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Sample records for air-filled pore space

  1. The pore space scramble

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  2. Tight dual models of pore spaces

    NASA Astrophysics Data System (ADS)

    Glantz, Roland; Hilpert, Markus

    2008-05-01

    The pore throats in a porous medium control permeability, drainage, and straining through their pore scale geometry and through the way they are connected via pore bodies on the macroscale. Likewise, imbibition is controlled through the geometry of the pore bodies (pore scale) and through the way the pore bodies are connected via pore throats on the macroscale. In an effort to account for both scales at the same time we recently introduced an image-based model for pore spaces that consists of two parts related by duality: (1) a decomposition of a polyhedral pore space into polyhedral pore bodies separated by polygonal pore throats and (2) a polygonal pore network that is homotopy equivalent to the pore space. In this paper we stick to the dual concept while amending the definition of the pore throats and, as a consequence, the other elements of the dual model. Formerly, the pore throats consisted of single two-dimensional Delaunay cells, while they now usually consist of more than one two-dimensional Delaunay cell and extend all the way into the narrowing ends of the pore channel cross sections. This is the first reason for naming the amended dual model "tight". The second reason is that the formation of the pore throats is now guided by an objective function that always attains its global optimum (tight optimization). At the end of the paper we report on simulations of drainage performed on tight dual models derived from simulated sphere packings and 3D gray-level images. The C-code for the generation of the tight dual model and the simulation of drainage is publicly available at https://jshare.johnshopkins.edu/mhilper1/public_html/tdm.html.

  3. Pore space morphology analysis using maximal inscribed spheres

    NASA Astrophysics Data System (ADS)

    Silin, Dmitriy; Patzek, Tad

    2006-11-01

    A new robust algorithm analyzing the geometry and connectivity of the pore space of sedimentary rock is based on fundamental concepts of mathematical morphology. The algorithm distinguishes between the “pore bodies” and “pore throats,” and establishes their respective volumes and connectivity. The proposed algorithm also produces a stick-and-ball diagram of the rock pore space. The tests on a pack of equal spheres, for which the results are verifiable, confirm its stability. The impact of image resolution on the algorithm output is investigated on the images of computer-generated pore space. One of distinctive features of our approach is that no image thinning is applied. Instead, the information about the skeleton is stored through the maximal inscribed balls or spheres (MIS) associated with each voxel. These maximal balls retain information about the entire pore space. Comparison with the results obtained by a thinning procedure preserving some topological properties of the pore space shows that our method produces more realistic estimates of the number and shapes of pore bodies and pore throats, and the pore coordination numbers. The distribution of maximal inscribed spheres makes possible simulation of mercury injection and computation of the corresponding dimensionless capillary pressure curve. It turns out that the calculated capillary pressure curve is a robust descriptor of the pore space geometry and, in particular, can be used to determine the quality of computer-based rock reconstruction.

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

    SciTech Connect

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

    1989-03-01

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

  5. Active pore space utilization in nanoporous carbon-based supercapacitors: Effects of conductivity and pore accessibility

    NASA Astrophysics Data System (ADS)

    Seredych, Mykola; Koscinski, Mikolaj; Sliwinska-Bartkowiak, Malgorzata; Bandosz, Teresa J.

    2012-12-01

    Composites of commercial graphene and nanoporous sodium-salt-polymer-derived carbons were prepared with 5 or 20 weight% graphene. The materials were characterized using the adsorption of nitrogen, SEM/EDX, thermal analysis, Raman spectroscopy and potentiometric titration. The samples' conductivity was also measured. The performance of the carbon composites in energy storage was linked to their porosity and electronic conductivity. The small pores (<0.7) were found as very active for double layer capacitance. It was demonstrated that when double layer capacitance is a predominant mechanism of charge storage, the degree of the pore space utilization for that storage can be increased by increasing the conductivity of the carbons. That active pore space utilization is defined as gravimetric capacitance per unit pore volume in pores smaller than 0.7 nm. Its magnitude is affected by conductivity of the carbon materials. The functional groups, besides pseudocapacitive contribution, increased the wettability and thus the degree of the pore space utilization. Graphene phase, owing to its conductivity, also took part in an insitu increase of the small pore accessibility and thus the capacitance of the composites via enhancing an electron transfer to small pores and thus imposing the reduction of groups blocking the pores for electrolyte ions.

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

    PubMed

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

    2012-07-01

    Characterization of porosity in carbonate rocks is important in the oil and gas industry since a major hydrocarbons field is formed by this lithology and they have a complex media porous. In this context, this research presents a study of the pore space in limestones rocks by x-ray microtomography. Total porosity, type of porosity and pore size distribution were evaluated from 3D high resolution images. Results show that carbonate rocks has a complex pore space system with different pores types at the same facies. PMID:22264795

  7. Transport pathways within percolating pore space networks of granular materials

    NASA Astrophysics Data System (ADS)

    Vo, Kevin; Walker, David M.; Tordesillas, Antoinette

    2013-06-01

    Granular media can be regarded as a mixture of two components: grains and the material filling the voids or pores between the grains. Pore properties give rise to a range of applications such as modelling ground water flow, carbon capture and sequestration. The grains within a dense granular material respond to deformation (e.g., shearing or compression) by rearranging to create local zones of compression and zones of dilatation (i.e., regions of high pore space). Descriptions of the deformation are typically focused on analysis of the solid skeleton via topology of physical contact networks of grains but an alternative perspective is to consider network representations of the evolving anisotropic pore space. We demonstrate how to construct pore space networks that express the local size of voids about a grain through network edge weights. We investigate sectors of the loading history when a percolating giant component of the pore space network exists. At these states the grains are in a configuration more prone to the efficient transport of material (e.g., fluid flow, mineral/gas deposits). These pathways can be found through examination of the weighted shortest paths percolating the boundaries of the material. In particular, network weights biased towards large void space results in efficient percolating pathways traversing the shear band in the direction of principal stress within a 2D granular assembly subject to high strains.

  8. Partitioning of habitable pore space in earthworm burrows.

    PubMed

    Gorres, Josef H; Amador, Jose A

    2010-03-01

    Earthworms affect macro-pore structure of soils. However, some studies suggest that earthworm burrow walls and casts themselves differ greatly in structure from surrounding soils, potentially creating habitat for microbivorours nematodes which accelerate the decomposition and C and N mineralization. In this study aggregates were sampled from the burrow walls of the anecic earthworm Lumbricus terrestris and bulk soil (not altered by earthworms) from mesocosm incubated in the lab for 0, 1, 3, 5 and 16 weeks. Pore volumes and pore sizes were measured in triplicate with Mercury Intrusion Porosimetry (MIP). This method is well suited to establish pore size structure in the context of habitat, because it measures the stepwise intrusion of mercury from the outside of the aggregate into ever smaller pores. The progress of mercury into the aggregate interior thus resembles potential paths of a nematode into accessible habitable pore spaces residing in an aggregate. Total specific pore volume, V(s), varied between 0.13 and 0.18 mL/g and increased from 3 to 16 weeks in both burrow and bulk soil. Differences between total V(s) of bulk and burrow samples were not significant on any sampling date. However, differences were significant for pore size fractions at the scale of nematode body diameter. PMID:22736839

  9. The Dimension of the Pore Space in Sponges

    ERIC Educational Resources Information Center

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

    2009-01-01

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

  10. Carbon turnover in pore spaces - CIPS model approach

    NASA Astrophysics Data System (ADS)

    Kuka, Katrin

    2010-05-01

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

  11. Effects of Inter- and Intra-aggregate Pore Space on the Soil-Gas Diffusivity Behavior in Unsaturated, Undisturbed Volcanic Ash Soils

    NASA Astrophysics Data System (ADS)

    Resurreccion, A. C.; Kawamoto, K.; Komatsu, T.; Moldrup, P.

    2006-12-01

    Volcanic ash soils (Andisols) have a unique dual porosity structure that results in good drainage and high soil- water retention. Despite of the complicated and highly developed soil structure, recent studies have reported a simple, highly linear relation between the soil-gas diffusion coefficient, Dp, and the soil-air content, ɛ, for several Japanese Andisols. In this study, we explain the linear Dp(ɛ) behavior from the effects of the inter- and intra-aggregate pore-size distributions. We couple the bimodal van Genuchten soil-water retention model with a general Dp(ɛ) model, ɛ^{X}, allowing the tortuosity- connectivity factor X to vary with pF (= log(-ψ; the soil-water matric potential in cm H2O)). Measured data suggest that the tortuosity-connectivity parameter X is at the minimum at pF 3 (where X ~ 2, following Buckingham, 1904), equal to the water retention point where a separation of inter- and intra-aggregate effects on Dp is observed. At pF < 3, the X values increased as pF decreased because of inactive/remote air-filled pore space entrapped by the inter-connected water films between inter-aggregate pore spaces. At pF > 3, X increased to a high value at very dry conditions due to remote air-filled space inside the intra-aggregate pores. By combining the complex dual porosity soil-water retention model with the power- law gas diffusivity model using a parabolic X(pF) function, the surprisingly simple linear behavior of Dp with ɛ was captured while the variation of Dp with pF followed a dual s-shaped curve similar to the water retention curve. A simple linear model to predict Dp(ɛ) is suggested, with slope C and threshold soil-air content, ɛth, calculated from the power-law model ɛ^{X} at pF 2 (near field capacity) and at pF 4.1 (near wilting point) using the same X value (= 2.3) at both pF in agreement with measured data. This linear Dp(ɛ) model performed better, especially at dry conditions, compared to the traditionally-used predictive models when

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

    PubMed

    Liebschner, Michael A K; Wettergreen, Matthew

    2012-01-01

    The goal of this area of research is to manipulate the pore space of scaffolds through the application of an intelligent design concept on dissolvable microparticles. To accomplish this goal, we developed an efficient and repeatable process for fabrication of microparticles from multiple materials using a combination of rapid prototyping (RP) and soft lithography. Phase changed 3D printing was used to create masters for PDMS molds. A photocrosslinkable polymer was then delivered into these molds to make geometrically complex 3D microparticles. This repeatable process has demonstrated to generate the objects with greater than 95% repeatability with complete pattern transfer. This process was illustrated for three different shapes of various complexities. The shapes were based on the extrusion of 2D shapes. This may allow simplification of the fabrication process in the future combined with a direct transfer of the findings. Altering the shapes of particles used for porous scaffold fabrication will allow for tailoring of the pore shapes, and therefore their biological function within a porous tissue engineering scaffold. Through permeation experiments, we have shown that the pore geometry may alter the permeability coefficient of scaffolds while influencing mechanical properties to a lesser extent. By selecting different porogen shapes, the nutrition transport and scaffold degradation can be significantly influenced with minimal effect on the mechanical integrity of the construct. In addition, the different shapes may allow a control of drug release by modifying their surface-to-volume ratio, which could modulate drug delivery over time. While soft lithography is currently used with photolithography, its high precision is offset by high cost of production. The employment of RP to a specific resolution offers a much less expensive alternative with increased throughput due to the speed of current RP systems. PMID:22692605

  13. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  15. 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

  16. 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

  17. 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

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

    PubMed

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

    2013-12-01

    We show how microparticles can be moved over long distances and precisely positioned in a low-loss air-filled hollow-core photonic crystal fiber using a coherent superposition of two co-propagating spatial modes, balanced by a backward-propagating fundamental mode. This creates a series of trapping positions spaced by half the beat-length between the forward-propagating modes (typically a fraction of a millimeter). The system allows a trapped microparticle to be moved along the fiber by continuously tuning the relative phase between the two forward-propagating modes. This mode-based optical conveyor belt combines long-range transport of microparticles with a positional accuracy of 1 µm. The technique also has potential uses in waveguide-based optofluidic systems. PMID:24514492

  19. Wave intensity analysis in air-filled flexible vessels.

    PubMed

    Clavica, Francesco; Parker, Kim H; Khir, Ashraf W

    2015-02-26

    Wave intensity analysis (WIA) is an analytical technique generally used to investigate the propagation of waves in the cardiovascular system. Despite its increasing usage in the cardiovascular system, to our knowledge WIA has never been applied to the respiratory system. Given the analogies between arteries and airways (i.e. fluid flow in flexible vessels), the aim of this work is to test the applicability of WIA with gas flow instead of liquid flow. The models employed in this study are similar to earlier studies used for arterial investigations. Simultaneous pressure (P) and velocity (U) measurements were initially made in a single tube and then in several flexible tubes connected in series. Wave speed was calculated using the foot-to-foot method (cf), which was used to separate analytically the measured P and U waveforms into their forward and backward components. Further, the data were used to calculate wave intensity, which was also separated into its forward and backward components. Although the measured wave speed was relatively high, the results showed that the onsets and the nature of reflections (compression/expansion) derived with WIA, corresponded well to those anticipated using the theory of waves in liquid-filled elastic tubes. On average the difference between the experimental and theoretical arrival time of reflection was 6.1% and 3.6% for the single vessel and multivessel experiment, respectively. The results suggest that WIA can provide relatively accurate information on reflections in air-filled flexible tubes, warranting further studies to explore the full potential of this technique in the respiratory system. PMID:25595424

  20. Pore space in sediments on continental blocks and sea level change

    SciTech Connect

    Hay, W.W.; Leslie, M.

    1985-01-01

    The problem of explaining geologically rapid sea level changes on an earth without major ice caps is vexing because it has been difficult to understand where the water which left the ocean was stored. One possible storage reservoir which has not been previously investigated is the pore space in sediment on the continental blocks. Cratonic sediments (165x10/sup 6/km/sup 3/) with an average porosity of about 20%, have a pore volume of 33x10/sup 6/km/sup 3/; geosynclinal sediments have a pore volume of 53x10/sup 6/km/sup 3/; coastal plain and continental shelf sediments have a pore volume of 30x10/sup 6/km/sup 3/. The total potential for water storage is equal to an impressive 320 meters of sea level change. However most of this pore space is below sea level and unavailable because it is permanently filled with water. The total pore space available within the upper 500m of sediment is 12.5x10/sup 6/km/sup 3/; within the upper 1000m of sediment, 24.8x10/sup 6/km/sup 3/. An approximation for the total pore space available above sea level space which could be filled with or emptied of ground water lies between these figures. Assuming that 18.6x10V2andkm/sup 3/ of pore space could respond to differing infiltration volumes of water as a result of climate changes, a maximum fluctuation of sea level of 52 meters could be accounted for. Interestingly, the time constants associated with filling or emptying this space are in the same order of magnitude as Milankovitch cycles.

