in DOM is roughly 2 times more than that in POM. The mean relative abundance of tyrosine-like was more than 50%, while tryptophan-like was about 18.6%-23.1%. Abundance of fulvic-like was much more than that of humic-like, but they were only a small proportion of organic matter fractions. Based on principal component analysis, the characteristics of DOM and POM distinctly were distributed along river source, rural region and urban region, proving that the river was deeply influenced by human activity. PMID:26197578

  11. 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.

  12. Pore Structure Reconstruction and Moisture Migration in Porous Media

    NASA Astrophysics Data System (ADS)

    Zheng, Jiayi; Shi, Xing; Shi, Juan; Chen, Zhenqian

    2014-09-01

    Three kinds of porous media (isotropic, perpendicular anisotropic and parallel anisotropic porous media) with the same porosity, different pore size distributions and fractal spectral dimensions were reconstructed by random growth method. It was aimed to theoretically study the impact of microscopic pore structure on water vapor diffusion process in porous media. The results show that pore size distribution can only denote the static characteristics of porous media but cannot effectively reflect the dynamic transport characteristics of porous media. Fractal spectral dimension can effectively analyze and reflect pores connectivity and moisture dynamic transport properties of porous media from the microscopic perspective. The pores connectivity and water vapor diffusion performance in pores of porous media get better with the increase of fractal spectral dimension of porous media. Fractal spectral dimension of parallel anisotropic porous media is more than that of perpendicular anisotropic porous media. Fractal spectral dimension of isotropic porous media is between parallel anisotropic porous media and perpendicular anisotropic porous media. Other macroscopic parameters such as equilibrium diffusion coefficient of water vapor, water vapor concentration variation at right boundary in equilibrium, the time when water vapor diffusion process reaches a stable state also can characterize the pores connectivity and water vapor diffusion properties of porous media.

  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.

  15. Structural Insights into Clostridium perfringens Delta Toxin Pore Formation

    PubMed Central

    Huyet, Jessica; Naylor, Claire E.; Savva, Christos G.; Gibert, Maryse; Popoff, Michel R.; Basak, Ajit K.

    2013-01-01

    Clostridium perfringens Delta toxin is one of the three hemolysin-like proteins produced by C. perfringens type C and possibly type B strains. One of the others, NetB, has been shown to be the major cause of Avian Nectrotic Enteritis, which following the reduction in use of antibiotics as growth promoters, has become an emerging disease of industrial poultry. Delta toxin itself is cytotoxic to the wide range of human and animal macrophages and platelets that present GM2 ganglioside on their membranes. It has sequence similarity with Staphylococcus aureus β-pore forming toxins and is expected to heptamerize and form pores in the lipid bilayer of host cell membranes. Nevertheless, its exact mode of action remains undetermined. Here we report the 2.4 Å crystal structure of monomeric Delta toxin. The superposition of this structure with the structure of the phospholipid-bound F component of S. aureus leucocidin (LukF) revealed that the glycerol molecules bound to Delta toxin and the phospholipids in LukF are accommodated in the same hydrophobic clefts, corresponding to where the toxin is expected to latch onto the membrane, though the binding sites show significant differences. From structure-based sequence alignment with the known structure of staphylococcal α-hemolysin, a model of the Delta toxin pore form has been built. Using electron microscopy, we have validated our model and characterized the Delta toxin pore on liposomes. These results highlight both similarities and differences in the mechanism of Delta toxin (and by extension NetB) cytotoxicity from that of the staphylococcal pore-forming toxins. PMID:23805259

  16. 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.

  17. Nanometer to Centimeter Scale Analysis and Modeling of Pore Structures

    NASA Astrophysics Data System (ADS)

    Wesolowski, D. J.; Anovitz, L.; Vlcek, L.; Rother, G.; Cole, D. R.

    2011-12-01

    The microstructure and evolution of pore space in rocks is a critically important factor controlling fluid flow. The size, distribution and connectivity of these confined geometries dictate how fluids including H2O and CO2, migrate into and through these micro- and nano-environments, wet and react with the solid. (Ultra)small-angle neutron scattering and autocorrelations derived from BSE imaging provide a method of quantifying pore structures in a statistically significant manner from the nanometer to the centimeter scale. Multifractal analysis provides additional constraints. These methods were used to characterize the pore features of a variety of potential CO2 geological storage formations and geothermal systems such as the shallow buried quartz arenites from the St. Peter Sandstone and the deeper Mt. Simon quartz arenite in Ohio as well as the Eau Claire shale and mudrocks from the Cranfield MS CO2 injection test and the normal temperature and high-temperature vapor-dominated parts of the Geysers geothermal system in California. For example, analyses of samples of St. Peter sandstone show total porosity correlates with changes in pores structure including pore size ratios, surface fractal dimensions, and lacunarity. These samples contain significant large-scale porosity, modified by quartz overgrowths, and neutron scattering results show significant sub-micron porosity, which may make up fifty percent or more of the total pore volume. While previous scattering data from sandstones suggest scattering is dominated by surface fractal behavior, our data are both fractal and pseudo-fractal. The scattering curves are composed of steps, modeled as polydispersed assemblages of pores with log-normal distributions. In some samples a surface-fractal overprint is present. There are also significant changes in the mono and multifractal dimensions of the pore structure as the pore fraction decreases. There are strong positive correlations between D(0) and image and total

  18. Application of low-voltage field-emission SEM to the study of internal pore structures of activated carbon

    SciTech Connect

    Liu, J.; Ornberg, R.L.

    1996-12-31

    Activated carbon has interesting and useful properties for industrial applications. It has been used extensively in purification, separation, chemical recovery and catalysis. To achieve a predictable performance of activated carbon materials, it is necessary to develop a comprehensive understanding of the pore structure including pore size, pore shape, and pore surface chemistry. Macropores (> 50 nm), mesopores (2-50 nm) and micropores (< 2 nm) generally coexist in activated carbon. It is thus desirable to synthesize activated carbon with controlled pore structures to optimize its performance. We previously reported the characterization of the surface pore structure of activated carbon by field emission SEM (FESEM) and the examination of the internal pore structure by HAADF/HRTEM techniques. However, both HAADF and HRTEM techniques give only limited information about the carbon pore structure. We report here some preliminary observation of the internal pore structure of activated carbon by high resolution low voltage FESEM technique.

  19. Structural characterization of water and ice in mesoporous SBA-15 silicas IV: partially filled cases for 86 Å pore diameter.

    PubMed

    Seyed-Yazdi, J; Dore, John C; Webber, J Beau W; Farman, H

    2013-11-20

    Previous papers in this series have involved the study of water/ice in a sample of a mesoporous SBA-15 silica with a pore size of 86 Å, filling-factors f of 1.15 and 0.95. The present paper extends the study to partially filled samples with f = 0.6 and 0.4. It is found that the ice formed in the pores has characteristics that differ markedly from those seen in the previous measurements. For f = 0.6, there is a significant amount of hexagonal ice, as seen by the presence of the normal ice triplet. For f = 0.4, the triplet peaks are not seen, indicating the predominant formation of cubic ice superimposed on a broad diffuse scattering peak that is attributed to a defective form of low-density amorphous ice. A parameter-fitting routine has been used (as previously) to extract the variation of the peak intensities and shapes with temperature. A separate component analysis procedure confirms these conclusions and emphasizes the role of plastic ice in the phase conversion process for the 260-200 K temperature region. A comparison of the liquid phase data for filling-factors of 0.4 and 0.95 indicates that the structural characteristics of the water vary according to the thickness of the layer, as suggested by computer predictions.

  20. Structural characterization of water and ice in mesoporous SBA-15 silicas IV: partially filled cases for 86 Å pore diameter.

    PubMed

    Seyed-Yazdi, J; Dore, John C; Webber, J Beau W; Farman, H

    2013-11-20

    Previous papers in this series have involved the study of water/ice in a sample of a mesoporous SBA-15 silica with a pore size of 86 Å, filling-factors f of 1.15 and 0.95. The present paper extends the study to partially filled samples with f = 0.6 and 0.4. It is found that the ice formed in the pores has characteristics that differ markedly from those seen in the previous measurements. For f = 0.6, there is a significant amount of hexagonal ice, as seen by the presence of the normal ice triplet. For f = 0.4, the triplet peaks are not seen, indicating the predominant formation of cubic ice superimposed on a broad diffuse scattering peak that is attributed to a defective form of low-density amorphous ice. A parameter-fitting routine has been used (as previously) to extract the variation of the peak intensities and shapes with temperature. A separate component analysis procedure confirms these conclusions and emphasizes the role of plastic ice in the phase conversion process for the 260-200 K temperature region. A comparison of the liquid phase data for filling-factors of 0.4 and 0.95 indicates that the structural characteristics of the water vary according to the thickness of the layer, as suggested by computer predictions. PMID:24132016

  1. 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

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

    PubMed

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

    2016-01-01

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

  3. Correlation between gas permeability and pore structure of coal matrix

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Yang, J.; Gao, F.; Li, Y.; Niu, H.; Gao, H.

    2012-04-01

    The sequestration of CO2 in unminable coal seams represents a promising option for CO2 geologic storage, because the injected CO2 may enhance coalbed methane recovery (CO2-ECBM), which could partly offset the costs of the storage process. The CO2-ECBM technology is based on the relative affinity of CO2 and CH4 to coals under given pressure and temperature conditions. The excess sorption capacity of coals for CO2 is generally higher than the sorption capacity for methane. The coal seams are characterized by a dual porosity structure including cleat and matrix pores. The cleats in the coal seams are considered as highways for gas and water flow, while the matrix is the storage location of gas by adsorption. The slow transport process of gas in coal matrix may constrain the efficiency of the displacement of CH4 by CO2 due to the compacted pore structure of the coal matrix. Therefore, a detailed understanding of the correlation between permeability of gas and pore structure in coal matrix is crucial for the CO2-ECBM processes. Yangquan coals originating from the Qingshui basin, which contains gas-rich coals in China, were selected for the tests in this study. Yangquan coals are classified as anthracite. In order to avoid the influence of coal cleats on fluid flow, small coal plugs (~6 mm in diameter, ~13 mm in length) were selected and fixed in the sample compartment by special glue. A test system for simultaneously measuring adsorption-porosity-permeability on the coal matrix blocks in its free state is constructed. The permeability of gas and porosity in coal plugs to He under different gas pressure and temperature conditions were simultaneously investigated. The permeability and excess sorption capacity of the coal plugs to He, N2, CH4 and CO2 were compared at a constant gas pressure and temperature. It is expected that gas break through a cleat-plug is much faster than that through a coal matrix-plug. Different sample plugs with the different pore structure results

  4. 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

  5. Characterisation of pore structures in nanoporous materials for advanced bionanotechnology.

    PubMed

    Heo, K; Yoon, J; Jin, K S; Jin, S; Ree, M

    2006-08-01

    Porous materials are potential candidates for applications in various fields, such as bionanotechnology, gas separation, catalysts and micro-electronics. In particular, their applications in bionanotechnology include biosensors, biomedical implants and microdevices, biosupporters, bio-encapsules, biomolecule separations and biomedical therapy. All these bionanotechnology applications utilise the shape, size and size distribution of pores in porous materials. Therefore the controlled creation of pores with desired shape, size and size distribution is most important in the development of nanoporous materials. Accordingly, the accurate evaluation of pore structure is necessary in the development of nanoporous materials and their applications. This article reviews recent developments in analytical techniques to characterise the pore structures of nanoporous materials.

  6. 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

  7. 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.

  8. 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

  9. Pore structure of single-wall carbon nanohorn aggregates

    NASA Astrophysics Data System (ADS)

    Murata, K.; Kaneko, K.; Kokai, F.; Takahashi, K.; Yudasaka, M.; Iijima, S.

    2000-11-01

    Single-wall carbon nanohorn aggregates were characterized by N 2 adsorption at 77 K and `particle density' measurement using the high pressure He buoyancy method. The single-wall carbon nanohorn aggregate had micropores and its pore volume was 0.11 ml g -1. The particle density was 1.25 g ml -1. The particle density was not equal to the solid density of graphite (2.27 g ml -1) , but it agreed within 15% with the density of the single-wall carbon nanohorn estimated using previous TEM data. Hence single-wall carbon nanohorns have closed micropores covered with single graphene walls. According to N 2 adsorption, single-wall carbon nanohorns have a considerably large surface area (308 m2 g-1) and open microporosity which has been ascribed to the inter-particle aggregate structure, the so-called ` dahlia flower type structure'.

  10. 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.

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

    PubMed Central

    Zhao, Haitao; Xiao, Qi; Huang, Donghui

    2014-01-01

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

  12. Pore Structure and the Low Frequency Permittivity of Sea Ice

    NASA Astrophysics Data System (ADS)

    O'Sadnick, M.; Ingham, M.; Eicken, H.

    2014-12-01

    Field and laboratory measurements of the dielectric permittivity of first-year sea ice both show that below a frequency of about 10 Hz the real part of the relative permittivity (ɛ') increases with decreasing frequency. Field measurements in Barrow, Alaska and McMurdo Sound suggest that this rise in low frequency ɛ' steepens as the ice warms, and is confined primarily to the upper 0.50m of the ice cover as it approaches maximum thickness. We propose that this behaviour may be related to membrane polarization occurring in the pore structure within the ice. With ice-liquid interfaces carrying a net charge, an electric double layer forms within the brine filled pores. Polarization occurs at grain boundaries, intragranular films and "necks" in the pore structure where the effective thickness of the double layer approaches the width of the pore resulting in differential transport of ions. This process is dependent on both the characteristic lengths and radii of pores relative to the length and radii of the "necks" or the geometry of inter/intragranular brine layers. By representing the measured dielectric permittivity in terms of a Cole-Cole model it is possible to show that the distribution of pore sizes evolves with temperature. Derived values of complex conductivity are also examined in relationship to the temporal evolution of pore geometry including smoothness of the pore-ice interface.

  13. 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.

  14. Nitrocellulose Templated Hierarchical Pore Structure in Mesoporous Thin Films

    SciTech Connect

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

    2006-01-01

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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

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

    PubMed

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

    2015-06-01

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

  1. Pore-structure models of hydraulic conductivity for permeable pavement

    NASA Astrophysics Data System (ADS)

    Kuang, X.; Sansalone, J.; Ying, G.; Ranieri, V.

    2011-03-01

    SummaryPermeable pavement functions as a porous infrastructure interface allowing the infiltration and evaporation of rainfall-runoff while functioning as a relatively smooth load-bearing surface for vehicular transport. Hydraulic conductivity ( k) of permeable pavement is an important hydraulic property and is a function of the pore structure. This study examines k for a cementitious permeable pavement (CPP) through a series of pore-structure models. Measurements utilized include hydraulic head as well as total porosity, ( ϕ t), effective porosity ( ϕ e), tortuosity ( L e/ L) and pore size distribution (PSD) indices generated through X-ray tomography (XRT). XRT results indicate that the permeable pavement pore matrix is hetero-disperse, with high tortuosity and ϕ t ≠ ϕ e. Power law models of k- ϕ t and k- ϕ e relationships are developed for a CPP mix design. Results indicate that the Krüger, Fair-Hatch, Hazen, Slichter, Beyer and Terzaghi models based on simple pore-structure indices do not reproduce measured k values. The conventional Kozeny-Carman model (KCM), a more parameterized pore-structure model, did not reproduce measured k values. This study proposes a modified KCM utilizing ϕ e, specific surface area (SSA) pe and weighted tortuosity ( L e/ L) w. Results demonstrate that such permeable pavement pore-structure parameters with the modified KCM can predict k. The k results are combined with continuous simulation modeling using historical rainfall to provide nomographs examining permeable pavement as a low impact development (LID) infrastructure component.

  2. Probing the pore wall structure of nanoporous carbons using adsorption.

    PubMed

    Nguyen, Thanh X; Bhatia, Suresh K

    2004-04-27

    Hitherto, adsorption has been traditionally used to study only the porous structure in disordered materials, while the structure of the solid phase skeleton has been probed by crystallographic methods such as X-ray diffraction. Here we show that for carbons density functional theory, suitably adapted to consider heterogeneity of the pore walls, can be reliably used to probe features of the solid structure hitherto accessibly only approximately even by crystallographic methods. We investigate a range of carbons and determine pore wall thickness distributions using argon adsorption, with results corroborated by X-ray diffraction.

  3. 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.

  4. 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.

  5. 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).

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    1996-12-01

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

  20. 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.

  1. 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

  2. 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).

  3. 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.

  4. 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.

  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. 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.

  7. Fabrication of Silicon Nitride Ceramics with Pore Gradient Structure

    SciTech Connect

    Zhang Lianmeng; Chen Fei; Shen Qiang; Yan Faqiang

    2008-02-15

    In the present study, Si{sub 3}N{sub 4} ceramics with pore gradient structure were prepared by spark plasma sintering (SPS) technique. Silicon nitride ceramics with different controlled porosities were prepared by using ZrP{sub 2}O{sub 7} as a binder material and heat treated at 1100 deg. C in a pressureless nitrogen atmosphere. Si{sub 3}N{sub 4} ceramics with controlled porosity of 34-47% were obtained. The distribution of porous structure was homogenous. Fully dense Si{sub 3}N{sub 4} ceramics could be sintered at 1400{approx}1600 deg. C by using MgO and alumina Al{sub 2}O{sub 3} as the sintering aids. Pore gradient structure was formed by laminating the Si{sub 3}N{sub 4} porous ceramics and powder mixture was used to obtain fully dense ceramics, and then sintering at 1400-1600 deg. C. Microstructure of sintered samples was observed by scanning electronic microscope (SEM) and the change of phase compositions was analyzed by X-ray diffraction (XRD). The results showed that these samples exhibited a good porous graded structure with a highly porous layer and a dense surface layer. The major phase of the Si{sub 3}N{sub 4} ceramics was still {alpha} phase.

  8. [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

  9. 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

  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.

  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. 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

  13. 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

  14. 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

  15. Synthesis and study on pore structure of SiO2/Al2O3 aerogel

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    In the current paper, the mixed SiO2/Al2O3 aerogel was synthesized by sol-gel method with subcritical drying and characterized. Tetraethoxysilane was used as a precursor of silicon sol. The flower-shaped alumina suspension was peptized to produce alumina sol. The aerogel texture, morphology, and structure were determined using scanning electron microscopy, X-ray diffraction, low-temperature nitrogen adsorption, and high-resolution spectroscopy. A special attention was paid to the pore structure of aerogel, and aerogel framework was formed by the spherical agglomerates containing spherical particles of silicon oxide and alumina nanopetals. The pore size distribution was bimodal with peaks of 5.5 nm and 77 nm.

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. A specific two-pore domain potassium channel blocker defines the structure of the TASK-1 open pore.

    PubMed

    Streit, Anne K; Netter, Michael F; Kempf, Franca; Walecki, Magdalena; Rinné, Susanne; Bollepalli, Murali K; Preisig-Müller, Regina; Renigunta, Vijay; Daut, Jürgen; Baukrowitz, Thomas; Sansom, Mark S P; Stansfeld, Phillip J; Decher, Niels

    2011-04-22

    Two-pore domain potassium (K(2P)) channels play a key role in setting the membrane potential of excitable cells. Despite their role as putative targets for drugs and general anesthetics, little is known about the structure and the drug binding site of K(2P) channels. We describe A1899 as a potent and highly selective blocker of the K(2P) channel TASK-1. As A1899 acts as an open-channel blocker and binds to residues forming the wall of the central cavity, the drug was used to further our understanding of the channel pore. Using alanine mutagenesis screens, we have identified residues in both pore loops, the M2 and M4 segments, and the halothane response element to form the drug binding site of TASK-1. Our experimental data were used to validate a K(2P) open-pore homology model of TASK-1, providing structural insights for future rational design of drugs targeting K(2P) channels.

  3. 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

  4. Crystal structure of a voltage-gated K+ channel pore module in a closed state in lipid membranes.

    PubMed

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

    2012-12-14

    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.

  5. 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

  6. Pore formation by antimicrobial peptides: structural tendencies in bulk and quasi-2D membrane systems

    NASA Astrophysics Data System (ADS)

    Gordon, Vernita; Yang, Lihua; Davis, Matthew; Som, A.; Tew, G.; Wong, Gerard

    2007-03-01

    Antimicrobial peptides are cationic, amphiphilic structures that are key components of innate immunity. A prototypical family of synthetic analogs are the phenylene ethynylene antimicrobial oligomers (AMOs), which have hydrophobic alkyl chains connected to cationic hydrophilic regions. Synchrotron small-angle x-ray scattering (SAXS) shows that when AMO is mixed with concentrated model membranes, initially in the form of Small Unilamellar Vesicles, the sample forms the inverted hexagonal phase. This is a 3-dimensional phase characterized by a regular array of size-defined water channels. We demonstrate how this structural tendency is expressed when AMOs interact with dilute model membranes in the form of Giant Unilamellar Vesicles (GUVs). Using confocal microscopy, we see that applying AMO to the GUVs causes small encapsulated molecules to be released while large molecules are retained, indicating that size-defined pores have been created. Examining the partial release of polydisperse intermediately-sized molecules allows a closer measurement of the pore size, and there are indications that this single-vesicle microscopy will allow elucidation of the kinetics of the pore-forming process.

  7. Synthesis and characterization of mesoporous ZnS with narrow size distribution of small pores

    NASA Astrophysics Data System (ADS)

    Nistor, L. C.; Mateescu, C. D.; Birjega, R.; Nistor, S. V.

    2008-08-01

    Pure, nanocrystalline cubic ZnS forming a stable mesoporous structure was synthesized at room temperature by a non-toxic surfactant-assisted liquid liquid reaction, in the 9.5 10.5 pH range of values. The appearance of an X-ray diffraction (XRD) peak in the region of very small angles (˜ 2°) reveals the presence of a porous material with a narrow pore size distribution, but with an irregular arrangement of the pores, a so-called worm hole or sponge-like material. The analysis of the wide angle XRD diffractograms shows the building blocks to be ZnS nanocrystals with cubic structure and average diameter of 2 nm. Transmission electron microscopy (TEM) investigations confirm the XRD results; ZnS crystallites of 2.5 nm with cubic (blende) structure are the building blocks of the pore walls with pore sizes from 1.9 to 2.5 nm, and a broader size distribution for samples with smaller pores. Textural measurements (N2 adsorption desorption isotherms) confirm the presence of mesoporous ZnS with a narrow range of small pore sizes. The relatively lower surface area of around 100 m2/g is attributed to some remaining organic molecules, which are filling the smallest pores. Their presence, confirmed by IR spectroscopy, seems to be responsible for the high stability of the resulting mesoporous ZnS as well.

  8. Rock-fabric/petrophysical classification of carbonate pore space for reservoir characterization

    SciTech Connect

    Lucia, F.J.

    1995-09-01

    This paper defines the important geologic parameters that can be described and mapped to allow accurate petrophysical quantification of carbonate geologic models. All pore space is divided into interparticle (intergrain and intercrystal) and vuggy pores. In nonvuggy carbonate rocks, permeability and capillary properties can be described in terms of particle size, sorting, and interparticle porosity (total porosity minus vuggy porosity). Particle size and sorting in limestones can be described using a modified Dunham approach, classifying packstone as grain dominated or mud dominated, depending on the presence or absence of intergrain pore space. To describe particle size and sorting in dolostones, dolomite crystal size must be added to the modified Dunham terminology. Larger dolomite crystal size improves petrophysical properties in mud-dominated fabrics, wheras variations in dolomite crystal size have little effect on the petrophysical properties of grain-dominated fabrics. A description of vuggy pore space that relates to petrophysical properties must be added to the description of interparticle pore space to complete the petrophysical characterization. Vuggy pore space is divided into separate vugs and touching vugs on the basis of vug interconnection. Separate vugs are fabric selective and are connected only through the interparticle pore network. Separate vug porosity contributes little to permeability and should be subtracted from total porosity to obtain interparticle porosity for permeability estimation. Separate-vug pore space is generally considered to by hydrocarbon filled in reservoirs; however, intragranular microporosity is composed of small pore sizes and may contain capillary-held connate water within the reservoir. Touching vugs are nonfabric selective and form an interconnected pore system independent of the interparticle system.

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

    PubMed

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

    2009-09-01

    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 alpha helix and a decrease in beta structure in pore formation. Spectral changes caused by a deletion mutation support the hypothesis that the 2beta2-2beta3 loop transforms into the transmembrane segment of the beta-barrel stem of the pore. Changes caused by selected point mutations indicate that the transition to alpha structure is dependent on residues of the luminal 2beta11-2beta12 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.

  10. 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.

  11. 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

  12. Characterizing 3-D flow velocity in evolving pore networks driven by CaCO3 precipitation and dissolution

    NASA Astrophysics Data System (ADS)

    Chojnicki, K. N.; Yoon, H.; Martinez, M. J.

    2015-12-01

    Understanding reactive flow in geomaterials is important for optimizing geologic carbon storage practices, such as using pore space efficiently. Flow paths can be complex in large degrees of geologic heterogeneities across scales. In addition, local heterogeneity can evolve as reactive transport processes alter the pore-scale morphology. For example, dissolved carbon dioxide may react with minerals in fractured rocks, confined aquifers, or faults, resulting in heterogeneous cementation (and/or dissolution) and evolving flow conditions. Both path and flow complexities are important and poorly characterized, making it difficult to determine their evolution with traditional 2-D transport models. Here we characterize the development of 3-D pore-scale flow with an evolving pore configuration due to calcium carbonate (CaCO3) precipitation and dissolution. A simple pattern of a microfluidic pore network is used initially and pore structures will become more complex due to precipitation and dissolution processes. At several stages of precipitation and dissolution, we directly visualize 3-D velocity vectors using micro particle image velocimetry and a laser scanning confocal microscope. Measured 3-D velocity vectors are then compared to 3-D simulated flow fields which will be used to simulate reactive transport. Our findings will highlight the importance of the 3-D flow dynamics and its impact on estimating reactive surface area over time. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114.

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Sheng, Yangping

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

  16. The role of pore structure on char reactivity. Quarterly progress report, October 1994--December 1994

    SciTech Connect

    Sarofim, A.F.

    1995-01-01

    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 soot 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 modeled.

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

    PubMed

    Nikoofard, Narges; Mashaghi, Alireza

    2016-02-28

    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.

  18. 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.

  19. Primary structure analysis of an integral membrane glycoprotein of the nuclear pore

    PubMed Central

    1989-01-01

    The complete primary structure of an integral membrane glycoprotein of the nuclear pore was deduced from the cDNA sequence. The cDNA encodes a polypeptide of 204,205 D containing a 25-residue-long signal sequence, two hydrophobic segments that could function as transmembrane segments, and 13 potential N-linked oligosaccharide addition sites. Endoglycosidase H reduces the molecular mass by approximately 9 kD suggesting that not all of these 13 sites are used. We discuss possible models for the topology of this protein in the pore membrane as well as a possible role in the formation of pores and pore complexes. PMID:2738089

  20. Neutron scattering in the plane of membranes: structure of alamethicin pores.

    PubMed Central

    He, K; Ludtke, S J; Worcester, D L; Huang, H W

    1996-01-01

    A technique of neutron in-plane scattering for studying the structures of peptide pores in membranes is described. Alamethicin in the inserted state was prepared and undeuterated and deuterated dilauroyl phosphatidylcholine (DLPC) hydrated with D2O or H2O. Neutron in-plane scattering showed a strong dependence on deuteration, clearly indicating that water is a part of the high-order structure of inserted alamethicin. The data are consistent with the simple barrel-stave model originally proposed by Baumann and Mueller. The theoretical curves computed with this model at four different deuteration conditions agree with the data in all cases. Both the diameter of the water pore and the effective outside diameter of the channel are determined accurately. Alamethicin forms pores in a narrow range of size. In a given sample condition, > 70% of the peptide forms pores of n and n +/- 1 monomers. The pore size varies with hydration and with lipid. In DLPC, the pores are made of n = 8-9 monomers, with a water pore approximately 18 A in diameter and with an effective outside diameter of approximately 40 A. In diphytanoyl phosphatidylcholine, the pores are made of n approximately 11 monomers, with a water pore approximately 26 A in diameter, with an effective outside diameter of approximately 50 A. Images FIGURE 1 PMID:8744303

  1. Three-dimensional structure of the anthrax toxin pore inserted into lipid nanodiscs and lipid vesicles

    PubMed Central

    Katayama, H.; Wang, J.; Tama, F.; Chollet, L.; Gogol, E. P.; Collier, R. J.; Fisher, M. T.

    2010-01-01

    A major goal in understanding the pathogenesis of the anthrax bacillus is to determine how the protective antigen (PA) pore mediates translocation of the enzymatic components of anthrax toxin across membranes. To obtain structural insights into this mechanism, we constructed PA-pore membrane complexes and visualized them by using negative-stain electron microscopy. Two populations of PA pores were visualized in membranes, vesicle-inserted and nanodisc-inserted, allowing us to reconstruct two virtually identical PA-pore structures at 22-Å resolution. Reconstruction of a domain 4-truncated PA pore inserted into nanodiscs showed that this domain does not significantly influence pore structure. Normal mode flexible fitting of the x-ray crystallographic coordinates of the PA prepore indicated that a prominent flange observed within the pore lumen is formed by the convergence of mobile loops carrying Phe427, a residue known to catalyze protein translocation. Our results have identified the location of a crucial functional element of the PA pore and documented the value of combining nanodisc technology with electron microscopy to examine the structures of membrane-interactive proteins. PMID:20142512

  2. 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.

  3. 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.

  4. 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.

  5. 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.

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

    PubMed Central

    Park, In; Pinnavaia, Thomas J.

    2009-01-01

    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 m2/g) and pore volumes (0.5–2.0 cm3/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

  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.

  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. Porosity, permeability, and pore structure of the tight Mesa Verde sandstone, Piceance Basin, CO

    SciTech Connect

    Soeder, D.J.; Randolph, P.L.

    1984-09-01

    Special core analyses on 44 tight Mesa Verde sandstone samples from the U.S. DOE Multiwell Experiment were combined with petrographic investigations in an attempt to relate the porosity and permeability of the cores to the pore structure of the rocks. Core analysis was performed on one inch (2.54 cm) diameter horizontal plug samples using a computerized steady-state flow measuring device. This equipment routinely measures flow rates with a resolution of better than 10/sup -6/ cm/sup 3//sec. All samples were selected from intervals expected to be gas productive on the basis of wireline well logs, and were taken from the portion of the interval that showed the lowest gamma ray log response. The core plugs were measured for dry permeability to gas, relative permeability at various water saturations, porosity to gas, and pore volume compressibility. Petrographic samples were taken directly off the plug ends and were analyzed with both an optical microscope and a scanning electron microscope. The petrographic study was explicitly directed toward observing the flow paths and pore structure that had been deduced from the core analysis data. Petrographic observations revealed that the pore geometry of sandstone can be broken down into three categories: grain-supported pores, solution pores connected by narrow intergranular slots (the most common pore structure in the Mesa Verde) and matrix supported grains. Core analysis measurements correlated fairly well with pore geometry. Solution pores connected by slots varied by a factor of two in porosity and pore volume compressibility; the dry permeability values fell within the range of 0.1 to 10.0 microdarcies. Calculation of slot-like flow path dimensions from the permeability data revealed a characteristic width of only about 0.1 micron. Special core analysis of the Mesa Verde also showed trends that correlated with various depositional environments in the formation.