  1. 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

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

    PubMed Central

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  4. Pore space analysis of NAPL distribution in sand-clay media

    USGS Publications Warehouse

    Matmon, D.; Hayden, N.J.

    2003-01-01

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

  5. Geometric and Topological Analysis of Three-Dimensional Porous Media: Pore Space Partitioning Based on Morphological Skeletonization.

    PubMed

    Liang; Ioannidis; Chatzis

    2000-01-01

    This article presents a versatile, rigorous, and efficient methodology for extracting various geometric and topological parameters of 3D discrete porous media. The new approach takes advantage of the morphological skeleton of the pore structure-a lower dimensional representation of the pore space akin to the topological "deformation retract". The skeleton is derived by a fully parallel thinning algorithm that fulfils two essential requirements: it generates a medial axis and preserves the connectivity of the pore space. Topological analysis is accomplished by classifying all skeleton points as node or link (branch) points according to the concept of lambda-adjacency in 3D discrete space. In this manner, node coordination number and link length distributions are directly obtained from the skeleton. Pore necks (throats) are identified through a search for minima in the hydraulic radius of individual pore space channels outlined by skeleton links. In addition to the determination of the size distribution of the constrictions (pore necks) that control nonwetting phase invasion, improved estimates of the distributions of effective hydraulic and electric conductivity of individual pore space channels are obtained. Furthermore, erection of planes at the location of pore necks results in partitioning of the pore space into its constituent pores. This enables the characterization of the pore space in terms of a pore volume distribution. The new methodology is illustrated by application to a regular cubic pore network and irregularly shaped 2D and 3D pore networks generated by stochastic simulation. In the latter case, important new results are obtained concerning the sensitivity of geometric and topological properties of the microstructure to the parameters of stochastic simulation, namely, the porosity and correlation function. It is found that model porous media reconstructed from the same porosity and correlation function can exhibit marked differences in geometry and

  6. 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

  7. Formation factor and the microscopic distribution of wetting phase in pore space of Berea sandstone

    SciTech Connect

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

    1992-11-01

    Experimental studies have been accomplished aimed at studying the formation factor of a partially saturated rock. The effective formation factors to an electrolyte solution of the pore spaces not occupied by a wetting raid (paraffin wax) have been measured at various saturations, after solidifying the wetting fluid in place. The experimental data is studied in light of the role of the pore structure on the wetting fluid invasion process with the aid of fluid distributions at each saturation regime, a complete rock pore cast, and its associated rock section. The effect of clay minerals on formation factor is studied. The surface conductance contribution of day minerals to overall electrical conductivity is assessed. The effect of partial hydrocarbon saturation on overall rock conductivity and on the Archei saturation exponent is discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  9. 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.

  10. Micromorphometric features of pore space in the plow horizons of loamy soils

    NASA Astrophysics Data System (ADS)

    Skvortsova, E. B.; Sanzharova, S. I.

    2007-04-01

    A computer-based analysis of thin sections has been applied to study pore space in the plow horizons of loamy soils in European Russia and Ukraine. Differences in the morphology of soil macro-and mesopores are shown. It is argued that agrogenic impacts result in the convergence of the shape and orientation of macropores in plowed loamy soils of the forest, forest-steppe, and steppe zones. At the same time, this convergence is not observed for the soil mesopores.

  11. Variation of Permeability with Porosity in Sandstone Diagenesis Interpreted with a Fractal Pore Space Model

    NASA Astrophysics Data System (ADS)

    Pape, H.; Clauser, C.; Iffland, J.

    Permeability is one of the key rock properties for the management of hydrocarbon and geothermal reservoirs as well as for aquifers. The fundamental equation for estimating permeability is the Kozeny-Carman equation. It is based on a capillary bundle model and relates permeability to porosity, tortuosity and an effective hydraulic pore radius which is defined by this equation. Whereas in clean sands the effective pore radius can be replaced by the specific surface or by the grain radius in a simple way, the resulting equations for permeability cannot be applied to consolidated rocks. Based on a fractal model for porous media, equations were therefore developed which adjust the measure of the specific surface and of the grain radius to the resolution length appropriate for the hydraulic process. These equations are calibrated by a large data set for permeability, formation factor, and porosity determined on sedimentary rocks. This fractal model yields tortuosity and effective pore radius as functions of porosity as well as a general permeability-porosity relationship, the coefficients of which are characteristic for different rock types. It can be applied to interpret the diagenetic evolution of the pore space of sedimentary rocks due to mechanical and chemical compaction with respect to porosity and permeability.

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

    NASA Astrophysics Data System (ADS)

    Weller, A.; Slater, L. D.

    2015-12-01

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

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

    USGS Publications Warehouse

    Lee, Myung W.; Waite, William F.

    2008-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  15. Thermal conductivity contrast due to gas saturated pore space-application in basin simulation

    SciTech Connect

    Poelchau, H.S.; Zwach, C.; Welte, D.H. ); Hantschel, T. ); Welte, D.H. Integrated Exploration Systems , Juelich )

    1996-01-01

    Calibration of thermal histories in basin modeling usually relies on matching temperature and vitrinite reflectance distribution in wells. The four main temperature, maximum depth of burial (or eroded overburden), and thermal conductivity of the individual layers of rocks. The last parameter can be used to match the fine structure of the vertical temperature distribution, thermal gradient changes and heat anomalies. While most commercial simulation packages use thermal conductivity values calculated with water as the pore fluid, we have experimented with using decreased conductivity resulting from high gas saturation in the pore space of specific formations in our modeling. One such case study is the Alberta Deep Basin in western Canada, where a large part of the lower Cretaceous section is thought to be gas saturated, underneath a water-saturated seal. Another case study comes from northwestern Siberia, where the largest gas accumulations on earth have been discovered. Results show that the thermal effect of gas in pores, as opposed to water, are significant and cannot be neglected in basin modeling. Such gas saturations can explain frequently observed sudden increases in vitrinite reflectance gradients or so called [open quote]kinky[close quote] reflection profiles. The gas effect can also be used to model heat anomalies in past geologic periods where hypothetical increased heatflow evens cannot be justified.

  16. Thermal conductivity contrast due to gas saturated pore space-application in basin simulation

    SciTech Connect

    Poelchau, H.S.; Zwach, C.; Welte, D.H.; Hantschel, T.; Welte, D.H.

    1996-12-31

    Calibration of thermal histories in basin modeling usually relies on matching temperature and vitrinite reflectance distribution in wells. The four main temperature, maximum depth of burial (or eroded overburden), and thermal conductivity of the individual layers of rocks. The last parameter can be used to match the fine structure of the vertical temperature distribution, thermal gradient changes and heat anomalies. While most commercial simulation packages use thermal conductivity values calculated with water as the pore fluid, we have experimented with using decreased conductivity resulting from high gas saturation in the pore space of specific formations in our modeling. One such case study is the Alberta Deep Basin in western Canada, where a large part of the lower Cretaceous section is thought to be gas saturated, underneath a water-saturated seal. Another case study comes from northwestern Siberia, where the largest gas accumulations on earth have been discovered. Results show that the thermal effect of gas in pores, as opposed to water, are significant and cannot be neglected in basin modeling. Such gas saturations can explain frequently observed sudden increases in vitrinite reflectance gradients or so called {open_quote}kinky{close_quote} reflection profiles. The gas effect can also be used to model heat anomalies in past geologic periods where hypothetical increased heatflow evens cannot be justified.

  17. Ultrasonic Pulse Waves Propagating through Cancellous Bone Phantoms with Aligned Pore Spaces

    NASA Astrophysics Data System (ADS)

    Hosokawa, Atsushi

    2006-05-01

    To elucidate the propagation phenomena of ultrasonic waves in cancellous bone related to trabecular structure, pulse waves propagating through three cancellous bone phantoms with different skeletal frames have been experimentally observed using a water-immersion ultrasonic technique. Skeletal frames with regularly aligned pore spaces were formed to imitate the orthotropic trabecular structure, using wire gauzes, punched plates and honeycomb ceramics. The propagations of the fast and slow waves, which were clearly observed in the direction of the trabecular alignment of cancellous bone, were investigated with the frame’s structures of these phantoms.

  18. 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.

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

    SciTech Connect

    Plum, M.; Brown, D.

    1993-01-01

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

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

    SciTech Connect

    Plum, M.; Brown, D.

    1993-06-01

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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  3. Theory of membrane capacitive deionization including the effect of the electrode pore space.

    PubMed

    Biesheuvel, P M; Zhao, R; Porada, S; van der Wal, A

    2011-08-01

    Membrane capacitive deionization (MCDI) is a technology for water desalination based on applying an electrical field between two oppositely placed porous electrodes. Ions are removed from the water flowing through a channel in between the electrodes and are stored inside the electrodes. Ion-exchange membranes are placed in front of the electrodes allowing for counterion transfer from the channel into the electrode, while retaining the coions inside the electrode structure. We set up an extended theory for MCDI which includes in the description for the porous electrodes not only the electrostatic double layers (EDLs) formed inside the porous (carbon) particles, but also incorporates the role of the transport pathways in the electrode, i.e., the interparticle pore space. Because in MCDI the coions are inhibited from leaving the electrode region, the interparticle porosity becomes available as a reservoir to store salt, thereby increasing the total salt storage capacity of the porous electrode. A second advantage of MCDI is that during ion desorption (ion release) the voltage can be reversed. In that case the interparticle porosity can be depleted of counterions, thereby increasing the salt uptake capacity and rate in the next cycle. In this work, we compare both experimentally and theoretically adsorption/desorption cycles of MCDI for desorption at zero voltage as well as for reversed voltage, and compare with results for CDI. To describe the EDL-structure a novel modified Donnan model is proposed valid for small pores relative to the Debye length. PMID:21592485

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

    PubMed Central

    Cowin, Stephen C.; Cardoso, Luis

    2015-01-01

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

  5. Bulk stress distributions in the pore space of sphere-packed beds under Darcy flow conditions.

    PubMed

    Pham, Ngoc H; Voronov, Roman S; Tummala, Naga Rajesh; Papavassiliou, Dimitrios V

    2014-03-01

    In this paper, bulk stress distributions in the pore space of columns packed with spheres are numerically computed with lattice Boltzmann simulations. Three different ideally packed and one randomly packed configuration of the columns are considered under Darcy flow conditions. The stress distributions change when the packing type changes. In the Darcy regime, the normalized stress distribution for a particular packing type is independent of the pressure difference that drives the flow and presents a common pattern. The three parameter (3P) log-normal distribution is found to describe the stress distributions in the randomly packed beds within statistical accuracy. In addition, the 3P log-normal distribution is still valid when highly porous scaffold geometries rather than sphere beds are examined. It is also shown that the 3P log-normal distribution can describe the bulk stress distribution in consolidated reservoir rocks like Berea sandstone. PMID:24730946

  6. Bulk stress distributions in the pore space of sphere-packed beds under Darcy flow conditions

    NASA Astrophysics Data System (ADS)

    Pham, Ngoc H.; Voronov, Roman S.; Tummala, Naga Rajesh; Papavassiliou, Dimitrios V.

    2014-03-01

    In this paper, bulk stress distributions in the pore space of columns packed with spheres are numerically computed with lattice Boltzmann simulations. Three different ideally packed and one randomly packed configuration of the columns are considered under Darcy flow conditions. The stress distributions change when the packing type changes. In the Darcy regime, the normalized stress distribution for a particular packing type is independent of the pressure difference that drives the flow and presents a common pattern. The three parameter (3P) log-normal distribution is found to describe the stress distributions in the randomly packed beds within statistical accuracy. In addition, the 3P log-normal distribution is still valid when highly porous scaffold geometries rather than sphere beds are examined. It is also shown that the 3P log-normal distribution can describe the bulk stress distribution in consolidated reservoir rocks like Berea sandstone.

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

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

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

  8. Morphological Functions with Parallel Sets for the Pore Space of X-ray CT Images of Soil Columns

    NASA Astrophysics Data System (ADS)

    San José Martínez, F.; Muñoz Ortega, F. J.; Caniego Monreal, F. J.; Peregrina, F.

    2016-03-01

    During the last few decades, new imaging techniques like X-ray computed tomography have made available rich and detailed information of the spatial arrangement of soil constituents, usually referred to as soil structure. Mathematical morphology provides a plethora of mathematical techniques to analyze and parameterize the geometry of soil structure. They provide a guide to design the process from image analysis to the generation of synthetic models of soil structure in order to investigate key features of flow and transport phenomena in soil. In this work, we explore the ability of morphological functions built over Minkowski functionals with parallel sets of the pore space to characterize and quantify pore space geometry of columns of intact soil. These morphological functions seem to discriminate the effects on soil pore space geometry of contrasting management practices in a Mediterranean vineyard, and they provide the first step toward identifying the statistical significance of the observed differences.

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

    PubMed

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

    2014-10-01

    A micro-gap air-filled ionisation chamber was designed for criticality dosimetry. The special feature of the chamber is its very small gap between electrodes of only 0.3 mm. This prevents ion recombination at high dose rates and minimises the influence of gas on secondary particles spectrum. The electrodes are made of polypropylene because of higher content of hydrogen in this material, when compared with soft tissue. The difference between neutron and gamma sensitivity in such chamber becomes practically negligible. The chamber's envelope contains two specially connected capacitors, one for polarising the electrodes and the other for collecting the ionisation charge. PMID:24324250

  10. Photospectroscopically observed pore-space correlations of a wetting fluid during the drying process in nanoporous Vycor glass.

    PubMed

    Ogawa, Shigeo; Nakamura, Jiro

    2015-04-01

    We use light scattering to study spatial correlations in the pore space of Vycor glass upon draining a wetting fluid. We analyze the transmission spectrum of forward-scattered light on the basis of the theory of dielectric constant fluctuation, whereas conventional light scattering analyzes the scattered light at small angles of monochromatic incident light. Assuming that the drained pores, which are surrounded by filled pores, exhibit long-range correlations of a fractal dimension of 2.5, we analytically derive the corresponding turbidity. The slight deviation from the λ(-4) Rayleigh wavelength dependence directly provides the correlation length of the interconnected network of drained pores. The estimated length, ranging from 0.5 to 18 nm at most, is almost the same order as that indirectly estimated from our previous simple effective Rayleigh scatterer model. PMID:26366762

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  12. Modeling diffusion control on organic matter decomposition in unsaturated soil pore space

    NASA Astrophysics Data System (ADS)

    Vogel, Laure; Pot, Valérie; Garnier, Patricia; Vieublé-Gonod, Laure; Nunan, Naoise; Raynaud, Xavier; Chenu, Claire

    2014-05-01

    Soil Organic Matter decomposition is affected by soil structure and water content, but field and laboratory studies about this issue conclude to highly variable outcomes. Variability could be explained by the discrepancy between the scale at which key processes occur and the measurements scale. We think that physical and biological interactions driving carbon transformation dynamics can be best understood at the pore scale. Because of the spatial disconnection between carbon sources and decomposers, the latter rely on nutrient transport unless they can actively move. In hydrostatic case, diffusion in soil pore space is thus thought to regulate biological activity. In unsaturated conditions, the heterogeneous distribution of water modifies diffusion pathways and rates, thus affects diffusion control on decomposition. Innovative imaging and modeling tools offer new means to address these effects. We have developed a new model based on the association between a 3D Lattice-Boltzmann Model and an adimensional decomposition module. We designed scenarios to study the impact of physical (geometry, saturation, decomposers position) and biological properties on decomposition. The model was applied on porous media with various morphologies. We selected three cubic images of 100 voxels side from µCT-scanned images of an undisturbed soil sample at 68µm resolution. We used LBM to perform phase separation and obtained water phase distributions at equilibrium for different saturation indices. We then simulated the diffusion of a simple soluble substrate (glucose) and its consumption by bacteria. The same mass of glucose was added as a pulse at the beginning of all simulations. Bacteria were placed in few voxels either regularly spaced or concentrated close to or far from the glucose source. We modulated physiological features of decomposers in order to weight them against abiotic conditions. We could evidence several effects creating unequal substrate access conditions for

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. Temperature-Dependent Pore Space of Sea Ice: X-ray Computed-Tomography and Dual Model Network Analysis

    NASA Astrophysics Data System (ADS)

    Pringle, D.; Miner, J.; Glantz, R.; Hilpert, M.; Eicken, H.

    2006-12-01

    Sea ice provides a mechanical and thermal barrier between the atmosphere and ocean at high latitudes and is an important component of the climate system. It is a composite material with temperature- and salinity- dependent volume fractions of ice, brine and air. Our present interest is the microstructural control of the (hydraulic) permeability, which affects the melt-season albedo (shortwave reflectance) of sea ice by enabling or restricting the drainage of surface meltwater, and is also relevant for other processes including nutrient delivery to microorganisms colonizing the lower layers of the ice sheet. At low temperatures, the relative brine volume (porosity) is small, the inclusions are disconnected, and the permeability is small. The relative brine volume increases with temperature, and the permeability increases strongly above a porosity of ~5%. We have imaged the pore space of natural and laboratory-grown sea ice with x-ray micro-computed tomography (CT) over a temperature range typical of that in the Arctic ( - 25°C to -3°C) and which spans corresponding changes in the permeability by several orders of magnitude. Based on our `Dual Model' approach, we identify pore bodies and throats from the segmented CT data to eventually derive a pore network. We characterize the temperature-dependence of the pore space connectivity and apply critical path analysis to investigate the dependence of permeability on pore microstructural evolution.

  15. Pore space evolution and elastic properties of platform carbonates (Urgonian limestone, Barremian-Aptian, SE France)

    NASA Astrophysics Data System (ADS)

    Fournier, François; Léonide, Philippe; Kleipool, Luuk; Toullec, Renault; Reijmer, John J. G.; Borgomano, Jean; Klootwijk, Thomas; Van Der Molen, Jeroen

    2014-07-01

    A dataset of 214 ultrasonic velocity and porosity measurements on Barremian-Aptian carbonates from Provence (SE France) provides well-constrained velocity-porosity transforms and allows the quantification of the impact of pore type and diagenetic history on these velocities. A numerical approach (EPAR: equivalent pore aspect ratio) was used to link diagenetic transformations, pore network evolution and elastic properties. Three categories of samples characterized by their dominant pore type were discriminated from the velocity and porosity database by means of the EPAR values derived from bulk (K-EPAR) and shear (μ-EPAR) moduli: 1) purely microporous limestones (low K- and μ-EPAR < 0.22), 2) samples with preserved intergranular and moldic pores (intermediate K- and μ-EPAR), and 3) vuggy limestones (K- and μ-EPAR > 0.3). Three velocity-porosity trajectories related to three diagenetic paths were defined and quantified from the Urgonian database: 1) EPAR-preserving micro-scale cementation of micrite, 2) non-EPAR-preserving dissolution with moldic pore development and 3) EPAR-preserving sparry calcite cementation of molds. Equivalent Pore Aspect Ratio can therefore be regarded as a robust tool to decipher diagenetic trends in velocity-porosity transforms and may help predicting pore architecture from subsurface data.

  16. Reconfigurable optothermal microparticle trap in air-filled hollow-core photonic crystal fiber.

    PubMed

    Schmidt, O A; Garbos, M K; Euser, T G; Russell, P St J

    2012-07-13

    We report a novel optothermal trapping mechanism that occurs in air-filled hollow-core photonic crystal fiber. In the confined environment of the core, the motion of a laser-guided particle is strongly influenced by the thermal-gradient-driven flow of air along the core surface. Known as "thermal creep flow," this can be induced either statically by local heating, or dynamically by the absorption (at a black mark placed on the fiber surface) of light scattered by the moving particle. The optothermal force on the particle, which can be accurately measured in hollow-core fiber by balancing it against the radiation forces, turns out to exceed the conventional thermophoretic force by 2 orders of magnitude. The system makes it possible to measure pN-scale forces accurately and to explore thermally driven flow in micron-scale structures. PMID:23030165

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

    NASA Technical Reports Server (NTRS)

    Nelson, D. A.

    1985-01-01

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

  18. Reconfigurable Optothermal Microparticle Trap in Air-Filled Hollow-Core Photonic Crystal Fiber

    NASA Astrophysics Data System (ADS)

    Schmidt, O. A.; Garbos, M. K.; Euser, T. G.; Russell, P. St. J.

    2012-07-01

    We report a novel optothermal trapping mechanism that occurs in air-filled hollow-core photonic crystal fiber. In the confined environment of the core, the motion of a laser-guided particle is strongly influenced by the thermal-gradient-driven flow of air along the core surface. Known as “thermal creep flow,” this can be induced either statically by local heating, or dynamically by the absorption (at a black mark placed on the fiber surface) of light scattered by the moving particle. The optothermal force on the particle, which can be accurately measured in hollow-core fiber by balancing it against the radiation forces, turns out to exceed the conventional thermophoretic force by 2 orders of magnitude. The system makes it possible to measure pN-scale forces accurately and to explore thermally driven flow in micron-scale structures.

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

    SciTech Connect

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

    1997-07-01

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

  20. Small-angle scattering studies of the pore spaces of shaly rocks

    NASA Astrophysics Data System (ADS)

    Hall, Peter L.; Mildner, David F. R.; Borst, Roger L.

    1986-02-01

    Small-angle neutron and X ray scattering (SANS and SAXS) measurements have been performed on shaly rocks from a variety of oil field locations. Thin core sections cut parallel to their bedding planes give circularly symmetric scattering patterns. On the basis of the model of Debye et al., the data indicate characteristic pore dimensions of 9-15 nm. Sections cut normal to the bedding planes exhibit elliptically symmetric scattering indicative of pores flattened in the direction of sedimentary compaction. Fourier inversion of the symmetric SANS data in all cases yields a broad distribution of pore diameters having peaks typically in the range 4-6 nm. These distributions are in reasonable agreement with distributions derived from nitrogen adsorption isotherms, although often in disagreement with nitrogen desorption or mercury porosimetry data. At higher scattering vectors, in the Porod region, differences between the SAXS and SANS data are observed which are explained in terms of the rather different sensitives of the two techniques to empty and filled pores. The data indicate that a significant component of the total porosity is due to pores of less than 2 nm in diameter, in which water is retained under ambient conditions. In several cases, pore dimensions measured by SANS increase after extraction of bitumens by methylene chloride solution, suggesting an intimate microscopic association of hydrocarbon and fine mineral grains.

  1. Pore space characteristics vs. stress-strain markers: two contrasting approaches on how to predict durability of porous natural stone

    NASA Astrophysics Data System (ADS)

    Prikryl, Richard; Weishauptova, Zuzana; Lokajicek, Tomas

    2016-04-01

    Pore space characteristics, specifically its textural properties derived from mercury porosimetry present useful data that are often employed as one of the proxies for the evaluation of the durability of porous construction materials, specifically of natural stone or bricks. Interconnected pore spaces present pathways for migration of moisture, water, or water-soluble salts in porous materials, but do not provide direct evidence on mechanical properties including resistance to brittle damage caused by various physical weathering processes. On contrary, experimentally derived rock mechanical properties are used very rarely for the estimation of the durability of natural stone. This concerns not only basic rock mechanical properties (strength) but also deformation (stress-strain behaviour) and energetic parameters derived from it. In the recent study, we are discussing both these approaches and looking for possible correlation or for mutual use of data from both types of tests.

  2. Estimation of water-filled and air-filled porosity in the unsaturated zone, Yucca Mountain, Nevada

    USGS Publications Warehouse

    Nelson, Philip H.

    1993-01-01

    The responses of density and dielectric logs are formulated in terms if the matrix properties, air-filled porosity and water-filled porosity. Porosity values obtained from logs from borehole USW G-2 are in reasonable agreement with estimates from core determinations.

  3. A magnetic resonance study of pore filling processes during spontaneous imbibition in Berea sandstone

    NASA Astrophysics Data System (ADS)

    Chen, Quan; Gingras, Murray K.; Balcom, Bruce J.

    2003-11-01

    A new magnetic resonance technique, DDIF (the decay of magnetization due to diffusion in the internal field), was combined with mercury porosimetry to investigate pore geometry, including pore- and throat-size distribution, and pore connectivity for porous media. A comparison of DDIF spectra for a fully water saturated Berea sandstone, with the partially saturated sample by centrifugation in air, indicated that DDIF can be used for the measurement of water filled pore size distribution in partially saturated porous media. Dynamic water imbibition into air-filled Berea sandstone was studied using the DDIF technique. Simultaneously, in situ three-dimensional saturation and capillary driven water penetration were monitored using Conical-SPRITE, which is a rapid, centric scanning, spin-density weighted single point three-dimensional magnetic resonance imaging technique. These measurements provide direct evidence for differences in the pore filling mechanisms for co-current imbibition and counter-current imbibition in Berea sandstone. During co-current imbibition, water flows through the pores and connected throats with a piston-type mechanism. Air is displaced from the sample by the leading edge of the waterfront, resulting in a macroscopic piston-like flow through the entire sample. During counter-current imbibition, water flows through the pores and connected throats with a film-like structure along the corners and surfaces of the pore space. Air escapes from the sample by flowing through the center of the pores and pore throats, in the opposite direction. Once the penetrating waterfronts meet, at the sample center, there is a global, uniform increase in water content.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  7. Characterisation of pore space geometry by 14C-PMMA impregnation - development work for in-situ studies

    NASA Astrophysics Data System (ADS)

    Kelokaski, M.; Sardini, P.; Möri, A.; Hellmuth, K.-H.; Siitari-Kauppi, M.

    2003-04-01

    The repository safety evaluation requires going from laboratory and surface-based field work underground to the repository level. Little is known about the changes of rock transport properties during sampling and decompression. Some recent investigations imply that non-conservative errors in transport properties derived from laboratory data may reach factors of 2--3. Recently at the Grimsel Test Site (GTS) progress with the in-situ resin impregnation using fluorescent dyes has been successful. During ten years time the PMMA method has been developed for characterisation of pore space geometry for low permeable granitic rocks. Rock matrices has been studied so far at laboratory circumstances. Impregnation with 14C-labelled methylmethacrylate (MMA) and autoradiography allows the investigation of the pattern of the spatial porosity distribution and quantitative measurement of mineral specific, local porosities. The quantitative petrography methods developed by University of Poitiers in combination with the PMMA method provide quantitative information on rock properties. The development of the PMMA method for in-situ to be tested at first at Grimsel Test Site and the necessary rock characterisation in the laboratory is reported here. The porosity parameters, hydraulic conductivity parameters, diffusive properties and mineralogical properties are measured with complementary methods. Highly conductive granite is impregnated with MMA using vacuum dried samples as well as water saturated ones. The intrusion pressure of MMA in water filled pores of different apertures will be the key point for the successful in-situ impregnation. Details of the development work will be given.

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

    SciTech Connect

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

    1994-04-01

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

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

    NASA Technical Reports Server (NTRS)

    Grugel, Richard N.

    2003-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  11. Accurate micro-computed tomography imaging of pore spaces in collagen-based scaffold.

    PubMed

    Zidek, Jan; Vojtova, Lucy; Abdel-Mohsen, A M; Chmelik, Jiri; Zikmund, Tomas; Brtnikova, Jana; Jakubicek, Roman; Zubal, Lukas; Jan, Jiri; Kaiser, Jozef

    2016-06-01

    In this work we have used X-ray micro-computed tomography (μCT) as a method to observe the morphology of 3D porous pure collagen and collagen-composite scaffolds useful in tissue engineering. Two aspects of visualizations were taken into consideration: improvement of the scan and investigation of its sensitivity to the scan parameters. Due to the low material density some parts of collagen scaffolds are invisible in a μCT scan. Therefore, here we present different contrast agents, which increase the contrast of the scanned biopolymeric sample for μCT visualization. The increase of contrast of collagenous scaffolds was performed with ceramic hydroxyapatite microparticles (HAp), silver ions (Ag(+)) and silver nanoparticles (Ag-NPs). Since a relatively small change in imaging parameters (e.g. in 3D volume rendering, threshold value and μCT acquisition conditions) leads to a completely different visualized pattern, we have optimized these parameters to obtain the most realistic picture for visual and qualitative evaluation of the biopolymeric scaffold. Moreover, scaffold images were stereoscopically visualized in order to better see the 3D biopolymer composite scaffold morphology. However, the optimized visualization has some discontinuities in zoomed view, which can be problematic for further analysis of interconnected pores by commonly used numerical methods. Therefore, we applied the locally adaptive method to solve discontinuities issue. The combination of contrast agent and imaging techniques presented in this paper help us to better understand the structure and morphology of the biopolymeric scaffold that is crucial in the design of new biomaterials useful in tissue engineering. PMID:27153826

  12. Optimum values of air-filling fraction for photonic crystal fibers with different configurations and fixed number of air rings.