  11. Investigation of the Effect of the Tortuous Pore Structure on Water Diffusion through a Polymer Film Using Lattice Boltzmann Simulations.

    PubMed

    Gebäck, Tobias; Marucci, Mariagrazia; Boissier, Catherine; Arnehed, Johan; Heintz, Alexei

    2015-04-23

    Understanding how the pore structure influences the mass transport through a porous material is important in several applications, not the least in the design of polymer film coatings intended to control drug release. In this study, a polymer film made of ethyl cellulose and hydroxypropyl cellulose was investigated. The 3D structure of the films was first experimentally characterized using confocal laser scanning microscopy data and then mathematically reconstructed for the whole film thickness. Lattice Boltzmann simulations were performed to compute the effective diffusion coefficient of water in the film and the results were compared to experimental data. The local porosities and pore sizes were also analyzed to determine how the properties of the internal film structure affect the water effective diffusion coefficient. The results show that the top part of the film has lower porosity, lower pore size, and lower connectivity, which results in a much lower effective diffusion coefficient in this part, largely determining the diffusion rate through the entire film. Furthermore, the local effective diffusion coefficients were not proportional to the local film porosity, indicating that the results cannot be explained by a single tortuosity factor. In summary, the proposed methodology of combining microscopy data, mass transport simulations, and pore space analysis can give valuable insights on how the film structure affects the mass transport through the film.

  12. 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.

  13. 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

  14. Characterization and investigation of the deformation behavior of porous magnesium scaffolds with entangled architectured pore channels.

    PubMed

    Jiang, Guofeng; Li, Qiuyan; Wang, Cunlong; Dong, Jie; He, Guo

    2016-12-01

    We report a kind of porous magnesium with entangled architectured pore structure for potential applications in biomedical implant. The pore size, spatial structure and Young׳s modulus of the as-prepared porous Mg are suitable for bone tissue engineering applications. Particularly, with regard to the load-bearing conditions, a new analytical model is employed to investigate its structure and mechanical response under compressive stress based on Gibson-Ashby model. It is found that there are three types of stress-strain behaviors in the large range of porosity from 20% to 80%. When the porosity is larger than an upper critical value, the porous magnesium exhibits densifying behavior with buckling deformation mechanism. When the porosity is smaller than a lower critical value, the porous magnesium exhibits shearing behavior with cracking along the maximum shear stress. Between the two critical porosities, both the buckling deformation and shearing behavior coexist. The upper critical porosity is experimentally determined to be 60% for 270μm pore size and 62% for 400μm pore size, while the lower critical porosity is 40% for 270μm pore size and 42% for 400μm pore size. A new analytical model could be used to accurately predict the mechanical response of the porous magnesium. No matter the calculated critical porosity or yielding stress in a large range of porosity by using the new model are well consistent with the experimental values. All these results could help to provide valuable data for developing the present porous magnesium for potential bio applications. PMID:27498424

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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)

  20. 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.

  1. 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)

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

    SciTech Connect

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

    2013-04-15

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

  3. Charge substitution for a deep-pore residue reveals structural dynamics during BK channel gating.

    PubMed

    Chen, Xixi; Aldrich, Richard W

    2011-08-01

    The pore-lining amino acids of ion channel proteins reside on the interface between a polar (the pore) and a nonpolar environment (the rest of the protein). The structural dynamics of this region, which physically controls ionic flow, are essential components of channel gating. Using large-conductance, Ca(2+)-dependent K(+) (BK) channels, we devised a systematic charge-substitution method to probe conformational changes in the pore region during channel gating. We identified a deep-pore residue (314 in hSlo1) as a marker of structural dynamics. We manipulated the charge states of this residue by substituting amino acids with different valence and pKa, and by adjusting intracellular pH. We found that the charged states of the 314 residues stabilized an open state of the BK channel. With models based on known structures of related channels, we postulate a dynamic rearrangement of the deep-pore region during BK channel opening/closing, which involves a change of the degree of pore exposure for 314.

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  6. 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).

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

  8. 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

  9. 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.

  10. 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.

  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.

  12. 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

  13. Predicting the permeability of sandstone from image analysis of pore structure

    NASA Astrophysics Data System (ADS)

    Lock, Peter A.; Jing, Xudong; Zimmerman, Robert W.; Schlueter, Erika M.

    2002-11-01

    A model is developed that allows accurate prediction of the permeability of a core sample of sedimentary rock, based on two-dimensional image analysis of its pore structure. The pore structure is idealized as consisting of a cubic network of pore tubes, with the tubes having an arbitrary distribution of cross-sectional areas and shapes. The areas and perimeters of the individual pores are estimated from image analysis of scanning electron micrographs of thin sections, with appropriate stereological corrections introduced to account for the angle between axis of the pore tube and plane of the thin section. The individual conductances of each tube are estimated from the measured areas and perimeters, using the hydraulic radius approximation. Variations in the pore diameter along the length of the tube are accounted for with a "constriction factor" whose derivation is based on laminar flow through an irregular tube. Effective-medium theory is used to find the effective single-tube conductance, based on the measured distribution of individual conductances. This procedure is applied to several consolidated North Sea reservoir sandstones, and some outcrop sandstones, with permeabilities ranging from 20 to 1400 mD. The predicted permeabilities are typically within a factor of 2 of the measured values, with an average error in logk of only 0.168.

  14. 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.

  15. Correlation between structure and mass distribution of the nuclear pore complex and of distinct pore complex components

    PubMed Central

    1990-01-01

    Nuclear pore complexes (NPCs) prepared from Xenopus laevis oocyte nuclear envelopes were studied in "intact" form (i.e., unexposed to detergent) and after detergent treatment by a combination of conventional transmission electron microscopy (CTEM) and quantitative scanning transmission electron microscopy (STEM). In correlation- averaged CTEM pictures of negatively stained intact NPCs and of distinct NPC components (i.e., "rings," "spoke" complexes, and "plug- spoke" complexes), several fine structural features arranged with octagonal symmetry about a central axis could reproducibly be identified. STEM micrographs of unstained/freeze-dried intact NPCs as well as of their components yielded comparable but less distinct features. Mass determination by STEM revealed the following molecular masses: intact NPC with plug, 124 +/- 11 MD; intact NPC without plug, 112 +/- 11 MD; heavy ring, 32 +/- 5 MD; light ring, 21 +/- 4 MD; plug- spoke complex, 66 +/- 8 MD; and spoke complex, 52 +/- 3 MD. Based on these combined CTEM and STEM data, a three-dimensional model of the NPC exhibiting eightfold centrosymmetry about an axis perpendicular to the plane of the nuclear envelope but asymmetric along this axis is proposed. This structural polarity of the NPC across the nuclear envelope is in accord with its well-documented functional polarity facilitating mediated nucleocytoplasmic exchange of molecules and particles. PMID:2324201

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Yoon, H.; Dewers, T. A.

    2012-12-01

    Accurate prediction of coupled geophysical and chemical processes at the pore scale requires realistic representation of pore structures. This is especially true for chalk materials, where pore networks are small and complex, and often characterized at sub-micron scale. Common techniques such as X-ray microtomography, microscopic imaging, or mercury intrusion porosimetry often show a limit on determining pore throat distributions and seal analysis of such fine-grained rocks. Focused ion beam-scanning electron microscope (FIB-SEM) and laser scanning confocal microscopy methods are used for 3D imaging of nanometer-to-micron scale microcrack and pore distributions in samples of the Cretaceous Selma Group Chalk. The Selma Chalk is considered the seal for oil and gas fields in the Mississippi Interior Salt Basin and a proposed regional-scale seal identified for CO2 sequestration sites. A series of image analysis techniques is used to process raw images in order to recover both nano-scale pore structure and continuous fracture networks. We apply 3D imaging techniques in interpreting FIB-SEM binary data for characterizing geometric pore body and throat distributions and other topological properties, and lattice-Boltzmann method (LBM) for obtaining permeability at several different scales. In particular, comparison of primary flow paths obtained from 3D image analysis and LBM demonstrates that image analysis results may have too many equally plausible flow paths, compared to LBM results. Upscaling of permeability and LB multiphase flow results with image dataset will be discussed with emphasis on understanding microfracture-matrix interaction during multiphase flow, and seal analysis for geologic CO2 storage. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114

  18. Changes of the local pore space structure quantified in heterogeneous porous media by 1H magnetic resonance relaxation tomography

    NASA Astrophysics Data System (ADS)

    Borgia, G. C.; Bortolotti, V.; Fantazzini, P.

    2001-08-01

    Magnetic resonance imaging and relaxation analysis are combined in a spatially resolved technique (relaxation tomography), which is able to quantify the parameters connected to the local structure in the internal regions of a porous material saturated by water, giving information on the pore space structure beyond the nominal instrumental resolution. Voxel-by-voxel longitudinal (T1) and transverse (T2) relaxation curves are acquired in order to obtain T1, T2 and S(0) maps, where S(0) is the extrapolation to zero time of the total equilibrium magnetization corrected for T2 decay. The proposed method permits evaluation of the porosity (ratio of pore space to total volume), at different length scales, from the sample to the voxel, not all achievable by traditional methods. More striking is its ability to describe how porosity is shared among different classes of surface-to-volume ratios of diffusion cells (the regions that the individual water molecules, starting at their particular positions, can experience by diffusion before relaxing). This is a consequence of the fact that relaxation times of water confined in a porous material can, under favorable circumstances, distinguish regions with the same local porosity but with different pore sizes and connections. So, parameters can be introduced, such as the microporosity fraction, defined as the fraction of the "micropore" volume with respect to the total pore volume, and several voxel average porosities, defined as the average porosities of the voxels characterized by particular classes of diffusion cells. Moreover, the imaging methods enable us to get all this information in a user-defined region of interest. The method has been applied to quantify changes in the structure of carbonate cores with wide distributions of pore sizes induced by repeated cycles of freezing and heating of the sample. With freezing, the microporosity fraction decreases significantly; the voxel average porosity of voxels with T1 shorter than

  19. 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.

  20. 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

  1. 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.

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

    SciTech Connect

    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.

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

    SciTech Connect

    2000-07-11

    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.

  4. Pore structure and function of synthetic nanopores with fixed charges: tip shape and rectification properties.

    PubMed

    Ramírez, Patricio; Apel, Pavel Yu; Cervera, Javier; Mafé, Salvador

    2008-08-01

    We present a complete theoretical study of the relationship between the structure (tip shape and dimensions) and function (selectivity and rectification) of asymmetric nanopores on the basis of previous experimental studies. The theoretical model uses a continuum approach based on the Nernst-Planck equations. According to our results, the nanopore transport properties, such as current-voltage (I-V) characteristics, conductance, rectification ratio, and selectivity, are dictated mainly by the shape of the pore tip (we have distinguished bullet-like, conical, trumpet-like, and hybrid shapes) and the concentration of pore surface charges. As a consequence, the nanopore performance in practical applications will depend not only on the base and tip openings but also on the pore shape. In particular, we show that the pore opening dimensions estimated from the pore conductance can be very different, depending on the pore shape assumed. The results obtained can also be of practical relevance for the design of nanopores, nanopipettes, and nanoelectrodes, where the electrical interactions between the charges attached to the nanostructure and the mobile charges confined in the reduced volume of the inside solution dictate the device performance in practical applications. Because single tracks are the elementary building blocks for nanoporous membranes, the understanding and control of their individual properties should also be crucial in protein separation, water desalination, and bio-molecule detection using arrays of identical nanopores.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  7. 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.

  8. 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.

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

    PubMed

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

    2008-04-16

    A "brick-and-mortar" assembly approach for creating porous carbon and carbon/metal oxide fibers on the micron scale with well-defined pore structure and interface is presented. A series of monodisperse silica@polyacrylonitrile (PAN) and silica@metal oxide@PAN core/shell particles were synthesized by emulsion polymerization and assembled into organic-inorganic composite fibers through a simple ice-templating strategy with the assistance of polyvinyl alcohol. Porous carbon and carbon/metal oxide fibers with well-controlled pores and interfaces were created by oxidative stabilization and carbonization of composite fibers followed by removal of silica cores with hydrofluoric acid or concentrated alkali. The pore structure and the carbon/metal oxide interfaces of the fibers impart to the fibers' lightweight and potential applications in catalysis, electrochemical energy, and gas or liquid separations and storage. PMID:18355006

  10. 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

  11. 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.

  12. 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.

  13. Proton Conduction in Sulfonated Organic-Inorganic Hybrid Monoliths with Hierarchical Pore Structure.

    PubMed

    von der Lehr, Martin; Seidler, Christopher F; Taffa, Dereje H; Wark, Michael; Smarsly, Bernd M; Marschall, Roland

    2016-09-28

    Porous organic-inorganic hybrid monoliths with hierarchical porosity exhibiting macro- and mesopores are prepared via sol-gel process under variation of the mesopore size. Organic moieties in the pore walls are incorporated by substituting up to 10% of the silicon precursor tetramethylorthosilicate with bisilylated benzene molecules. After functionalization with sulfonic acid groups, the resulting sulfonated hybrid monoliths featuring a bimodal pore structure are investigated regarding proton conduction depending on temperature and relative humidity. The hierarchical pore system and controlled mesopore design turn out to be crucial for sulfonation and proton conduction. These sulfonated hybrid hierarchical monoliths containing only 10% organic precursor exhibit higher proton conduction at different relative humidities than sulfonated periodic mesoporous organosilica made of 100% bisilylated precursors exhibiting solely mesopores, even with a lower concentration of sulfonic acid groups. PMID:27598017

  14. 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

  15. Proton Conduction in Sulfonated Organic-Inorganic Hybrid Monoliths with Hierarchical Pore Structure.

    PubMed

    von der Lehr, Martin; Seidler, Christopher F; Taffa, Dereje H; Wark, Michael; Smarsly, Bernd M; Marschall, Roland

    2016-09-28

    Porous organic-inorganic hybrid monoliths with hierarchical porosity exhibiting macro- and mesopores are prepared via sol-gel process under variation of the mesopore size. Organic moieties in the pore walls are incorporated by substituting up to 10% of the silicon precursor tetramethylorthosilicate with bisilylated benzene molecules. After functionalization with sulfonic acid groups, the resulting sulfonated hybrid monoliths featuring a bimodal pore structure are investigated regarding proton conduction depending on temperature and relative humidity. The hierarchical pore system and controlled mesopore design turn out to be crucial for sulfonation and proton conduction. These sulfonated hybrid hierarchical monoliths containing only 10% organic precursor exhibit higher proton conduction at different relative humidities than sulfonated periodic mesoporous organosilica made of 100% bisilylated precursors exhibiting solely mesopores, even with a lower concentration of sulfonic acid groups.

  16. 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.

  17. 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.

  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.

  19. Microporous metal organic framework [M2(hfipbb)2(ted)] (M=Zn, Co; H2hfipbb=4,4-(hexafluoroisopropylidene)-bis(benzoic acid); ted=triethylenediamine): Synthesis, structure analysis, pore characterization, small gas adsorption and CO2/N2 separation properties

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    Carbon dioxide is a greenhouse gas that is a major contributor to global warming. Developing methods that can effectively capture CO2 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 CO2 from power plant waste gases. In this work we report the synthesis, crystal structure analysis and pore characterization of two microporous MOF structures, [M2(hfipbb)2(ted)] (M=Zn (1), Co (2); H2hfipbb=4,4-(hexafluoroisopropylidene)-bis(benzoic acid); ted=triethylenediamine). The CO2 and N2 adsorption experiments and IAST calculations are carried out on [Zn2(hfipbb)2(ted)] under conditions that mimic post-combustion flue gas mixtures emitted from power plants. The results show that the framework interacts with CO2 strongly, giving rise to relatively high isosteric heats of adsorption (up to 28 kJ/mol), and high adsorption selectivity for CO2 over N2, making it promising for capturing and separating CO2 from CO2/N2 mixtures.

  20. 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.

  1. The investigation of gadolinium oxide porous structure and refinement of the pore size distribution based on the NLDFT-models

    NASA Astrophysics Data System (ADS)

    Mashkovtsev, Maxim A.; Botalov, Maxim S.; Smyshlyaev, Denis V.; Kasimova, Renata E.; Bereskina, Polina A.; Vereshchagin, Artem O.

    2016-09-01

    The study focuses on the characterization of gadolinium oxide surface by the method of low-temperature adsorption/desorption of nitrogen. The specific surface area of gadolinium oxide, the average pore diameter and fractal dimensions were determined. The refinement of the pore distribution was performed on the basis of the NLDFT model. It was shown that there were three kinds of pores with average sizes of 150, 300 and 600 Å.

  2. 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.

  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. Influence of Pore Structure on SIP Properties Deduced from Micro-Scale Modelling

    NASA Astrophysics Data System (ADS)

    Volkmann, Jan; Klitzsch, Norbert; Wiens, Eugen; Mohnke, Oliver

    2010-05-01

    In geophysics frequency dependent complex resistivity measurements are called Spectral Induced Polarization (SIP). In other fields this method is known as Impedance Spectroscopy. In the last two decades many empirical relations were proposed which relate the frequency dependent electrical properties of water saturated rocks to structural properties such as pore radius and inner surface area, or to hydraulic conductivity. Unfortunately, these relations are not universal; they apply only for specific rock types and water compositions. In order to quantify the influence of inner rock structure (as well as of electrochemical water and rock properties) on the frequency dependent electrical properties we model the charge transport processes at the pore space using Comsol Multiphysics. In the frequency domain the effect of Induced Polarization (IP) is characterised by a phase shift between a measured electric current and an alternating voltage applied to the ground. A possible origin of this behaviour particularly for nonconducting rock minerals can be seen in the membrane polarization model as proposed by Marshall and Madden. This model describes a system of electrolyte filled pores. Different mobilities of cations and anions in the small pores cause a membrane effect and thus an electrical polarization. We aim to find a more realistic way of modelling the membrane polarization effect than using the simple Marshall and Madden model. The electric double layer, the origin of the Induced Polarization effect, is caused by surface charges located at the electrolyte rock interface. Thus, the EDL as a boundary effect is accounted for by reduced ion mobilities at the inner surface area. The governing equations and boundary conditions for a system of larger and smaller pores with applied voltage are expressed in frequency domain using a time harmonic approach, the electric current is determined to obtain information about amplitude and phase of the complex resistivity. The

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

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

    PubMed

    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

  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. 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

  13. Blockers of VacA provide insights into the structure of the pore.

    PubMed Central

    Tombola, F; Del Giudice, G; Papini, E; Zoratti, M

    2000-01-01

    The cytotoxic effects of the Helicobacter pylori toxin VacA, an important etiogenic factor in human gastric diseases, are due to its ability to form anion-selective pores in target cell membranes. We have studied the inhibition of channel activity by 5-nitro-2-(3-phenylpropylamino) benzoic acid (NPPB) and 4, 4'-diisothiocyanatostilbene-2,2'-disulfonic acid (DIDS), representatives of two popular classes of chloride channel blockers, to gain information on the mechanism of blocking and on the unknown structure of the VacA pore. The data indicate that both compounds produce a fast block by binding to separate but mutually exclusive sites within the channel lumen. DIDS binds close to the pore opening on the side of protein insertion, whereas NPPB blocks at a position in the opposite half of the channel. Although DIDS reaches the blocking site by traveling along the lumen, inhibition by NPPB appears to involve mainly partition of the compound into the membrane, voltage-independent diffusion from it to the inhibitory position, and voltage-dependent exit. The data are consistent with a pore that can be more easily entered from the side of protein insertion than from the opposite end. PMID:10920018

  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. 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...

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

  17. 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.

  18. A Novel Approach to Estimate Iron Distribution Within Different Pore Domains of Structured Media.

    SciTech Connect

    Kamolpornwijit, Wiwat; Brooks, Scott C.; Kim, Y.; Scheibe, Timothy D.

    2007-11-25

    The success and long-term performance of bioremediation processes employing iron-reducing bacteria depends on several factors. A crucial factor is the availability of Fe(III) as an electron acceptor which may be dictated by both chemical (e.g., oxide mineralogy) and physical (distribution of Fe(III) in space) effects. The iron content of subsurface media usually is obtained through different extraction techniques performed in a well-mixed batch experiment. For structured media where preferential flow prevails over the matrix flow, however, the iron content determined from homogenized samples may not well represent the iron content available for microbial activity. Metal reducing bacteria may be physically excluded from a significant fraction of pores due to their sizes. In this study we performed Fe(III) oxide extraction on an intact core of saprolite where intact structure was preserved. An unsaturated flow setup was modified to allow the extraction of oxalate-extractable Fe(III) oxides under two pore tensions, 15 and 0 cm of water. The result suggested the existence of Fe(III) oxide distribution with its mass mainly contained within the finer pore domain of matrix potential larger than 15 cm. Less than 15.5% mass (an upper bound) of oxalate-extractable Fe (III) oxides were present in domains of pore tension less than 15 cm. Hence the use of extraction results from well mixed batch extraction techniques can overestimate the quantity of Fe(III) oxides accessible to bacteria in structured media. To the extent that Fe (III) oxide minerals play an important role in contaminant biogeochemistry and solute transport, the distribution of Fe(III) oxides in structured subsurface media are critical to our understanding of these processes.

  19. 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.

  20. 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

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

    2016-07-13

    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.

  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. Self-assembly of hybrid dendrons with complex primary structure into functional helical pores.

    PubMed

    Percec, Virgil; Smidrkal, Jan; Peterca, Mihai; Mitchell, Catherine M; Nummelin, Sami; Dulcey, Andrés E; Sienkowska, Monika J; Heiney, Paul A

    2007-01-01

    The synthesis of three libraries of self-assembling hybrid dendrons containing a primary structure based on the sequence (4-3,4-3,5)12G2-CO(2)CH(3) generated from benzyl ether, biphenyl-4-methyl ether, and AB(2) repeat units constructed from (AB)(y)--AB(2) combinations of benzyl ethers, is reported. The structural and retrostructural analysis of their supramolecular dendrimers facilitated the discovery of new architectural principles that lead to the assembly of functional helical pores. The self-assembly of an example of hybrid dendron containing -H, -CO(2)CH(3), -CH(2)OH, -COOH, -COOK, -CONH(2), -CONHCH(3), -CO(2)(CH(2))(2)OCH(3), -(R) and -(S)-CONHCH(CH(3))C(2)H(5) as X-groups at the apex demonstrated that these self-assembling dendrons provide the simplest strategy for the design and synthesis of porous columns containing a diversity of hydrophilic and hydrophobic functional groups in the inner part of the pore. The results reported here expand the scope and limitations of dendrons available for the self-assembly of functional pores that previously were generated mostly from dendritic dipeptides, to simpler architectures based on hybrid dendrons. PMID:17304597

  11. 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.

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

    PubMed Central

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

    2014-01-01

    The transport of cargo across the nuclear membrane is highly selective and accomplished by a poorly understood mechanism involving hundreds of nucleoporins lining the inside of the nuclear pore complex (NPC). Currently, there is no clear picture of the overall structure formed by this collection of proteins within the pore, primarily due to their disordered nature. We perform coarse-grained simulations of both individual nucleoporins and grafted rings of nups mimicking the in vivo geometry of the NPC and supplement this with polymer brush modeling. Our results indicate that different regions or blocks of an individual NPC protein can have distinctly different forms of disorder and that this property appears to be a conserved functional feature. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture that can exist in distinct morphologies depending on the effective interaction energy between the phenylalanine glycine (FG) domains of different nups. Because the interactions between FG domains may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability. PMID:24806932

  13. 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

  14. 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

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

    NASA Astrophysics Data System (ADS)

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

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

  16. Structure, Dynamics, Evolution, and Function of a Major Scaffold Component in the Nuclear Pore Complex

    PubMed Central

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

    2013-01-01

    Summary The nuclear pore complex, composed of proteins termed nucleoporins (Nups), is responsible for nucleocytoplasmic transport in eukaryotes. Nuclear pore complexes (NPCs) form an annular structure composed of the nuclear ring, cytoplasmic ring, a membrane ring, and two inner rings. Nup192 is a major component of the NPC’s inner ring. We report the crystal structure of Saccharomyces cerevisiae Nup192 residues 2–960 [ScNup192(2–960)], which adopts an α-helical fold with three domains (i.e., D1, D2, and D3). Small angle X-ray scattering and electron microscopy (EM) studies reveal that ScNup192(2–960) could undergo long-range transition between “open” and “closed” conformations. We obtained a structural model of full-length ScNup192 based on EM, the structure of ScNup192(2–960), and homology modeling. Evolutionary analyses using the ScNup192(2–960) structure suggest that NPCs and vesicle-coating complexes are descended from a common membrane-coating ancestral complex. We show that suppression of Nup192 expression leads to compromised nuclear transport and hypothesize a role for Nup192 in modulating the permeability of the NPC central channel. PMID:23499021

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

    PubMed

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

    2013-04-01

    The nuclear pore complex, composed of proteins termed nucleoporins (Nups), is responsible for nucleocytoplasmic transport in eukaryotes. Nuclear pore complexes (NPCs) form an annular structure composed of the nuclear ring, cytoplasmic ring, a membrane ring, and two inner rings. Nup192 is a major component of the NPC's inner ring. We report the crystal structure of Saccharomyces cerevisiae Nup192 residues 2-960 [ScNup192(2-960)], which adopts an α-helical fold with three domains (i.e., D1, D2, and D3). Small angle X-ray scattering and electron microscopy (EM) studies reveal that ScNup192(2-960) could undergo long-range transition between "open" and "closed" conformations. We obtained a structural model of full-length ScNup192 based on EM, the structure of ScNup192(2-960), and homology modeling. Evolutionary analyses using the ScNup192(2-960) structure suggest that NPCs and vesicle-coating complexes are descended from a common membrane-coating ancestral complex. We show that suppression of Nup192 expression leads to compromised nuclear transport and hypothesize a role for Nup192 in modulating the permeability of the NPC central channel. PMID:23499021

  18. 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.

  19. Development and validation of pore structure models for adsorption in activated carbons

    SciTech Connect

    Davies, G.M.; Seaton, N.A.

    1999-09-14

    Predicting adsorption over a range of operating conditions and the improvement of the adsorbent itself are two important aspects that arise in the industrial application of adsorption. Both of these aspects can be addressed using molecular simulation techniques in conjunction with an appropriate model of the internal structure of the adsorbent. The internal structure of activated carbons is particularly difficult to model due to the fact that the structure is only locally crystalline and that most of the void volumes within the structure have length scales comparable to small molecules. This paper presents a systematic method to develop suitable models of the internal structure that are based on networks of regularly shaped model pores. Important aspects that are addressed include the realism and consistency of the resulting models. The method is illustrated using the adsorption of pure methane and ethane, and binary mixtures of these components, over a wide range of operating conditions onto four activated carbons.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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'.

  5. 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

  6. Characterization of pore scale NAPL morphology in homogeneous sands as a function of grain size and NAPL dissolution.

    PubMed

    Cho, Jaehyun; Annable, Michael D

    2005-11-01

    In this study, we investigate pore scale morphology of nonaqueous phase liquids (NAPLs) trapped in different pore sizes using tracer techniques. Specific interfacial area and saturation of NAPL trapped in homogeneous sands were measured using the interfacial and partitioning tracer techniques. The observed NAPL-water interfacial areas increased in a log-linear fashion with decreasing sand grain size, but showed no clear trend with residual NAPL saturation formed in the various grain sizes. The measured values were used to calculate the NAPL morphology index, which characterizes the spatial NAPL distribution within the pore space. The NAPL morphology indices, increased exponentially with decreasing grain size, indicating that the NAPL becomes smaller, but more blobs. For a fixed grain size, the specific interfacial area and saturation of the NAPL were measured following changes caused by dissolution using alcohol. The observed interfacial areas showed a decrease linearly as a function of the NAPL saturation.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. Structural evolution of the membrane-coating module of the nuclear pore complex

    PubMed Central

    Liu, Xiaoping; Mitchell, Jana M.; Wozniak, Richard W.; Blobel, Günter; Fan, Jie

    2012-01-01

    The coatomer module of the nuclear pore complex borders the cylinder-like nuclear pore-membrane domain of the nuclear envelope. In evolution, a single coatomer module increases in size from hetero-heptamer (Saccharomyces cerevisiae) to hetero-octamer (Schizosaccharomyces pombe) to hetero-nonamer (Metazoa). Notably, the heptamer–octamer transition proceeds through the acquisition of the nucleoporin Nup37. How Nup37 contacts the heptamer remained unknown. Using recombinant nucleoporins, we show that Sp-Nup37 specifically binds the Sp-Nup120 member of the hetero-heptamer but does not bind an Sc-Nup120 homolog. To elucidate the Nup37–Nup120 interaction at the atomic level, we carried out crystallographic analyses of Sp-Nup37 alone and in a complex with an N-terminal, ∼110-kDa fragment of Sp-Nup120 comprising residues 1–950. Corroborating structural predictions, we determined that Nup37 folds into a seven-bladed β-propeller. Several disordered surface regions of the Nup37 β-propeller assume structure when bound to Sp-Nup120. The N-terminal domain of Sp-Nup1201–950 also folds into a seven-bladed propeller with a markedly protruding 6D–7A insert and is followed by a contorted helical domain. Conspicuously, this 6D–7A insert contains an extension of 50 residues which also is highly conserved in Metazoa but is absent in Sc-Nup120. Strikingly, numerous contacts with the Nup37 β-propeller are located on this extension of the 6D–7A insert. Another contact region is situated toward the end of the helical region of Sp-Nup1201–950. Our findings provide information about the evolution and the assembly of the coatomer module of the nuclear pore complex. PMID:23019579

  16. 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.

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

    PubMed

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

    2008-11-01

    In the present work, we propose the use of the Laser Scanning Confocal Microscopy (LSCM) to determine the effect of water repellents on rock's pore-network configuration and interconnection. The rocks studied are sandstones of Miocene age, a building material that is commonly found in the architectural heritage of Tunisia. The porosity quantitative data of treated and untreated samples, obtained by mercury porosimetry tests, were compared. The results show a slight decrease in total porosity with the water repellent treatment, which reduced both microporosity and macroporosity. This reduction produced a modification in pore size distribution and a shift of the pore access size mode interval toward smaller pore diameters (from the 30-40 microm to the 20-30 microm intervals). The water repellent was observed in SEM images as a continuous film coating grain surfaces; moreover, it was easily visualized in LSCM, by staining the water repellent with Epodye fluorochrome, and the coating thickness was straightforwardly measured (1.5-2 microm). In fact, the combination of mercury intrusion porosimetry data and LSCM observations suggests that the porosity reduction and the shift of the pore diameter mode were mainly due to the general reduction of pore diameters, but also to the plugging of the smallest pores (less than 3-4 microm in diameter) by the water repellent film. Finally, the LSCM technique enabled the reconstruction of 3D views of the water repellent coating film in the pore network, indicating that its distribution was uniform and continuous over the 100 microm thick sample. The LSCM imaging facilitates the integration and interpretation of mercury porosimetry and SEM data. PMID:18767050

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

    PubMed

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

    2015-05-20

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

  19. 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.

  20. 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

  1. Structural characterization of submerged granular packings

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  2. 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

  3. 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

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

    SciTech Connect

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

    2015-07-01

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

  5. 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

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

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  7. Active structural growth in central Taiwan in relationship to large earthquakes and pore-fluid pressures

    NASA Astrophysics Data System (ADS)

    Yue, Li-Fan

    Central Taiwan is subject to a substantial long-term earthquake risk with a population of five million and two disastrous earthquakes in the last century, the 1935 ML=7.1 Tuntzuchiao and 1999 Mw=7.6 Chi-Chi earthquakes. Rich data from these earthquakes combined with substantial surface and subsurface data accumulated from petroleum exploration form the basis for these studies of the growth of structures in successive large earthquakes and their relationships to pore-fluid pressures. Chapter 1 documents the structural context of the bedding-parallel Chelungpu thrust that slipped in the Chi-Chi earthquake by showing for this richly instrumented earthquake the close geometric relationships between the complex 3D fault shape and the heterogeneous coseismic displacements constrained by geodesy and seismology. Chapter 2 studies the accumulation of deformation by successive large earthquakes by studying the deformation of flights of fluvial terraces deposited over the Chelungpu and adjacent Changhua thrusts, showing the deformation on a timescale of tens of thousands of years. Furthermore these two structures, involving the same stratigraphic sequence, show fundamentally different kinematics of deformation with associated contrasting hanging-wall structural geometries. The heights and shapes of deformed terraces allowed testing of existing theories of fault-related folding. Furthermore terrace dating constrains a combined shortening rate of 37 mm/yr, which is 45% of the total Taiwan plate-tectonic rate, and indicates a substantial earthquake risk for the Changhua thrust. Chapter 3 addresses the long-standing problem of the mechanics of long-thing thrust sheets, such as the Chelungpu and Changhua thrusts in western Taiwan, by presenting a natural test for the classic Hubbert-Rubey hypothesis, which argues that ambient excess pore-fluid pressure substantially reduces the effective fault friction allowing the thrusts to move. Pore-fluid pressure data obtained from 76 wells

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

  11. Characterization of Two-pore Channel 2 (TPCN2)-mediated Ca2+ Currents in Isolated Lysosomes*

    PubMed Central

    Schieder, Michael; Rötzer, Katrin; Brüggemann, Andrea; Biel, Martin; Wahl-Schott, Christian A.

    2010-01-01

    Two-pore channels (TPCNs) have been proposed to form lysosomal Ca2+ release channels that are activated by nicotinic acid adenine dinucleotide phosphate. Here, we employ a glass chip-based method to record for the first time nicotinic acid adenine dinucleotide phosphate -dependent currents through a two-pore channel (TPCN2) from intact lysosomes. We show that TPCN2 is a highly selective Ca2+ channel that is regulated by intralysosomal pH. Using site-directed mutagenesis, we identify an amino acid residue in the putative pore region that is crucial for conferring high Ca2+ selectivity. Our glass chip-based method will provide electrophysiological access not only to lysosomal TPCN channels but also to a broad range of other intracellular ion channels. PMID:20495006

  12. Characterization of two-pore channel 2 (TPCN2)-mediated Ca2+ currents in isolated lysosomes.

    PubMed

    Schieder, Michael; Rötzer, Katrin; Brüggemann, Andrea; Biel, Martin; Wahl-Schott, Christian A

    2010-07-01

    Two-pore channels (TPCNs) have been proposed to form lysosomal Ca(2+) release channels that are activated by nicotinic acid adenine dinucleotide phosphate. Here, we employ a glass chip-based method to record for the first time nicotinic acid adenine dinucleotide phosphate -dependent currents through a two-pore channel (TPCN2) from intact lysosomes. We show that TPCN2 is a highly selective Ca(2+) channel that is regulated by intralysosomal pH. Using site-directed mutagenesis, we identify an amino acid residue in the putative pore region that is crucial for conferring high Ca(2+) selectivity. Our glass chip-based method will provide electrophysiological access not only to lysosomal TPCN channels but also to a broad range of other intracellular ion channels.

  13. Zymogen granule exocytosis is characterized by long fusion pore openings and preservation of vesicle lipid identity

    PubMed Central

    Thorn, Peter; Fogarty, Kevin E.; Parker, Ian

    2004-01-01

    The dynamics of the fusion pore that forms between a secretory vesicle and the plasma membrane are important in the regulation of both exocytosis and endocytosis. Here, we describe characteristics of fusion during zymogen granule exocytosis in exocrine pancreatic acinar cells. By using fluorescence recovery after photobleaching techniques, we show that the fusion pore remains open to allow free aqueous exchange with the vesicle lumen. There is no lipid interchange between the plasma and granule membranes during this time, and at the end of its life, the intact granule shrinks in situ, probably by a gradual pinching off of membrane patches. We propose that the protracted fusion pore lifetime is adapted to permit compound exocytosis, whereby the lingering primary granule acts as a conduit through which the contents of a secondary granule can be released. The lack of lipid intermixing may then facilitate selective recycling of granule membrane and preservation of apical membrane integrity. PMID:15090649

  14. Influence of pore structure on the effectiveness of a biogenic carbonate surface treatment for limestone conservation.

    PubMed

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

    2011-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Erdogan, S. T.

    2015-12-01

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

  16. Thermodynamics of a fluid confined to a slit pore with structured walls

    SciTech Connect

    Diestler, D.J. ); Schoen, M. ); Curry, J.E.; Cushman, J.H. )

    1994-06-15

    In this article we extend our previous thermodynamic analysis of films confined to slit pores with smooth walls (i.e., plane--parallel solid surfaces without molecular structure) to the situation in which the walls themselves possess structure. Structured-wall models are frequently employed to interpret experiments performed with the surface forces apparatus (SFA), in which thin films (1--10 molecular diameters thick) are subjected to shear stress by moving the walls laterally over one another at constant temperature, chemical potential, and normal stress or load. The periodic structure of the walls is reflected in a periodic variation of the shear stress with the lateral alignment (i.e., shear strain) of the walls. We demonstrate by means of a solvable two-dimensional model that the molecular length scale imposed by the structure of the walls precludes the derivation of a simple mechanical expression for the grand potential analogous to that which holds in the smooth-wall case. This conclusion is borne out by the results of a grand-canonical Monte Carlo simulation of the three-dimensional prototypal model consisting of a Lennard-Jones (12,6) fluid confined between fcc (100) walls. Criteria for the thermodynamic stability of thin films confined by structured walls are derived and applied to the SFA.

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

    SciTech Connect

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

    2015-10-27

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

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

    SciTech Connect

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

    2013-08-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  20. Rotaxane-Like Structures Threaded through the Pores of Hollow Porous Nanocapusles.

    PubMed

    Dergunov, Sergey A; Ehterami, Nasim; Pinkhassik, Eugene

    2016-09-26

    Nanocapsules with molecules threaded through the porous shells may lead to advanced cell-mimicking functional devices. Herein, we show the feasibility of synthesizing such hybrid nanostructures by using vesicle-templated polymer nanocapsules with controlled nanopores. Ship-in-a-bottle assembly inside a nanocapsule created an internal unit. An external unit was then connected to an entrapped internal unit through pre-attached linker threaded through a nanopore in the shell of the nanocapsule. Both internal and external units are larger than the pore size and cannot cross the shell, producing a rotaxane-like structure. Successful synthesis was achieved with fairly short linkers (six and ten carbon atoms in a chain), creating an opportunity for facile synthesis of functional devices capable of cross-shell communication. PMID:27471052

  1. Structure-assisted functional anchor implantation in robust metal-organic frameworks with ultralarge pores.

    PubMed

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

    2015-02-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

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

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

    PubMed Central

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Giliazetdinova, Dina; Korost, Dmitry; Gerke, Kirill

    2015-04-01

    Oil and gas generation is a complex superposition of processes which take place in the interiors and are not readily observable in nature in human life time-frames. During burial of the source rocks organic matter is transformed into a mixture of high-molecular compounds - precursors of oil and gas (kerogen). Specific thermobaric conditions trigger formation of low molecular weight hydrocarbon compounds. Generation of sufficient quantities of hydrocarbons leads to the primary fluid migration. For series of our experiments we selected mainly siliceous-carbonate composition shale rocks from Domanic horizon of South-Tatar arch. Rock samples were heated in the pyrolyzer to temperatures closely corresponding to different catagenesis stages. X-ray microtomography method was used to monitor changes in the morphology of the pore space within studied shale rocks. By routine measurements we made sure that all samples (10 in total) had similar composition of organic and mineral phases. All samples in the collection were grouped according to initial structure and amount of organics and processed separately to: 1) study the influence of organic matter content on the changing morphology of the rock under thermal effects; 2) study the effect of initial structure on the primary migration processes for samples with similar organic matter content. An additional experiment was conducted to study the dynamics of changes in the structure of the pore space and prove the validity of our approach. At each stage of heating the morphology of altered rocks was characterized by formation of new pores and channels connecting primary voids. However, it was noted that the samples with a relatively low content of the organic matter had less changes in pore space morphology, in contrast to rocks with a high organic content. Second part of the study also revealed significant differences in resulting pore structures depending on initial structure of the unaltered rocks and connectivity of original

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  7. Hierarchical pore structure of calcium phosphate scaffolds by a combination of gel-casting and multiple tape-casting methods.

    PubMed

    Sánchez-Salcedo, S; Werner, J; Vallet-Regí, M

    2008-07-01

    The objective of this work was to design hierarchical pore structure scaffolds with potential applications in bone tissue regeneration. For that purpose, a bioceramic material such as biphasic calcium phosphate, which consists of a mixture of hydroxyapatite and beta-tricalcium phosphate, was selected. Multilayer pieces (MLP) with hierarchical pore structure were developed employing a new technique that combines gel casting and adding porogens, using multiple tape-casting methods. Pieces with functionally graded porosity were fabricated using porogens with different sizes. The porogens used were Porlat K85 and Porlat K86 with diameters <150 microm and 150-300 microm, respectively. Two types of sintered tapes, with different porosity, no cracking and enough interconnection size were selected. MLP with hierarchical pore structure were designed by the multiple tape-casting method. Interconnected pores whose sizes increase from interior tapes (1.6-3.6 microm) towards exterior tapes (20-51.5 microm) and interpenetration between tapes were achieved. Delamination or cracking were not observed after heat treatment. The flexural strength of pieces was investigated by the three-point bending test. This new combination of methods offers the possibility of manufacturing scaffolds with interconnected pore sizes ranging from 1.6 to 51.5 microm.

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

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

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

  9. Precipitation and Dissolution of Uranyl Phosphates in a Microfluidic Pore Structure

    NASA Astrophysics Data System (ADS)

    Werth, C. J.; Fanizza, M.; Strathmann, T.; Finneran, K.; Oostrom, M.; Zhang, C.; Wietsma, T. W.; Hess, N. J.

    2011-12-01

    The abiotic precipitation of uranium (U(VI)) was evaluated in a microfluidic pore structure (i.e. micromodel) to assess the efficacy of using a phosphate amendment to immobilize uranium in groundwater and mitigate the risk of this contaminant to potential down-gradient receptor sites. U(VI) was mixed transverse to the direction of flow with hydrogen phosphate (HPO42-), in the presence or absence of calcium (Ca2+) or sulfate (SO42-), in order to identify precipitation rates, the morphology and types of minerals formed, and the stability of these minerals to dissolution with and without bicarbonate (HCO3-) present. Raman backscattering spectroscopy and micro X-ray diffraction (μ-XRD) results both showed that the only mineral precipitated was chernikovite (also known as hydrogen uranyl phosphate; UO2HPO4), even though the formation of other minerals were thermodynamically favored depending on the experimental conditions. Precipitation and dissolution rates varied with influent conditions. Relative to when only U(VI) and HPO42- were present, precipitation rates were 2.3 times slower when SO42- was present, and 1.4 times faster when Ca2+ was present. These rates were inversely related to the size of crystals formed during precipitation. Dissolution rates for chernikovite increased with increasing HCO3- concentrations, consistent with formation of uranyl carbonate complexes in aqueous solution, and they were the fastest for chernikovite formed in the presence of SO42-, and slowest for the chernikovite formed in the presence of Ca2+. These rates are related to the ratios of mineral-water interfacial area to mineral volume. Fluorescent tracer studies and laser confocal microscopy images showed that densely aggregated precipitates blocked pores and reduced permeability. The results suggest that changes in the solute conditions evaluated affect precipitation rates, crystal morphology, and crystal stability, but not mineral type.

  10. Microporous silica prepared by organic templating: Relationship between the molecular template and pore structure

    SciTech Connect

    Lu, Y.; Brinker, C.J. |; Cao, G.; Kale, R.P.; Prabakar, S.; Lopez, G.P.

    1999-05-01

    Microporous silica materials with a controlled pore size and a narrow pore size distribution have been prepared by sol-gel processing using an organic-templating approach. Microporous networks were formed by pyrolytic removal of organic ligands (methacryloxypropyl groups) from organic/inorganic hybrid materials synthesized by copolymerization of 3-methacryloxypropylsilane (MPS) and tetraethoxysilane (TEOS). Molecular simulations and experimental measurements were conducted to examine the relationship between the microstructural characteristics of the porous silica (e.g., pore size, total pore volume, and pore connectivity) and the size and amount of organic template ligands added. Adsorption measurements suggest that the final porosity of the microporous silica is due to both primary pores (those present in the hybrid material prior to pyrolysis) and secondary pores (those created by pyrolytic removal of organic templates). Primary pores were inaccessible to N{sub 2} at 77 K but accessible to CO{sub 2} at 195 K; secondary pores were accessible to both N{sub 2} (at 77 K) and CO{sub 2} (at 195 K) in adsorption measurements. Primary porosity decreases with the amount of organic ligands added because of the enhanced densification of MPS/TEOS hybrid materials as the mole fraction of trifunctional MPS moieties increases. Pore volumes measured by nitrogen adsorption experiments at 77 K suggest that the secondary (template-derived) porosity exhibits a percolation behavior as the template concentration is increased. Gas permeation experiments indicate that the secondary pores are approximately 5 {angstrom} in diameter, consistent with predictions based on molecular simulations.

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

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed

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

    2013-06-01

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

  14. Tomographic Analysis of Reactive Flow Induced Pore Structure Changes in Column Experiments

    SciTech Connect

    Cai, Rong; Lindquist, W.Brent; Um, Wooyong; Jones, Keith W.

    2009-09-23

    We utilize synchrotron X-ray computed microtomography to capture and quantify snapshots in time of dissolution and secondary precipitation in the microstructure of Hanford sediments exposed to simulated caustic waste in flow-column experiments. The experiment is complicated somewhat as logis- tics dictated that the column spent significant amounts of time in a sealed state (acting as a batch reactor). Changes accompanying a net reduction in porosity of 4% were quantified including: 1) a 25% net decrease in pores resulting from a 38% loss in the number of pores less than < 10-4 MM3 in volume and a 13% increase in the number of pores of larger size; and 2) a 38% decrease in the number of throats. The loss of throats resulted in de- creased coordination number for pores of all sizes and significant reduction in the number of pore pathways.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  18. Molecular and functional characterization of the p62 complex, an assembly of nuclear pore complex glycoproteins

    PubMed Central

    1996-01-01

    Macromolecular trafficking across the nuclear envelope involves interactions between cytosolic transport factors and nuclear pore complex proteins. The p62 complex, an assembly of 62, 58, 54, and 45-kD O-linked glycoproteins-localized near the central gated channel of the nuclear pore complex, has been directly implicated in nuclear protein import. The cDNA cloning of rat p62 was reported previously. We have now carried out cDNA cloning of rat p58, p54, and p45. We found that p58 contains regions with FG (Phe, Gly) and PA (Pro, Ala) repeats at both its NH2 and COOH termini separated by a predicted alpha-helical coiled-coil region, while p54 has an NH2-terminal FG and PA repeat region and a COOH-terminal predicted coiled-coil region. p45 and p58 appear to be generated by alternative splicing, with p45 containing the NH2-terminal FG repeat region and the coiled-coil region of p58. Using immunogold electron microscopy, we found that p58/p45 and p54 are localized on both sides of the nuclear pore complex, like p62. Previous studies have shown that immobilized recombinant p62 can bind the cytosolic nuclear import factor NTF2 and thereby deplete transport activity from cytosol. We have now found that immobilized recombinant p58 and p54 also can deplete nuclear transport activity from cytosol, and that p62, p58, and p54 bind directly to the cytosolic nuclear import factors p97 and NTF2. At least in the case of p58, this involves FG repeat regions. Moreover, p58 can bind to a complex containing transport ligand, the nuclear localization sequence receptor (Srp1 alpha) and p97. These data support a model in which the p62 complex binds to a multicomponent particle consisting of transport ligand and cytosolic factors to achieve accumulation of ligand near the central gated channel of the nuclear pore complex. PMID:8707840

  19. The Water Permeability and Pore Entrance Structure of Aquaporin-4 Depend on Lipid Bilayer Thickness.

    PubMed

    Tong, Jihong; Wu, Zhe; Briggs, Margaret M; Schulten, Klaus; McIntosh, Thomas J

    2016-07-12

    Aquaporin-4 (AQP4), the primary water channel in glial cells of the mammalian brain, plays a critical role in water transport in the central nervous system. Previous experiments have shown that the water permeability of AQP4 depends on the cholesterol content in the lipid bilayer, but it was not clear whether changes in permeability were due to direct cholesterol-AQP4 interactions or to indirect effects caused by cholesterol-induced changes in bilayer elasticity or bilayer thickness. To determine the effects resulting only from bilayer thickness, here we use a combination of experiments and simulations to analyze AQP4 in cholesterol-free phospholipid bilayers with similar elastic properties but different hydrocarbon core thicknesses previously determined by x-ray diffraction. The channel (unit) water permeabilities of AQP4 measured by osmotic-gradient experiments were 3.5 ± 0.2 × 10(-13) cm(3)/s (mean ± SE), 3.0 ± 0.3 × 10(-13) cm(3)/s, 2.5 ± 0.2 × 10(-13) cm(3)/s, and 0.9 ± 0.1 × 10(-13) cm(3)/s in bilayers containing (C22:1)(C22:1)PC, (C20:1)(C20:1)PC, (C16:0)(C18:1)PC, and (C13:0)(C13:0)PC, respectively. Channel permeabilities obtained by molecular dynamics (MD) simulations were 3.3 ± 0.1 × 10(-13) cm(3)/s and 2.5 ± 0.1 × 10(-13) cm(3)/s in (C22:1)(C22:1)PC and (C14:0)(C14:0)PC bilayers, respectively. Both the osmotic-gradient and MD-simulation results indicated that AQP4 channel permeability decreased with decreasing bilayer hydrocarbon thickness. The MD simulations also suggested structural modifications in AQP4 in response to changes in bilayer thickness. Although the simulations showed no appreciable changes to the radius of the pore located in the hydrocarbon region of the bilayers, the simulations indicated that there were changes in both pore length and α-helix organization near the cytoplasmic vestibule of the channel. These structural changes, caused by mismatch between the hydrophobic length of AQP4 and the bilayer hydrocarbon

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

    PubMed

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

    2016-04-01

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

  1. Templated synthesis of porous particles with tunable pore structures from nanoscale building blocks

    NASA Astrophysics Data System (ADS)

    Wu, Zhiwang

    Porous silica, carbon, titania and carbon/silica composite micro- or nano-materials have been synthesized by the templated self-assembly approaches through an aerosol-assisted process or hydrothermal technique. Porous silica particles with controllable hierarchical pore structure (from hexagonal to lamellar or hierarchical) have been prepared through tuning the hydrophilic and hydrophobic balance among silicate, cetyltrimethylammonium bromide (CTAB), and hydrophobic poly(propylene oxide) (PPO, H[OCH(CH 3)CH2nOH) additives during a dynamic aerosol-assisted process. Aerosol-assisted self-assembly of hollow silica microspheres with microporous shell (HSMMS) are prepared by utilizing the block copolymer F127's aggregating behavior in basic solution and the self-assembly between silicate and amphiphilic tetrapropylammonium hydroxide (TPAOH) molecules. Interactions of TPAOH with both F127 and silicate are necessary for avoiding the phase separation between silicate and F127 aggregates because of the lack of hydrogen bonding interactions. Therefore, F127 aggregates with various sizes act as the core template while TPAOH molecules or TPAOH aggregates formed by excessive TPAOH molecules stay in the silica shell. Removal of F127 and TPAOH by solvent extraction results in the HSMMS materials. Mesoporous carbon/silica composite with both meso- and molecular ordering has been synthesized by carbonization of as-synthesized phenylene/silica/surfactant hybrid by co-assembly of BTEB and Pluronic surfactant P123. Removal of silica from carbon/silica composite results in the mesoporous carbon which retains some of the meso-ordering and has many worm-like pores due to silica dissolution. This mesoporous carbon has potential applications in such field as hydrogen storage, catalysis, and other areas. Hollow carbon microspheres with micropores in the shell and carbon nanotubes on the outer surface have been prepared using resols as the carbon precursor and hydrophobic PPO additives as

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

    DOE PAGESBeta

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

    2015-07-01

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

  3. Selectivity Mechanism of the Nuclear Pore Complex Characterized by Single Cargo Tracking

    PubMed Central

    Lowe, Alan R.; Siegel, Jake J.; Kalab, Petr; Siu, Merek; Weis, Karsten; Liphardt, Jan T.

    2010-01-01

    The Nuclear Pore Complex (NPC) mediates all exchange between the cytoplasm and the nucleus. Small molecules can passively diffuse through the NPC, while larger cargos require transport receptors to translocate1. How the NPC facilitates the translocation of transport receptor/cargo complexes remains unclear. Here, we track single protein-functionalized Quantum Dot (QD) cargos as they translocate the NPC. Import proceeds by successive sub-steps comprising cargo capture, filtering and translocation, and release into the nucleus. The majority of QDs are rejected at one of these steps and return to the cytoplasm including very large cargos that abort at a size-selective barrier. Cargo movement in the central channel is subdiffusive and cargos that can bind more transport receptors diffuse more freely. Without Ran, cargos still explore the entire NPC, but have a markedly reduced probability of exit into the nucleus, suggesting that NPC entry and exit steps are not equivalent and that the pore is functionally asymmetric to importing cargos. The overall selectivity of the NPC appears to arise from the cumulative action of multiple reversible sub-steps and a final irreversible exit step. PMID:20811366

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

    SciTech Connect

    Misra, R.; Benson, S.A.

    1988-02-01

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

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

    SciTech Connect

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

    1998-05-01

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

  6. Pore Structure and Limit Pressure of Gas Slippage Effect in Tight Sandstone

    PubMed Central

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

    2013-01-01

    Gas slip effect is an important mechanism that the gas flow is different from liquid flow in porous media. It is generally considered that the lower the permeability in porous media is, the more severe slip effect of gas flow will be. We design and then carry out experiments with the increase of backpressure at the outlet of the core samples based on the definition of gas slip effect and in view of different levels of permeability of tight sandstone reservoir. This study inspects a limit pressure of the gas slip effect in tight sandstones and analyzes the characteristic parameter of capillary pressure curves. The experimental results indicate that gas slip effect can be eliminated when the backpressure reaches a limit pressure. When the backpressure exceeds the limit pressure, the measured gas permeability is a relatively stable value whose range is less than 3% for a given core sample. It is also found that the limit pressure increases with the decreasing in permeability and has close relation with pore structure of the core samples. The results have an important influence on correlation study on gas flow in porous medium, and are beneficial to reduce the workload of laboratory experiment. PMID:24379747

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

    PubMed

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

    2013-01-01

    Gas slip effect is an important mechanism that the gas flow is different from liquid flow in porous media. It is generally considered that the lower the permeability in porous media is, the more severe slip effect of gas flow will be. We design and then carry out experiments with the increase of backpressure at the outlet of the core samples based on the definition of gas slip effect and in view of different levels of permeability of tight sandstone reservoir. This study inspects a limit pressure of the gas slip effect in tight sandstones and analyzes the characteristic parameter of capillary pressure curves. The experimental results indicate that gas slip effect can be eliminated when the backpressure reaches a limit pressure. When the backpressure exceeds the limit pressure, the measured gas permeability is a relatively stable value whose range is less than 3% for a given core sample. It is also found that the limit pressure increases with the decreasing in permeability and has close relation with pore structure of the core samples. The results have an important influence on correlation study on gas flow in porous medium, and are beneficial to reduce the workload of laboratory experiment. PMID:24379747

  8. Surface area and pore structure properties of urethane-based copolymers containing β-cyclodextrin.

    PubMed

    Wilson, Lee D; Mohamed, Mohamed H; Headley, John V

    2011-05-01

    The surface area and pore structure characteristics were investigated for a series of aliphatic- and aromatic-based polyurethane (PU) copolymers containing a macromolecular porogen (β-cyclodextrin). The bi-functional diisocyanates used as crosslinker units were: 1,6-hexamethylene, 4,4'-dicyclohexylmethane, 4,4'-diphenylmethane, 1,4-phenylene, and 1,5-naphthalene diisocyanate, respectively. The macromolecular porogen content was controlled by fixing the composition of β-CD and varying the co-monomer mole ratio from unity to larger integer values. Nitrogen adsorption results reveal that copolymer materials with variable mole ratios (β-CD: crosslinker) from 1:1 to 1:3 displayed relatively low BET surface areas (SA∼10(1) m(2)/g) and mesopore diameters (∼16-29 nm). In contrast, a dye adsorption method in aqueous solution with p-nitrophenol (PNP) at pH=4.60 and 295 K provided estimates of the surface area (1.5-6.2×10(2) m(2)/g) for the corresponding copolymer materials. Variation of the copolymer SA was attributed to the type of diisocyanate crosslinker and its relative mole ratio. The differences in the estimated SA values from porosimetry and the UV-Vis dye adsorption method for these nanoporous copolymers were attributed to the role of solvent as evidenced by swelling of the copolymer framework in aqueous solution and the respective temperature conditions. PMID:21349528

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

    PubMed

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

    2013-01-01

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

  10. [Structure and function of pore-forming proteins from bacteria of the genus Yersinia: I. Isolation and a comparison of physicochemical properties and functional activity of Yersinia porins].

    PubMed

    Vostrikova, O P; Kim, N Iu; Likhatskaia, G N; Guzev, K V; Vakorina, T I; Khomenko, V A; Novikova, O D; Solov'eva, T F

    2006-01-01

    The molecular organization and functional activity of porins isolated from the outer membrane (OM) of the Yersinia enterocolitica and three phylogenetically close nonpathogenic Yersinia species (Y. intermedia, Y. kristensenii, and Y. frederiksenii) cultured at 6-8 degrees C were comparatively studied for the first time. The proteins were isolated in two molecular forms (trimeric and monomeric), and their spatial structures were characterized by the methods of optical spectroscopy, CD and intrinsic protein fluorescence. The studied porins were shown to belong to the beta-structural proteins (they have 59-96% total beta structures and 0-17% alpha helices). The spatial structures of the proteins were demonstrated to depend on the nature of the detergent used for solubilization. Unlike the enterobacterial pore-forming proteins, the porin trimers are less stable to sodium dodecyl sulfate (SDS). The spatial structures of the porins become more compact after the substitution of octyl beta-D-glucoside for SDS: the content of beta structures increases and the accessibility of Trp residues to solvent decreases. It was established with the use of the technique of bilayer lipid membranes that the functional properties of the porins are similar to those of the OmpF proteins of Gram-negative bacteria. Trimers are functionally active forms of the porins. Special features of the pore-forming activity of the Yersinia porins were revealed to depend on the microorganism species and the value of the membrane potential.

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

    PubMed

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

    2012-11-21

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

  12. Quantitative characterization of pore-scale disorder effects on transport in ``homogeneous'' granular media

    NASA Astrophysics Data System (ADS)

    Cortis, Andrea; Chen, Youjian; Scher, Harvey; Berkowitz, Brian

    2004-10-01

    Breakthrough curves (BTC) of a passive tracer in macroscopically homogeneous granular materials (well-sorted, unconsolidated sands or glass beads) were measured in a series of column experiments. The early and late arrival times are observed to differ systematically from theoretical predictions based on solution of the advective-dispersion equation for uniform porous media. We propose that subtle and residual pore-scale disorder effects in the porous media can account for these observations. We determine an ensemble-averaged distribution of particle transfer rates (based on a master equation for the local flux-averaged concentration) which incorporates these effects, and utilize it to calculate BTC that are in excellent agreement with the entire series of observations. Theoretical prediction of the dependence of the effective macroscopic parameters on measurable quantities is also in excellent agreement with the observations.

  13. Hierarchical structured Ni nanoring and hollow sphere arrays by morphology inheritance based on ordered through-pore template and electrodeposition.