    PubMed

    Zendehnam, Akbar; Hosseinpour, Maryam; Mirzaei, Mahmood; Hedayati, Kambiz

    2014-02-20

    In this study, a Gaussian amp function related to the Gaussian family is employed to approximate the output intensity profile of various arrangements of air holes in photonic crystal fibers (PCFs) with a fixed number of air rings (N=4). It is shown that d/Λ=0.5 can be the best minimum value of air-filling fraction for all of the studied PCFs when λ=1.35  μm, whereas, for λ=1.55 and 1.65 μm, d/Λ=0.6 is suitable for achieving the maximum output intensity with very low confinement loss. PMID:24663304

  13. Impact of pore space topology on permeability, cut-off frequencies and validity of wave propagation theories

    NASA Astrophysics Data System (ADS)

    Sarout, Joël.

    2012-04-01

    For the first time, a comprehensive and quantitative analysis of the domains of validity of popular wave propagation theories for porous/cracked media is provided. The case of a simple, yet versatile rock microstructure is detailed. The microstructural parameters controlling the applicability of the scattering theories, the effective medium theories, the quasi-static (Gassmann limit) and dynamic (inertial) poroelasticity are analysed in terms of pores/cracks characteristic size, geometry and connectivity. To this end, a new permeability model is devised combining the hydraulic radius and percolation concepts. The predictions of this model are compared to published micromechanical models of permeability for the limiting cases of capillary tubes and penny-shaped cracks. It is also compared to published experimental data on natural rocks in these limiting cases. It explicitly accounts for pore space topology around the percolation threshold and far above it. Thanks to this permeability model, the scattering, squirt-flow and Biot cut-off frequencies are quantitatively compared. This comparison leads to an explicit mapping of the domains of validity of these wave propagation theories as a function of the rock's actual microstructure. How this mapping impacts seismic, geophysical and ultrasonic wave velocity data interpretation is discussed. The methodology demonstrated here and the outcomes of this analysis are meant to constitute a quantitative guide for the selection of the most suitable modelling strategy to be employed for prediction and/or interpretation of rocks elastic properties in laboratory-or field-scale applications when information regarding the rock's microstructure is available.

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

    PubMed

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

    2016-09-25

    A microporous Cu-MOF with optimized open metal sites and pore space was constructed based on a designed bent ligand; it exhibits high-capacity multiple gas storage under atmospheric pressure and efficient catalytic activity for chemical fixation of CO2 under mild conditions. PMID:27550833

  15. Capillary hysteresis in the pore space of a packing of spheres measured by the movement of blobs

    SciTech Connect

    Mason, G.; Yadav, G.D.

    1983-09-01

    The effect of the flow of surrounding liquid on the initial movement of a liquid blob in a packing of spheres was used to test the hypothesis that the capillary meniscus radius of a pore when filling is the same as the largest meniscus radius of the same pore when emptying. The agreement between experiment and theory confirmed this hypothesis and indicated that the multiple interconnections between the pores are instrumental in developing the capillary hysteresis exhibited by an assembly of pores. 12 references.

  16. Preparation and in vitro evaluation of poly(D,L-lactide-co-glycolide) air-filled nanocapsules as a contrast agent for ultrasound imaging.

    PubMed

    Néstor, Mendoza-Muñoz; Kei, Noriega-Peláez Eddy; Guadalupe, Nava-Arzaluz María; Elisa, Mendoza-Elvira Susana; Adriana, Ganem-Quintanar; David, Quintanar-Guerrero

    2011-10-01

    The aim of this study was to prepare air-filled nanocapsules intended ultrasound contrast agents (UCAs) with a biodegradable polymeric shell composed of poly(d,l-lactide-co-glycolide) (PLGA). Because of their size, current commercial UCAs are not capable of penetrating the irregular vasculature that feeds growing tumors. The new generation of UCAs should be designed on the nanoscale to enhance tumor detection, in addition, the polymeric shell in contrast with monomolecular stabilized UCAs improves the mechanical properties against ultrasound pressure and lack of stability. The preparation method of air-filled nanocapsules was based on a modification of the double-emulsion solvent evaporation technique. Air-filled nanocapsules with a mean diameter of 370±96nm were obtained. Electronic microscopies revealed spherical-shaped particles with smooth surfaces and a capsular morphology, with a shell thickness of ∼50nm. Air-filled nanocapsules showed echogenic power in vitro, providing an enhancement of up to 15dB at a concentration of 0.045mg/mL at a frequency of 10MHz. Loss of signal for air-filled nanocapsules was 2dB after 30min, suggesting high stability. The prepared contrast agent in this work has the potential to be used in ultrasound imaging. PMID:21570702

  17. Isolating scattering resonances of an air-filled spherical shell using iterative, single-channel time reversal.

    PubMed

    Waters, Zachary J; Dzikowicz, Benjamin R; Simpson, Harry J

    2012-01-01

    Iterative, single-channel time reversal is employed to isolate backscattering resonances of an air-filled spherical shell in a frequency range of 0.5-20 kHz. Numerical simulations of free-field target scattering suggest improved isolation of the dominant target response frequency in the presence of varying levels of stochastic noise, compared to processing returns from a single transmission and also coherent averaging. To test the efficacy of the technique in a realistic littoral environment, monostatic scattering experiments are conducted in the Gulf of Mexico near Panama City, Florida. The time reversal technique is applied to returns from a hollow spherical shell target sitting proud on a sandy bottom in 14 m deep water. Distinct resonances in the scattering response of the target are isolated, depending upon the bandwidth of the sonar system utilized. PMID:22280594

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  19. Spectral Evidence for Ionization in Air-Filled Glow Discharge Tubes: Application to Sprites

    NASA Astrophysics Data System (ADS)

    Armstrong, R. A.; Williams, E. R.; Golka, R. K.; Williams, D. R.

    2001-12-01

    The question of ionization in sprites and the evidence for VLF backscatter from sprites has motivated a quantitative spectral analysis of the various (classical) regions of the glow discharge tube under DC excitation and at air densities appropriate for sprites in the mesosphere. A PR-650 colorimeter (Photo Research, Inc.) has enabled calibrated irradiance measurements for localized zones along the axis of the discharge tube--in the dominantly blue negative glow, in the Faraday dark space and in the red/pink positive column. Consistent with historical nomenclature, nitrogen first and second positive emission is dominant in the positive column (associated with neutral N2), and nitrogen first negative emission, with a prominent peak at 4278 A, is dominant in the blue negative glow (associated with ionized N2+). Whereas nitrogen first and second positive emission are also detected in the negative glow, no spectral evidence for ionization (no 4279, no 3914, no Meinel) is found in the red/pink positive column. This negative result is attributed not to an absence of ionization in the positive column, but rather to a sparse population of N2+ relative to neutral nitrogen in this region, and to the prominent emission in the blue part of the spectrum due to nitrogen second positive. A similar interpretation may be appropriate for the time-integrated spectra from the red body of sprites, also lacking direct evidence for ionization.

  20. 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

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

    PubMed

    Saâdi, Zakaria

    2014-05-01

    The radon exhalation rate at the earth's surface from soil or rock with radium as its source is the main mechanism behind the radon activity concentrations observed in both indoor and outdoor environments. During the last two decades, many subsurface radon transport models have used Rogers and Nielson's formula for modeling the unsaturated soil bulk radon diffusion coefficient. This formula uses an "air-filled effective porosity" to account for radon adsorption and radon dissolution in the groundwater. This formula is reviewed here, and its hypotheses are examined for accuracy in dealing with subsurface radon transport problems. The author shows its limitations by comparing one dimensional steady-state analytical solutions of the two-phase (air/water) transport equation (Fick's law) with Rogers and Nielson's formula. For radon diffusion-dominated transport, the calculated Rogers and Nielson's radon exhalation rate is shown to be unrealistic as it is independent of the values of the radon adsorption and groundwater dissolution coefficients. For convective and diffusive transport, radon exhalation rates calculated using Fick's law and this formula agree only for high values of gas-phase velocity and groundwater saturation. However, these conditions are not usually met in most shallow subsurface environments where radon migration takes place under low gas phase velocities and low water saturation. PMID:24670909

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  3. Modification of textural properties of pore space in sedimentary rocks by conservation agents: mercury porosimetry study and indirect interpretation of durability

    NASA Astrophysics Data System (ADS)

    Zamrazilova, Lenka; Weishauptova, Zuzana; Prikrylova, Jirina; Sykorova, Ivana; Prikryl, Richard

    2014-05-01

    Textural properties of porous sedimentary rocks (various types of sandstone, clayey-calcareous silicites, bioclastic limestones) have been modified by applying some conventional conservation agents (lime water, water glass, esters of silicon acid) used for consolidation and/or hydrophobization treatments of natural stone. Many of these treatments are applied in practice without knowing the real effect on material properties. To partly fill this gap in knowledge, laboratory-scale study performed on disc-like specimens was focused on the detailed investigation of textural properties of pore space of above mentioned types of natural stone by means of mercury porosimetry and on indirect evaluation of durability from pore space textural properties. Depth of penetration of treatments in some of the studied rocks was also controlled by microscopic techniques. Our results show significant variability in the effectiveness of various treatments for different lithologies not only in terms of total porosity change but also in terms of modification of pore size distribution and specific surface area. Data obtained confirm importance of the detailed trials of the effect of specific conservation agents on respective stone types before their final application in real scale.

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  5. Small bowel necrosis as a consequence of spontaneous deflation and migration of an air-filled intragastric balloon - a potentially life-threatening complication.

    PubMed

    Drozdowski, Robert; Wyleżoł, Mariusz; Frączek, Mariusz; Hevelke, Piotr; Giaro, Marcin; Sobański, Paweł

    2014-06-01

    Intragastric balloon placement is a common method of treatment of obesity and is often used by non-surgical teams in endoscopy departments. The likelihood of spontaneous intragastric balloon damage is a well-known phenomenon. We describe a patient who was disqualified from surgical obesity treatment and in whom intragastric fluid-filled balloons had already been inserted twice and removed due to their intolerance. Therefore we qualified this patient for placement of the air-filled balloon Heliosphere BAG. Two months after the planned check-up, he arrived at the surgery department complaining of nausea and vomiting and due to symptoms of ileus diagnosed with an X-ray and ultrasound examination we qualified him for emergency surgery. We would like to emphasise the following issues: the necessity of air-filled balloon removal according to the producer's instructions and multidisciplinary specialist team care along with appropriate diagnostic tools in every case of intragastric balloon insertion. PMID:25097704

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

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

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

  7. Single-mode pumped high air-fill fraction photonic crystal fiber taper for high-power deep-blue supercontinuum sources.

    PubMed

    Sørensen, Simon T; Larsen, Casper; Jakobsen, Christian; Thomsen, Carsten L; Bang, Ole

    2014-02-15

    Dispersion control with axially nonuniform photonic crystal fibers (PCFs) permits supercontinuum (SC) generation into the deep-blue from an ytterbium pump laser. In this Letter, we exploit the full degrees of freedom afforded by PCFs to fabricate a fiber with longitudinally increasing air-fill fraction and decreasing diameter directly on the draw-tower. We demonstrate SC generation extending down to 375 nm in one such monolithic fiber device that is single-mode at 1064 nm at the input end. PMID:24562287

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

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

  9. Reconstruction and analysis of fuel cell gas diffusion layers using fiber spacing rather than pore size data: Questioned validity of widely-used porosity-based thermal conductivity models

    NASA Astrophysics Data System (ADS)

    Sadeghifar, Hamidreza

    2016-03-01

    Porosity and pore size data have long been used for reconstructing (two directional) fibrous materials. The present study is aimed to explain the overlooked fact that pore size parameter, bundling several other geometric parameters together, cannot be directly used for the reconstruction and geometrical modeling of gas diffusion layers (GDLs) of fuel cells. Instead, it has to be converted to fiber spacing, for which purpose it is a useful parameter. A technical approach is presented on how to reach fiber spacing from pore size (diameter) data. The reason why GDLs with the same porosity, fiber diameter and angle, but with unequal fiber spacing, may have different properties is also explained by providing physical evidence. The present study clearly demonstrates that the traditional notion that fibrous materials with lower porosity have higher thermal conductivity does not necessary hold. In addition, it is shown that GDLs with the same porosity and the same pore size may have different fiber spacing and thus, distinct properties. It is found that the thermal conductivity models based solely upon porosity can be off by several hundred percent and must be either discarded or used over the narrow range of conditions under which they have been formulated.

  10. 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

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

    NASA Astrophysics Data System (ADS)

    Vialle, S.; Mavko, G. M.

    2012-04-01

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

  12. Pore Velocity Estimation Uncertainties

    NASA Astrophysics Data System (ADS)

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

    1982-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  14. Rapid assessment of methanotrophic capacity of compost-based materials considering the effects of air-filled porosity, water content and dissolved organic carbon.

    PubMed

    Mancebo, Uriel; Hettiaratchi, J Patrick A

    2015-02-01

    Since the global warming potential of CH4 is 25 times that of CO2 on a 100-year time horizon, the development of methanotrophic applications for the conversion of CH4 to CO2 is emerging as an area of interest for researchers and practicing engineers. Compost exhibits most of the characteristics required for methanotroph growth media and has been used in several projects. This paper presents results from a study that was undertaken to assess the influence of physical and chemical characteristics of compost-based materials on the biological oxidation of CH4 when used in methane biofilters. The results showed that easily-measurable parameters, such as air filled porosity, water content and dissolved organic carbon, are correlated with maximum CH4 removal rates. The results obtained were used to develop an empirical relationship that could be regarded as a rapid assessment tool for the estimation of the performance of compost-based materials in engineered methanotrophic applications. PMID:25484123

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  18. Evaporative modeling for idealized lithographic pores

    NASA Astrophysics Data System (ADS)

    Oinuma, Ryoji; Best, Frederick

    2002-01-01

    As a demand for the high performance and small size electronics devices increased, the heat removal from those electronic devices for space use is getting critical factor more than devices on the earth due to the limitation of the size. The purpose of this paper is to show a study of optimized size of coherent pores or slits in the evaporative wick of a heat pipe to cool down the high heat flux density heat source. Our system considered in this paper consists of a plate heat source, the evaporative wick with coherent pores and conducting walls connecting between the heat source and the evaporator. The evaporation rate of working fluid along the meniscus interface in a micro-order pore or slit was calculated based on the kinetic theory and the statistical rate theory to find a proper diameter of pores to cool down the heat source effectively. The results show the smaller diameter of pores is preferred to achieve the smallest total size of the evaporator although it will involve the cost issue. As a demand for the high performance and small size electronics devices increased, the heat removal from those electronic devices for space use is getting critical factor more than devices on the earth due to the limitation of the size. The purpose of this paper is to show a study of optimized size of coherent pores or slits in the evaporative wick of a heat pipe to cool down the high heat flux density heat source. Our system considered in this paper consists of a plate heat source, the evaporative wick with coherent pores and conducting walls connecting between the heat source and the evaporator. The evaporation rate of working fluid along the meniscus interface in a micro-order pore or slit was calculated based on the kinetic theory and the statistical rate theory to find a proper diameter of pores to cool down the heat source effectively. The results show that the smaller diameter of pores uses the pore for evaporation effectively and is preferred to achieve the smallest

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

    NASA Astrophysics Data System (ADS)

    Chander, Ramesh; Tomar, S. K.