    PubMed

    Duan, Guotao; Cai, Weiping; Luo, Yuanyuan; Li, Zhigang; Lei, Yong

    2006-08-17

    Fabrication of micro/nano-hierarchical Ni ordered nanostructured arrays is demonstrated by electrochemical deposition on the ordered alumina through-pore template induced by solution-dipping the colloidal monolayer. The morphology of the Ni nanostructured arrays exhibits a ringlike or hollow spherical structure depending on the template geometry and appropriate deposition parameters. The skeletons of the arrays are of floc- or flakelet-like fine structure on the nanoscale. The formation of such morphologies is attributed to the preferential growth along the inner wall of the alumina pores, while the nanoflakelet fine structure originates from a morphology inheritance process or the transitional product Ni(OH)2 which leads to the final nanostructured Ni crystals. This morphology inherence could be useful in the field of nanofabrication. Such micro/nano-hierarchically structured arrays show good magnetic properties and will find applications in the fields of catalysis, magnetics, optoelectrics, surface-enhanced Raman scattering (SERS), and new nanodevices.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  16. Structural Basis for Recognition of the Pore-Forming Toxin Intermedilysin by Human Complement Receptor CD59

    PubMed Central

    Johnson, Steven; Brooks, Nicholas J.; Smith, Richard A.G.; Lea, Susan M.; Bubeck, Doryen

    2013-01-01

    Summary Pore-forming proteins containing the structurally conserved membrane attack complex/perforin fold play an important role in immunity and host-pathogen interactions. Intermedilysin (ILY) is an archetypal member of a cholesterol-dependent cytolysin subclass that hijacks the complement receptor CD59 to make cytotoxic pores in human cells. ILY directly competes for the membrane attack complex binding site on CD59, rendering cells susceptible to complement lysis. To understand how these bacterial pores form in lipid bilayers and the role CD59 plays in complement regulation, we determined the crystal structure of human CD59 bound to ILY. Here, we show the ILY-CD59 complex at 3.5 Å resolution and identify two interfaces mediating this host-pathogen interaction. An ILY-derived peptide based on the binding site inhibits pore formation in a CD59-containing liposome model system. These data provide insight into how CD59 coordinates ILY monomers, nucleating an early prepore state, and suggest a potential mechanism of inhibition for the complement terminal pathway. PMID:23665225

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

    SciTech Connect

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

    2012-11-21

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  20. Characterization of a Ligand Binding Site in the Human Transient Receptor Potential Ankyrin 1 Pore

    PubMed Central

    Klement, Göran; Eisele, Lina; Malinowsky, David; Nolting, Andreas; Svensson, Mats; Terp, Gitte; Weigelt, Dirk; Dabrowski, Michael

    2013-01-01

    The pharmacology and regulation of Transient Receptor Potential Ankyrin 1 (TRPA1) ion channel activity is intricate due to the physiological function as an integrator of multiple chemical, mechanical, and temperature stimuli as well as differences in species pharmacology. In this study, we describe and compare the current inhibition efficacy of human TRPA1 on three different TRPA1 antagonists. We used a homology model of TRPA1 based on Kv1.2 to select pore vestibule residues available for interaction with ligands entering the vestibule. Site-directed mutation constructs were expressed in Xenopus oocytes and their functionality and pharmacology assessed to support and improve our homology model. Based on the functional pharmacology results we propose an antagonist-binding site in the vestibule of the TRPA1 ion channel. We use the results to describe the proposed intravestibular ligand-binding site in TRPA1 in detail. Based on the single site substitutions, we designed a human TRPA1 receptor by substituting several residues in the vestibule and adjacent regions from the rat receptor to address and explain observed species pharmacology differences. In parallel, the lack of effect on HC-030031 inhibition by the vestibule substitutions suggests that this molecule interacts with TRPA1 via a binding site not situated in the vestibule. PMID:23442958

  1. Characterization of a ligand binding site in the human transient receptor potential ankyrin 1 pore.

    PubMed

    Klement, Göran; Eisele, Lina; Malinowsky, David; Nolting, Andreas; Svensson, Mats; Terp, Gitte; Weigelt, Dirk; Dabrowski, Michael

    2013-02-19

    The pharmacology and regulation of Transient Receptor Potential Ankyrin 1 (TRPA1) ion channel activity is intricate due to the physiological function as an integrator of multiple chemical, mechanical, and temperature stimuli as well as differences in species pharmacology. In this study, we describe and compare the current inhibition efficacy of human TRPA1 on three different TRPA1 antagonists. We used a homology model of TRPA1 based on Kv1.2 to select pore vestibule residues available for interaction with ligands entering the vestibule. Site-directed mutation constructs were expressed in Xenopus oocytes and their functionality and pharmacology assessed to support and improve our homology model. Based on the functional pharmacology results we propose an antagonist-binding site in the vestibule of the TRPA1 ion channel. We use the results to describe the proposed intravestibular ligand-binding site in TRPA1 in detail. Based on the single site substitutions, we designed a human TRPA1 receptor by substituting several residues in the vestibule and adjacent regions from the rat receptor to address and explain observed species pharmacology differences. In parallel, the lack of effect on HC-030031 inhibition by the vestibule substitutions suggests that this molecule interacts with TRPA1 via a binding site not situated in the vestibule.

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

    SciTech Connect

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

    2004-03-15

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

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

    SciTech Connect

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

    2012-04-30

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

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

    NASA Astrophysics Data System (ADS)

    Kravchenko, Alexandra; Grandy, Stuart A.

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1998-10-01

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

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

    PubMed

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

    2014-07-20

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

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

    PubMed

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

    2014-07-20

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Bradshaw, Patrick C; Pfeiffer, Douglas R

    2013-12-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

    The nuclear pore complex (NPC) is an enormous proteinaceous complex composed of multiple copies of about 30 different proteins called nucleoporins. In this study, we analyzed the composition of the NPC in the model organism Schizosaccharomyces pombe using strains in which individual nucleoporins were tagged with GFP. We identified 31 proteins as nucleoporins by their localization to the nuclear periphery. Gene disruption analysis in previous studies coupled with gene disruption analysis in the present study indicates that 15 of these nucleoporins are essential for vegetative cell growth and the other 16 nucleoporins are non-essential. Among the 16 non-essential nucleoporins, 11 are required for normal progression through meiosis and their disruption caused abnormal spore formation or poor spore viability. Based on fluorescence measurements of GFP-fused nucleoporins, we estimated the composition of the NPC in S. pombe and found that the organization of the S. pombe NPC is largely similar to that of other organisms; a single NPC was estimated as being 45.8–47.8 MDa in size. We also used fluorescence measurements of single NPCs and quantitative western blotting to analyze the composition of the Nup107-Nup160 subcomplex, which plays an indispensable role in NPC organization and function. Our analysis revealed low amounts of Nup107 and Nup131 and high amounts of Nup132 in the Nup107-Nup160 subcomplex, suggesting that the composition of this complex in S. pombe may differ from that in S. cerevisiae and humans. Comparative analysis of NPCs in various organisms will lead to a comprehensive understanding of the functional architecture of the NPC. PMID:24637836

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

    PubMed

    Tian, Zhenghong; Bu, Jingwu

    2014-01-01

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

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

    PubMed Central

    Tian, Zhenghong; Bu, Jingwu

    2014-01-01

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

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

    SciTech Connect

    Sotirchos, S.V.

    1991-05-01

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

  15. Characterization and modeling of the stress and pore-fluid dependent acoustic properties of fractured porous rocks

    NASA Astrophysics Data System (ADS)

    Almrabat, Abdulhadi M.

    The thesis presents the results of a study of the characterization and modeling of the stress and pore-fluid dependent acoustic properties of fractured porous rocks. A new laboratory High Pressure and High Temperature (HPHT) triaxial testing system was developed to characterize the seismic properties of sandstone under different levels of effective stress confinement and changes in pore-fluid composition. An intact and fractured of Berea sandstones core samples were used in the experimental studies. The laboratory test results were used to develop analytical models for stress-level and pore-fluid dependent seismic velocity of sandstones. Models for stress-dependent P and S-wave seismic velocities of sandstone were then developed based on the assumption that stress-dependencies come from the nonlinear elastic response of micro-fractures contained in the sample under normal and shear loading. The contact shear stiffness was assumed to increase linearly with the normal stress across a micro-fracture, while the contact normal stiffness was assumed to vary as a power law with the micro-fracture normal stress. Both nonlinear fracture normal and shear contact models were validated by experimental data available in the literature. To test the dependency of seismic velocity of sandstone on changes in pore-fluid composition, another series of tests were conducted where P and S-wave velocities were monitored during injection of supercritical CO 2 in samples of Berea sandstone initially saturated with saline water and under constant confining stress. Changes in seismic wave velocity were measured at different levels of supercritical CO2 saturation as the initial saline water as pore-fluid was displaced by supercritical CO 2. It was found that the P- iv wave velocity significantly decreased while the S-wave velocity remained almost constant as the sample supercritical CO2 saturation increased. The dependency of the seismic velocity on changes on pore fluid composition during

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  17. Effects of steam activation on the pore structure and surface chemistry of activated carbon derived from bamboo waste

    NASA Astrophysics Data System (ADS)

    Zhang, Yan-Juan; Xing, Zhen-Jiao; Duan, Zheng-Kang; Li, Meng; Wang, Yin

    2014-10-01

    The effects of steam activation on the pore structure evolution and surface chemistry of activated carbon (AC) obtained from bamboo waste were investigated. Nitrogen adsorption-desorption isotherms revealed that higher steam activation temperatures and/or times promoted the creation of new micropores and widened the existing micropores, consequently decreasing the surface area and total pore volume. Optimum conditions included an activation temperature of 850 °C, activation time of 120 min, and steam flush generated from deionized water of 0.2 cm3 min-1. Under these conditions, AC with a BET surface area of 1210 m2 g-1 and total pore volume of 0.542 cm-3 g-1was obtained. Changes in surface chemistry were determined through Boehm titration, pH measurement, Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS). Results revealed the presence of a large number of basic groups on the surface of the pyrolyzed char and AC. Steam activation did not affect the species of oxygen-containing groups but changed the contents of these species when compared with pyrolyzed char. Scanning electron microscopy was used to observe the surface morphology of the products. AC obtained under optimum conditions showed a monolayer adsorption capacity of 330 mg g-1 for methylene blue (MB), which demonstrates its excellent potential for MB adsorption applications.

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

    NASA Astrophysics Data System (ADS)

    Xu, Dongchao; Zhao, Hongbo; Hao, Qing

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

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

    SciTech Connect

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

    2015-06-28

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

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

    SciTech Connect

    Sotirchos, S.V.

    1989-01-01

    A research program is proposed for the investigation of the dependence of the sorptive capacity of metal/metal oxide desulfurization sorbents on their pore size distribution and their intraparticle diffusivity. Integrated reaction/adsorption systems, chromatographic and gravimetric, will be used for successive reactivity, adsorption, and well as diffusivity, measurements. Single particle models that have been developed by our research group for gas-solid reactions with solid product will be used as basis for experimental data analysis and development of a general mathematical model for fixed-bed desulfurization and sorbent regeneration.

  1. A capillary network model for filter cake based on pore structure analysis

    SciTech Connect

    Miller, J.D.; Lin, C.L.

    1996-12-31

    Dewatering of fine coal by continuous filtration involves filter cake formation and removal of surface moisture by drawing air through the capillaries of the cake. In order to gain a better understanding of the complex transport phenomena that occur in the filter cake, analysis of the effect of three-dimensional pore geometry on the effective transport properties of the filter cake is necessary. This paper provides information on the techniques and methodology necessary to provide a detailed three-dimensional analysis of a completely interconnected porous system. In addition, a conceptual capillary network model based on a 3-D interconnected porous system is proposed.

  2. Assessment of material degradation considering the characteristics of its pore structure

    NASA Astrophysics Data System (ADS)

    Kočí, Jan; Černý, Robert

    2016-07-01

    In this paper a simple damage function for the relative assessment of the material degradation is presented. The damage function is based on the analysis of temperature and moisture content fields in the investigated material together with its pore size distribution function. In this way the relative assessment of frost induced damage can be provided. The application of the damage function is demonstrated on several wall assemblies exposed to several environmental loads in the Czech Republic and the comparison of weather year severity to the studied constructions is presented.

  3. Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex

    PubMed Central

    Kampmann, Martin; Blobel, Günter

    2009-01-01

    Summary The Nuclear Pore Complex (NPC) mediates nucleocytoplasmic transport in all eukaryotes and is among the largest cellular assemblies of proteins, collectively referred to as nucleoporins (nups). Nups are organized into distinct subcomplexes. We optimized the isolation of a putative membrane-coating subcomplex of the NPC, the heptameric Nup84 complex, and analyzed its structure by electron microscopy (EM). Our data confirm the previously reported Y-shape. We discerned additional structural details, including specific hinge regions at which the particle shows great flexibility. We determined the three-dimensional structures of two conformers, mapped the localization of two nups within the subcomplex and docked known crystal structures into the EM maps. The free ends of the Y-shaped particle are formed by beta-propellers; the connecting segments consist of alpha-solenoids. Strikingly, the same organizational principle is found in the clathrin triskelion, which was proposed to share a common evolutionary origin with the heptameric complex. PMID:19503077

  4. Improving the capacitive deionisation performance by optimising pore structures of the electrodes.

    PubMed

    Zou, L; Li, L; Song, H; Morris, G

    2010-01-01

    In this paper, three types of ordered mesoporous carbons (OMCs) were synthesised by an original template method and a modified sol-gel process involving nickel salts. The effects of pore arrangement pattern (ordered and random), and pore size distribution (mesoporous and microporous) on the desalination performance were investigated by comparing mesoporous carbons with activated carbons (ACs). It is found that the mesoporous carbons prepared by addition of nickel salts demonstrated higher specific capacitances than mesoporous carbons without nickel salts and the activated carbon electrodes. Their electrosorptive deionisation properties were also compared in a dilute NaCl solution (conductivity 100 microS cm(-1)), the amount of adsorbed ions are measured by a flow though apparatus in the laboratory. It is found that the amounts of the adsorbed ions are 15.9 micromol g(-1) for OMCs involving nickel in the synthesis process, 10.3 micromol g(-1) for OMC not involving nickel salts and 4.7 micromol g(-1) for ACs.

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

    SciTech Connect

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

    2013-02-15

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

  6. Characterization of differential pore-forming activities of ESAT-6 proteins from Mycobacterium tuberculosis and Mycobacterium smegmatis.

    PubMed

    Peng, Xiuli; Jiang, Guozhong; Liu, Wei; Zhang, Qi; Qian, Wei; Sun, Jianjun

    2016-02-01

    Mycobacterium tuberculosis ESAT-6 (MtbESAT-6) plays essential roles in pathogenesis. MtbESAT-6 exhibits a unique pore-forming activity (PFA) that is not found in its ortholog from non-pathogenic Mycobacterium smegmatis (MsESAT-6). Here, we characterized the differential PFAs and found that exchange of I25-H26/T25-A26 between two proteins reciprocally affected their PFAs. MtbESAT-6(IH/TA) had ~ 40% reduction, while MsESAT-6(TA/IH) fully acquired its activity similar to MtbESAT-6. Mutations of A17E, K38T, N67L or R74Q on MtbESAT-6(IH/TA) further reduced the activity, with MtbESAT-6(IH/TA-17) being the lowest. This study suggests I25-H26 as the pH-sensor essential for MsESAT-6 to fully acquire the activity, while multiple residues contributed to MtbESAT-6 PFA.

  7. Structural characterization of thin film photonic crystals

    SciTech Connect

    Subramania, G.; Biswas, R.; Constant, K.; Sigalas, M. M.; Ho, K. M.

    2001-06-15

    We quantitatively analyze the structure of thin film inverse-opal photonic crystals composed of ordered arrays of air pores in a background of titania. Ordering of the sphere template and introduction of the titania background were performed simultaneously in the thin film photonic crystals. Nondestructive optical measurements of backfilling with high refractive index liquids, angle-resolved reflectivity, and optical spectroscopy were combined with band-structure calculations. The analysis reveals a thin film photonic crystal structure with a very high filling fraction (92{endash}94%) of air and a substantial compression along the c axis ({similar_to}22{endash}25%).

  8. The effect of external magnetic fields on the pore structure of polyurethane foams loaded with magnetic microparticles

    NASA Astrophysics Data System (ADS)

    Schümann, M.; Seelig, N.; Odenbach, S.

    2015-10-01

    Elastic matrices loaded with magnetic microparticles are a new kind of magnetic hybrid material gaining a lot of scientific interest during the last few years. The central advantage of those materials is given by the possibility to control the mechanical properties by external stimuli, in this case external magnetic fields. Due to their extraordinary elastic properties, polyurethane foams are a promising matrix material for a new approach to synthesize such magnetic hybrid materials. A key to a deeper understanding of this new material is the investigation on how the inner structure of the hybrid material is controllable by the application of an external magnetic field during the polymerization. This paper presents a convenient method for analysis of structural changes of magnetically influenced particle loaded polyurethane foams. The geometry and size of up to 40 000 individual pores was evaluated by means of x-ray microtomography and digital image processing. A modest impact of the magnetic field on the pore structure was found with the utilized foam material, proving the convenient applicability of this method for future investigation with magnetic hybrid foams.

  9. Model Inspired by Nuclear Pore Complex Suggests Possible Roles for Nuclear Transport Receptors in Determining Its Structure

    PubMed Central

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

    2013-01-01

    Nuclear transport receptors (NTRs) mediate nucleocytoplasmic transport via their affinity for unstructured proteins (polymers) in the nuclear pore complex (NPC). Here, we have modeled the effect of NTRs on polymeric structure in the nanopore confinement of the NPC central conduit. The model explicitly takes into account inter- and intramolecular interactions, as well as the finite size of the NTRs (∼20% of the NPC channel diameter). It reproduces various proposed scenarios for the channel structure, ranging from a central polymer condensate (selective phase) to brushlike polymer arrangements localized at the channel wall (virtual gate, reduction of dimensionality), with the transport receptors lining the polymer surface. In addition, it predicts a new structure in which NTRs become an integral part of the transport barrier by forming a cross-linked network with the unstructured proteins stretching across the pore. The model provides specific and distinctive predictions for the equilibrium spatial distributions of NTRs for these different scenarios that can be experimentally verified by, e.g., superresolution fluorescence microscopy. Moreover, it suggests mechanisms by which globular macromolecules (colloidal particles) can cause polymer-coated nanopores to switch between open and closed configurations, a possible explanation of the biological function of the NPC, and suggests potential technological applications for filtration and single-molecule sensing. PMID:24359750

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  11. The EEEE locus is the sole high-affinity Ca(2+) binding structure in the pore of a voltage-gated Ca(2+) channel: block by ca(2+) entering from the intracellular pore entrance.

    PubMed

    Cibulsky, S M; Sather, W A

    2000-09-01

    Selective permeability in voltage-gated Ca(2+) channels is dependent upon a quartet of pore-localized glutamate residues (EEEE locus). The EEEE locus is widely believed to comprise the sole high-affinity Ca(2+) binding site in the pore, which represents an overturning of earlier models that had postulated two high-affinity Ca(2+) binding sites. The current view is based on site-directed mutagenesis work in which Ca(2+) binding affinity was attenuated by single and double substitutions in the EEEE locus, and eliminated by quadruple alanine (AAAA), glutamine (QQQQ), or aspartate (DDDD) substitutions. However, interpretation of the mutagenesis work can be criticized on the grounds that EEEE locus mutations may have additionally disrupted the integrity of a second, non-EEEE locus high-affinity site, and that such a second site may have remained undetected because the mutated pore was probed only from the extracellular pore entrance. Here, we describe the results of experiments designed to test the strength of these criticisms of the single high-affinity locus model of selective permeability in Ca(2+) channels. First, substituted-cysteine accessibility experiments indicate that pore structure in the vicinity of the EEEE locus is not extensively disrupted as a consequence of the quadruple AAAA mutations, suggesting in turn that the quadruple mutations do not distort pore structure to such an extent that a second high affinity site would likely be destroyed. Second, the postulated second high-affinity site was not detected by probing from the intracellularly oriented pore entrance of AAAA and QQQQ mutants. Using inside-out patches, we found that, whereas micromolar Ca(2+) produced substantial block of outward Li(+) current in wild-type channels, internal Ca(2+) concentrations up to 1 mM did not produce detectable block of outward Li(+) current in the AAAA or QQQQ mutants. These results indicate that the EEEE locus is indeed the sole high-affinity Ca(2+) binding locus in

  12. Appraisal of a cementitious material for waste disposal: Neutron imaging studies of pore structure and sorptivity

    SciTech Connect

    McGlinn, Peter J.; Beer, Frikkie C. de; Aldridge, Laurence P.; Radebe, Mabuti J.; Nshimirimana, Robert; Brew, Daniel R.M.; Payne, Timothy E.; Olufson, Kylie P.

    2010-08-15

    Cementitious materials are conventionally used in conditioning intermediate and low level radioactive waste. In this study a candidate cement-based wasteform has been investigated using neutron imaging to characterise the wasteform for disposal in a repository for radioactive materials. Imaging showed both the pore size distribution and the extent of the cracking that had occurred in the samples. The rate of the water penetration measured both by conventional sorptivity measurements and neutron imaging was greater than in pastes made from Ordinary Portland Cement. The ability of the cracks to distribute the water through the sample in a very short time was also evident. The study highlights the significant potential of neutron imaging in the investigation of cementitious materials. The technique has the advantage of visualising and measuring, non-destructively, material distribution within macroscopic samples and is particularly useful in defining movement of water through the cementitious materials.

  13. Unique Electronic Structure in a Porous Ga-In Bimetallic Oxide Nano-Photocatalyst with Atomically Thin Pore Walls.

    PubMed

    Chen, Hui; Yu, Guangtao; Li, Guo-Dong; Xie, Tengfeng; Sun, Yuanhui; Liu, Jingwei; Li, Hui; Huang, Xuri; Wang, Dejun; Asefa, Tewodros; Chen, Wei; Zou, Xiaoxin

    2016-09-12

    A facile synthetic route is presented that produces a porous Ga-In bimetallic oxide nanophotocatalyst with atomically thin pore walls. The material has an unprecedented electronic structure arising from its ultrathin walls. The bottom of the conduction band and the top of the valence band of the material are distributed on two opposite surfaces separated with a small electrostatic potential difference. This not only shortens the distance by which the photogenerated charges travel from the sites where they are generated to the sites where they catalyze the reactions, but also facilitates charge separations in the material. The porous structure within the walls results in a large density of exposed surface reactive/catalytic sites. Because of these optimized electronic and surface structures, the material exhibits superior photocatalytic activity toward the hydrogen evolution reaction (HER). PMID:27529769

  14. Unique Electronic Structure in a Porous Ga-In Bimetallic Oxide Nano-Photocatalyst with Atomically Thin Pore Walls.

    PubMed

    Chen, Hui; Yu, Guangtao; Li, Guo-Dong; Xie, Tengfeng; Sun, Yuanhui; Liu, Jingwei; Li, Hui; Huang, Xuri; Wang, Dejun; Asefa, Tewodros; Chen, Wei; Zou, Xiaoxin

    2016-09-12

    A facile synthetic route is presented that produces a porous Ga-In bimetallic oxide nanophotocatalyst with atomically thin pore walls. The material has an unprecedented electronic structure arising from its ultrathin walls. The bottom of the conduction band and the top of the valence band of the material are distributed on two opposite surfaces separated with a small electrostatic potential difference. This not only shortens the distance by which the photogenerated charges travel from the sites where they are generated to the sites where they catalyze the reactions, but also facilitates charge separations in the material. The porous structure within the walls results in a large density of exposed surface reactive/catalytic sites. Because of these optimized electronic and surface structures, the material exhibits superior photocatalytic activity toward the hydrogen evolution reaction (HER).

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

    PubMed

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

    2016-09-01

    Crystal (Cry) proteins from Bacillus thuringiensis (Bt) are globally used in agriculture as proteinaceous insecticides. Numerous crystal structures have been determined, and most exhibit conserved three-dimensional architectures. Recently, we have identified a novel nematicidal mechanism by which Cry6Aa triggers cell death through a necrosis-signaling pathway via an interaction with the host protease ASP-1. However, we found little sequence conservation of Cry6Aa in our functional study. Here, we report the 1.90 angstrom (Å) resolution structure of the proteolytic form of Cry6Aa (1-396), determined by X-ray crystallography. The structure of Cry6Aa is highly similar to those of the pathogenic toxin family of ClyA-type α-pore-forming toxins (α-PFTs), which are characterized by a bipartite structure comprising a head domain and a tail domain, thus suggesting that Cry6Aa exhibits a previously undescribed nematicidal mode of action. This structure also provides a framework for the functional study of other nematicidal toxins. PMID:27381865

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

    SciTech Connect

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

    2012-03-26

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

  17. THE STRUCTURES OF COILED-COIL DOMAINS FROM TYPE THREE SECRETION SYSTEM TRANSLOCATORS REVEAL HOMOLOGY TO PORE-FORMING TOXINS

    PubMed Central

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

    2012-01-01

    Many pathogenic Gram-negative bacteria utilize type III secretion systems (T3SS) to alter the normal functions of target cells. Shigella flexneri uses its T3SS to invade human intestinal cells to cause bacillary dysentery (shigellosis) which is responsible for over one million deaths per year. The Shigella type III secretion apparatus (T3SA) is comprised of a basal body spanning both bacterial membranes and an exposed oligomeric needle. Host altering effectors are secreted through this energized unidirectional conduit to promote bacterial invasion. The active needle tip complex of S. flexneri is composed of a tip protein, IpaD, and two pore-forming translocators, IpaB and IpaC. While the atomic structure of IpaD has been elucidated and studied, structural data on the hydrophobic translocators from the T3SS family remain elusive. We present here the crystal structures of a protease-stable fragment identified within the N-terminal regions of IpaB from S. flexneri and SipB from Salmonella enterica serovar Typhimurium determined at 2.1 Å and 2.8 Å limiting resolution, respectively. These newly identified domains are comprised of extended length (114 Å in IpaB and 71 Å in SipB) coiled-coil motifs that display a high degree of structural homology to one another despite the fact that they share only 21% sequence identity. Further structural comparisons also reveal substantial similarity to the coiled-coil regions of pore-forming proteins from other Gram-negative pathogens, notably colicin Ia. This suggests that these mechanistically-separate and functionally-distinct membrane-targeting proteins may have diverged from a common ancestor during the course of pathogen-specific evolutionary events. PMID:22321794

  18. Synthesis of microtubes with a surface of "house of cards" structure via needlelike particles and control of their pore size.

    PubMed

    Mitsuhashi, Kohei; Tagami, Naoki; Tanabe, Katsuyuki; Ohkubo, Takahiro; Sakai, Hideki; Koishi, Masumi; Abe, Masahiko

    2005-04-12

    The conditions for synthesizing microtubes with a surface of "house of cards" structure via needlelike particles were examined in detail. Magnesium carbonate trihydrate was formed as a metastable phase in the reaction process using magnesium hydroxide and carbon dioxide as starting materials. Subsequently, in the formation of basic magnesium carbonate from magnesium carbonate trihydrate, microtubes with a surface of house of cards structure were obtained via needlelike particles of magnesium carbonate trihydrate under certain conditions where the temperature and added amount of sodium hydroxide were properly controlled. The pore size of the microtubes could be controlled within a range of 0.5-6 microm by adjusting the condition of needlelike particle formation. In addition, the sustainability of naphthalene release from the microtube was found to be about 6 times higher than that from naphthalene crystal. PMID:15807617

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

    PubMed Central

    Qian, Tingting; Li, Jinhong; Deng, Yong

    2016-01-01

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

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

    PubMed

    Qian, Tingting; Li, Jinhong; Deng, Yong

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Qian, Tingting; Li, Jinhong; Deng, Yong

    2016-09-01

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

  2. Damping characterization in large structures

    NASA Technical Reports Server (NTRS)

    Eke, Fidelis O.; Eke, Estelle M.

    1991-01-01

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

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

    PubMed Central

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

    2011-01-01

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

  4. Structural characterization of porous low-k thin films prepared by different techniques using x-ray porosimetry

    NASA Astrophysics Data System (ADS)

    Lee, Hae-Jeong; Soles, Christopher L.; Liu, Da-Wei; Bauer, Barry J.; Lin, Eric K.; Wu, Wen-li; Grill, Alfred

    2004-03-01

    Three different types of porous low-k dielectric films, with similar dielectric constants, are characterized using x-ray porosimetry (XRP). XRP is used to extract critical structural information, such as the average density, wall density, porosity, and pore size distribution. The materials include a plasma-enhanced-chemical-vapor-deposited carbon-doped oxide film composed of Si, C, O, and H (SiCOH) and two spin cast silsesquioxane type films—methylsilsesquioxane with a polymeric porogen (porous MSQ) and hydrogensilsesquioxane with a high boiling point solvent (porous HSQ). The porous SiCOH film displays the smallest pore sizes, while porous HSQ film has both the highest density wall material and porosity. The porous MSQ film exhibits a broad range of pores with the largest average pore size. We demonstrate that the average pore size obtained by the well-established method of neutron scattering and x-ray reflectivity is in good agreement with the XRP results.

  5. Recent Advances in Characterizing Depositional Facies and Pore Network Modeling in Context of Carbon Capture Storage: An Example from the Cambrian Mt. Simon Sandstone in the Illinois Basin

    NASA Astrophysics Data System (ADS)

    Freiburg, J. T.; Nathan, W.; Best, J.; Reesink, A.; Ritzi, R. W., Jr.; Pendleton, J.; Dominic, D. F.; Tudek, J.; Kohanpur, A. H.

    2015-12-01

    In order to understand subsurface flow dynamics, including CO2 plume migration and capillary trapping, a diverse set of geologic properties within the reservoir, from the pore scale to the basin scale, must be understood and quantified. The uncertainty about site-specific geology stems from the inherent variation in rock types, depositional environments, and diagenesis. In collaboration with geocellular and multiphase modeling, detailed characterization of the Lower Mt. Simon Sandstone (LMSS), a reservoir utilized for carbon capture storage, is supporting data-driven conceptual models to better understand reservoir heterogeneity and its relationship to reservoir properties. This includes characterization of sedimentary facies and pore scale modeling of the reservoir The Cambrian-age Lower Mt. Simon Sandstone (LMSS) is a reservoir utilized for two-different carbon capture storage projects in the Illinois Basin, USA. The LMSS is interpreted to have formed in a braided river environment comprising a hierarchy of stratification, with larger scale depositional facies comprising assemblages of smaller scale facies. The proportions, geometries, length scales, and petrophysical attributes of the depositional facies, and of the textural facies they comprise, are being quantified. Based on examination of core and analog outcrop in adjacent areas, the LMSS is comprised of five dominant depositional facies, the most abundant facies being planar to trough cross-bedded sandstones produced by subaqueous sand dunes. This facies has the best reservoir conditions with porosity up to 27% and permeability up to 470 mD. Three-dimensional pore network modeling via micro computed tomography of this facies shows well-connected and unobstructed pore throats and pore space. This presentation will outline the depositional heterogeneity of the LMSS, its relationship to diagenetic fabrics, and its influence on fluid movement within the reservoir.

  6. A Novel Approach to Estimate the Distribution of Reducible Iron Within Different Pore Fractions of Structured Media.

    NASA Astrophysics Data System (ADS)

    Kamolpornwijit, W.; Brooks, S. C.; Kim, Y.; Scheibe, T. D.

    2005-12-01

    The success of bioremediation processes employing iron reducing bacteria depends on several factors; one of the crucial factors is the availability of Fe(III) as an electron acceptor. The iron content of subsurface media usually is obtained through different extraction techniques performed in a well-mixed batch experiment. For structured media where preferential flow prevails over the matrix flow, however, the iron content from homogenized samples may not well represent the iron content available for microbial activity. Results from the batch experiments may overestimate the availability of reducible iron. As microbes remain within the macro- and mesopores due to their cellular size restriction, the iron content within micropores may play an insignificant role during the biostimulation process. In this new approach, we extract Fe from different pore classes of intact cores of structured saprolite. The extracting solution (0.2 M ammonium oxalate) is introduced to an unsaturated column at specific tension. Unit gradient across the cores is maintained with a Marriotte device and vacuum chamber at the column inlet and outlet, respectively. Nonreactive tracers are included in the extractant solution to quantify transport properties. When the iron content in the effluent falls below detection limit, the tension is decreased (higher degree of saturation). The process is repeated until the column is operated at saturated conditions. The distribution of extractable iron within different pore fractions will be obtained directly from the experiment. In this study we will estimate the flow distribution, affected area, and mass concentration of iron using transport parameters obtained from non reactive tracer tests under both saturated and unsaturated conditions. The study will provide a novel approach supplementing the bulk extraction procedures which is critical to the success of bioremediation processes especially in structured media.

  7. Effect of hydrogel particle additives on water-accessible pore structure of sandy soils: a custom pressure plate apparatus and capillary bundle model.

    PubMed

    Wei, Y; Durian, D J

    2013-05-01

    To probe the effects of hydrogel particle additives on the water-accessible pore structure of sandy soils, we introduce a custom pressure plate method in which the volume of water expelled from a wet granular packing is measured as a function of applied pressure. Using a capillary bundle model, we show that the differential change in retained water per pressure increment is directly related to the cumulative cross-sectional area distribution f(r) of the water-accessible pores with radii less than r. This is validated by measurements of water expelled from a model sandy soil composed of 2-mm-diameter glass beads. In particular, it is found that the expelled water is dramatically dependent on sample height and that analysis using the capillary bundle model gives the same pore size distribution for all samples. The distribution is found to be approximately log normal, and the total cross-sectional area fraction of the accessible pore space is found to be f(0)=0.34. We then report on how the pore distribution and total water-accessible area fraction are affected by superabsorbent hydrogel particle additives, uniformly mixed into a fixed-height sample at varying concentrations. Under both fixed volume and free swelling conditions, the total area fraction of water-accessible pore space in a packing decreases exponentially as the gel concentration increases. The size distribution of the pores is significantly modified by the swollen hydrogel particles, such that large pores are clogged while small pores are formed.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    SciTech Connect

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

    2012-10-23

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

  10. Velocities in Solar Pores

    NASA Astrophysics Data System (ADS)

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

    1996-05-01

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

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

    SciTech Connect

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

    1994-11-07

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

  12. Hydrodeoxygenation of heavy oils derived from low-temperature coal gasification over NiW catalysts-effect of pore structure

    SciTech Connect

    Dieter Leckel

    2008-01-15

    The effect of the pore structure on the hydroprocessing of heavy distillate oils derived from low-temperature coal gasification residues was studied using four NiW catalysts with different pore size distributions. The hydroprocessing was conducted at a pressure of 17.5 MPa, a temperature range of 370-410{sup o}C, and a 0.50 h{sup -1} space velocity. The degree of hydrodeoxygenation (HDO) in terms of phenolics removal was influenced by the catalyst pore structure, with the most preferable peak pore diameter for HDO ranging between 6.8 and 16 nm. The catalyst with the highest volume of pores in the 3.5-6 nm range showed the lowest HDO activity. The apparent activation energies for the HDO reaction varied between 59 and 87 kJ/mol, whereby the lowest values are obtained for the catalysts with a peak pore diameter of 11 and 16 nm. 30 refs., 5 figs., 6 tabs.

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

    PubMed

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

    2014-02-28

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

  14. Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers

    PubMed Central

    Leontiadou, Hari; Mark, Alan E.; Marrink, Siewert J.

    2004-01-01

    Hydrophilic pores are formed in peptide free lipid bilayers under mechanical stress. It has been proposed that the transport of ionic species across such membranes is largely determined by the existence of such meta-stable hydrophilic pores. To study the properties of these structures and understand the mechanism by which pore expansion leads to membrane rupture, a series of molecular dynamics simulations of a dipalmitoylphosphatidylcholine (DPPC) bilayer have been conducted. The system was simulated in two different states; first, as a bilayer containing a meta-stable pore and second, as an equilibrated bilayer without a pore. Surface tension in both cases was applied to study the formation and stability of hydrophilic pores inside the bilayers. It is observed that below a critical threshold tension of ∼38 mN/m the pores are stabilized. The minimum radius at which a pore can be stabilized is 0.7 nm. Based on the critical threshold tension the line tension of the bilayer was estimated to be ∼3 × 10−11 N, in good agreement with experimental measurements. The flux of water molecules through these stabilized pores was analyzed, and the structure and size of the pores characterized. When the lateral pressure exceeds the threshold tension, the pores become unstable and start to expand causing the rupture of the membrane. In the simulations the mechanical threshold tension necessary to cause rupture of the membrane on a nanosecond timescale is much higher in the case of the equilibrated bilayers, as compared with membranes containing preexisting pores. PMID:15041656

  15. Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex

    SciTech Connect

    Yoshida, Kimihisa; Seo, Hyuk-Soo; Debler, Erik W.; Blobel, Günter; Hoelz, André

    2012-07-25

    So far, only a few of the interactions between the {approx}30 nucleoporins comprising the modular structure of the nuclear pore complex have been defined at atomic resolution. Here we report the crystal structure, at 2.6 {angstrom} resolution, of a heterotrimeric complex, composed of fragments of three cytoplasmically oriented nucleoporins of yeast: Nup82, Nup116, and Nup159. Our data show that the Nup82 fragment, representing more than the N-terminal half of the molecule, folds into an extensively decorated, seven-bladed {beta}-propeller that forms the centerpiece of this heterotrimeric complex and anchors both a C-terminal fragment of Nup116 and the C-terminal tail of Nup159. Binding between Nup116 and Nup82 is mutually reinforced via two loops, one emanating from the Nup82 {beta}-propeller and the other one from the {beta}-sandwich fold of Nup116, each contacting binding pockets in their counterparts. The Nup82-Nup159 interaction occurs through an amphipathic {alpha}-helix of Nup159, which is cradled in a large hydrophobic groove that is generated from several large surface decorations of the Nup82 {beta}-propeller. Although Nup159 and Nup116 fragments bind to the Nup82 {beta}-propeller in close vicinity, there are no direct contacts between them, consistent with the noncooperative binding that was detected biochemically. Extensive mutagenesis delineated hot-spot residues for these interactions. We also showed that the Nup82 {beta}-propeller binds to other yeast Nup116 family members, Nup145N, Nup100 and to the mammalian homolog, Nup98. Notably, each of the three nucleoporins contains additional nuclear pore complex binding sites, distinct from those that were defined here in the heterotrimeric Nup82 {center_dot} Nup159 {center_dot} Nup116 complex.

  16. Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex

    PubMed Central

    Yoshida, Kimihisa; Seo, Hyuk-Soo; Debler, Erik W.; Blobel, Günter; Hoelz, André

    2011-01-01

    So far, only a few of the interactions between the ≈30 nucleoporins comprising the modular structure of the nuclear pore complex have been defined at atomic resolution. Here we report the crystal structure, at 2.6 Å resolution, of a heterotrimeric complex, composed of fragments of three cytoplasmically oriented nucleoporins of yeast: Nup82, Nup116, and Nup159. Our data show that the Nup82 fragment, representing more than the N-terminal half of the molecule, folds into an extensively decorated, seven-bladed β-propeller that forms the centerpiece of this heterotrimeric complex and anchors both a C-terminal fragment of Nup116 and the C-terminal tail of Nup159. Binding between Nup116 and Nup82 is mutually reinforced via two loops, one emanating from the Nup82 β-propeller and the other one from the β-sandwich fold of Nup116, each contacting binding pockets in their counterparts. The Nup82-Nup159 interaction occurs through an amphipathic α-helix of Nup159, which is cradled in a large hydrophobic groove that is generated from several large surface decorations of the Nup82 β-propeller. Although Nup159 and Nup116 fragments bind to the Nup82 β-propeller in close vicinity, there are no direct contacts between them, consistent with the noncooperative binding that was detected biochemically. Extensive mutagenesis delineated hot-spot residues for these interactions. We also showed that the Nup82 β-propeller binds to other yeast Nup116 family members, Nup145N, Nup100 and to the mammalian homolog, Nup98. Notably, each of the three nucleoporins contains additional nuclear pore complex binding sites, distinct from those that were defined here in the heterotrimeric Nup82•Nup159•Nup116 complex. PMID:21930948

  17. Automated Characterization Of Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    SciTech Connect

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

    2012-10-23

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

  19. Atomic Structure of the Nuclear Pore Complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata

    PubMed Central

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

    2012-01-01

    The nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and cytoplasm. The yeast NPC is an eight-fold symmetric annular structure composed of ~456 polypeptide chains contributed by ~30 distinct proteins termed nucleoporins (Nups). Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N-terminal “FG” repeats containing a Gle2p-binding sequence motif (GLEBS motif) and a NPC targeting domain at its C-terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882-1034 [CgNup116(882-1034)], at 1.94 Å resolution. The X-ray structure of CgNup116(882-1034) is consistent with the molecular envelope determined in solution by Small Angle X-ray Scattering (SAXS). Structural similarities of CgNup116(882-1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiaeNup145N, and human Nup98 are discussed. PMID:22544723

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

    PubMed

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

    2012-08-01

    The nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and the cytoplasm. The yeast NPC is an eightfold symmetric annular structure composed of ~456 polypeptide chains contributed by ~30 distinct proteins termed nucleoporins. Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N-terminal "FG" repeats containing a Gle2p-binding sequence motif and a NPC targeting domain at its C-terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882-1034 [CgNup116(882-1034)], at 1.94 Å resolution. The X-ray structure of CgNup116(882-1034) is consistent with the molecular envelope determined in solution by small-angle X-ray scattering. Structural similarities of CgNup116(882-1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiae Nup145N, and human Nup98 are discussed. PMID:22544723

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-10-01

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

  3. Structure-function of proteins interacting with the α1 pore-forming subunit of high-voltage-activated calcium channels

    PubMed Central

    Neely, Alan; Hidalgo, Patricia

    2014-01-01

    Openings of high-voltage-activated (HVA) calcium channels lead to a transient increase in calcium concentration that in turn activate a plethora of cellular functions, including muscle contraction, secretion and gene transcription. To coordinate all these responses calcium channels form supramolecular assemblies containing effectors and regulatory proteins that couple calcium influx to the downstream signal cascades and to feedback elements. According to the original biochemical characterization of skeletal muscle Dihydropyridine receptors, HVA calcium channels are multi-subunit protein complexes consisting of a pore-forming subunit (α1) associated with four additional polypeptide chains β, α2, δ, and γ, often referred to as accessory subunits. Twenty-five years after the first purification of a high-voltage calcium channel, the concept of a flexible stoichiometry to expand the repertoire of mechanisms that regulate calcium channel influx has emerged. Several other proteins have been identified that associate directly with the α1-subunit, including calmodulin and multiple members of the small and large GTPase family. Some of these proteins only interact with a subset of α1-subunits and during specific stages of biogenesis. More strikingly, most of the α1-subunit interacting proteins, such as the β-subunit and small GTPases, regulate both gating and trafficking through a variety of mechanisms. Modulation of channel activity covers almost all biophysical properties of the channel. Likewise, regulation of the number of channels in the plasma membrane is performed by altering the release of the α1-subunit from the endoplasmic reticulum, by reducing its degradation or enhancing its recycling back to the cell surface. In this review, we discuss the structural basis, interplay and functional role of selected proteins that interact with the central pore-forming subunit of HVA calcium channels. PMID:24917826

  4. A Forward Analysis on the Applicability of Tracer Breakthrough in Revealing the Pore Structure of Tight Gas Sandstone and Carbonate Rocks

    NASA Astrophysics Data System (ADS)

    Mehmani, A.; Mehmani, Y.; Prodanovic, M.; Balhoff, M.

    2015-12-01

    Be it fuel production for energy consumption or carbon storage and sequestration to mitigate global warming, tight gas sandstone and carbonate formations offer a new and largely available potential for these purposes. Exploring and developing these formations however is hampered by uncertainties in quantifying their pore structure due to considerable heterogeneity and existence of pores in multiple length scales. We explore tracer breakthrough profiles (TBP) as a macroscopic property to infer the complex pore space topology of tight gas sandstone and carbonate rocks at the core scale. The following features were modeled via three-dimensional multiscale networks: microporosity within dissolved grains and pore-filling clay, cementation in the absence and presence of microporosity (each classified into uniform, pore preferred, and throat-preferred modes), layering, vug, and microcrack inclusion. A priori knowledge of the extent and location of each process was assumed to be known. With the exception of an equal importance of macropores and pore-filling micropores, TBPs show little sensitivity to the fraction of micropores present. In general, significant sensitivity of the TBPs was observed for uniform and throat-preferred cementation. Layering parallel to the fluid flow direction had a considerable impact on TBPs whereas layering perpendicular to flow did not. Microcrack orientations seemed of minor importance in affecting TBPs.

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

    PubMed

    Kim, Kwangmoo; Stroud, D

    2013-08-26

    We have calculated the photonic band structures of metallic inverse opals and of periodic linear chains of spherical pores in a metallic host, below a plasma frequency ωp. In both cases, we use a tight-binding approximation, assuming a Drude dielectric function for the metallic component, but without making the quasistatic approximation. The tight-binding modes are linear combinations of the single-cavity transverse magnetic (TM) modes. For the inverse-opal structures, the lowest modes are analogous to those constructed from the three degenerate atomic p-states in fcc crystals. For the linear chains, in the limit of small spheres compared to a wavelength, the results bear some qualitative resemblance to the dispersion relation for metal spheres in an insulating host, as calculated by Brongersma et al. [Phys. Rev. B 62, R16356 (2000)]. Because the electromagnetic fields of these modes decay exponentially in the metal, there are no radiative losses, in contrast to the case of arrays of metallic spheres in air. We suggest that this tight-binding approach to photonic band structures of such metallic inverse materials may be a useful approach for studying photonic crystals containing metallic components, even beyond the quasistatic approximation. PMID:24105532

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

    NASA Astrophysics Data System (ADS)

    Kim, Kwangmoo; Stroud, David

    2014-03-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

  8. Pore - to - Core Modeling of Soil Organic Matter Decomposition in 3D Soil Structures

    NASA Astrophysics Data System (ADS)

    Falconer, R. E.; Battaia, G.; Baveye, P.; Otten, W.

    2013-12-01

    There is a growing body of literature supporting the need for microbial contributions to be considered explicitly in carbon-climate models. There is also overwhelming evidence that physical protection within aggregates can play a significant role in organic matter dynamics. Yet current models of soil organic matter dynamics divide soil organic matter into conceptual pools with distinct turnover times, assuming that a combination of biochemical and physical properties control decay without explicit description. Albeit robust in their application, such models are not capable to account for changes in soil structure or microbial populations, or accurately predict the effect of wetness or priming. A spatially explicit model is presented that accounts for microbial dynamics and physical processes, permitting consideration of the heterogeneity of the physical and chemical microenvironments at scales relevant for microbes. Exemplified for fungi, we investigate how micro-scale processes manifest at the core scale with particular emphasis on evolution of CO2 and biomass distribution. The microbial model is based upon previous (Falconer et al, 2012) and includes the following processes: uptake, translocation, recycling, enzyme production, growth, spread and respiration. The model is parameterised through a combination of literature data and parameter estimation (Cazelles et al., 2012).The Carbon model comprises two pools, particulate organic matter which through enzymatic activity is converted into dissolved organic matter. The microbial and carbon dynamics occur within a 3D soil structure obtained by X-ray CT. We show that CO2 is affected not only by the amount of Carbon in the soil but also by microbial dynamics, soil structure and the spatial distribution of OM. The same amount of OM can result in substantially different respiration rates, with surprisingly more CO2 with increased clustering of OM. We can explain this from the colony dynamics, production of enzymes and

  9. Porous structure of fibre networks formed by a foaming process: a comparative study of different characterization techniques.

    PubMed

    Al-Qararah, Ahmad M; Ekman, Axel; Hjelt, Tuomo; Kiiskinen, Harri; Timonen, Jussi; Ketoja, Jukka A

    2016-10-01

    Recent developments in making fibre materials using the foam-forming technology have raised a need to characterize the porous structure at low material density. In order to find an effective choice among all structure-characterization methods, both two-dimensional and three-dimensional techniques were used to explore the porous structure of foam-formed samples made with two different types of cellulose fibre. These techniques included X-ray microtomography, scanning electron microscopy, light microscopy, direct surface imaging using a CCD camera and mercury intrusion porosimetry. The mean pore radius for a varying type of fibre and for varying foam properties was described similarly by all imaging methods. X-ray microtomography provided the most extensive information about the sheet structure, and showed more pronounced effects of varying foam properties than the two-dimensional imaging techniques. The two-dimensional methods slightly underestimated the mean pore size of samples containing stiff CTMP fibres with void radii exceeding 100 μm, and overestimated the pore size for the samples containing flexible kraft fibres with all void radii below 100 μm. The direct rapid surface imaging with a CCD camera showed surprisingly strong agreement with the other imaging techniques. Mercury intrusion porosimetry was able to characterize pore sizes also in the submicron region and led to an increased relative volume of the pores in the range of the mean bubble size of the foam. This may be related to the penetration channels created by the foam-fibre interaction.

  10. Small-angle x-ray scattering investigation of the effect of heating temperature on the submicroscopic pore structure of wood charcoal

    SciTech Connect

    Schmidt, P.W.; Cutter, B.E.; Kalliat, M.

    1984-04-01

    In order to learn about the effects of higher preparation temperatures, we recently examined a series of charcoals from black cherry (Prunus serotina Ehrh.) wood heated to temperatures from 600/sup 0/ to 2000/sup 0/C. The results are summarized in this report. In addition to obtaining some information about the pore structure of black cherry charcoal, we have developed a general picture of how the charcoal porosity depends on the temperature to which the wood was heated during pyrolysis. These results have led us to propose that the macropores in charcoals are similar to those in wood and that the main effect which pyrolysis at temperatures above 400/sup 0/C exerts on the pore structure is to cause the micropores and transitional pores to grow, while leaving the macropores almost unchanged.

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

    NASA Astrophysics Data System (ADS)

    Han, J.; Keehm, Y.

    2011-12-01

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

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

    PubMed

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

    2010-03-01

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

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

    PubMed Central

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-08-01

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

  15. 3D bioprinting matrices with controlled pore structure and release function guide in vitro self-organization of sweat gland

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Jani, Divyang; Valkov, Eugene; Stewart, Murray

    2014-06-01

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

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

    PubMed

    Jani, Divyang; Valkov, Eugene; Stewart, Murray

    2014-06-01

    The conserved Sac3:Thp1:Sem1:Sus1:Cdc31 (TREX2) complex binds to nuclear pore complexes (NPCs) and, in addition to integrating mRNA nuclear export with preceding steps in the gene expression pathway, facilitates re-positioning of highly regulated actively transcribing genes (such as GAL1) to NPCs. Although TREX2 is thought to bind NPC protein Nup1, defining the precise role of this interaction has been frustrated by the complex pleiotropic phenotype exhibited by nup1Δ strains. To provide a structural framework for understanding the binding of TREX2 to NPCs and its function in the gene expression pathway, we have determined the structure of the Nup1:TREX2 interaction interface and used this information to engineer a Sac3 variant that impairs NPC binding while not compromising TREX2 assembly. This variant inhibited the NPC association of both de-repressed and activated GAL1 and also produced mRNA export and growth defects. These results indicate that the TREX2:Nup1 interaction facilitates the efficient nuclear export of bulk mRNA together with the re-positioning of GAL1 to NPCs that is required for transcriptional control that is mediated by removal of SUMO from repressors by NPC-bound Ulp1. PMID:24705649

  18. Structural and dipolar properties of the voltage-dependent pore former alamethicin in octanol/dioxane.

    PubMed Central

    Schwarz, G; Savko, P

    1982-01-01

    Dielectric constant and loss of the membrane-active peptide alamethicin in octanol/dioxane mixtures have been measured at frequencies between 5 kHz and 50 MHz. On the basis of a rotational mechanism of dipolar orientation, the observed dispersion provides information regarding size, shape, and dipole moment of the structural entities which the solute may assume in media of diverse lipophilicity. Particularly detailed results are obtained in a pure octanol solvent where an apparent molecular weight of alamethicin could be determined. It turns out that in this quite lipophilic medium most of the peptide material exists as a monomer particle that has approximate length and diameter of 35 and 13 A, respectively. It carries a dipole moment of approximately 75 Debye units (directed nearly parallel to the long axis). At our concentrations of a few milligrams per milliliters, appreciable formation of dimers by head-to-tail linkage is indicated. When the octanol content is reduced by adding greater amounts of dioxane, larger particles are encountered. This is accompanied by a decrease of the effective polarity. The inherent increase of hydrophilicity in the dioxane-enriched solvent apparently favors another monomer conformation that has a low dipole moment and easily aggregates to some kind of micelle. PMID:7115881

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  20. Nucleoporins as components of the nuclear pore complex core structure and Tpr as the architectural element of the nuclear basket.

    PubMed

    Krull, Sandra; Thyberg, Johan; Björkroth, Birgitta; Rackwitz, Hans-Richard; Cordes, Volker C

    2004-09-01

    The vertebrate nuclear pore complex (NPC) is a macromolecular assembly of protein subcomplexes forming a structure of eightfold radial symmetry. The NPC core consists of globular subunits sandwiched between two coaxial ring-like structures of which the ring facing the nuclear interior is capped by a fibrous structure called the nuclear basket. By postembedding immunoelectron microscopy, we have mapped the positions of several human NPC proteins relative to the NPC core and its associated basket, including Nup93, Nup96, Nup98, Nup107, Nup153, Nup205, and the coiled coil-dominated 267-kDa protein Tpr. To further assess their contributions to NPC and basket architecture, the genes encoding Nup93, Nup96, Nup107, and Nup205 were posttranscriptionally silenced by RNA interference (RNAi) in HeLa cells, complementing recent RNAi experiments on Nup153 and Tpr. We show that Nup96 and Nup107 are core elements of the NPC proper that are essential for NPC assembly and docking of Nup153 and Tpr to the NPC. Nup93 and Nup205 are other NPC core elements that are important for long-term maintenance of NPCs but initially dispensable for the anchoring of Nup153 and Tpr. Immunogold-labeling for Nup98 also results in preferential labeling of NPC core regions, whereas Nup153 is shown to bind via its amino-terminal domain to the nuclear coaxial ring linking the NPC core structures and Tpr. The position of Tpr in turn is shown to coincide with that of the nuclear basket, with different Tpr protein domains corresponding to distinct basket segments. We propose a model in which Tpr constitutes the central architectural element that forms the scaffold of the nuclear basket.

  1. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola

    PubMed Central

    Dhakshnamoorthy, Balasundaresan; Rohaim, Ahmed; Rui, Huan; Blachowicz, Lydia; Roux, Benoît

    2016-01-01

    The selectivity filter is an essential functional element of K+ channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca2+ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca2+ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca2+ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel. PMID:27678077

  2. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola

    NASA Astrophysics Data System (ADS)

    Dhakshnamoorthy, Balasundaresan; Rohaim, Ahmed; Rui, Huan; Blachowicz, Lydia; Roux, Benoît

    2016-09-01

    The selectivity filter is an essential functional element of K+ channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca2+ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca2+ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca2+ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel.

  3. Crystal structure of Cry51Aa1: A potential novel insecticidal aerolysin-type β-pore-forming toxin from Bacillus thuringiensis.

    PubMed

    Xu, Chengchen; Chinte, Unmesh; Chen, Lirong; Yao, Qingqing; Meng, Ying; Zhou, Dayong; Bi, Li-Jun; Rose, John; Adang, Michael J; Wang, Bi-Cheng; Yu, Ziniu; Sun, Ming

    2015-07-01

    The structures of several Bacillus thuringiensis (Bt) insecticidal crystal proteins have been determined by crystallographic methods and a close relationship has been explicated between specific toxicities and conserved three-dimensional architectures. In this study, as a representative of the coleopteran- and hemipteran-specific Cry51A group, the complete structure of Cry51Aa1 protoxin has been determined by X-ray crystallography at 1.65 Å resolution. This is the first report of a coleopteran-active Bt insecticidal toxin with high structural similarity to the aerolysin-type β-pore forming toxins (β-PFTs). Moreover, study of featured residues and structural elements reveal their possible roles in receptor binding and pore formation events. This study provides new insights into the action of aerolysin-type β-PFTs from a structural perspective, and could be useful for the control of coleopteran and hemipteran insect pests in agricultures.

  4. Characterization of reactive flow-induced evolution of carbonate rocks using digital core analysis- part 1: Assessment of pore-scale mineral dissolution and deposition.

    PubMed

    Qajar, Jafar; Arns, Christoph H

    2016-09-01

    The application of X-ray micro-computed tomography (μ-CT) for quantitatively characterizing reactive-flow induced pore structure evolution including local particle detachment, displacement and deposition in carbonate rocks is investigated. In the studies conducted in this field of research, the experimental procedure has involved alternating steps of imaging and ex-situ core sample alteration. Practically, it is impossible to return the sample, with micron precision, to the same position and orientation. Furthermore, successive images of a sample in pre- and post-alteration states are usually taken at different conditions such as different scales, resolutions and signal-to-noise ratios. These conditions accompanying with subresolution features in the images make voxel-by-voxel comparisons of successive images problematic. In this paper, we first address the respective challenges in voxel-wise interpretation of successive images of carbonate rocks subject to reactive flow. Reactive coreflood in two carbonate cores with different rock types are considered. For the first rock, we used the experimental and imaging results published by Qajar et al. (2013) which showed a quasi-uniform dissolution regime. A similar reactive core flood was conducted in the second rock which resulted in wormhole-like dissolution regime. We particularly examine the major image processing operations such as transformation of images to the same grey-scale, noise filtering and segmentation thresholding and propose quantitative methods to evaluate the effectiveness of these operations in voxel-wise analysis of successive images of a sample. In the second part, we generalize the methodology based on the three-phase segmentation of normalized images, microporosity assignment and 2D histogram of image intensities to estimate grey-scale changes of individual image voxels for a general case where the greyscale images are segmented into arbitrary number of phases. The results show that local (voxel

  5. Characterization of reactive flow-induced evolution of carbonate rocks using digital core analysis- part 1: Assessment of pore-scale mineral dissolution and deposition

    NASA Astrophysics Data System (ADS)

    Qajar, Jafar; Arns, Christoph H.

    2016-09-01

    The application of X-ray micro-computed tomography (μ-CT) for quantitatively characterizing reactive-flow induced pore structure evolution including local particle detachment, displacement and deposition in carbonate rocks is investigated. In the studies conducted in this field of research, the experimental procedure has involved alternating steps of imaging and ex-situ core sample alteration. Practically, it is impossible to return the sample, with micron precision, to the same position and orientation. Furthermore, successive images of a sample in pre- and post-alteration states are usually taken at different conditions such as different scales, resolutions and signal-to-noise ratios. These conditions accompanying with subresolution features in the images make voxel-by-voxel comparisons of successive images problematic. In this paper, we first address the respective challenges in voxel-wise interpretation of successive images of carbonate rocks subject to reactive flow. Reactive coreflood in two carbonate cores with different rock types are considered. For the first rock, we used the experimental and imaging results published by Qajar et al. (2013) which showed a quasi-uniform dissolution regime. A similar reactive core flood was conducted in the second rock which resulted in wormhole-like dissolution regime. We particularly examine the major image processing operations such as transformation of images to the same grey-scale, noise filtering and segmentation thresholding and propose quantitative methods to evaluate the effectiveness of these operations in voxel-wise analysis of successive images of a sample. In the second part, we generalize the methodology based on the three-phase segmentation of normalized images, microporosity assignment and 2D histogram of image intensities to estimate grey-scale changes of individual image voxels for a general case where the greyscale images are segmented into arbitrary number of phases. The results show that local (voxel

  6. Characterization of reactive flow-induced evolution of carbonate rocks using digital core analysis- part 1: Assessment of pore-scale mineral dissolution and deposition.

    PubMed

    Qajar, Jafar; Arns, Christoph H

    2016-09-01

    The application of X-ray micro-computed tomography (μ-CT) for quantitatively characterizing reactive-flow induced pore structure evolution including local particle detachment, displacement and deposition in carbonate rocks is investigated. In the studies conducted in this field of research, the experimental procedure has involved alternating steps of imaging and ex-situ core sample alteration. Practically, it is impossible to return the sample, with micron precision, to the same position and orientation. Furthermore, successive images of a sample in pre- and post-alteration states are usually taken at different conditions such as different scales, resolutions and signal-to-noise ratios. These conditions accompanying with subresolution features in the images make voxel-by-voxel comparisons of successive images problematic. In this paper, we first address the respective challenges in voxel-wise interpretation of successive images of carbonate rocks subject to reactive flow. Reactive coreflood in two carbonate cores with different rock types are considered. For the first rock, we used the experimental and imaging results published by Qajar et al. (2013) which showed a quasi-uniform dissolution regime. A similar reactive core flood was conducted in the second rock which resulted in wormhole-like dissolution regime. We particularly examine the major image processing operations such as transformation of images to the same grey-scale, noise filtering and segmentation thresholding and propose quantitative methods to evaluate the effectiveness of these operations in voxel-wise analysis of successive images of a sample. In the second part, we generalize the methodology based on the three-phase segmentation of normalized images, microporosity assignment and 2D histogram of image intensities to estimate grey-scale changes of individual image voxels for a general case where the greyscale images are segmented into arbitrary number of phases. The results show that local (voxel

  7. Effects of Temperature and Pore Structure on High Surface Area-Activated Carbon Obtained from Peanut Shells.

    PubMed

    Kalpana, D; Lee, Y S

    2016-03-01

    Activated carbon was synthesized from peanut shells by treating with H3PO4 with an intention to enhance the surface area and to find its electrochemical performance in EDLC as electrode material. The powdered peanut shells were pyrolyzed at three different temperatures namely 300 degrees C, 600 degrees C and 800 degrees C respectively. The structural and surface properties of the pyrolyzed carbon materials were studied using N2 adsorption/desorption, Raman, TEM and SEM analysis. There has been remarkable increase in the surface area of the carbon pyrolyzed at 600 degrees C due to the effect of pore generations. The surface area of the 600 degrees C pyrolyzed sample was found to be 1629 m2/g. The electrochemical properties of all the samples were evaluated by cyclic voltammetry, impedance spectroscopy, and galvanostatic charge-discharge tests. The system showed excellent cycleability and a maximum specific capacitance of 291 Fg(-1) was obtained in a 0.1 M H2SO4 electrolyte solution. The effects of the various properties of the activated carbon on the EDLC performance are discussed. PMID:27455740

  8. Effects of Temperature and Pore Structure on High Surface Area-Activated Carbon Obtained from Peanut Shells.

    PubMed

    Kalpana, D; Lee, Y S

    2016-03-01

    Activated carbon was synthesized from peanut shells by treating with H3PO4 with an intention to enhance the surface area and to find its electrochemical performance in EDLC as electrode material. The powdered peanut shells were pyrolyzed at three different temperatures namely 300 degrees C, 600 degrees C and 800 degrees C respectively. The structural and surface properties of the pyrolyzed carbon materials were studied using N2 adsorption/desorption, Raman, TEM and SEM analysis. There has been remarkable increase in the surface area of the carbon pyrolyzed at 600 degrees C due to the effect of pore generations. The surface area of the 600 degrees C pyrolyzed sample was found to be 1629 m2/g. The electrochemical properties of all the samples were evaluated by cyclic voltammetry, impedance spectroscopy, and galvanostatic charge-discharge tests. The system showed excellent cycleability and a maximum specific capacitance of 291 Fg(-1) was obtained in a 0.1 M H2SO4 electrolyte solution. The effects of the various properties of the activated carbon on the EDLC performance are discussed.