    2014-10-01

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

  20. Emulsion formation at the Pore-Scale

    NASA Astrophysics Data System (ADS)

    Armstrong, R. T.; Van Den Bos, P.; Berg, S.

    2012-12-01

    The use of surfactant cocktails to produce ultra-low interfacial tension between water and oil is an enhanced oil recovery method. In phase behavior tests three distinct emulsion phases are observed: (1) oil-in-water emulsion; (2) microemulsion; and (3) water-in-oil emulsion. However, it is unknown how phase behavior manifests at the pore-scale in a porous media system. What is the time scale needed for microemulsion formation? Where in the pore-space do the microemulsions form? And in what order do the different emulsion phases arrange during oil bank formation? To answer these questions micromodel experiments were conducted. These experiments are used to build a conceptual model for phase behavior at the pore-scale.

  1. Pore pressure embrittlement in a volcanic edifice

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  2. Low pore connectivity in natural rock

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

  3. Low pore connectivity in natural rock.

    PubMed

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

    2012-05-15

    As repositories for CO(2) and radioactive waste, as oil and gas reservoirs, and as contaminated sites needing remediation, rock formations play a central role in energy and environmental management. The connectivity of the rock's porespace strongly affects fluid flow and solute transport. This work examines pore connectivity and its implications for fluid flow and chemical transport. Three experimental approaches (imbibition, tracer concentration profiles, and imaging) were used in combination with network modeling. In the imbibition results, three types of imbibition slope [log (cumulative imbibition) vs. log (imbibition time)] were found: the classical 0.5, plus 0.26, and 0.26 transitioning to 0.5. The imbibition slope of 0.26 seen in Indiana sandstone, metagraywacke, and Barnett shale indicates low pore connectivity, in contrast to the slope of 0.5 seen in the well-connected Berea sandstone. In the tracer profile work, rocks exhibited different distances to the plateau porosity, consistent with the pore connectivity from the imbibition tests. Injection of a molten metal into connected pore spaces, followed by 2-D imaging of the solidified alloy in polished thin sections, allowed direct assessment of pore structure and lateral connection in the rock samples. Pore-scale network modeling gave results consistent with measurements, confirming pore connectivity as the underlying cause of both anomalous behaviors: imbibition slope not having the classical value of 0.5, and accessible porosity being a function of distance from the edge. A poorly connected porespace will exhibit anomalous behavior in fluid flow and chemical transport, such as a lower imbibition slope (in air-water system) and diffusion rate than expected from classical behavior. PMID:22507286

  4. Low Pore Connectivity in Natural Rock

    SciTech Connect

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

    2012-05-15

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

  5. Organization of the Mitochondrial Apoptotic BAK Pore

    PubMed Central

    Aluvila, Sreevidya; Mandal, Tirtha; Hustedt, Eric; Fajer, Peter; Choe, Jun Yong; Oh, Kyoung Joon

    2014-01-01

    The multidomain pro-apoptotic Bcl-2 family proteins BAK and BAX are believed to form large oligomeric pores in the mitochondrial outer membrane during apoptosis. Formation of these pores results in the release of apoptotic factors including cytochrome c from the intermembrane space into the cytoplasm, where they initiate the cascade of events that lead to cell death. Using the site-directed spin labeling method of electron paramagnetic resonance (EPR) spectroscopy, we have determined the conformational changes that occur in BAK when the protein targets to the membrane and forms pores. The data showed that helices α1 and α6 disengage from the rest of the domain, leaving helices α2-α5 as a folded unit. Helices α2-α5 were shown to form a dimeric structure, which is structurally homologous to the recently reported BAX “BH3-in-groove homodimer.” Furthermore, the EPR data and a chemical cross-linking study demonstrated the existence of a hitherto unknown interface between BAK BH3-in-groove homodimers in the oligomeric BAK. This novel interface involves the C termini of α3 and α5 helices. The results provide further insights into the organization of the BAK oligomeric pores by the BAK homodimers during mitochondrial apoptosis, enabling the proposal of a BAK-induced lipidic pore with the topography of a “worm hole.” PMID:24337568

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  7. Pore-scale imaging and modelling

    NASA Astrophysics Data System (ADS)

    Blunt, Martin J.; Bijeljic, Branko; Dong, Hu; Gharbi, Oussama; Iglauer, Stefan; Mostaghimi, Peyman; Paluszny, Adriana; Pentland, Christopher

    2013-01-01

    Pore-scale imaging and modelling - digital core analysis - is becoming a routine service in the oil and gas industry, and has potential applications in contaminant transport and carbon dioxide storage. This paper briefly describes the underlying technology, namely imaging of the pore space of rocks from the nanometre scale upwards, coupled with a suite of different numerical techniques for simulating single and multiphase flow and transport through these images. Three example applications are then described, illustrating the range of scientific problems that can be tackled: dispersion in different rock samples that predicts the anomalous transport behaviour characteristic of highly heterogeneous carbonates; imaging of super-critical carbon dioxide in sandstone to demonstrate the possibility of capillary trapping in geological carbon storage; and the computation of relative permeability for mixed-wet carbonates and implications for oilfield waterflood recovery. The paper concludes by discussing limitations and challenges, including finding representative samples, imaging and simulating flow and transport in pore spaces over many orders of magnitude in size, the determination of wettability, and upscaling to the field scale. We conclude that pore-scale modelling is likely to become more widely applied in the oil industry including assessment of unconventional oil and gas resources. It has the potential to transform our understanding of multiphase flow processes, facilitating more efficient oil and gas recovery, effective contaminant removal and safe carbon dioxide storage.

  8. Pore dynamics in lipid membranes

    NASA Astrophysics Data System (ADS)

    Gozen, I.; Dommersnes, P.

    2014-09-01

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

  9. Cilia and Nuclear Pore Proteins: Pore No More?

    PubMed

    Obado, Samson O; Rout, Michael P

    2016-09-12

    Nuclear pore proteins at the base of cilia were thought to regulate transport into cilia. In this issue of Developmental Cell, Del Viso et al. (2016) challenge this view, showing instead that pore proteins localize to ciliary basal bodies and that their perturbation leads to congenital heart disease. PMID:27623377

  10. Silicon Pore Optics Technology

    NASA Astrophysics Data System (ADS)

    Beijersbergen, Marco; Collon, M. J.; Günther, R.; Partapsing, R.; Ackermann, M.; Olde Riekerink, M.; Cooper-Jensen, C.; Christensen, F.; Freyberg, M.; Krumrey, M.; Erhard, M.; van Baren, C.; Wallace, K.; Bavdaz, M.

    2009-01-01

    Silicon pore optics have been developed over the last years to enable future astrophysical X-ray telescopes and have now become a candidate mirror technology for the IXO mission. Scientific requirements demand an angular resolution better than 5” and a large effective area of several square meters at photon energies of 1 keV. This paper discusses the performance of the latest generation of these novel light, stiff and modular X-ray optics, based on ribbed plates made from commercial high grade 12” silicon wafers. Stacks with several tens of silicon plates have been assembled in the course of an ESA technology development program, by bending the plates into an accurate shape and directly bonding them on top of each other. Several mirror modules, using two stacks each, have been aligned and integrated to form the conical approximation of a Wolter-I design. This paper presents the status of the technology, addresses and discusses a number of activities in the ongoing ESA technology development and shows the latest results of full area measurements at the long-beamline MPE X-ray test facility (PANTER) and the PTB beam line at the BESSY electron storage ring in Berlin.

  11. Pore Scale Analysis of Oil Shale/Sands Pyrolysis

    SciTech Connect

    Lin, Chen-Luh; Miller, Jan

    2011-03-01

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

  12. Relationship between the Averaged Deposition Rate Coefficients for Colloids in a Single Pore and Various Pore-scale Parameters

    NASA Astrophysics Data System (ADS)

    Narayanan, S.; Mohan Kumar, M.; Hassanizadeh, S. M.; Raoof, A.

    2014-12-01

    The colloid deposition behavior observed at the Darcy scale represents an average of the processes occurring at the pore scale. Hence, a better understanding of the processes occurring at the Darcy scale can be obtained by studying colloid transport at the pore-scale and then upscaling the results. In this study, we have developed a mathematical model to simulate the transport of colloids in a cylindrical pore by considering various processes such as advection, diffusion, colloid-soil surface interactions and hydrodynamic wall effects. The pore space is divided into three different regions, namely, the bulk, diffusion and potential regions, based on the dominant processes acting in each of these regions. In the bulk region, colloid transport is governed by advection and diffusion; whereas in the diffusion region, colloid mobility due to diffusion is retarded by hydrodynamic wall effects. Colloid-solid interaction forces dominate the transport in the potential region where colloid deposition occurs and are calculated using DLVO theory. The expressions for mass transfer rate coefficients between the diffusion and potential regions have been derived for different DLVO energy profiles. These are incorporated in the pore-scale equations in the form of a boundary condition at the diffusion-potential region interface. The model results are used to obtain the colloid breakthrough curve at the end of a long pore, and then it is fitted with 1D advection-dispersion-adsorption model so as to determine the averaged attachment and detachment rate coefficients at the scale of a single pore. A sensitivity analysis of the model to six pore-scale parameters (colloid and wall surface potentials, solution ionic strength, average pore-water velocity, colloid radius, and pore radius) is carried out so as to find the relation between the averaged deposition rate coefficients at pore scale vs the pore-scale parameters. We found an hyper exponential relation between the colloid attachment

  13. 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.

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

    PubMed

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

    2013-01-01

    The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities. PMID:24391805

  15. Impact of Matric Potential and Pore Size Distribution on Growth Dynamics of Filamentous and Non-Filamentous Soil Bacteria

    PubMed Central

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

    2013-01-01

    The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities. PMID:24391805

  16. Soil hydraulic properties and REV study using X-ray microtomography and pore-scale modelling: saturated hydraulic conductivity

    NASA Astrophysics Data System (ADS)

    Gerke, Kirill; Khirevich, Siarhei; Sizonenko, Timofey; Karsanina, Marina; Umarova, Aminat; Korost, Dmitry; Matthai, Stephan; Mallants, Dirk

    2016-04-01

    To verify pore-scale modelling approach for determination of soil saturated hydraulic conductivity properties we scanned three cylindrical soil samples taken from A, Ah and B horizons using X-ray microtomography method. Resulting 3D soil images with resolutions of 15.25-20.96 μm were segmented into pores and solids and their maximum inscribed cube subvolumes were used as input data for three major pore-scale modelling methods to simulate saturated flow - lattice-Boltzmann method, finite-difference solution of the Stokes problem, and pore-network model. Provided that imaging resolution is high enough to capture the backbone of effective porosity and the main conducting pores all three methods resulted in simulated soil permeabilities close to experimental values for Ah and B samples. The resolution of A sample was not enough for an accurate modelling and we concluded that this soil requires multi-scale imaging to cover all relevant heterogeneities. We demonstrate that popular SWV method to choose segmentation threshold resulted in oversegmentation and order of magnitude higher permeability values. Careful manual thresholding combined with local segmentation algorithm provided much more accurate results. Detailed analysis of water retention curves showed that air-filled porosity at relevant pressure stages cannot be used for verification of the segmentation results. Representativity analysis by simulating flow in increasing soil volume up to 2.8 cm3 revealed no representative elementary volume (REV) within Ah sample and non-uniqueness of REV for B sample. The latter was explained by soil structure non-stationarity. We further speculate that structures soil horizons can exhibit no REV at all. We discuss numerous advantages of coupled imaging and pore-scale modelling approach and show how it can become a successor of the conventional soil coring method to parametrize large scale continuum models.

  17. Reactive transport in porous media: pore-network model approach compared to pore-scale model.

    PubMed

    Varloteaux, Clément; Vu, Minh Tan; Békri, Samir; Adler, Pierre M

    2013-02-01

    Accurate determination of three macroscopic parameters governing reactive transport in porous media, namely, the apparent solute velocity, the dispersion, and the apparent reaction rate, is of key importance for predicting solute migration through reservoir aquifers. Two methods are proposed to calculate these parameters as functions of the Péclet and the Péclet-Dahmköhler numbers. In the first method called the pore-scale model (PSM), the porous medium is discretized by the level set method; the Stokes and convection-diffusion equations with reaction at the wall are solved by a finite-difference scheme. In the second method, called the pore-network model (PNM), the void space of the porous medium is represented by an idealized geometry of pore bodies joined by pore throats; the flow field is computed by solving Kirchhoff's laws and transport calculations are performed in the asymptotic regime where the solute concentration undergoes an exponential evolution with time. Two synthetic geometries of porous media are addressed by using both numerical codes. The first geometry is constructed in order to validate the hypotheses implemented in PNM. PSM is also used for a better understanding of the various reaction patterns observed in the asymptotic regime. Despite the PNM approximations, a very good agreement between the models is obtained, which shows that PNM is an accurate description of reactive transport. PNM, which can address much larger pore volumes than PSM, is used to evaluate the influence of the concentration distribution on macroscopic properties of a large irregular network reconstructed from microtomography images. The role of the dimensionless numbers and of the location and size of the largest pore bodies is highlighted. PMID:23496613

  18. CFTR: what's it like inside the pore?

    PubMed

    Liu, Xuehong; Smith, Stephen S; Dawson, David C

    2003-11-01

    The Cystic Fibrosis Conductance Regulator (CFTR) functions as a cAMP-activated, anion-selective channel, but the structural basis for anion permeation is not well understood. Here we summarize recent studies aimed at understanding how anions move through the CFTR channel, and the nature of the environment anions experience inside the pore. From these studies it is apparent that anion permeability selectivity and anion binding selectivity of the pore are consistent with a model based on a "dielectric tunnel." The selectivity pattern for halides and pseudohalides can be predicted if it is assumed that permeant anions partition between bulk water and a polarizable space that is characterized by an effective dielectric constant of about 19. Covalent labeling of engineered cysteines and pH titration of engineered cysteines and histidines lead to the conclusion that the CFTR anion conduction path includes a positively charged outer vestibule. A residue in transmembrane segment 6 (TM6) (R334) appears to reside in the outer vestibule of the CFTR pore where it creates a positive electrostatic potential that enhances anion conduction. PMID:14598388

  19. Triggered pore-forming agents

    DOEpatents

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

    1998-01-01

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

  20. Space.

    ERIC Educational Resources Information Center

    Web Feet K-8, 2001

    2001-01-01

    This annotated subject guide to Web sites and additional resources focuses on space and astronomy. Specifies age levels for resources that include Web sites, CD-ROMS and software, videos, books, audios, and magazines; offers professional resources; and presents a relevant class activity. (LRW)

  1. 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.