  9. Structural characterization of multimetallic nanoparticles

    NASA Astrophysics Data System (ADS)

    Mukundan, Vineetha

    Bimetallic and trimetallic alloy nanoparticles have enhanced catalytic activities due to their unique structural properties. Using in situ time-resolved synchrotron based x-ray diffraction, we investigated the structural properties of nanoscale catalysts undergoing various heat treatments. Thermal treatment brings about changes in particle size, morphology, dispersion of metals on support, alloying, surface electronic properties, etc. First, the mechanisms of coalescence and grain growth in PtNiCo nanoparticles supported on planar silica on silicon were examined in detail in the temperature range 400-900°C. The sintering process in PtNiCo nanoparticles was found to be accompanied by lattice contraction and L10 chemical ordering. The mass transport involved in sintering is attributed to grain boundary diffusion and its corresponding activation energy is estimated from the data analysis. Nanoscale alloying and phase transformations in physical mixtures of Pd and Cu ultrafine nanoparticles were also investigated in real time with in situ synchrotron based x-ray diffraction complemented by ex situ high-resolution transmission electron microscopy. PdCu nanoparticles are interesting because they are found to be more efficient as catalysts in ethanol oxidation reaction (EOR) than monometallic Pd catalysts. The combination of metal support interaction and reactive/non-reactive environment was found to determine the thermal evolution and ultimate structure of this binary system. The composition of the as prepared Pd:Cu mixture in this study was 34% Pd and 66% Cu. At 300°C, the nanoparticles supported on silica and carbon black intermix to form a chemically ordered CsCl-type (B2) alloy phase. The B2 phase transforms into a disordered fcc alloy at higher temperature (>450°C). The alloy nanoparticles supported on silica and carbon black are homogeneous in volume, but evidence was found of Pd surface enrichment. In sharp contrast, when supported on alumina, the two metals

  10. Relevance of Pore Structure and Diffusion-Accessible Porosity for Calcium-Bromide Diffusion in Na-Montmorillonite

    NASA Astrophysics Data System (ADS)

    Tinnacher, R. M.; Davis, J. A.

    2013-12-01

    Bentonite is an important hydraulic barrier material in many geotechnical applications, such as geosynthetic clay liners at solid waste landfills, or as proposed backfill material in engineered barrier systems at nuclear waste repositories. The limited permeability of bentonite is at least partially the result of its low porosity and the swelling of Na-montmorillonite, its major mineralogical component, in water. Due to these characteristics, the transport of contaminants through bentonite layers is expected to be limited and dominated by diffusion processes. In bentonite, the majority of the connected porosity is associated with montmorillonite particles, which consist of stacks of negatively-charged smectite layers. As a result, compacted smectite has two types of porosities: (1) large pores between clay particles, where diffusion is less affected by electric-double-layer forces, and (2) very thin interlayer spaces within individual clay particles, where diffusion is strongly impacted by surface charge and ionic strength. As diffusion is expected to take place differently in these two volumes, this essentially creates two 'small-scale diffusion pathways', where each may become dominant under different system conditions. Furthermore, for surface-reactive solutes, these two porous regimes differ with regards to surface complexation reactions. Electrostatic and hydration forces only are thought to govern interlayer binding, whereas chemical bonding with surface ligands is dominant for reactions at edge sites of layered clay particles and for iron oxide nanoparticles on outer basal planes. In this presentation, we will demonstrate the relevance of clay pore structure and diffusion-accessible porosity for solute diffusion rates, and hence, contaminant mobility in bentonites. First, we will discuss the effects of chemical solution conditions on montmorillonite properties, such as clay surface charge, diffusion-accessible porosity, clay tortuosity and constrictivity

  11. Preparation of sandwich-structured graphene/mesoporous silica composites with C8-modified pore wall for highly efficient selective enrichment of endogenous peptides for mass spectrometry analysis.

    PubMed

    Yin, Peng; Wang, Yuhua; Li, Yan; Deng, Chunhui; Zhang, Xiangmin; Yang, Pengyuan

    2012-09-01

    In this study, sandwich-structured graphene/mesoporous silica composites (C8-modified graphene@mSiO(2)) were synthesized by coating mesoporous silica onto hydrophilic graphene nanosheets through a surfactant-mediated cocondensation sol-gel process. The newly prepared C8-modified graphene@mSiO(2) nanocomposites possess unique properties of extended plate-like morphology, good water dispersibility, highly open pore structure, uniform pore size (2.8 nm), high surface area (632 m(2)/g), and C8-modified-interior pore walls. The unique structure of the C8-modified graphene@mSiO(2) composite nanosheets not only provide extended planes with hydrophilic surface that prevents aggregation in solution, but also offer a huge number of C8-modified mesopores with high surface area that can ensure an efficient adsorption of peptides through hydrophobic-hydrophobic interaction between C8-moified pore walls and target molecules. The obtained C8-modified graphene@mSiO(2) materials were utilized for size selectively and specifically enriching peptides in standard peptide mixtures and endogenous peptides in real biological samples (mouse brain tissue). PMID:22837154

  12. Preparation and characterization of SNARE-containing nanodiscs and direct study of cargo release through fusion pores.

    PubMed

    Shi, Lei; Howan, Kevin; Shen, Qing-Tao; Wang, Yong Jian; Rothman, James E; Pincet, Frédéric

    2013-05-01

    This protocol describes an assay that uses suspended nanomembranes called nanodiscs to analyze fusion events. A nanodisc is a lipid bilayer wrapped by membrane scaffold proteins. Fluorescent lipids and a protein that is part of a fusion machinery, VAMP2 in the example detailed herein, are included in the nanodiscs. Upon fusion of a nanodisc with a nonfluorescent liposome containing cognate proteins (for instance, the VAMP2 cognate syntaxin1/SNAP-25 complex), the fluorescent lipids are dispersed in the liposome and the increase in fluorescence, initially quenched in the nanodisc, is monitored on a plate reader. Because the scaffold proteins restrain pore expansion, the fusion pore eventually reseals. A reducing agent, such as dithionite, which can quench the fluorescence of accessible lipids, can then be used to determine the number of fusion events. A fluorescence-based approach can also be used to monitor the release of encapsulated cargo. From data on the total cargo release and the number of the much faster lipid-mixing events, the researcher may determine the amount of cargo released per fusion event. This assay requires 3 d for preparation and 4 h for data acquisition and analysis. PMID:23598444

  13. Validation of a Fluid–Structure Interaction Model of Solute Transport in Pores of Cyclically Deformed Tissue Scaffolds

    PubMed Central

    Op Den Buijs, Jorn; Ritman, Erik L.

    2010-01-01

    Convection induced by repetitive compression of porous tissue scaffolds enhances solute transport inside the scaffold. Our previous experiments have shown that pore size, shape, and orientation with respect to strain direction greatly influence loading-induced solute transport. The objective of this study was to develop a computational model of deformation-induced solute transport in porous tissue scaffolds, which included the pore geometry of the scaffold. This geometry consisted of a cubic scaffold with single channel in the middle of the scaffold, immersed in a fluid reservoir. Cylindrical pores with circular or elliptic cross section, and spheroid pores were modeled. The scaffold was cyclically compressed from one side, causing fluid motion and dispersion of solute inside the scaffold pore. Scaffold deformation was solved using the finite element method, and fluid flow and solute transport were solved using the finite volume method. The distortion of the scaffold–fluid interface was transferred as a boundary condition to the fluid flow solver. Both convection and diffusion were included in the computations. The solute transport rates in the different scaffold pore geometries agreed well with our previous experimental results obtained with X-ray microimaging. This model will be used to explore transport properties of a spectrum of novel scaffold designs. PMID:20136371

  14. Health Monitoring for Airframe Structural Characterization

    NASA Technical Reports Server (NTRS)

    Munns, Thomas E.; Kent, Renee M.; Bartolini, Antony; Gause, Charles B.; Borinski, Jason W.; Dietz, Jason; Elster, Jennifer L.; Boyd, Clark; Vicari, Larry; Ray, Asok; Cooper, E. G. (Technical Monitor)

    2002-01-01

    This study established requirements for structural health monitoring systems, identified and characterized a prototype structural sensor system, developed sensor interpretation algorithms, and demonstrated the sensor systems on operationally realistic test articles. Fiber-optic corrosion sensors (i.e., moisture and metal ion sensors) and low-cycle fatigue sensors (i.e., strain and acoustic emission sensors) were evaluated to validate their suitability for monitoring aging degradation; characterize the sensor performance in aircraft environments; and demonstrate placement processes and multiplexing schemes. In addition, a unique micromachined multimeasure and sensor concept was developed and demonstrated. The results show that structural degradation of aircraft materials could be effectively detected and characterized using available and emerging sensors. A key component of the structural health monitoring capability is the ability to interpret the information provided by sensor system in order to characterize the structural condition. Novel deterministic and stochastic fatigue damage development and growth models were developed for this program. These models enable real time characterization and assessment of structural fatigue damage.

  15. Pore structure effects on Ca-based sorbent sulfation capacity at medium temperatures: activated carbon as sorbent/catalyst support.

    PubMed

    Tseng, Hui-Hsin; Wey, Ming-Yen; Lin, Chiou-Liang; Chang, Yu-Chen

    2002-11-01

    The reaction between three different Ca-based sorbents and SO2 were studied in a medium temperature range (473-773 K). The largest SO2 capture was found with Ca(OH)2 at 773 K, 126.31 mg SO2 x g Ca(OH)2(-1), and the influence of SO2 concentration on the sorbent utilization was observed. Investigations of the internal porous structure of Ca-based sorbents showed that the initial reaction rate was controlled by the surface area, and once the sulfated products were produced, pore structure dominated. To increase the surface area of Ca-based sorbents available to interact with and retain SO2, one kind of CaO/ activated carbon (AC) sorbent/catalyst was prepared to study the effect of AC on the dispersion of Ca-based materials. The results indicated that the Ca-based material dispersed on high-surface-area AC had more capacities for SO2 than unsupported Ca-based sorbents. The initial reaction rates of the reaction between SO2 and Ca-based sorbents and the prepared CaO/AC sorbents/catalysts were measured. Results showed that the reaction rate apparently increased with the presence of AC. It was concluded that CaO/AC was the active material in the desulfurization reaction. AC acting as the support can play a role to supply O2 to increase the affinity to SO2. Moreover, when AC is acting as a support, the surface oxygen functional group formed on the surface of AC can serve as a new site for SO2 adsorption.

  16. Metal-organic frameworks: structure, properties, methods of synthesis and characterization

    NASA Astrophysics Data System (ADS)

    Butova, V. V.; Soldatov, M. A.; Guda, A. A.; Lomachenko, K. A.; Lamberti, C.

    2016-03-01

    This review deals with key methods of synthesis and characterization of metal-organic frameworks (MOFs). The modular structure affords a wide variety of MOFs with different active metal sites and organic linkers. These compounds represent a new stage of development of porous materials in which the pore size and the active site structure can be modified within wide limits. The set of experimental methods considered in this review is sufficient for studying the short-range and long-range order of the MOF crystal structure, determining the morphology of samples and elucidating the processes that occur at the active metal site in the course of chemical reactions. The interest in metal-organic frameworks results, first of all, from their numerous possible applications, ranging from gas separation and storage to chemical reactions within the pores. The bibliography includes 362 references.

  17. Novel in situ multiharmonic EQCM-D approach to characterize complex carbon pore architectures for capacitive deionization of brackish water.

    PubMed

    Shpigel, Netanel; Levi, Mikhael D; Sigalov, Sergey; Aurbach, Doron; Daikhin, Leonid; Presser, Volker

    2016-03-23

    Multiharmonic analysis by electrochemical quartz-crystal microbalance with dissipation monitoring (EQCM-D) is introduced as an excellent tool for quantitative studying electrosorption of ions from aqueous solution in mesoporous (BP-880) or mixed micro-mesoporous (BP-2000) carbon electrodes. Finding the optimal conditions for gravimetric analysis of the ionic content in the charged carbon electrodes, we propose a novel approach to modeling the charge-dependent gravimetric characteristics by incorporation of Gouy-Chapman-Stern electric double layer model for ions electrosorption into meso- and micro-mesoporous carbon electrodes. All three parameters of the gravimetric equation evaluated by fitting it to the experimental mass changes curves were validated using supplementary nitrogen gas sorption analysis and complementing atomic force microscopy. Important overlap between gravimetric EQCM-D analysis of the ionic content of porous carbon electrodes and the classical capacitive deionization models has been established. The necessity and usefulness of non-gravimetric EQCM-D characterizations of complex carbon architectures, providing insight into their unique viscoelastic behavior and porous structure changes, have been discussed in detail.

  18. Using noble gases in the pore water of ocean sediments to characterize CH4 seepage off the coast of New Zealand

    NASA Astrophysics Data System (ADS)

    Tomonaga, Yama; Brennwald, Matthias S.; Kipfer, Rolf

    2013-04-01

    Newly developed analytical techniques to determine the abundances of noble gases in sediment pore water [1, 5] allow noble-gas concentrations and isotope ratios to be measured easily and routinely in unconsolidated lacustrine sediments [6, 7]. We applied these techniques for the first time to ocean sediments to investigate an active cold methane seepage system located in the South Pacific off the coast of New Zealand using 3He-4He ratios determined in the sediment pore water. Our results [8] show that more 3He-rich fluids are released in the vicinity of the Pacific-Australian subduction zone than at the forearc stations located closer to the New Zealand coast. However, the 3He-4He isotope signature in the sediment column indicates that only a minor part of the He emanating from deeper strata originates from a (depleted) mantle source. Hence, most He in the pore water is produced locally by the radioactive decay of U and Th in the sediment minerals or in the underlying crustal rocks. Such an occurrence of isotopically heavy crustal He also suggests that the source of the largest fraction of methane is a near-surface geochemical reservoir. This finding is in line with a previous δ13C study in the water column which concluded that the emanating methane is most likely of biological origin and is formed in the upper few meters of the sediment column [2]. The prevalence of isotopically heavy He agrees well with the outcome of other previous studies on island arc systems [3, 4] which indicate that the forearc regions are characterized by crustal He emission, whereas the volcanic arc region is characterized by the presence of mantle He associated with rising magma. References [1] Brennwald, M. S., Hofer, M., Peeters, F., Aeschbach-Hertig, W., Strassmann, K., Kipfer, R., and Imboden, D. M. (2003). Analysis of dissolved noble gases in the pore water of lacustrine sediments. Limnol. Oceanogr.: Methods 1, 51-62. [2] Faure, K., Greinert, J., Schneider von Deimling, J., Mc

  19. Fabrication, characterization, and application of microresonators and resonant structures

    NASA Astrophysics Data System (ADS)

    Cohoon, Gregory A.

    Optical resonators are structures that allow light to circulate and store energy for a duration of time. This work primarily looks at the fabrication, characterization, and application of whispering gallery mode microresonators and the analysis of organic photonic crystal-like structures and simulation of their resonant effects. Whispering gallery mode (WGM) microresonators are a class of cylindrically symmetric optical resonator which light circulates around the equator of the structure. These resonators are named after acoustic whispering galleries, where a whisper can be heard anywhere along the perimeter of a circular room. These optical structures are known for their ultra high Q-factor and their low mode volume. Q-factor describes the photon lifetime in the cavity and is responsible for the energy buildup within the cavity and sharp spectral characteristics of WGM resonators. The energy buildup is ideal for non-linear optics and the sharp spectral features are beneficial for sensing applications. Characterization of microbubble resonators is done by coupling light from a tunable laser source via tapered optical fiber into the cavity. The fabrication of quality tapered optical fiber on the order of 1--2 microm is critical to working on WGM resonators. The measurement of Q-factors up to 2x10 8 and mode spectra are possible with these resonators and experimental techniques. This work focuses on microdisk and microbubble WGM resonators. The microdisk resonators are fabricated by femtosecond laser micromachining. The micromachined resonators are fabricated by ablating rotating optical fiber to generate the disk shape and then heated to reflow the surface to improve optical quality. These resonators have a spares mode spectrum and display a Q factor as high a 2x106. The microbubble resonators are hollow microresonators fabricated by heating a pressurized capillary tube which forms a bubble in the area exposed to heat. These have a wall thickness of 2--5 microm and

  20. X-ray and Cryo-electron Microscopy Structures of Monalysin Pore-forming Toxin Reveal Multimerization of the Pro-form*

    PubMed Central

    Leone, Philippe; Bebeacua, Cecilia; Opota, Onya; Kellenberger, Christine; Klaholz, Bruno; Orlov, Igor; Cambillau, Christian; Lemaitre, Bruno; Roussel, Alain

    2015-01-01

    β-Barrel pore-forming toxins (β-PFT), a large family of bacterial toxins, are generally secreted as water-soluble monomers and can form oligomeric pores in membranes following proteolytic cleavage and interaction with cell surface receptors. Monalysin has been recently identified as a β-PFT that contributes to the virulence of Pseudomonas entomophila against Drosophila. It is secreted as a pro-protein that becomes active upon cleavage. Here we report the crystal and cryo-electron microscopy structure of the pro-form of Monalysin as well as the crystal structures of the cleaved form and of an inactive mutant lacking the membrane-spanning region. The overall structure of Monalysin displays an elongated shape, which resembles those of β-pore-forming toxins, such as Aerolysin, but is devoid of a receptor-binding domain. X-ray crystallography, cryo-electron microscopy, and light-scattering studies show that pro-Monalysin forms a stable doughnut-like 18-mer complex composed of two disk-shaped nonamers held together by N-terminal swapping of the pro-peptides. This observation is in contrast with the monomeric pro-form of the other β-PFTs that are receptor-dependent for membrane interaction. The membrane-spanning region of pro-Monalysin is fully buried in the center of the doughnut, suggesting that upon cleavage of pro-peptides, the two disk-shaped nonamers can, and have to, dissociate to leave the transmembrane segments free to deploy and lead to pore formation. In contrast with other toxins, the delivery of 18 subunits at once, nearby the cell surface, may be used to bypass the requirement of receptor-dependent concentration to reach the threshold for oligomerization into the pore-forming complex. PMID:25847242

  1. Fabrication and Structure Characterization of Alumina-Aluminum Interpenetrating Phase Composites

    NASA Astrophysics Data System (ADS)

    Dolata, Anna J.

    2016-01-01

    Alumina-Aluminum composites with interpenetrating networks structure belong to advanced materials with potentially better properties when compared with composites reinforced by particles or fibers. The paper presents the experimental results of fabrication and structure characterization of Al matrix composites locally reinforced via Al2O3 ceramic foam. The composites were obtained using centrifugal infiltration of porous ceramics by liquid aluminum alloy. Both scanning electron microscopy (SEM + EDS) and x-ray tomography were used to determine the structure of foams and composites especially in reinforced areas. The quality of castings, degree of pore filling in ceramic foams by Al alloy, and microstructure in area of interface were assessed.

  2. Fabrication and Structure Characterization of Alumina-Aluminum Interpenetrating Phase Composites

    NASA Astrophysics Data System (ADS)

    Dolata, Anna J.

    2016-08-01

    Alumina-Aluminum composites with interpenetrating networks structure belong to advanced materials with potentially better properties when compared with composites reinforced by particles or fibers. The paper presents the experimental results of fabrication and structure characterization of Al matrix composites locally reinforced via Al2O3 ceramic foam. The composites were obtained using centrifugal infiltration of porous ceramics by liquid aluminum alloy. Both scanning electron microscopy (SEM + EDS) and x-ray tomography were used to determine the structure of foams and composites especially in reinforced areas. The quality of castings, degree of pore filling in ceramic foams by Al alloy, and microstructure in area of interface were assessed.

  3. Modelling the effect of pore structure and wetting angles on capillary rise in soils having different wettabilities

    NASA Astrophysics Data System (ADS)

    Czachor, Henryk

    2006-09-01

    SummaryCapillary rise in axis symmetrical sinusoidal capillary (SC) has been modelled. Analytical formula for meniscus radius, capillary pressure and meniscus rate in SC have been found. Capillary shape described by wall waviness highly influences all of them. The limit between wettability and repellency in such capillary is described by critical value of contact angle θc which is related to the pore geometry by the equation ctg( θc) = πd2, where d2 - pore wall waviness. Kinetics of capillary rise in sinusoidal capillary has been determined by numerical integration of meniscus rate equation for a wide range of pore wall waviness and several values of contact angles. Application of Washburn theory to the data obtained from simulation gives the contact angle value much higher than the true one. In contrast, the obtained pore radius value is usually well correlated with capillary neck. However, in some cases a calculated radius can be even smaller. Above conclusions have been qualitatively confirmed by experiments performed on glass beads and soils. Contact angle measured on flat glass was 27.4°. The calculations concerning the data from capillary rise experiments on 90-1000 μm fraction of glass powder and Washburn theory gave values ca. 80°. The contact angle values for peat soils and loamy sand have close values, which supports the opinion that non-cylindrical shape of soil pores highly influences both the wettability/repellency and the water flux in soils.

  4. Experiments In Characterizing Vibrations Of A Structure

    NASA Technical Reports Server (NTRS)

    Yam, Yeung; Hadaegh, Fred Y.; Bayard, David S.

    1993-01-01

    Report discusses experiments conducted to test methods of identification of vibrational and coupled rotational/vibrational modes of flexible structure. Report one in series that chronicle development of integrated system of methods, sensors, actuators, analog and digital signal-processing equipment, and algorithms to suppress vibrations in large, flexible structure even when dynamics of structure partly unknown and/or changing. Two prior articles describing aspects of research, "Autonomous Frequency-Domain Indentification" (NPO-18099), and "Automated Characterization Of Vibrations Of A Structure" (NPO-18141).

  5. Development of an in-situ soil structure characterization methodology

    NASA Astrophysics Data System (ADS)

    Debos, Endre; Kriston, Sandor

    2015-04-01

    The agricultural cultivation has several direct and indirect effects on the soil properties, among which the soil structure degradation is the best known and most detectable one. Soil structure degradation leads to several water and nutrient management problems, which reduce the efficiency of agricultural production. There are several innovative technological approaches aiming to reduce these negative impacts on the soil structure. The tests, validation and optimization of these methods require an adequate technology to measure the impacts on the complex soil system. This study aims to develop an in-situ soil structure and root development testing methodology, which can be used in field experiments and which allows one to follow the real time changes in the soil structure - evolution / degradation and its quantitative characterization. The method is adapted from remote sensing image processing technology. A specifically transformed A/4 size scanner is placed into the soil into a safe depth that cannot be reached by the agrotechnical treatments. Only the scanner USB cable comes to the surface to allow the image acquisition without any soil disturbance. Several images from the same place can be taken throughout the vegetation season to follow the soil consolidation and structure development after the last tillage treatment for the seedbed preparation. The scanned image of the soil profile is classified using supervised image classification, namely the maximum likelihood classification algorithm. The resulting image has two principal classes, soil matrix and pore space and other complementary classes to cover the occurring thematic classes, like roots, stones. The calculated data is calibrated with filed sampled porosity data. As the scanner is buried under the soil with no changes in light conditions, the image processing can be automated for better temporal comparison. Besides the total porosity each pore size fractions and their distributions can be calculated for

  6. Structural characterization of unusually stable polycyclic ozonides

    NASA Astrophysics Data System (ADS)

    Cusati, R. C.; Pereira, U. A.; Barbosa, L. C. A.; Maltha, C. R. A.; Carneiro, José W. M.; Corrêa, R. S.; Doriguetto, A. C.

    2015-02-01

    The single crystal structure of seven tri- and tetracyclic ozonides derived from 8-oxabicycle[3.2.1]oct-6-en-3-ones have been characterized by X-ray diffraction method. Five ozonides (4, 5, 6, 7 and 8) crystallize in the monoclinic crystal system with P21/c space group. Compound 3 crystallize in the unusual centrosymmetric space group R 3 bar m, which represents ∼0.04% of the total number of structures know. The supramolecular structure of 3 forms infinite channels in a hexagram fashion, resulting in a honeycomb-like structure. Semi-empirical (PM6) and density functional theory methods (DFT) with the B3LYP functional and the 6-31G(d) basis set were used to optimize the geometries and compute structural parameters (bond lengths, angles and dihedral angles) that could be compared to the refined crystal structure. The theoretical results show good agreements with the experimental structure.

  7. Structure of a prokaryotic sodium channel pore reveals essential gating elements and an outer ion binding site common to eukaryotic channels

    PubMed Central

    Shaya, David; Findeisen, Felix; Abderemane-Ali, Fayal; Arrigoni, Cristina; Wong, Stephanie; Nurva, Shailika Reddy; Loussouarn, Gildas; Minor, Daniel L.

    2013-01-01

    Voltage-gated sodium channels (NaVs) are central elements of cellular excitation. Notwithstanding advances from recent bacterial NaV (BacNaV) structures, key questions about gating and ion selectivity remain. Here, we present a closed conformation of NaVAe1p, a pore-only BacNaV derived from NaVAe1, a BacNaV from the arsenite oxidizer Alkalilimnicola ehrlichei found in Mono Lake, California, that provides insight into both fundamental properties. The structure reveals a pore domain in which the pore-lining S6 helix connects to a helical cytoplasmic tail. Electrophysiological studies of full-length BacNaVs show that two elements defined by the NaVAe1p structure, an S6 activation gate position and the cytoplasmic tail ‘neck’, are central to BacNaV gating. The structure also reveals the selectivity filter ion entry site, termed the ‘outer ion’ site. Comparison with mammalian voltage-gated calcium channel (CaV) selectivity filters, together with functional studies shows that this site forms a previously unknown determinant of CaV high affinity calcium binding. Our findings underscore commonalities between BacNaVs and eukaryotic voltage-gated channels and provide a framework for understanding gating and ion permeation in this superfamily. PMID:24120938

  8. Electrochemical Characterization of Semiconductor Materials and Structures

    NASA Technical Reports Server (NTRS)

    1997-01-01

    The objective of this investigation was to demonstrate the applicability of electrochemical techniques for characterization of complex device structures based on InP and GaAs, Ge, InGaAs, InSb, InAs and InSb, including: (1) accurate EC-V net majority carrier concentration depth profiling, and (2) surface and bulk structural and electrical type defect densities. Our motivation for this R&D effort was as follows: Advanced space solar cells and thermophotovoltaic (TPV) cells are fabricated using a large variety of III-V materials based on InP and GaAs for solar cells and low bandgap materials such as Ge, InGaAs, InAs and InSb for TPV applications. At the present time for complex device structures using these materials, however, there is no simple way to assess the quality of these structures prior to device fabrication. Therefore, process optimization is a very time consuming and a costly endeavor. Completion of this R&D effort would have had unquestionable benefits for space solar cell and TPV cells, since electrochemical characterization of the above cell structures, if properly designed can provide many useful structural and electrical material information virtually at any depth inside various layers and at the interfaces. This, could have been applied for step-by-step process optimization, which could have been used for fabrication of new generation high efficiency, low cost space PV and TPV cells. The four projects were as follows: (1) Electrochemical characterization of Germanium Substrates and Structures for TPV and other Device applications; (2) Electrochemical characterization of InP and GaAs based structures grown on InP, GaAs, and Si of Ge substrates for space solar cell applications; (3) Electrochemical characterization of InGaAs based structures grown on Ge Substrates,using InP as a buffer layer for TPV applications; (4) Electrochemical characterization of InSb and InAs bases structures for TPV applications.

  9. Electrochemical characterization of InP structures

    NASA Technical Reports Server (NTRS)

    Faur, Maria; Faur, Mircea; Vargas-Aburto, Carlos; Wilt, David M.; Goradia, Manju

    1992-01-01

    Electrochemical (EC) techniques represent a simple and yet accurate method to characterize InP and related materials structures. With EC techniques, uncertainties in the measurements arising from factors such as surface effects, the composition and thickness of a front dead layer, the contacts, etc., can be significantly reduced when both a suitable electrolyte is used and the measuring conditions are carefully selected. In this work, the use of photoelectrochemical techniques with InP structures is reported. The work focuses on both the characterization and the optimization of structures grown by thermal diffusion and by epitaxial methods. Characterization of the structures is done by studying the variation in the density of surface states, number of defects, and net majority carrier concentration as a function of material removed. A step-by-step optimization process of n(sup +)p and p(sup+)n InP structures is also described. This involves the passivation and subsequent removal of damaged layers in order to extract the performance parameters of solar cells fabricated with these structures.

  10. Integrated Pore-Water and Geophysical Investigations StreamlineCharacterization of Ground-Water Discharges to Surface Water

    EPA Science Inventory

    This issue of Technology News and Trends highlights strategies and tools for characterizing or monitoring remediation of sites with contaminated sediment. Addressing these sites often relies upon dynamic workplans that involve more efficient, cost-effective, and practical methods...

  11. Proliferation and osteogenic differentiation of human bone marrow stromal cells on alginate-gelatine-hydroxyapatite scaffolds with anisotropic pore structure.

    PubMed

    Bernhardt, A; Despang, F; Lode, A; Demmler, A; Hanke, T; Gelinsky, M

    2009-01-01

    Porous mineralized scaffolds are required for various applications in bone engineering. In particular, tube-like pores with controlled orientation inside the scaffold may support homogeneous cell seeding as well as sufficient nutrient supply and may facilitate blood vessel ingrowth. Scaffolds with parallely orientated tube-like pores were generated by diffusion-controlled ionotropic gelation of alginate. Incorporation of hydroxyapatite (HA) during the gelation process yielded stable scaffolds with an average pore diameter of approximately 90 microm. To evaluate the potential use of alginate-gelatine-HA scaffolds for bone tissue engineering, in vitro tests with human bone marrow stromal cells (hBMSCs) were carried out. We analysed biocompatibility and cell penetration into the capillary pores by microscopic methods. hBMSCs were also cultivated on alginate-gelatine-HA scaffolds for 3 weeks in the presence and absence of osteogenic supplements. We studied proliferation and osteogenic differentiation in terms of total lactate dehydrogenase (LDH) activity, DNA content and alkaline phosphatase (ALP) activity and found a 10-14-fold increase of cell number after 2 weeks of cultivation, as well as an increase of specific ALP activity for osteogenic-induced hBMSCs. Furthermore, the expression of bone-related genes [ALP, bone sialoprotein II (BSPII)] was analysed. We found an increase of ALP as well as BSPII expression for osteogenic-induced hBMSCs on alginate-gelatin-HA scaffolds.

  12. Ion and water transport in a Nafion{reg_sign} membrane pore: A statistical mechanical model with molecular structure

    SciTech Connect

    Paddison, S.J.; Zawodzinski, T.A. Jr.; Paul, R.