  2. 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

  3. Can ash clog soil pores?

    NASA Astrophysics Data System (ADS)

    Stoof, Cathelijne; Stoof, Cathelijne; Gevaert, Anouk; Gevaert, Anouk; Baver, Christine; Baver, Christine; Hassanpour, Bahareh; Hassanpour, Bahareh; Morales, Veronica; Morales, Veronica; Zhang, Wei; Zhang, Wei; Martin, Deborah; Martin, Deborah; Steenhuis, Tammo; Steenhuis, Tammo

    2015-04-01

    Wildfire can greatly increase a landscape's vulnerability to flooding and erosion events, and ash is thought to play a large role in controlling runoff and erosion processes after wildfire. Although ash can store rainfall and thereby reduce runoff and erosion for a limited period after wildfires, it has also been hypothesized to clog soil pores and reduce infiltration. Several researchers have attributed the commonly observed increase in runoff and erosion after fire to the potential pore-clogging effect of ash. Evidence is however incomplete, as to date, research has solely focused on identifying the presence of ash in the soil, with the actual flow processes associated with the infiltration and pore-clogging of ash remaining a major unknown. In several laboratory experiments, we tested the hypothesis that ash causes pore clogging to the point that infiltration is hampered and ponding occurs. We first visualized and quantified pore-scale infiltration of water and ash in sand of a range of textures and at various infiltration rates, using a digital bright field microscope capturing both photo and video. While these visualization experiments confirm field and lab observation of ash washing into soil pores, we did not observe any clogging of pores, and have not been able to create conditions for which this does occur. Additional electrochemical analysis and measurement of saturated hydraulic conductivity indicate that pore clogging by ash is not plausible. Electrochemical analysis showed that ash and sand are both negatively charged, showing that attachment of ash to sand and any resulting clogging is unlikely. Ash also had quite high saturated conductivity, and systems where ash was mixed in or lying on top of sand had similarly high hydraulic conductivity. Based on these various experiments, we cannot confirm the hypothesis that pore clogging by ash contributes to the frequently observed increase in post-fire runoff, at least for the medium to coarse sands

  4. Development of a closed pore insulation material

    NASA Technical Reports Server (NTRS)

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

    1973-01-01

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

  5. 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.

  6. Geostatistical Modeling of Pore Velocity

    SciTech Connect

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

    1981-06-01

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

  7. Pore opening dynamics in the exocytosis of serotonin

    NASA Astrophysics Data System (ADS)

    Ramirez-Santiago, Guillermo; Cercos, Montserrat G.; Martinez-Valencia, Alejandro; Salinas Hernandez, Israel; Rodríguez-Sosa, Leonardo; de-Miguel, Francisco F.

    2015-03-01

    The current view of the exocytosis of transmitter molecules is that it starts with the formation of a fusion pore that connects the intravesicular and the extracellular spaces, and is completed by the release of the rest of the transmitter contained in the vesicle upon the full fusion and collapse of the vesicle with the plasma membrane. However, under certain circumstances, a rapid closure of the pore before the full vesicle fusion produces only a partial release of the transmitter. Here we show that whole release of the transmitter occurs through fusion pores that remain opened for tens of milliseconds without vesicle collapse. This was demonstrated through amperometric measurements of serotonin release from electrodense vesicles in the axon of leech Retzius neurons and mathematical modelling. By modeling transmitter release with a diffusion equation subjected to boundary conditions that are defined by the experiment, we showed that those pores with a fast half rise time constant remained opened and allowed the full quantum release without vesicle collapse, whereas pores with a slow rise time constant closed rapidly, thus producing partial release. We conclude that a full transmitter release may occur through the fusion pore in the absence of vesicle collapse. This work was founded by a DGAPA-UNAM grants IN200914 and IN118410 CONACYT GRANT 130031, and CONACyT doctoral fellowships.

  8. Restricted Transport in Small Pores

    PubMed Central

    Anderson, John L.; Quinn, John A.

    1974-01-01

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

  9. Closed-pore Insulation Thermal Protection System Design Concept Development

    NASA Technical Reports Server (NTRS)

    Varisco, A.; Harris, H. G.

    1973-01-01

    The development of a unique closed-pore ceramic foam insulation (CPI) produced from low cost fly ash cenospheres is reported for space shuttle external thermal protection. Two basic design approaches were developed: bonded and mechanically fastened. A description of the concepts is presented in addition to fabrication and test results.

  10. Applications of fluorescence microscopy to study of pores in tight rocks

    SciTech Connect

    Soeder, D.J. )

    1990-01-01

    Observation of pore structures in thin section by traditional impregnation with blue-dyed epoxy becomes difficult when the pores are smaller than about 1 {mu}m and/or linear in shape. These types of pores are common in many low-permeability gas reservoirs, such as coal, shale, and tight sandstone. Incident-light fluorescence microscopy can be used to observe small, narrow pore structures in tight rocks. This common medical technique can be adapted to petrography by staining the impregnation epoxy with fluorescent rhodamine B dye along with the usual blue dye, and using an incident-light microscope equipped for epifluorescence to observe the prepared thin section. Under excitation of green light at a wavelength of 5,400 {angstrom}, rhodamine fluoresces a brilliant reddish orange, clearly showing impregnated pore spaces. A dichromatic interference filter in the light path passes the reddish orange light and blocks nonfluorescing mineral grains so that only the pore structure is visible. Fluorescing epoxy behaves as an emission source, and even submicron-size pores, which may be narrower than the wavelengths of visible light, become visible if they are impregnated. The incident-light configuration of the microscope also allows the observation of impregnated pore spaces in opaque materials such as coal. Fluorescence microscopy not only has potential for studying pore structures in tight sedimentary rocks, but also can be applied to crystalline rocks and other materials with narrow, linear, or small pores. 9 figs.

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

    SciTech Connect

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

    2006-01-30

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

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

    SciTech Connect

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

    2006-02-21

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

  13. Membrane pores induced by magainin.

    PubMed

    Ludtke, S J; He, K; Heller, W T; Harroun, T A; Yang, L; Huang, H W

    1996-10-29

    Magainin, found in the skin of Xenopus laevis, belongs to a broad class of antimicrobial peptides which kill bacteria by permeabilizing the cytoplasmic membrane but do not lyse eukaryotic cells. The 23-residue peptide has been shown to form an amphiphilic helix when associated with membranes. However, its molecular mechanism of action has been controversial. Oriented circular dichroism has detected helical magainin oriented perpendicular to the plane of the membrane at high peptide concentrations, but Raman, fluorescence, differential scanning calorimetry, and NMR all indicate that the peptide is associated with the head groups of the lipid bilayer. Here we show that neutron in-plane scattering detects pores formed by magainin 2 in membranes only when a substantial fraction of the peptide is oriented perpendicular to the membrane. The pores are almost twice as large as the alamethicin pores. On the basis of the in-plane scattering data, we propose a toroidal (or wormhole) model, which differs from the barrel-stave model of alamethicin in that the lipid bends back on itself like the inside of a torus. The bending requires a lateral expansion in the head group region of the bilayer. Magainin monomers play the role of fillers in the expansion region thereby stabilizing the pore. This molecular configuration is consistent with all published magainin data. PMID:8901513

  14. Triggered pore-forming agents

    DOEpatents

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

    1998-07-07

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

  15. Upscaling porosity-permeability relation in porous media; reactive pore-scale modeling

    NASA Astrophysics Data System (ADS)

    Raoof, A.; Spiers, C.; Hassanizadeh, S. M.

    2012-04-01

    The main objective of this research is to gain a better understanding of the relation between porosity-permeability evolution at the local scale and its manifestation at larger (REV) scales. Continuum pore space changes during the progress of chemical reactions in porous media. Such phenomena takes place in reservoir rock in which CO2 is to be stored. In the present approach, the microscopic pore space is modeled using a Multi-Directional Pore Network (MDPN), which allows for a distribution of pore coordination number ranging between one and 26. This topological property, together with geometrical distributions of pore sizes are used to mimic the microstructure of real porous media at the REV scale. In order to simulate transport of multi-component chemical species, mass balance equations are solved within each element of the network (i.e., pore body and pore throat). We have considered both advective and diffusive transport processes within the pore spaces and have used a Reaction Network Simulator to model multi-component chemical reactions, allowing for both equilibrium and kinetic calculations. By averaging over the network domain, we calculate the evolution of porosity and permeability as well as of flux-averaged concentration breakthrough curves. We have obtained constitutive relations linking porosity and permeability as the pore space involve during dissolution of calcium carbonate within calcite-cemented sandstone, under conditions relevant to geological storage of CO2. Results show that transition between advection- and diffusion- dominated transport, along with the distribution of reactive sites between pore bodies and pore throats, play a key role in determining evolution of porosity and permeability.

  16. Precipitation in pores: A geochemical frontier

    SciTech Connect

    Stack, Andrew G.

    2015-07-29

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

  17. Precipitation in pores: A geochemical frontier

    DOE PAGESBeta

    Stack, Andrew G.

    2015-07-29

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

  18. Network representation of pore scale imagery for percolation models

    NASA Astrophysics Data System (ADS)

    Klise, K. A.; McKenna, S. A.; Read, E.; Karpyn, Z. T.; Celauro, J.

    2012-12-01

    Multiphase flow under capillary dominated flow regimes is driven by an intricate relationship between pore geometry, material and fluid properties. In this research, high-resolution micro-computed tomography (CT) imaging experiments are used to investigate structural and surface properties of bead packs, and how they influence percolation pathways. Coreflood experiments use a mix of hydrophilic and hydrophobic beads to track the influence of variable contact angle on capillary flow. While high-resolution CT images can render micron scale representation of the pore space, data must be upscaled to capture pore and pore throat geometry for use in percolation models. In this analysis, the pore space is upscaled into a network representation based on properties of the medial axis. Finding the medial axis using micron scale images is computationally expensive. Here, we compare the efficiency and accuracy of medial axes using erosion-based and watershed algorithms. The resulting network representation is defined as a ball-and-stick model which represents pores and pore throats. The ball-and-stick model can be further reduced by eliminating sections of the network that fall below a capillary pressure threshold. In a system of mixed hydrophilic and hydrophobic beads, capillary pressure can change significantly throughout the network based on the interaction between surface and fluid properties. The upscaled network representations are used in percolation models to estimate transport pathway. Current results use a basic percolation model that sequentially fills neighboring pores with the highest potential. Future work will expand the percolation model to include additional mechanics, such as trapping, vacating pores, and viscous fingering. Results from the coreflood experiments will be used to validate upscaling techniques and percolation models. Preliminary results show that the relative strength of water-wet and oil-wet surfaces has a significant impact on percolation

  19. Defeating the pores of Kohn.

    PubMed

    Ng, Calvin S H; Lau, Rainbow W H; Lau, Kelvin K W; Underwood, Malcolm J; Yim, Anthony P C

    2014-01-01

    In the treatment of emphysema with an endobronchial valve, entire lobar treatment is important in achieving adequate atelectasis. This case illustrates that without treatment of the entire lobe, it can fail to collapse even after several years, leading to treatment failure. Intralobar collateral ventilation through the pores of Kohn is demonstrated in this case, as endobronchial valve blockage of the remaining patent anterior segment resulted in the desired atelectasis and significant improvements in pulmonary function. PMID:24585656

  20. Impacts of Hydrate Pore Habit on Physical Properties of Hydrate Bearing Sediments

    NASA Astrophysics Data System (ADS)

    Seol, Y.; Dai, S.; Choi, J. H.

    2014-12-01

    The physical properties of gas hydrate bearing sediments, to a large extent, are governed by the volume fraction and spatial distribution of the hydrate phase. For sediments containing the same amount of hydrates, their overall physical properties may vary several orders of magnitude depending on hydrate pore habit. We investigate the interplay among hydrate formation methods, hydrate pore habits, and fundamental physical properties of hydrate bearing sediments. We have developed a new method to synthesize noncementing hydrate in sands, a multi-properties characterization chamber to test the hydrate bearing sediments, and pore network models to simulate fluid flow processes in hydrate bearing sediments. We have found that (1) the growth pattern of hydrate crystal in the pore spaces of water saturated sediments is dominated by the relative magnitude of the capillary force (between hydrate crystal and pore fluid) and the skeleton force, which will result in pore-filling or grain-displacing type of hydrate pore character; (2) the existing capillary tube models of water permeability in hydrate bearing sediments are sensitive to pore geometry and hydrate pore habit; and (3) preliminary CT results suggest that hydrate nucleation in partially water saturated sands tends to agglomerate in patches, rather than in an uniformly-distributed contact-cementing morphology. Additional CT results with a small amount of fines (5wt%) and visualization via micro-CT of hydrate pore habits in sediments using different hydrate formation methods will be discussed.

  1. 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.

  2. Experimental and theoretical pore-scale study of thermal field responses to drying of porous surfaces

    NASA Astrophysics Data System (ADS)

    Aminzadeh, M.; Or, D.

    2015-12-01

    The drying of porous surfaces involves pores invasion at a sequence reflecting their respective capillary size (large pores invaded first similar to drainage). The emptying of an evaporating pore is accompanied by changes in the thermal field forming on the surface around the invaded pore that consequently affects surface temperature and energy partitioning over the drying surface. A novel experimental system was designed to systematically evaluate the coupling between surface temperature and evaporative flux from individual and clusters of pores drilled into rough glass surfaces connected to a liquid reservoir. Details of thermal fields around individual evaporating pores were observed for sparse and dense pore spacings including measurements of evaporating flux dynamics and results were compared with PCEB model [Aminzadeh and Or, 2014] predictions. We observed drying-induced pore emptying sequences of sintered glass bead surfaces by visual and thermal imaging using high resolution infrared imager. The links between pore emptying sequence at a drying surface inferred from pore size distribution, and surface temperature dynamics offer a possibility of predicting energy partitioning over drying terrestrial surfaces.