    1998-12-31

    With the well established importance of the coupling of water and protons through electroosmotic drag in operating PEFCs the authors present here a derivation of a mathematical model that focuses on the computation of the mobility of an hydronium ion through an arbitrary cylindrical pore of a PEM with a non-uniform charge distribution on the walls of the pore. The total Hamiltonian is derived for the hydronium ion as it moves through the hydrated pore and is effected by the net potential due to interaction with the solvent molecules and the pendant side chains. The corresponding probability density is derived through solution of the Liouville equation. This probability density is then used to compute the friction tensor for the hydronium ion. The authors find two types of contributions: (a) due to the solvent-ion interactions for which they adopt the conventional continuum model; (b) due to the interaction between the pendant charges and the hydronium ion. The latter is a new result and displays the role of the non-uniform nature of the charge distribution on the pore wall.

  13. Use of 3D X-ray Computed Microtomography to Observe in situ Sediment Structure and Colloidal Zirconia Deposits at the Pore Scale

    NASA Astrophysics Data System (ADS)

    Chen, C.; Packman, A. I.; Keane, D. T.; Gaillard, J.

    2006-12-01

    We are using X-ray Micro-Tomography (XMT) to study in situ sediment structure using the facilities of the DuPont-Northwestern-Dow Collaborative Access Team (DND-CAT), Advanced Photon Source (APS), Argonne National Laboratory. Images of a sediment sample are taken at a number of different angles as the incident x- ray beam passes through it, and a three-dimensional view of the interior of the sample is then reconstructed from these maps using Computed Tomography (CT). These 3D images allow us to observe sediment structure with near-micron-scale resolution. We are also using difference tomography to resolve the distribution of zirconium in sediment cores. Column experiments were performed to observe the deposition of colloidal zirconia (Zr) particles in porous media composed of glass beads. Reconstructed 3D maps of Zr deposition demonstrate strong pore-scale heterogeneity. Most zirconia particles accumulated at the upstream sides of collector beads and in narrow pore throats. Statistical analysis of deposition clusters reveals the average, large-scale filtration behavior. Reconstructed 3D pore structure data were used to investigate scale dependency and the effects of local variation within the porous medium. Statistical representative elementary volumes were calculated for quantities such as porosity, specific surface area, and permeability. Finally, preliminary experiments in flume were conducted in order to investigate zirconia deposition in streambeds at the scale of characteristic topographic features (bedforms).

  14. Synthesis, characterization, and biodistribution of multiple 89Zr-labeled pore-expanded mesoporous silica nanoparticles for PET

    NASA Astrophysics Data System (ADS)

    Miller, Larissa; Winter, Gordon; Baur, Benjamin; Witulla, Barbara; Solbach, Christoph; Reske, Sven; Lindén, Mika

    2014-04-01

    Functional nanoparticles are highly interesting imaging agents for positron emission tomography (PET) due to the possibility of multiple incorporation of positron emitting radionuclides thus increasing the signal strength. Furthermore, long-term nanoparticle biodistribution tests with increased signal-to-noise ratio can be achieved with nanoparticles carrying long-lived isotopes. Mesoporous silica nanoparticles, MSNs, have recently attracted a lot of interest as both imaging agents and carriers for drugs in vitro and in vivo. Here we present results related to the synthesis of PET imageable MSNs carrying the long-lived 89Zr isotope (half-life of 78.4 hours). Here, 89Zr4+ was immobilized through covalent attachment of the complexing agent p-isothiocyanatobenzyldesferrioxamine (DFO-NCS) to large-pore MSNs. Due to the presence of the high DFO content on the MSNs, quantitative 89Zr4+ labeling was achieved within just a few minutes, and no subsequent purification step was needed in order to remove non-complexed 89Zr4+. The stability of the 89Zr-labeled MSNs against leaching of 89Zr4+ was verified for 24 hours. The high signal strength of the 89Zr-DFO-MSNs was evidenced by successful PET imaging using a mouse model at particle loadings one order of magnitude lower than those previously applied in PET-MSN studies. The biodistribution followed the same trends as previously observed for MSNs of different sizes and surface functionalities. Taken together, our results suggest that 89Zr-DFO-MSNs are promising PET imaging agents for long-term in vivo imaging.Functional nanoparticles are highly interesting imaging agents for positron emission tomography (PET) due to the possibility of multiple incorporation of positron emitting radionuclides thus increasing the signal strength. Furthermore, long-term nanoparticle biodistribution tests with increased signal-to-noise ratio can be achieved with nanoparticles carrying long-lived isotopes. Mesoporous silica nanoparticles, MSNs, have

  15. Characterization of the microbial community colonizing the anal and vulvar pores of helminths from the hindgut of zebras.

    PubMed Central

    Mackie, R I; Krecek, R C; Els, H J; van Niekerk, J P; Kirschner, L M; Baecker, A A

    1989-01-01

    Scanning and transmission electron microscopy were used to examine the adherence and in situ morphology of the microbial community colonizing the anal and vulvar pores of the subfamily Cyathostominae (Nematoda: Strongylidae) from the colon of Burchell's zebra (Equus burchelli antiquorum). Two different morphological types of asporogenous rod were prominent in the microbial community. One was a thin, septate, filamentous organism (0.4 to 0.5 micron by 2 to 3 microns) with blunt ends, which was more prominent at the site of attachment. The other was a larger (1.8 to 2.4 microns by 5 to 10 microns) multicellular rod with round ends in the form of a trichome. Spiral- and vibrio-shaped bacteria were also present in the thin sections. The septate filaments were shown to contain a cell spacer similar to those described in Methanospirillum hungatei. Attachment to the cuticle was by means of an amorphous electron-dense material with fibrillar appearance and not by specialized holdfast segments. Ten isolates were obtained from a habitat-simulating medium on which a homogenate from the posterior region was plated. Antibodies were raised to whole cells of five rod-shaped isolates in rabbits and fluorescein isothiocyanate labeled. Positive bright-yellow fluorescence was obtained with one of the clostridial isolates. The results are discussed with reference to other bacteria with similar morphology, the nature of this unique interrelationship between the microbial community and its parasitic host inside the equine hindgut, and the possibility of biological control of parasitic helminths. Images PMID:2667460

  16. Electrochemical Characterization of Semiconductor Materials and Structures

    NASA Technical Reports Server (NTRS)

    1997-01-01

    For a period covering October 1, 1995 through August 12, 1996, the research group at CSU has conducted theoretical and experimental research on "Electrochemical Characterization of Semiconductor Materials and Structures. " The objective of this investigation was to demonstrate the applicability of electrochemical techniques for characterization of complex device structures based on InP and GaAs, Ge, InGaAs, InSb, InAs and InSb, including: (1) accurate EC-V net majority carrier concentration depth profiling, and (2) surface and bulk structural and electrical type defect densities. Our motivation for this R&D effort was as follows: "Advanced space solar cells and ThermoPhotoVoltaic (TPV) cells are fabricated using a large variety of III-V materials based on InP and GaAs for solar cells and low bandgap materials such as Ge, InGaAs, InAs and InSb for TPV applications. At the present time for complex device structures using these materials, however, there is no simple way to assess the quality of these structures prior to device fabrication. Therefore, process optimization is a very time consuming and a costly endeavor". Completion of this R&D effort would have had unquestionable benefits for space solar cell and TPV cells, since electrochemical characterization of the above cell structures, if properly designed can provide many useful structural and electrical material information virtually at any depth inside various layers and at the interfaces. This, could have been applied for step-by-step process optimization, which could have been used for fabrication of new generation high efficiency, low cost space PV and TPV cells.

  17. Poring over two-pore channel pore mutants

    PubMed Central

    Penny, Christopher J.; Patel, Sandip

    2016-01-01

    Two-pore channels are members of the voltage-gated ion channel superfamily. They localise to the endolysosomal system and are likely targets for the Ca2+ mobilising messenger NAADP. In this brief review, we relate mutagenesis of the TPC pore to a recently published homology model and discuss how pore mutants are informing us of TPC function. Molecular physiology of these ubiquitous proteins is thus emerging. PMID:27226934

  18. Improving bone repair of femoral and radial defects in rabbit by incorporating PRP into PLGA/CPC composite scaffold with unidirectional pore structure.

    PubMed

    He, Fupo; Chen, Yan; Li, Jiyan; Lin, Bomiao; Ouyang, Yi; Yu, Bo; Xia, Yuanyou; Yu, Bo; Ye, Jiandong

    2015-04-01

    In this study, a platelet-rich plasma poly(lactic-co-glycolic acid) (PRP-PLGA)/calcium phosphate cement (CPC) composite scaffold was prepared by incorporating PRP into PLGA/CPC scaffold with unidirectional pore structure, which was fabricated by the unidirectional freeze casting of CPC slurry and the following infiltration of PLGA. The results from in vitro cell experiments and in vivo implantation in femoral defects manifested that incorporation of PRP into PLGA/CPC scaffold improved in vitro cell response (cell attachment, proliferation, and differentiation), and markedly boosted bone formation, angiogenesis and material degradation. The incorporation of PRP into scaffold showed more outstanding improvement in osteogenesis as the scaffolds were used to repair the segmental radial defects, especially at the early stage. The new bone tissues grew along the unidirectional lamellar pores of scaffold. At 12 weeks postimplantation, the segmental radial defects treated with PRP-PLGA/CPC scaffold had almost recuperated, whereas treated with the scaffold without PRP was far from healed. Taken together, the PRP-PLGA/CPC scaffold with unidirectional pore structure is a promising candidate to repair bone defects at various sites.

  19. The dependence of phase change enthalpy on the pore structure and interfacial groups in hydrated salts/silica composites via sol-gel.

    PubMed

    Wu, Yuping; Wang, Tao

    2015-06-15

    It was found that the procedures for incorporating hydrated salts into silica, including mixing with sol in an instant (S1 procedure), mixing with sol via drop by drop (S2 procedure) and mixing until the sol forming the gel (S3 procedure), had pronounced effects on the phase change enthalpy of hydrated salts/silica composite via sol-gel process. The discrepancy of phase change enthalpies of the composites with the same content of hydrated salts can be as high as 40 kJ/kg. To unveil the mechanism behind, the pore structure of silica matrix and interfacial functional groups were investigated extensively. It was revealed that different incorporation procedures resulted in distinct pore structure of silica matrix and different intensities of interfacial Si-OH groups. The S3 procedure was beneficial to induce the silica matrix with bigger pore size and fewer Si-OH groups. Consequently, the phase change enthalpy of the hydrated salts/silica composite prepared by this procedure was the highest because of its lower size confinement effects and weaker adsorption by Si-OH groups. This study will provide insight into the preparation of shape-stabilized phase change materials for thermal energy storage applications.

  20. Pore-water chemistry from the ICDP-USGS coer hole in the Chesapeake Bay impact structure--Implications for paleohydrology, microbial habitat, and water resources

    USGS Publications Warehouse

    Sanford, Ward E.; Voytek, Mary A.; Powars, David S.; Jones, Blair F.; Cozzarelli, Isabelle M.; Eganhouse, Robert P.; Cockell, Charles S.

    2009-01-01

    We investigated the groundwater system of the Chesapeake Bay impact structure by analyzing the pore-water chemistry in cores taken from a 1766-m-deep drill hole 10 km north of Cape Charles, Virginia. Pore water was extracted using high-speed centrifuges from over 100 cores sampled from a 1300 m section of the drill hole. The pore-water samples were analyzed for major cations and anions, stable isotopes of water and sulfate, dissolved and total carbon, and bioavailable iron. The results reveal a broad transition between fresh and saline water from 100 to 500 m depth in the post-impact sediment section, and an underlying syn-impact section that is almost entirely filled with brine. The presence of brine in the lowermost post-impact section and the trend in the dissolved chloride with depth suggest a transport process dominated by molecular diffusion and slow, compaction-driven, upward flow. Major ion results indicate residual effects of diagenesis from heating, and a pre-impact origin for the brine. High levels of dissolved organic carbon (6-95 mg/L) and the distribution of electron acceptors indicate an environment that may be favorable for microbial activity throughout the drilled section. The concentration and extent of the brine is much greater than had previously been observed, suggesting its occurrence may be common in the inner crater. However, groundwater flow conditions in the structure may reduce the salt-water-intrusion hazard associated with the brine.

  1. Pore-water chemistry from the ICDP-USGS core hole in the Chesapeake Bay impact structure-Implications for paleohydrology, microbial habitat, and water resources

    USGS Publications Warehouse

    Sanford, W.E.; Voytek, M.A.; Powars, D.S.; Jones, B.F.; Cozzarelli, I.M.; Cockell, C.S.; Eganhouse, R.P.

    2009-01-01

    We investigated the groundwater system of the Chesapeake Bay impact structure by analyzing the pore-water chemistry in cores taken from a 1766-m-deep drill hole 10 km north of Cape Charles, Virginia. Pore water was extracted using high-speed centrifuges from over 100 cores sampled from a 1300 m section of the drill hole. The pore-water samples were analyzed for major cations and anions, stable isotopes of water and sulfate, dissolved and total carbon, and bioavailable iron. The results reveal a broad transition between freshwater and saline water from 100 to 500 m depth in the postimpact sediment section, and an underlying synimpact section that is almost entirely filled with brine. The presence of brine in the lowermost postimpact section and the trend in dissolved chloride with depth suggest a transport process dominated by molecular diffusion and slow, compaction-driven, upward flow. Major ion results indicate residual effects of diagenesis from heating, and a pre-impact origin for the brine. High levels of dissolved organic carbon (6-95 mg/L) and the distribution of electron acceptors indicate an environment that may be favorable for microbial activity throughout the drilled section. The concentration and extent of the brine is much greater than had previously been observed, suggesting that its occurrence may be common in the inner crater. However, groundwater-flow conditions in the structure may reduce the saltwater-intrusion hazard associated with the brine. ?? 2009 The Geological Society of America.

  2. Effect of the internal motions of an adsorbate on the characteristics of adsorption for structurally heterogenous surfaces of slit-like pores

    NASA Astrophysics Data System (ADS)

    Tovbin, Yu. K.; Zaitseva, E. S.; Rabinovich, A. B.

    2016-01-01

    The effect of internal motions of an adsorbate on the local characteristics of adsorption and layering phase diagrams are studied for structurally heterogeneous surfaces of slit-like pores. A molecular model describing adsorbate distributions inside slit-like pores, which is based on discrete distribution functions (lattice gas model), is used for the calculation. Molecular distributions are calculated by the Lennard-Jones potential (12-6) in a quasi-chemical approximation reflecting the effects of direct correlations of interacting particles and for the combined interaction of an adsorbate with walls in the average potential approximation (9-3) and the short-range Lennard-Jones potential for structurally heterogeneous surface areas. The conclusion is made that internal motions reflect the vibrational motion of molecules within a modified quasi-dimer model and a displacement of the adsorbate during its translational motion inside cells. It was found that the taking into account of internal motions decreases the critical temperature of adsorbate layering in slit-like pores.

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

    PubMed

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

    2016-01-01

    Electro-spun nanofiber web is highly attractive as a separator for lithium ion batteries because of its high electrical properties. In moving toward wider battery applications of the nanofiber separators, a deeper understanding on the structure and property relationship is highly meaningful. In this regard, we prepared electro-spun poly(vinylidene fluoride) (PVdF) webs with various thicknesses (10.5~100 µm) and investigated their structures and electrochemical performances. As the thickness of the web is decreased, a decrease of porosity and an increase of pore size are resulted in. For the 10.5 µm-thick separator, a minor short-circuit was detected, stressing the importance of reducing pore-size on prevention of short-circuit. However, above the thickness of 21 µm, well-connected, submicron-sized pores are generated, and, with lowering the separator thickness, discharge capacity and rate capability are enhanced owing to the lowered area-specific resistance. PMID:27398553

  4. A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels

    PubMed Central

    Napolitano, Luisa Maria Rosaria; Bisha, Ina; De March, Matteo; Marchesi, Arin; Arcangeletti, Manuel; Demitri, Nicola; Mazzolini, Monica; Rodriguez, Alex; Magistrato, Alessandra; Onesti, Silvia; Laio, Alessandro; Torre, Vincent

    2015-01-01

    Cyclic nucleotide-gated (CNG) ion channels, despite a significant homology with the highly selective K+ channels, do not discriminate among monovalent alkali cations and are permeable also to several organic cations. We combined electrophysiology, molecular dynamics (MD) simulations, and X-ray crystallography to demonstrate that the pore of CNG channels is highly flexible. When a CNG mimic is crystallized in the presence of a variety of monovalent cations, including Na+, Cs+, and dimethylammonium (DMA+), the side chain of Glu66 in the selectivity filter shows multiple conformations and the diameter of the pore changes significantly. MD simulations indicate that Glu66 and the prolines in the outer vestibule undergo large fluctuations, which are modulated by the ionic species and the voltage. This flexibility underlies the coupling between gating and permeation and the poor ionic selectivity of CNG channels. PMID:26100907

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

    NASA Astrophysics Data System (ADS)

    Saif, T.

    2015-12-01

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

  6. Designed membrane channels and pores.

    PubMed

    Bayley, H

    1999-02-01

    Advances in the synthesis and assembly of designed membrane channels and pores include addressable template-assisted synthetic protein (TASP) syntheses of helix bundles, the production of a new class of nanotubes and the ability to purify hetero-oligomeric pores. Channels and pores with altered functional properties and with built-in triggers and switches have been prepared. Progress in applications has been greatest in sensor technology, where sensor elements based on ligand activation, channel selectivity and channel block have been made. Structural information about natural membrane proteins is emerging to inspire new designs.

  7. Structure characterization of the 26S proteasome

    PubMed Central

    Kim, Ho Min; Yu, Yadong; Cheng, Yifan

    2010-01-01

    In all eukaryotic cells, 26S proteasome plays an essential role in the process of ATP-dependent protein degradation. In this review, we focus on structure characterization of the 26S proteasome. Although the progress towards a high-resolution structure of the 26S proteasome has been slow, the recently solved structures of various proteasomal subcomplexes have greatly enhanced our understanding of this large machinery. In addition to having an ATP-dependent proteolytic function, the 26S proteasome is also involved in many non-proteolytic cellular activities, which are often mediated by subunits in its 19S regulatory complex. Thus, we include a detailed discussion of the structures of 19S subunits, including proteasomal ATPases, ubiquitin receptors, deubiquitinating enzymes and subunits that contain PCI domain. PMID:20800708

  8. Structural Characterization of Sm(III)(EDTMP).

    PubMed

    Yang, Y; Pushie, M J; Cooper, D M L; Doschak, M R

    2015-11-01

    Samarium-153 ethylenediamine-N,N,N',N'-tetrakis(methylenephosphonic acid) ((153)Sm-EDTMP, or samarium lexidronam), also known by its registered trademark name Quadramet, is an approved therapeutic radiopharmaceutical used in the palliative treatment of painful bone metastases. Typically, patients with prostate, breast, or lung cancer are most likely to go on to require bone pain palliation treatment due to bone metastases. Sm(EDTMP) is a bone-seeking drug which accumulates on rapidly growing bone, thereby delivering a highly region-specific dose of radiation, chiefly through β particle emission. Even with its widespread clinical use, the structure of Sm(EDTMP) has not yet been characterized at atomic resolution, despite attempts to crystallize the complex. Herein, we prepared a 1:1 complex of the cold (stable isotope) of Sm(EDTMP) under alkaline conditions and then isolated and characterized the complex using conventional spectroscopic techniques, as well as with extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional structure calculations, using natural abundance Sm. We present the atomic resolution structure of [Sm(III)(EDTMP)-8H](5-) for the first time, supported by the EXAFS data and complementary spectroscopic techniques, which demonstrate that the samarium coordination environment in solution is in agreement with the structure that has long been conjectured.

  9. Synthesis and structural characterization of CZTS nanoparticles

    SciTech Connect

    Lydia, R.; Reddy, P. Sreedhara

    2013-06-03

    The CZTS nanoparticles were successfully synthesized by Chemical co-precipitation method with different pH values in the range of 6 to 8. The synthesized nanoparticles were characterized by X-ray diffraction, scanning electron microscopy and energy dispersive spectroscopy. XRD studies revealed that the CZTS nanoparticles exhibited Kesterite Structure with preferential orientation along the (112) direction. Sample at pH value of 7 reached the nearly stoichiometric ratio.

  10. Transport of Ions and Particles Through Single Pores of Controlled Geometry and Surface Chemistry

    NASA Astrophysics Data System (ADS)

    Pevarnik, Matthew A.

    Synthetic nanopores are a powerful tool to control the transport of ions, molecules, and water at the molecular level, mimicking biological systems. In this research, polymer pores are prepared of different geometries, sizes, and surface chemistry to utilize features seen in naturally occurring systems. Specifically, it was one of the goals of this research to prepare and characterize single polymer pores that rectify the current due to a combination of electrostatic and hydrophobic interactions, similar to naturally occurring ion channels. Prior to modification, aqueous electrolytic solutions are able to conduct readily through the single polymer pores, but after the chemisorption of hydrophobic chemical groups, the pore demonstrates open and closed states. This behavior is also observed to be voltage dependent. Increasing voltage increases the probability of the pore to be in the open states. There is also a voltage range where the pore does not conduct at all. The hydrophobic gating was studied as a function of pore diameter and charge of the residual groups and could be used for an on demand drug delivery system. Another technique that was utilized in this research is the resistive-pulse technique, which is a powerful approach to detect single molecules and particles. A single particle passing through a pore can be observed as a transient drop of the transmembrane current. This research focuses on resistive-pulse sensing experiments performed with track-etched polymer pores characterized by an undulating diameter along the pore length. The resistive pulses generated by spherical beads passing through these pores have a repeatable pattern of large variations corresponding to these diameter changes. We show that this pattern of variations enables the unambiguous resolution of multiple particles simultaneously in the pore, the detection of transient sticking of particles within the pore, and confirmation whether any individual particle completely translocates the

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

    SciTech Connect

    Tomutsa, Liviu; Silin, Dmitriy

    2004-08-19

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  13. Porous structure of fibre networks formed by a foaming process: a comparative study of different characterization techniques.

    PubMed

    Al-Qararah, Ahmad M; Ekman, Axel; Hjelt, Tuomo; Kiiskinen, Harri; Timonen, Jussi; Ketoja, Jukka A

    2016-10-01

    Recent developments in making fibre materials using the foam-forming technology have raised a need to characterize the porous structure at low material density. In order to find an effective choice among all structure-characterization methods, both two-dimensional and three-dimensional techniques were used to explore the porous structure of foam-formed samples made with two different types of cellulose fibre. These techniques included X-ray microtomography, scanning electron microscopy, light microscopy, direct surface imaging using a CCD camera and mercury intrusion porosimetry. The mean pore radius for a varying type of fibre and for varying foam properties was described similarly by all imaging methods. X-ray microtomography provided the most extensive information about the sheet structure, and showed more pronounced effects of varying foam properties than the two-dimensional imaging techniques. The two-dimensional methods slightly underestimated the mean pore size of samples containing stiff CTMP fibres with void radii exceeding 100 μm, and overestimated the pore size for the samples containing flexible kraft fibres with all void radii below 100 μm. The direct rapid surface imaging with a CCD camera showed surprisingly strong agreement with the other imaging techniques. Mercury intrusion porosimetry was able to characterize pore sizes also in the submicron region and led to an increased relative volume of the pores in the range of the mean bubble size of the foam. This may be related to the penetration channels created by the foam-fibre interaction. PMID:27159162

  14. The impact of pore structure and surface roughness on capillary trapping for 2-D and 3-D porous media: Comparison with percolation theory

    NASA Astrophysics Data System (ADS)

    Geistlinger, Helmut; Ataei-Dadavi, Iman; Mohammadian, Sadjad; Vogel, Hans-Jörg

    2015-11-01

    We study the impact of pore structure and surface roughness on capillary trapping of nonwetting gas phase during imbibition with water for capillary numbers between 10-7 and 5 × 10-5, within glass beads, natural sands, glass beads monolayers, and 2-D micromodels. The materials exhibit different roughness of the pore-solid interface. We found that glass beads and natural sands, which exhibit nearly the same grain size distribution, pore size distribution, and connectivity, showed a significant difference of the trapped gas phase of about 15%. This difference can be explained by the microstructure of the pore-solid interface. Based on the visualization of the trapping dynamics within glass beads monolayers and 2-D micromodels, we could show that bypass trapping controls the trapping process in glass beads monolayers, while snap-off trapping controls the trapping process in 2-D micromodels. We conclude that these different trapping processes are the reason for the different trapping efficiency, when comparing glass beads packs with natural sand packs. Moreover, for small capillary numbers of 10-6, we found that the cluster size distribution of trapped gas clusters of all 2-D and 3-D porous media can be described by a universal power law behavior predicted from percolation theory. This cannot be expected a priori for 2-D porous media, because bicontinuity of the two bulk phases is violated. Obviously, bicontinuity holds for the thin-film water phase and the bulk gas phase. The snap-off trapping process leads to ordinary bond percolation in front of the advancing bulk water phase and is the reason for the observed universal power law behavior in 2-D micromodels with rough surfaces.

  15. Pore structure and reactivity changes in hot coal gas desulfurization sorbents. Technical progress report, October--December 1988

    SciTech Connect

    Sotirchos, S.V.

    1989-01-01

    A research program is proposed for the investigation of the dependence of the sorptive capacity of metal/metal oxide desulfurization sorbents on their pore size distribution and their intraparticle diffusivity. Integrated reaction/adsorption systems, chromatographic and gravimetric, will be used for successive reactivity, adsorption, and well as diffusivity, measurements. Single particle models that have been developed by our research group for gas-solid reactions with solid product will be used as basis for experimental data analysis and development of a general mathematical model for fixed-bed desulfurization and sorbent regeneration.

  16. Estimating permeability using median pore-throat radius obtained from mercury intrusion porosimetry

    NASA Astrophysics Data System (ADS)

    Gao, Zhiye; Hu, Qinhong

    2013-04-01

    Mercury intrusion porosimetry (MIP) has been widely used to characterize the pore structure for various types of porous media. Several relationships between permeability and pore structure information (e.g., porosity and pore-size distribution) have been developed in the literature. This work is to introduce a new, and simpler, empirical equation to predict permeability by solely using the median pore-throat radius (r50), which is the pore-throat radius corresponding to 50% mercury saturation. The total of 18 samples used in this work have a wide range of permeability, from 10-6 to 103 mD, which makes the new equation more applicable. The predicted permeabilities by using the new equation are comparable with permeability values obtained from other measurement methods, as shown from ten samples with permeability data measured with nitrogen.

  17. Soils, Pores, and NMR

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  18. Characterization of multi-scale porous structure of fly ash/phosphate geopolymer hollow sphere structures: from submillimeter to nano-scale.

    PubMed

    Li, Ruifeng; Wu, Gaohui; Jiang, Longtao; Sun, Dongli

    2015-01-01

    In the present work, the porous structure of fly ash/phosphate geopolymer hollow sphere structures (FPGHSS), prepared by pre-bonding and curing technology, has been characterized by multi-resolution methods from sub-millimeter to nano-scale. Micro-CT and confocal microscopy could provide the macroscopic distribution of porous structure on sub-millimeter scale, and hollow fly ashes with sphere shape and several sub-millimeter open cells with irregular shape were identified. SEM is more suitable to illustrate the distribution of micro-sized open and closed cells, and it was found that the open cells of FPGHSS were mainly formed in the interstitial porosity between fly ashes. Mercury porosimeter measurement showed that the micro-sized open cell of FPGHSS demonstrated a normal/bimodal distribution, and the peaks of pore size distribution were mainly around 100 and 10 μm. TEM observation revealed that the phosphate geopolymer was mainly composed of the porous area with nano-pores and dense areas, which were amorphous Al-O-P phase and α-Al2O3 respectively. The pore size of nano-pores demonstrated a quasi-normal distribution from about 10 to 100 nm. Therefore, detailed information of the porous structure of FPGHSS could be revealed using multiple methods.

  19. X-ray Crystallographic Structures of a Trimer, Dodecamer, and Annular Pore Formed by an Aβ17-36 β-Hairpin.

    PubMed

    Kreutzer, Adam G; Hamza, Imane L; Spencer, Ryan K; Nowick, James S

    2016-04-01

    High-resolution structures of oligomers formed by the β-amyloid peptide Aβ are needed to understand the molecular basis of Alzheimer's disease and develop therapies. This paper presents the X-ray crystallographic structures of oligomers formed by a 20-residue peptide segment derived from Aβ. The development of a peptide in which Aβ17-36 is stabilized as a β-hairpin is described, and the X-ray crystallographic structures of oligomers it forms are reported. Two covalent constraints act in tandem to stabilize the Aβ17-36 peptide in a hairpin conformation: a δ-linked ornithine turn connecting positions 17 and 36 to create a macrocycle and an intramolecular disulfide linkage between positions 24 and 29. An N-methyl group at position 33 blocks uncontrolled aggregation. The peptide readily crystallizes as a folded β-hairpin, which assembles hierarchically in the crystal lattice. Three β-hairpin monomers assemble to form a triangular trimer, four trimers assemble in a tetrahedral arrangement to form a dodecamer, and five dodecamers pack together to form an annular pore. This hierarchical assembly provides a model, in which full-length Aβ transitions from an unfolded monomer to a folded β-hairpin, which assembles to form oligomers that further pack to form an annular pore. This model may provide a better understanding of the molecular basis of Alzheimer's disease at atomic resolution.

  20. Unified method for the total pore volume and pore size distribution of hierarchical zeolites from argon adsorption and mercury intrusion.

    PubMed

    Kenvin, Jeffrey; Jagiello, Jacek; Mitchell, Sharon; Pérez-Ramírez, Javier

    2015-02-01

    A generalized approach to determine the complete distribution of macropores, mesopores, and micropores from argon adsorption and mercury porosimetry is developed and validated for advanced zeolite catalysts with hierarchically structured pore systems in powder and shaped forms. Rather than using a fragmented approach of simple overlays from individual techniques, a unified approach that utilizes a kernel constructed from model isotherms and model intrusion curves is used to calculate the complete pore size distribution and the total pore volume of the material. An added benefit of a single full-range pore size distribution is that the cumulative pore area and the area distribution are also obtained without the need for additional modeling. The resulting complete pore size distribution and the kernel accurately model both the adsorption isotherm and the mercury porosimetry. By bridging the data analysis of two primary characterization tools, this methodology fills an existing gap in the library of familiar methods for porosity assessment in the design of materials with multilevel porosity for novel technological applications.