  3. DESIGN INFORMATION ON FINE PORE AERATION SYSTEMS

    EPA Science Inventory

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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  6. Pore Formation and Mobility Furnace within the MSG

    NASA Technical Reports Server (NTRS)

    2003-01-01

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

  7. Zeolitic BIF Crystal Directly Producing Noble-Metal Nanoparticles in Its Pores for Catalysis

    PubMed Central

    Zhang, Hai-Xia; Liu, Meng; Bu, Xianhui; Zhang, Jian

    2014-01-01

    As an integral part of a porous framework and uniformly distributed throughout the internal pore space, the high density of the exposed B–H bond in zeolite-like porous BIF-20 (BIF = Boron Imidazolate Framework) is shown here to effectively produce nanoparticles within its confined pore space. Small noble-metal nanoparticles (Ag or Au) are directly synthesized into its pores without the need for any external reducing agent or photochemical reactions, and the resulting Ag@BIF-20 (or Au@BIF-20) samples show high catalytic activities for the reduction of 4-nitrophenol. PMID:24473155

  8. 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.

  9. 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).

  10. 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

  11. pH controlled gating of toxic protein pores by dendrimers

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    SciTech Connect

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

    2011-01-01

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

  13. Pore-scale simulation of calcium carbonate precipitation and dissolution under highly supersaturated conditions in a microfludic pore network

    NASA Astrophysics Data System (ADS)

    Yoon, H.; Dewers, T. A.; Valocchi, A. J.; Werth, C. J.

    2011-12-01

    Dissolved CO2 during geological CO2 storage may react with minerals in fractured rocks or confined aquifers and cause mineral precipitation. The overall rate of reaction can be affected by coupled processes among hydrodynamics, transport, and reactions at pore-scale. Pore-scale models of coupled fluid flow, reactive transport, and CaCO3 precipitation and dissolution are applied to account for transient experimental results of CaCO3 precipitation and dissolution under highly supersaturated conditions in a microfluidic pore network (i.e., micromodel). Pore-scale experiments in the micromodel are used as a basis for understanding coupled physics of systems perturbed by geological CO2 injection. In the micromodel, precipitation is induced by transverse mixing along the centerline in pore bodies. Overall, the pore-scale model qualitatively captured the governing physics of reactions such as precipitate morphology, precipitation rate, and maximum precipitation area in first few pore spaces. In particular, we found that proper estimation of the effective diffusion coefficient and the reactive surface area is necessary to adequately simulate precipitation and dissolution rates. As the model domain increases, the effect of flow patterns affected by precipitation on the overall reaction rate also increases. The model is also applied to account for the effect of different reaction rate laws on mineral precipitation and dissolution at pore-scale. Reaction rate laws tested include the linear rate law, nonlinear power law, and newly-developed rate law based on in-situ measurements at nano scale in the literature. Progress on novel methods for upscaling pore-scale models for reactive transport are discussed, and are being applied to mineral precipitation patterns observed in natural analogues. H.Y. and T. D. were 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  15. Applications of fluorescence microscopy to study of pores in tight rocks

    SciTech Connect

    Soeder, D.J.

    1987-05-01

    Observation of pore structures in thin section using the traditional method of impregnation with blue-dyed epoxy becomes difficult when the pores are smaller than about 1 micrometer and/or linear in shape. These types of pores are common in many gas-bearing tight formations, including coal seams, black shales, and lenticular sandstones. Incident-light fluorescence microscopy can be utilized for observation of small, narrow pore structures in tight rocks. Adaptation of this common medical technique to petrography is accomplished by staining the epoxy with fluorescent Rhodamine-B dye instead of the usual blue material, impregnating under vacuum, and preparing a polished thin section in the normal manner. The thin section is observed using an incident-light microscope equipped for fluorescence, which usually involves only a simple lamp and filter change on an existing, universal-type microscope. Under excitation of green light at a wavelength of 540 nm, the Rhodamine fluoresces a brilliant reddish orange, clearly showing impregnated pore space. A dichromatic interference filter in the light path allows only the reddish orange light to pass through, blacking out the mineral grains such that only the pore structure is visible. The incident-light configuration of the microscope has the advantage of inducing brighter fluorescence at higher magnifications due to the more intense concentration of the exciter beam through higher-power objectives. This technique also permits observation of impregnated pore space narrower than the wave-lengths of visible light. Epoxy fluorescing in pores this small behaves like a point source and makes the pore visible. Fluorescence microscopy has much promise for studying pore structures in tight sedimentary rocks and can also be applied to crystalline rocks and other materials containing narrow, linear, or small pores.

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

    DOE PAGESBeta

    Mehmani, Yashar; Schoenherr, Martin; Pasquali, Andrea; Perkins, William A.; Kim, Kyungjoo; Perego, Mauro; Parks, Michael L.; Balhoff, Matthew T.; Richmond, Marshall C.; Geier, Martin; et al

    2015-09-28

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

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

    SciTech Connect

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

    2015-09-28

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

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

    SciTech Connect

    Qian, Shuo

    2011-01-01

    Human LL-37 is a multifunctional cathelicidin peptide that has shown a wide spectrum of antimicrobial activity by permeabilizing microbial membranes similar to other antimicrobial peptides; however, its molecular mechanism has not been clarified. Two independent experiments revealed LL-37 bound to membranes in the {alpha}-helical form with the axis lying in the plane of membrane. This led to the conclusion that membrane permeabilization by LL-37 is a nonpore carpet-like mechanism of action. Here we report the detection of transmembrane pores induced by LL-37. The pore formation coincided with LL-37 helices aligning approximately normal to the plane of the membrane. We observed an unusual phenomenon of LL-37 embedded in stacked membranes, which are commonly used in peptide orientation studies. The membrane-bound LL-37 was found in the normal orientation only when the membrane spacing in the multilayers exceeded its fully hydrated value. This was achieved by swelling the stacked membranes with excessive water to a swollen state. The transmembrane pores were detected and investigated in swollen states by means of oriented circular dichroism, neutron in-plane scattering, and x-ray lamellar diffraction. The results are consistent with the effect of LL-37 on giant unilamellar vesicles. The detected pores had a water channel of radius 2333 {angstrom}. The molecular mechanism of pore formation by LL-37 is consistent with the two-state model exhibited by magainin and other small pore-forming peptides. The discovery that peptide-membrane interactions in swollen states are different from those in less hydrated states may have implications for other large membrane-active peptides and proteins studied in stacked membranes.

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

    NASA Astrophysics Data System (ADS)

    Morishige, Kunimitsu; Kataoka, Takaaki

    2015-07-01

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

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

    SciTech Connect

    Morishige, Kunimitsu Kataoka, Takaaki

    2015-07-21

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

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

    PubMed

    Morishige, Kunimitsu; Kataoka, Takaaki

    2015-07-21

    To obtain insights into the mechanism of the melting-point depression of rare gas solids confined in crystalline carbon pores, we examined the freezing and melting behavior of Xe and Ar confined to the crystalline pores of ordered mesoporous carbons as well as compressed exfoliated graphite compared to the amorphous pores of ordered mesoporous silicas, by means of X-ray diffraction. For the Xe and Ar confined to the crystalline carbon pores, there was no appreciable thermal hysteresis between freezing and melting. Furthermore, the position of the main diffraction peak did not change appreciably on freezing and melting. This strongly suggests that the liquids confined in the carbon pores form a multilayered structure parallel to the smooth walls. For the Xe and Ar confined to the amorphous silica pores, on the other hand, the position of the main diffraction peak shifted into higher scattering angle on freezing suggested that the density of the confined solid is distinctly larger than for the confined liquid. Using compressed exfoliated graphite with carbon walls of higher crystallinity, we observed that three-dimensional (3D) microcrystals of Xe confined in the slit-shaped pores melted to leave the unmelted bilayers on the pore walls below the bulk triple point. The lattice spacing of the 3D microcrystals confined is larger by ∼0.7% than that of the bilayer next to the pore walls in the vicinity of the melting point. PMID:26203042

  2. Nuclear pores. Architecture of the nuclear pore complex coat.

    PubMed

    Stuwe, Tobias; Correia, Ana R; Lin, Daniel H; Paduch, Marcin; Lu, Vincent T; Kossiakoff, Anthony A; Hoelz, André

    2015-03-01

    The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. Despite half a century of structural characterization, the architecture of the NPC remains unknown. Here we present the crystal structure of a reconstituted ~400-kilodalton coat nucleoporin complex (CNC) from Saccharomyces cerevisiae at a 7.4 angstrom resolution. The crystal structure revealed a curved Y-shaped architecture and the molecular details of the coat nucleoporin interactions forming the central "triskelion" of the Y. A structural comparison of the yeast CNC with an electron microscopy reconstruction of its human counterpart suggested the evolutionary conservation of the elucidated architecture. Moreover, 32 copies of the CNC crystal structure docked readily into a cryoelectron tomographic reconstruction of the fully assembled human NPC, thereby accounting for ~16 megadalton of its mass. PMID:25745173

  3. pH controlled gating of toxic protein pores by dendrimers.

    PubMed

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

    2016-07-14

    Designing effective nanoscale blockers for membrane inserted pores formed by pore forming toxins, which are expressed by several virulent bacterial strains, on a target cell membrane is a challenging and active area of research. Here we demonstrate that PAMAM dendrimers can act as effective pH controlled gating devices once the pore has been formed. We have used fully atomistic molecular dynamics (MD) simulations to characterize the cytolysin A (ClyA) protein pores modified with fifth generation (G5) PAMAM dendrimers. Our results show that the PAMAM dendrimer, in either its protonated (P) or non-protonated (NP) states can spontaneously enter the protein lumen. Protonated dendrimers interact strongly with the negatively charged protein pore lumen. As a consequence, P dendrimers assume a more expanded configuration efficiently blocking the pore when compared with the more compact configuration adopted by the neutral NP dendrimers creating a greater void space for the passage of water and ions. To quantify the effective blockage of the protein pore, we have calculated the pore conductance as well as the residence times by applying a weak force on the ions/water. Ionic currents are reduced by 91% for the P dendrimers and 31% for the NP dendrimers. The preferential binding of Cl(-) counter ions to the P dendrimer creates a zone of high Cl(-) concentration in the vicinity of the internalized dendrimer and a high concentration of K(+) ions in the transmembrane region of the pore lumen. In addition to steric effects, this induced charge segregation for the P dendrimer effectively blocks ionic transport through the pore. Our investigation shows that the bio-compatible PAMAM dendrimers can potentially be used to develop therapeutic protocols based on the pH sensitive gating of pores formed by pore forming toxins to mitigate bacterial infections. PMID:27328315

  4. Incomplete pneumolysin oligomers form membrane pores.

    PubMed

    Sonnen, Andreas F-P; Plitzko, Jürgen M; Gilbert, Robert J C

    2014-01-01

    Pneumolysin is a member of the cholesterol-dependent cytolysin (CDC) family of pore-forming proteins that are produced as water-soluble monomers or dimers, bind to target membranes and oligomerize into large ring-shaped assemblies comprising approximately 40 subunits and approximately 30 nm across. This pre-pore assembly then refolds to punch a large hole in the lipid bilayer. However, in addition to forming large pores, pneumolysin and other CDCs form smaller lesions characterized by low electrical conductance. Owing to the observation of arc-like (rather than full-ring) oligomers by electron microscopy, it has been hypothesized that smaller oligomers explain smaller functional pores. To investigate whether this is the case, we performed cryo-electron tomography of pneumolysin oligomers on model lipid membranes. We then used sub-tomogram classification and averaging to determine representative membrane-bound low-resolution structures and identified pre-pores versus pores by the presence of membrane within the oligomeric curve. We found pre-pore and pore forms of both complete (ring) and incomplete (arc) oligomers and conclude that arc-shaped oligomeric assemblies of pneumolysin can form pores. As the CDCs are evolutionarily related to the membrane attack complex/perforin family of proteins, which also form variably sized pores, our findings are of relevance to that class of proteins as well. PMID:24759615

  5. Effects of pore volume-transmissivity correlation on transport phenomena

    NASA Astrophysics Data System (ADS)

    Lunati, Ivan; Kinzelbach, Wolfgang; Sørensen, Ivan

    2003-12-01

    The relevant velocity that describes transport phenomena in a porous medium is the pore velocity. For this reason, one needs not only to describe the variability of transmissivity, which fully determines the Darcy velocity field for given source terms and boundary conditions, but also any variability of the pore volume. We demonstrate that hydraulically equivalent media with exactly the same transmissivity field can produce dramatic differences in the displacement of a solute if they have different pore volume distributions. In particular, we demonstrate that correlation between pore volume and transmissivity leads to a much smoother and more homogeneous solute distribution. This was observed in a laboratory experiment performed in artificial fractures made of two plexiglass plates into which a space-dependent aperture distribution was milled. Using visualization by a light transmission technique, we observe that the solute behaviour is much smoother and more regular after the fractures are filled with glass powder, which plays the role of a homogeneous fault gouge material. This is due to a perfect correlation between pore volume and transmissivity that causes pore velocity to be not directly dependent on the transmissivity, but only indirectly through the hydraulic gradient, which is a much smoother function due to the diffusive behaviour of the flow equation acting as a filter. This smoothing property of the pore volume-transmissivity correlation is also supported by numerical simulations of tracer tests in a dipole flow field. Three different conceptual models are used: an empty fracture, a rough-walled fracture filled with a homogeneous material and a parallel-plate fracture with a heterogeneous fault gouge. All three models are hydraulically equivalent, yet they have a different pore volume distribution. Even if piezometric heads and specific flow rates are exactly the same at any point of the domain, the transport process differs dramatically. These

  6. Inertial effects during irreversible meniscus reconfiguration in angular pores

    NASA Astrophysics Data System (ADS)