  1. Prevention of the water flooding by micronizing the pore structure of gas diffusion layer for polymer electrolyte fuel cell

    NASA Astrophysics Data System (ADS)

    Hiramitsu, Yusuke; Sato, Hitoshi; Hori, Michio

    In polymer electrolyte fuel cells, high humidity must be established to maintain high proton conductivity in the polymer electrolyte. However, the water that is produced electrochemically at the cathode catalyst layer can condense in the cell and cause an obstruction to the diffusion of reaction gas in the gas diffusion layer and the gas channel. This leads to a sudden decrease of the cell voltage. To combat this, strict water management techniques are required, which usually focus on the gas diffusion layer. In this study, the use of specially treated carbon paper as a flood-proof gas diffusion layer under extremely high humidity conditions was investigated experimentally. The results indicated that flooding originates at the interface between the gas diffusion layer and the catalyst layer, and that such flooding could be eliminated by control of the pore size in the gas diffusion layer at this interface.

  2. Diffractaic acid: Crystalline structure and physicochemical characterization

    NASA Astrophysics Data System (ADS)

    de Castro Fonseca, Jéssica; de Oliveira, Yara Santiago; Bezerra, Beatriz P.; Ellena, Javier; Honda, Neli Kika; Silva, Camilla V. N. S.; da Silva Santos, Noemia Pereira; Santos-Magalhães, Nereide Stela; Ayala, Alejandro Pedro

    2016-08-01

    Diffractaic acid (DA) is a secondary metabolite of lichens that belongs to the chemical class of depsides, and some relevant pharmacological properties are associated with this natural product, such as antioxidant, antiulcerogenic and gastroprotective effects. Considering the relevant biological activities and taking into account that the activities are intrinsically related to the structure, the main goal of this study was to elucidate the structure of diffractaic acid by single crystal X-ray diffraction as well to characterize its physicochemical properties by powder X-ray diffraction, thermal analysis and vibrational spectroscopy. It was observed that DA belongs to the monoclinic crystal system, crystallizing in the space group P21/c with the following cell parameters: a = 18.535(7) Å, b = 4.0439(18) Å, c = 23.964(6) Å, β = 91.55(3)°. The crystal packing is characterized by difractaic acid dimers, which are reflected in the vibrational spectrum. These observations were supported by quantum mechanical calculations.

  3. Thermomechanical characterization and modeling for TSV structures

    NASA Astrophysics Data System (ADS)

    Jiang, Tengfei; Ryu, Suk-Kyu; Zhao, Qiu; Im, Jay; Ho, Paul S.; Huang, Rui

    2014-06-01

    Continual scaling of devices and on-chip wiring has brought significant challenges for materials and processes beyond the 32-nm technology node in microelectronics. Recently, three-dimensional (3-D) integration with through-silicon vias (TSVs) has emerged as an effective solution to meet the future technology requirements. Among others, thermo-mechanical reliability is a key concern for the development of TSV structures used in die stacking as 3-D interconnects. This paper presents experimental measurements of the thermal stresses in TSV structures and analyses of interfacial reliability. The micro-Raman measurements were made to characterize the local distribution of the near-surface stresses in Si around TSVs. On the other hand, the precision wafer curvature technique was employed to measure the average stress and deformation in the TSV structures subject to thermal cycling. To understand the elastic and plastic behavior of TSVs, the microstructural evolution of the Cu vias was analyzed using focused ion beam (FIB) and electron backscattering diffraction (EBSD) techniques. Furthermore, the impact of thermal stresses on interfacial reliability of TSV structures was investigated by a shear-lag cohesive zone model that predicts the critical temperatures and critical via diameters.

  4. Thermomechanical characterization and modeling for TSV structures

    SciTech Connect

    Jiang, Tengfei; Zhao, Qiu; Im, Jay; Ho, Paul S.; Ryu, Suk-Kyu; Huang, Rui

    2014-06-19

    Continual scaling of devices and on-chip wiring has brought significant challenges for materials and processes beyond the 32-nm technology node in microelectronics. Recently, three-dimensional (3-D) integration with through-silicon vias (TSVs) has emerged as an effective solution to meet the future technology requirements. Among others, thermo-mechanical reliability is a key concern for the development of TSV structures used in die stacking as 3-D interconnects. This paper presents experimental measurements of the thermal stresses in TSV structures and analyses of interfacial reliability. The micro-Raman measurements were made to characterize the local distribution of the near-surface stresses in Si around TSVs. On the other hand, the precision wafer curvature technique was employed to measure the average stress and deformation in the TSV structures subject to thermal cycling. To understand the elastic and plastic behavior of TSVs, the microstructural evolution of the Cu vias was analyzed using focused ion beam (FIB) and electron backscattering diffraction (EBSD) techniques. Furthermore, the impact of thermal stresses on interfacial reliability of TSV structures was investigated by a shear-lag cohesive zone model that predicts the critical temperatures and critical via diameters.

  5. Structural characterization of the human proteome.

    PubMed

    Müller, Arne; MacCallum, Robert M; Sternberg, Michael J E

    2002-11-01

    This paper reports an analysis of the encoded proteins (the proteome) of the genomes of human, fly, worm, yeast, and representatives of bacteria and archaea in terms of the three-dimensional structures of their globular domains together with a general sequence-based study. We show that 39% of the human proteome can be assigned to known structures. We estimate that for 77% of the proteome, there is some functional annotation, but only 26% of the proteome can be assigned to standard sequence motifs that characterize function. Of the human protein sequences, 13% are transmembrane proteins, but only 3% of the residues in the proteome form membrane-spanning regions. There are substantial differences in the composition of globular domains of transmembrane proteins between the proteomes we have analyzed. Commonly occurring structural superfamilies are identified within the proteome. The frequencies of these superfamilies enable us to estimate that 98% of the human proteome evolved by domain duplication, with four of the 10 most duplicated superfamilies specific for multicellular organisms. The zinc-finger superfamily is massively duplicated in human compared to fly and worm, and occurrence of domains in repeats is more common in metazoa than in single cellular organisms. Structural superfamilies over- and underrepresented in human disease genes have been identified. Data and results can be downloaded and analyzed via web-based applications at http://www.sbg.bio.ic.ac.uk.

  6. Structural and functional studies of Nup107/Nup133 interaction and its implications for the architecture of the nuclear pore complex

    SciTech Connect

    Boehmer, T.; Jeudy, S.; Berke, I.C.; Schwartz, T.U.

    2008-07-03

    Nuclear pore complexes (NPCs) are 4060 MDa protein assemblies embedded in the nuclear envelope of eukaryotic cells. NPCs exclusively mediate all transport between cytoplasm and nucleus. The nucleoporins that build the NPC are arranged in a stable core of module-like subcomplexes with eight-fold rotational symmetry. To gain insight into the intricate assembly of the NPC, we have solved the crystal structure of a protein complex between two nucleoporins, human Nup107 and Nup133. Both proteins form elongated structures that interact tightly via a compact interface in tail-to-tail fashion. Additional experiments using structure-guided mutants show that Nup107 is the critical anchor for Nup133 to the NPC, positioning Nup133 at the periphery of the NPC. The significant topological differences between Nup107 and Nup133 suggest that {alpha}-helical nucleoporin domains of the NPC scaffold fall in different classes and fulfill largely nonredundant functions.

  7. Effects of manual threshold setting on image analysis results of a sandstone sample structural characterization by X-ray microtomography.

    PubMed

    Moreira, Anderson C; Appoloni, Carlos R; Mantovani, Iara F; Fernandes, Jaquiel S; Marques, Leonardo C; Nagata, Rodrigo; Fernandes, Celso P

    2012-06-01

    Binarization process plays an important role in structural characterization by means of micro-CT images analysis. The choice of the correct threshold to separate porous phase from the material is the procedure for binary images creation. Slight variations of the threshold level led to substantial variations in physical parameters determination. The aim of this work is to evaluate these variations based on manual threshold settings data of five operators. Porosity and pore size distribution of a sandstone sample were determined.

  8. Structural characterization of rotor blades through photogrammetry

    NASA Astrophysics Data System (ADS)

    Bernardini, Giovanni; Serafini, Jacopo; Enei, Claudio; Mattioni, Luca; Ficuciello, Corrado; Vezzari, Valerio

    2016-06-01

    This paper deals with the use of photogrammetry for the experimental identification of structural and inertial properties of helicopter rotor blades4. The identification procedure is based upon theoretical/numerical algorithms for the evaluation of mass and flexural stiffness distributions which are an extension of those proposed in the past by Larsen, whereas the torsional properties (stiffness and shear center position) are determined through the Euler-Bernoulli beam theory. The identification algorithms require the knowledge of the blade displacement field produced by known steady loads. These data are experimentally obtained through photogrammetric detection technique, which allows the identification of 3D coordinates of labeled points (markers) on the structure through the correlation of 2D digital photos. Indeed, the displacement field is simply evaluated by comparing the markers positions on the loaded configuration with those on the reference one. The proposed identification procedure, numerically and experimentally validated in the past by the authors, has been here applied to the structural characterization of two main rotor blades, designed for ultra-light helicopters. Strain gauges measurements have been used to assess the accuracy of the identified properties through natural frequencies comparison as well as to evaluate the blades damping characteristics.

  9. Structural characterization of rotor blades through photogrammetry

    NASA Astrophysics Data System (ADS)

    Bernardini, Giovanni; Serafini, Jacopo; Enei, Claudio; Mattioni, Luca; Ficuciello, Corrado; Vezzari, Valerio

    2016-06-01

    This paper deals with the use of photogrammetry for the experimental identification of structural and inertial properties of helicopter rotor blades4. The identification procedure is based upon theoretical/numerical algorithms for the evaluation of mass and flexural stiffness distributions which are an extension of those proposed in the past by Larsen, whereas the torsional properties (stiffness and shear center position) are determined through the Euler–Bernoulli beam theory. The identification algorithms require the knowledge of the blade displacement field produced by known steady loads. These data are experimentally obtained through photogrammetric detection technique, which allows the identification of 3D coordinates of labeled points (markers) on the structure through the correlation of 2D digital photos. Indeed, the displacement field is simply evaluated by comparing the markers positions on the loaded configuration with those on the reference one. The proposed identification procedure, numerically and experimentally validated in the past by the authors, has been here applied to the structural characterization of two main rotor blades, designed for ultra-light helicopters. Strain gauges measurements have been used to assess the accuracy of the identified properties through natural frequencies comparison as well as to evaluate the blades damping characteristics.

  10. Effect of non-solvent additives on the morphology, pore structure, and direct contact membrane distillation performance of PVDF-CTFE hydrophobic membranes.

    PubMed

    Zheng, Libing; Wu, Zhenjun; Zhang, Yong; Wei, Yuansong; Wang, Jun

    2016-07-01

    Four common types of additives for polymer membrane preparation including organic macromolecule and micromolecule additives, inorganic salts and acids, and the strong non-solvent H2O were used to prepare poly (vinylidene fluoride-co-chlorotrifluoroethylene) (PVDF-CTFE) hydrophobic flat-sheet membranes. Membrane properties including morphology, porosity, hydrophobicity, pore size and pore distribution were investigated, and the permeability was evaluated via direct contact membrane distillation (DCMD) of 3.5g/L NaCl solution in a DCMD configuration. Both inorganic and organic micromolecule additives were found to slightly influence membrane hydrophobicity. Polyethylene glycol (PEG), organic acids, LiCl, MgCl2, and LiCl/H2O mixtures were proved to be effective additives to PVDF-CTFE membranes due to their pore-controlling effects and the capacity to improve the properties and performance of the resultant membranes. The occurrence of a pre-gelation process showed that when organic and inorganic micromolecules were added to PVDF-CTFE solution, the resultant membranes presented a high interconnectivity structure. The membrane prepared with dibutyl phthalate (DBP) showed a nonporous surface and symmetrical cross-section. When H2O and LiCl/H2O mixtures were also used as additives, they were beneficial for solid-liquid demixing, especially when LiCl/H2O mixed additives were used. The membrane prepared with 5% LiCl+2% H2O achieved a flux of 24.53kg/(m(2)·hr) with 99.98% salt rejection. This study is expected to offer a reference not only for PVDF-CTFE membrane preparation but also for other polymer membranes. PMID:27372116

  11. Effect of non-solvent additives on the morphology, pore structure, and direct contact membrane distillation performance of PVDF-CTFE hydrophobic membranes.

    PubMed

    Zheng, Libing; Wu, Zhenjun; Zhang, Yong; Wei, Yuansong; Wang, Jun

    2016-07-01

    Four common types of additives for polymer membrane preparation including organic macromolecule and micromolecule additives, inorganic salts and acids, and the strong non-solvent H2O were used to prepare poly (vinylidene fluoride-co-chlorotrifluoroethylene) (PVDF-CTFE) hydrophobic flat-sheet membranes. Membrane properties including morphology, porosity, hydrophobicity, pore size and pore distribution were investigated, and the permeability was evaluated via direct contact membrane distillation (DCMD) of 3.5g/L NaCl solution in a DCMD configuration. Both inorganic and organic micromolecule additives were found to slightly influence membrane hydrophobicity. Polyethylene glycol (PEG), organic acids, LiCl, MgCl2, and LiCl/H2O mixtures were proved to be effective additives to PVDF-CTFE membranes due to their pore-controlling effects and the capacity to improve the properties and performance of the resultant membranes. The occurrence of a pre-gelation process showed that when organic and inorganic micromolecules were added to PVDF-CTFE solution, the resultant membranes presented a high interconnectivity structure. The membrane prepared with dibutyl phthalate (DBP) showed a nonporous surface and symmetrical cross-section. When H2O and LiCl/H2O mixtures were also used as additives, they were beneficial for solid-liquid demixing, especially when LiCl/H2O mixed additives were used. The membrane prepared with 5% LiCl+2% H2O achieved a flux of 24.53kg/(m(2)·hr) with 99.98% salt rejection. This study is expected to offer a reference not only for PVDF-CTFE membrane preparation but also for other polymer membranes.

  12. Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters.

    PubMed

    Miyoshi, Tatsuo; Iwatsuki, Teruki; Naganuma, Takeshi

    2005-02-01

    A total of 247 clones of 16S rRNA genes from microorganisms captured by 0.2- and 0.1-microm-pore-size filters from sedimentary and granite rock aquifers were amplified and yielded 37 operational taxonomic units (OTUs). Fifteen OTUs captured by 0.1-microm-pore-size filters were affiliated with the candidate divisions OD1 and OP11, representing novel lineages. On the other hand, OTUs captured by 0.2-microm-pore-size filters were largely affiliated with Betaproteobacteria.

  13. Structural characterization of copolymer embedded magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Nedelcu, G. G.; Nastro, A.; Filippelli, L.; Cazacu, M.; Iacob, M.; Rossi, C. Oliviero; Popa, A.; Toloman, D.; Dobromir, M.; Iacomi, F.

    2015-10-01

    Small magnetic nanoparticles (Fe3O4) were synthesized by co-precipitation and coated by emulsion polymerization with poly(methyl methacrylate-co-acrylic acid) (PMMA-co-AAc) to create surface functional groups that can attach drug molecules and other biomolecules. The coated and uncoated magnetite nanoparticles were stored for two years in normal closed ships and than characterized by Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, vibrating sample magnetometry, and electron paramagnetic resonance spectroscopy. The solid phase transformation of magnetite to maghemite, as well as an increase in particle size were evidenced for the uncoated nanoparticles. The coated nanoparticles preserved their magnetite structure and magnetic properties. The influences of monomers and surfactant layers on interactions between the magnetic nanoparticles evidenced that the thickness of the polymer has a significant effect on magnetic properties.

  14. The structural homology between uteroglobin and the pore-forming domain of colicin A suggests a possible mechanism of action for uteroglobin.

    PubMed Central

    de la Cruz, X.; Lee, B.

    1996-01-01

    Although the exact physiological function of uteroglobin is not known, it has been suggested that it may function by inhibiting phospholipase A2. We have found that the uteroglobin fold is embedded in that of the poreforming domain of colicin A. Colicin A is an antibiotic protein that kills sensitive Escherichia coli cells by forming a pore in their phospholipid membrane. The RMS deviation between the C alpha atoms after the structural alignment is 2.39 A for the 52 superimposed residues. In the alignment, uteroglobin helices 1, 2, 3, and 4 align with colicin A helices 6, 7, 3, and 4, respectively. The motif is strongly amphipathic in both proteins. On the basis of this common structural motif and of known experimental data on both proteins, we propose that UG binds to the membrane surface by lying on it monotopically. The phospholipase A2 inhibition would follow this initial binding step. PMID:8732757

  15. Titanium(IV) in the organic-structure-directing-agent-free synthesis of hydrophobic and large-pore molecular sieves as redox catalysts.

    PubMed

    Wang, Jingui; Yokoi, Toshiyuki; Kondo, Junko N; Tatsumi, Takashi; Zhao, Yanli

    2015-08-10

    Titanium(IV) incorporated into the framework of molecular sieves can be used as a highly active and sustainable catalyst for the oxidation of industrially important organic molecules. Unfortunately, the current process for the incorporation of titanium(IV) requires a large amount of expensive organic molecules used as organic-structure-directing agents (OSDAs), and this significantly increases the production costs and causes environmental problems owing to the removal of OSDAs by pyrolysis. Herein, an OSDA-free process was developed to incorporate titanium(IV) into BEA-type molecular sieves for the first time. More importantly, the hydrophobic environment and the robust, 3 D, and large pore structure of the titanium(IV)-incorporated molecular sieves fabricated from the OSDA-free process created a catalyst that was extremely active and selective for the epoxidation of bulky cyclooctene in comparison to Ti-incorporated BEA-type molecular sieves synthesized with OSDAs and commercial titanosilicate TS-1.

  16. Thermophysical property and pore structure evolution in stressed and non-stressed neutron irradiated IG-110 nuclear graphite

    DOE PAGESBeta

    Snead, Lance L.; Contescu, C. I.; Byun, T. S.; Porter, W.

    2016-04-23

    The nuclear graphite, IG-110, was irradiated with and without a compressive load of 5 MPa at ~400 C up to 9.3x1025 n/m2 (E>0.1 MeV.) Following irradiation physical properties were studied to compare the effect of graphite irradiation on microstructure developed under compression and in stress-free condition. Properties included: dimensional change, thermal conductivity, dynamic modulus, and CTE. The effect of stress on open internal porosity was determined through nitrogen adsorption. The IG-110 graphite experienced irradiation-induced creep that is differentiated from irradiation-induced swelling. Irradiation under stress resulted in somewhat greater thermal conductivity and coefficient of thermal expansion. While a significant increase inmore » dynamic modulus occurs, no differentiation between materials irradiated with and without compressive stress was observed. Nitrogen adsorption analysis suggests a difference in pore evolution in the 0.3-40 nm range for graphite irradiated with and without stress, but this evolution is seen to be a small contributor to the overall dimensional change.« less

  17. Thermophysical property and pore structure evolution in stressed and non-stressed neutron irradiated IG-110 nuclear graphite

    NASA Astrophysics Data System (ADS)

    Snead, L. L.; Contescu, C. I.; Byun, T. S.; Porter, W.

    2016-08-01

    The nuclear graphite, IG-110, was irradiated with and without a compressive load of 5 MPa at ∼400 °C up to 9.3 × 1025 n/m2 (E > 0.1 MeV). Following irradiation physical properties were studied to compare the effect of graphite irradiation on microstructure developed under compression and in stress-free conditions. Properties included: dimensional change, thermal conductivity, dynamic modulus, and CTE. The effect of stress on open internal porosity was determined through nitrogen adsorption. The IG-110 graphite experienced irradiation-induced creep that is differentiated from irradiation-induced swelling. Irradiation under stress resulted in somewhat greater thermal conductivity and coefficient of thermal expansion. While a significant increase in dynamic modulus occurs, no differentiation between materials irradiated with and without compressive stress was observed. Nitrogen adsorption analysis suggests a difference in pore evolution in the 0.3-40 nm range for graphite irradiated with and without stress, but this evolution is seen to be a small contributor to the overall dimensional change.

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

    SciTech Connect

    Peters, Catherine A

    2013-05-15

    This project addressed the scaling of geochemical reactions to core and field scales, and the interrelationship between reaction rates and flow in porous media. We targeted reactive transport problems relevant to the Hanford site specifically the reaction of highly caustic, radioactive waste solutions with subsurface sediments, and the immobilization of 90Sr and 129I through mineral incorporation and passive flow blockage, respectively. We addressed the correlation of results for pore-scale fluid-soil interaction with field-scale fluid flow, with the specific goals of (i) predicting attenuation of radionuclide concentration; (ii) estimating changes in flow rates through changes of soil permeabilities; and (iii) estimating effective reaction rates. In supplemental work, we also simulated reactive transport systems relevant to geologic carbon sequestration. As a whole, this research generated a better understanding of reactive transport in porous media, and resulted in more accurate methods for reaction rate upscaling and improved prediction of permeability evolution. These scientific advancements will ultimately lead to better tools for management and remediation of DOE legacy waste problems.

  19. Effects of pore-size and shape distributions on diffusion pore imaging by nuclear magnetic resonance

    NASA Astrophysics Data System (ADS)

    Kuder, Tristan Anselm; Laun, Frederik Bernd

    2015-08-01

    In medical imaging and porous media research, NMR diffusion measurements are extensively used to investigate the structure of diffusion restrictions such as cell membranes. Recently, several methods have been proposed to unambiguously determine the shape of arbitrary closed pores or cells filled with an NMR-visible medium by diffusion experiments. The first approach uses a combination of a long and a short diffusion-weighting gradient pulse, while the other techniques employ short gradient pulses only. While the eventual aim of these methods is to determine pore-size and shape distributions, the focus has been so far on identical pores. Thus, the aim of this work is to investigate the ability of these different methods to resolve pore-size and orientation distributions. Simulations were performed comparing the various pore imaging techniques employing different distributions of pore size and orientation and varying timing parameters. The long-narrow gradient profile is most advantageous to investigate pore distributions, because average pore images can be directly obtained. The short-gradient methods suppress larger pores or induce a considerable blurring. Moreover, pore-shape-specific artifacts occur; for example, the central part of a distribution of cylinders may be largely underestimated. Depending on the actual pore distribution, short-gradient methods may nonetheless yield good approximations of the average pore shape. Furthermore, the application of short-gradient methods can be advantageous to differentiate whether pore-size distributions or intensity distributions, e.g., due to surface relaxation, are predominant.

  20. A thermodynamic approach to Alamethicin pore formation

    PubMed Central

    Rahaman, Asif; Lazaridis, Themis

    2013-01-01

    The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11 Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6 Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8 Å pore and the octamer in an 11 Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted “barrel-stave” model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself. PMID:24071593

  1. Investigation of the pore structure and morphology of cellulose acetate membranes using small-angle neutron scattering. 1: Cellulose acetate active layer membranes

    SciTech Connect

    Kulkarni, S.; Krause, S. ); Wignall, G.D. . Solid State Div.); Hammouda, B. . Center for High Resolution Neutron Scattering)

    1994-11-07

    The structure of ultrathin cellulose acetate membranes, known as active layer membranes, has been investigated using small-angle neutron scattering. These membranes are known to have structural and functional similarity to the surface or skin layer in commercial reverse-osmosis (RO) membranes and hence are useful model systems for understanding the structure of the RO membrane skin layer. Active layer membranes were studied after swelling them with either D[sub 2]O or CD[sub 3]OD. The results in both cases clearly indicated the presence of very small (10--20 [angstrom]) porous structures in the membrane. The presence of such pores has been a subject of long-standing controversy in this area. The data were analyzed using a modified Debye-Bueche analysis and the resultant membrane structure was seen to agree well with structural information from electron microscopic studies. Finally, a possible explanation for the differences in scattering observed between the D[sub 2]O swollen membranes and the CD[sub 3]OD swollen membranes has been presented.

  2. Structural Characterization of Bimetallic Nanocrystal Electrocatalysts

    SciTech Connect

    Cullen, David A

    2016-01-01

    Late transition metal nanocrystals find applications in heterogeneous catalysis such as plasmon-enhanced catalysis and as electrode materials for fuel cells, a zero-emission and sustainable energy technology. Their commercial viability for automotive transportation has steadily increased in recent years, almost exclusively due to the discovery of more efficient bimetallic nanocatalysts for the oxygen reduction reaction (ORR) at the cathode. Despite improvements to catalyst design, achieving high activity while maintaining durability is essential to further enhance their performance for this and other important applications in catalysis. Electronic effects arising from the generation of metal-metal interfaces, from plasmonic metals, and from lattice distortions, can vastly improve sorption properties at catalytic surfaces, while increasing durability.[1] Multimetallic lattice-strained nanoparticles are thus an interesting opportunity for fundamental research.[2,3] A colloidal synthesis approach is demonstrated to produce AuPd alloy and Pd@Au core-shell nanoicosahedra as catalysts for electro-oxidations. The nanoparticles are characterized using aberration-corrected scanning transmission electron microscopy (ac-STEM) and large solid angle energy dispersive X-ray spectroscopy (EDS) on an FEI Talos 4-detector STEM/EDS system. Figure 1 shows bright-field (BF) and high-angle annular dark-field (HAADF) ac-STEM images of the alloy and core-shell nanoicosahedra together with EDS line-scans and elemental maps. These structures are unique in that the presence of twin boundaries, alloying, and core-shell morphology could create highly strained surfaces and interfaces. The shell thickness of the core-shell structures observed in HAADF-STEM images is tuned by adjusting the ratio between metal precursors (Figure 2a-f) to produce shells ranging from a few to several monolayers. Specific activity was measured in ethanol electro-oxidation to examine the effect of shell thickness on

  3. Isolation and characterization of a proteinaceous subnuclear fraction composed of nuclear matrix, peripheral lamina, and nuclear pore complexes from embryos of Drosophila melanogaster.

    PubMed

    Fisher, P A; Berrios, M; Blobel, G

    1982-03-01

    Morphologically intact nuclei have been prepared from embryos of Drosophila melanogaster by a simple and rapid procedure. These nuclei have been further treated with high concentrations of DNase I and RNase A followed by sequential extraction with 2% Triton X-100 and 1 M NaCl to produce a structurally and biochemically distinct preparation designated Drosophila subnuclear fraction I (DSNF-I). As seen by phase-contrast microscopy, DSNF-I is composed of material which closely resembles unfractionated nuclei; residual internal nuclear structures including nucleolar remnants are clearly visible. By transmission electron microscopy, nuclear lamina, pore complexes, and a nuclear matrix are similarly identified. Biochemically, DSNF-I is composed almost entirely of protein (greater than 93%). SDS PAGE analysis reveals several major polypeptides; species at 174,000, 74,000, and 42,000 predominate. A polypeptide coincident with the Coomassie Blue-stainable 174-kdalton band has been shown by a novel technique of lectin affinity labeling to be a glycoprotein; a glycoprotein of similar or identical molecular weight has been found to be a component of nuclear envelope fractions isolated from the livers of rats, guinea pigs, opossums, and chickens. Antisera against several of the polypeptides in DSNF-I have been obtained from rabbits, and all of them show only little or no cross-reactivity with Drosophila cytoplasmic fractions. Initial results of immunocytochemical studies, while failing to positively localize either the 174- or 16-kdalton polypeptides, demonstrate a nuclear localization of the 74-kdalton antigen in all of several interphase cell types obtained from both Drosophila embryos and third-instar larvae. PMID:6177701

  4. Structural Characterization of Crystalline Ice Nanoclusters

    NASA Technical Reports Server (NTRS)

    Blake, David

    2000-01-01

    Water ice nanoclusters are useful analogs for studying a variety of processes that occur within icy grains in the extraterrestrial environment. The surface of ice nanoclusters prepared in the laboratory is similar to the surface of interstellar ice grains. In cold molecular clouds, the silicate cores of interstellar grains are typically approx. 100 nm in diameter and have a coating of impure amorphous water ice. Depositional, thermal and radiolytic processes leave the surface and subsurface molecules in a disordered state. In this state, structural defects become mobile and reactions of trapped gases and small molecules can occur. The large surface area of nanocluster deposits relative to their bulk allows for routine observation of such surface-mediated processes. Furthermore, the disordered surface and subsurface layers in nanocluster deposits mimic the structure of amorphous ice rinds found on interstellar dust grains. Transmission Electron Microscopy (TEM has been used tn characterize the crystallinity, growth mechanism, and size distribution of nanoclusters formed from a mixture of water vapor with an inert carrier gas that has been rapidly cooled to 77K. E M imaging reveals a Gaussian size distribution around a modal diameter that increases from approx. 15 to 30 nm as the percentage of water vapor within the mixture increases from 0.5 to 2.007, respectively . TEM bright and dark field imaging also reveals the crystalline nature of the clusters. h4any of the clusters show a mosaic structure in which crystalline domains originate at the center Other images show mirror planes that are separated by approx. 10 nm. Electron diffraction patterns of these clusters show that the clusters are composed of cubic ice with only a small hexagonal component. Further, the crystalline domain size is approximately the same as the modal diameter suggesting that the clusters are single crystals.

  5. Combination of metamorphism and deformation affect the nano-scale pore structures and macromolecule characteristics of high-rank deformed coals

    NASA Astrophysics Data System (ADS)

    Zhang, W.; Li, H.; Ju, Y.

    2013-12-01

    Coal constitutes a large proportion of total energy supply in the world. Coalbed Methane (CBM) composes the greenhouse gases, which has attracted more and more scientists' concern and attention. The adsorption/desorption characteristics and mechanism of CBM on high-rank deformed coals are in favor of enhancing gas recovery, reducing coal mining accidents and carbon emission. Although the influence factors of CBM adsorption/desorption on different coals have been intensively studied, the combined action of metamorphism and deformation on high-rank coals have been rarely researched. Nevertheless. Metamorphism and deformation are the most fundamental driving forces that cause the changes of inner structures and compositions in coal strata, and then alter the adsorption/desorption capacities of CBM on different coalbeds. South of Qinshui Basin in Shanxi province developed with abundant high-rank coals is the first demonstrate area of CBM development in China. Meanwhile Southwest of Fujian province represents high metamorphic-deformed coals region due to the intense volcanic activities. Therefore samples were taken in both areas to elaborate the adsorption/desorption characteristics and mechanism of CBM. Based on hand specimens description, coal macerals testing, proximate analysis, ultimate analysis and vitrinite reflectance testing, the physical properties and composition characteristics of high-rank deformed coals have been studied. Combined with liquid nitrogen adsorption experiments, Transmission Electron Microscopy (TEM) observation, Fourier Transform Infrared Spectrometry (FTIR) and Nuclear Magnetic Resonance (NMR) experiments, the results show that nano-pores increase and become homogenization with metamorphic-deformation enhancement, stacking of the macromolecular basic structural units (BSU) enhances, aromatic compound increases while aliphatic chain compound and oxygen-containing function groups decrease. Comparing to coal adsorption/desorption isotherm

  6. Gas Hydrate and Pore Pressure

    NASA Astrophysics Data System (ADS)

    Tinivella, Umberta; Giustiniani, Michela

    2014-05-01

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

  7. Pore Characterization of Shale Rock and Shale Interaction with Fluids at Reservoir Pressure-Temperature Conditions Using Small-Angle Neutron Scattering

    NASA Astrophysics Data System (ADS)

    Ding, M.; Hjelm, R.; Watkins, E.; Xu, H.; Pawar,