    Ferrari, Andrea; Lunati, Ivan

    2014-12-01

    In porous media, the dynamics of the invading front between two immiscible fluids is often characterized by abrupt reconfigurations caused by local instabilities of the interface. As a prototype of these phenomena we consider the dynamics of a meniscus in a corner as it can be encountered in angular pores. We investigate this process in detail by means of direct numerical simulations that solve the Navier-Stokes equations in the pore space and employ the Volume of Fluid method (VOF) to track the evolution of the interface. We show that for a quasi-static displacement, the numerically calculated surface energy agrees well with the analytical solutions that we have derived for pores with circular and square cross sections. However, the spontaneous reconfigurations are irreversible and cannot be controlled by the injection rate: they are characterized by the amount of surface energy that is spontaneously released and transformed into kinetic energy. The resulting local velocities can be orders of magnitude larger than the injection velocity and they induce damped oscillations of the interface that possess their own time scales and depend only on fluid properties and pore geometry. In complex media (we consider a network of cubic pores) reconfigurations are so frequent and oscillations last long enough that increasing inertial effects leads to a different fluid distribution by influencing the selection of the next pore to be invaded. This calls into question simple pore-filling rules based only on capillary forces. Also, we demonstrate that inertial effects during irreversible reconfigurations can influence the work done by the external forces that is related to the pressure drop in Darcy's law. This suggests that these phenomena have to be considered when upscaling multiphase flow because local oscillations of the menisci affect macroscopic quantities and modify the constitutive relationships to be used in macro-scale models. These results can be extrapolated to other

  7. Open-pore polyurethane product

    DOEpatents

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

    1974-02-17

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

  8. Atomic Structure of Graphene Subnanometer Pores.

    PubMed

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

    2015-12-22

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

  9. Pore formation and translocation of melittin.

    PubMed Central

    Matsuzaki, K; Yoneyama, S; Miyajima, K

    1997-01-01

    Melittin, a bee venom, is a basic amphiphilic peptide, which mainly acts on the lipid matrix of membranes, lysing various cells. To elucidate the molecular mechanism, we investigated its interactions with phospholipid vesicles. The peptide formed a pore with a short lifetime in the membrane, as revealed by the release of an anionic fluorescent dye, calcein, from the liposomes. Our new double-labeling method clarified that the pore size increased with the peptide-to-lipid ratio. Upon the disintegration of the pore, a fraction of the peptides translocated across the bilayer. The pore formation was coupled with the translocation, which was proved by three fluorescence experiments recently developed by our laboratory. A novel model for the melittin pore formation was discussed in comparison with other pore-forming peptides. PMID:9251799

  10. Micromodel Experimental Observations and Numerical Simulations of Pore-Scale Colloidal Transport Processes

    NASA Astrophysics Data System (ADS)

    Scheibe, T. D.; Richmond, M. C.; Naoyuki, O.; Dragila, M. I.

    2008-05-01

    Pore-scale colloid movement was observed in microfluidic cells with variable flow rate and pore geometry. Colloid particles were observed to be mostly excluded from certain regions in the pore space, and the geometry of the excluded regions was observed to vary with flow velocity. High resolution numerical simulations of three- dimensional flow and particle transport were performed to facilitate interpretation of the experimental results. Of particular interest is the observation that colloidal particle paths were asymmetric in the vicinity of a pore constriction, leading to larger excluded zones downstream of grains, even though the simulated streamlines were symmetric. Alternative explanations tested using the pore-scale model include the effects of particle inertia, gravity forces, and surface attraction forces.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  12. Modeling the interaction of ultrasound with pores

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

  13. A novel architecture for pore network modelling with applications to permeability of porous media

    NASA Astrophysics Data System (ADS)

    Jivkov, Andrey P.; Hollis, Cathy; Etiese, Friday; McDonald, Samuel A.; Withers, Philip J.

    2013-04-01

    SummaryNetwork models of porous media are beneficial for predicting the evolution of macroscopic mass transport properties. This work proposes a novel bi-regular network model based on truncated octahedral support. With the model, pore systems with different pore coordination spectra for a given average coordination number can be constructed to match experimental data. This feature and the maximum allowed pore coordination of 14 make the proposed model more realistic and flexible than the existing models based on cubic supports. Limestone is used as a study material to illustrate the model performance. Experimental pore space data for this material obtained by X-ray tomography (CT) are used for constructing microstructure-informed model realisations. It is demonstrated that with these realisations the experimentally measured permeability of the material can be predicted. The model is further used to assess the effects of pore connectivity and porosity on the permeability. It is shown that the effect of pore connectivity is substantially stronger than the effect of porosity. A strategy for calculating the evolution of permeability with damage-related pore space changes is also described. The results reveal the effects of the mechanical properties of the medium on the permeability evolution as a function of damage evolution. Developments of this strategy are suggested for deriving mechanism-based constitutive laws for engineering applications.

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

    SciTech Connect

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

    2010-10-19

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

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  17. Three-dimensional analysis of pore effect on composite elasticity by means of finite element method

    NASA Astrophysics Data System (ADS)

    Yoneda, A.

    2015-12-01

    A three-dimensional buffer-layer finite element method (FEM) model was developed to investigate the porosity effect on macroscopic elasticity. Using the three-dimensional model, the effect of pores on bulk effective elastic properties were systematically analyzed by changing the degree of porosity, the aspect ratio of the ellipsoidal pore, and the elasticity of the material. The present results in 3D space was compared with the previous ones in 2D space. Derivatives of normalized elastic stiffness constants with respect to needle-type porosity are integers, if the Poisson ratio of a matrix material is zero; those derivatives of normalized stiffness elastic constants for C33, C44, C11, and C66 converge to -1, -2, -3, and -4, respectively, at the corresponding condition. We proposed a criterion of R <~1/3, where the mutual interaction between pores becomes negligible for macroscopic composite elasticity. These derivatives are nearly constant below 5% porosity in the case of spherical pore, suggesting that the interaction between neighboring pores is insignificant if the representative size of the pore is less than one-third of the mean distance between neighboring pores. The relations we obtained in this work were successfully applied to invert bulk modulus and rigidity of Cmcm-CaIrO3 as a case study; the performance of the inverting scheme was confirmed through this assessment. Thus the present scheme is applicable to predict macroscopic elasticity of porous object as well.

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

    SciTech Connect

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

    2012-04-01

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

  19. Upscaling of Transport Parameters in Reacting Porous Media; Pore-Scale Modelling

    NASA Astrophysics Data System (ADS)

    Raoof, Amir; Nick, Hamidreza M.; Hassanizadeh, Majid

    2014-05-01

    Pore scale modelling provides a tool for upscaling of flow and transport parameters in porous media. We use PoreFlow, a pore-network modelling tool capable of simulating fluid flow and multi-component reactive and adsorptive transport under saturated and variably saturated conditions. Simulations include: pore network generator, drainage simulator, calculation of pressure and velocity distributions, and modelling of reactive solute transport accounting for advection and diffusion. The pore space is represented using a multi-directional pore-network capable of capturing the random structure of a given porous media with user-defined directional connectivities for anisotropic pore structures. The chemical reactions can occur within the liquid phase, as well as between the liquid and solid phases which may result in an evolution of porosity and permeability. Potential applications are geological sequestration of CO2, affecting the reservoir rock transport properties as well as influencing the wellbore integrity, and acid-gas injection during enhanced oil recovery. Other examples will be provided, showing use of pore-scale information to determine macro-scale properties such as permeability-porosity changes, solute dispersivity, adsorption reaction coefficients, effective diffusion and tortuosity. Such information can be used as constitutive relations within continuum scale governing equations to model physical and chemical processes more accurately at the larger scales.

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

    PubMed Central

    Liu, Jianjun; Song, Rui; Cui, Mengmeng

    2014-01-01

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

  1. Improving the ruggedness of silicon pore optics

    NASA Astrophysics Data System (ADS)

    Ackermann, Marcelo D.; Collon, Maximilien J.; Günther, Ramses; Partapsing, Rakesh; Bavdaz, Marcos; Wallace, Kotska; Wille, Eric; van Baren, Coen; Kampf, Dirk; Erhard, Markus

    2010-07-01

    In this paper we present the latest developments on the ruggedisation of the Silicon Pore Optics (SPO) mirror modules. SPO is one of the candidate technologies for producing the X-ray optics for the future space based Xray telescope, the International X-ray Observatory (IXO). To produce SPO mirror modules, Si mirrors are first bonded together using direct Si bonding to form a stack. These stacks are the glued into brackets, which then connect to the supporting optical bench by invar pins. The combination of brackets and invar pins now forms a full isostatic mount, and is rugged enough to allow the mirror module to survive the high loads of a launch. The mounting system furthermore allows for a certain level of manufacturing tolerances for the support structure, and ensures interchangeability of the mirror modules within one single ring of the optical bench. To prove this, a test interface has been designed and manufactured, on which a single, full fledged mirror module will be mounted to be exposed to environmental tests.

  2. 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.

  3. Low Pore Connectivity Increases Bacterial Diversity in Soil▿

    PubMed Central

    Carson, Jennifer K.; Gonzalez-Quiñones, Vanesa; Murphy, Daniel V.; Hinz, Christoph; Shaw, Jeremy A.; Gleeson, Deirdre B.

    2010-01-01

    One of soil microbiology's most intriguing puzzles is how so many different bacterial species can coexist in small volumes of soil when competition theory predicts that less competitive species should decline and eventually disappear. We provide evidence supporting the theory that low pore connectivity caused by low water potential (and therefore low water content) increases the diversity of a complex bacterial community in soil. We altered the pore connectivity of a soil by decreasing water potential and increasing the content of silt- and clay-sized particles. Two textures were created, without altering the chemical properties or mineral composition of the soil, by adding silt- and clay-sized particles of quartz to a quartz-based sandy soil at rates of 0% (sand) or 10% (silt+clay). Both textures were incubated at several water potentials, and the effect on the active bacterial communities was measured using terminal restriction fragment length polymorphism (TRFLP) of bacterial 16S rRNA. Bacterial richness and diversity increased as water potential decreased and soil became drier (P < 0.012), but they were not affected by texture (P > 0.553). Bacterial diversity increased at water potentials of ≤2.5 kPa in sand and ≤4.0 kPa in silt+clay, equivalent to ≤56% water-filled pore space (WFPS) in both textures. The bacterial community structure in soil was affected by both water potential and texture (P < 0.001) and was correlated with WFPS (sum of squared correlations [δ2] = 0.88, P < 0.001). These findings suggest that low pore connectivity is commonly experienced by soil bacteria under field conditions and that the theory of pore connectivity may provide a fundamental principle to explain the high diversity of bacteria in soil. PMID:20418420

  4. Nanofiltration membranes with narrowed pore size distribution via pore wall modification.

    PubMed

    Du, Yong; Lv, Yan; Qiu, Wen-Ze; Wu, Jian; Xu, Zhi-Kang

    2016-06-30

    We propose a novel strategy for narrowing down the pore size distribution of ready-made nanofiltration membranes (NFMs) via pore wall modification. NFMs were subjected to the filtration of a highly reactive molecule solution, during which large pores were selectively reduced in size. The as-treated NFMs have high monovalent ion/divalent ion selectivity. PMID:27321407

  5. Experimental evidence of the role of pores on movement and distribution of bacteria in soil

    NASA Astrophysics Data System (ADS)

    Kravchenko, Alexandra N.; Rose, Joan B.; Marsh, Terence L.; Guber, Andrey K.

    2014-05-01

    It has been generally recognized that micro-scale heterogeneity in soil environments can have a substantial effect on movement, fate, and survival of soil microorganisms. However, only recently the development of tools for micro-scale soil analyses, including X-ray computed micro-tomography (μ-CT), enabled quantitative analyses of these effects. The long-term goal of our work is to explore how differences in micro-scale characteristics of pore structures influence movement, spatial distribution patterns, and activities of soil microorganisms. Using X-ray μ-CT we found that differences in land use and management practices lead to development of contrasting patterns in pore size-distributions within intact soil aggregates. Then our experiments with Escherichia coli added to intact soil aggregates demonstrated that the differences in pore structures can lead to substantial differences in bacteria redistribution and movement within the aggregates. Specifically, we observed more uniform E.coli redistribution in aggregates with homogeneously spread pores, while heterogeneous pore structures resulted in heterogeneous E.coli patterns. Water flow driven by capillary forces through intact aggregate pores appeared to be the main contributor to the movement patterns of the introduced bacteria. Influence of pore structure on E.coli distribution within the aggregates further continued after the aggregates were subjected to saturated water flow. E. coli's resumed movement with saturated water flow and subsequent redistribution within the soil matrix was influenced by porosity, abundance of medium and large pores, pore tortuosity, and flow rates, indicating that greater flow accompanied by less convoluted pores facilitated E. coli transport within the intra-aggregate space. We also found that intra-aggregate heterogeneity of pore structures can have an effect on spatial distribution patterns of indigenous microbial populations. Preliminary analysis showed that in aggregates from

  6. The impact of wettability and connectivity on relative permeability in carbonates: A pore network modeling analysis

    NASA Astrophysics Data System (ADS)

    Gharbi, Oussama; Blunt, Martin J.

    2012-12-01

    We use pore network modeling to study the impact of wettability and connectivity on waterflood relative permeability for a set of six carbonate samples. Four quarry samples are studied, Indiana, Portland, Guiting, and Mount Gambier, along with two subsurface samples obtained from a deep saline Middle Eastern aquifer. The pore space is imaged in three dimensions using X-ray microtomography at a resolution of a few microns. The images are segmented into pore and solid, and a topologically representative network of pores and throats is extracted from these images. We then simulate quasi-static displacement in the networks. We represent mixed-wet behavior by varying the oil-wet fraction of the pore space. The relative permeability is strongly dependent on both the wettability and the average coordination number of the network. We show that traditional measures of wettability based on the point where the relative permeability curves cross are not reliable. Good agreement is found between our calculations and measurements of relative permeability on carbonates in the literature. This work helps establish a library of benchmark samples for multiphase flow and transport computations. The implications of the results for field-scale displacement mechanisms are discussed, and the efficiency of waterflooding as an oil recovery process in carbonate reservoirs is assessed depending on the wettability and pore space connectivity.

  7. Application of GA in optimization of pore network models generated by multi-cellular growth algorithms

    NASA Astrophysics Data System (ADS)

    Jamshidi, Saeid; Boozarjomehry, Ramin Bozorgmehry; Pishvaie, Mahmoud Reza

    2009-10-01

    In pore network modeling, the void space of a rock sample is represented at the microscopic scale by a network of pores connected by throats. Construction of a reasonable representation of the geometry and topology of the pore space will lead to a reliable prediction of the properties of porous media. Recently, the theory of multi-cellular growth (or L-systems) has been used as a flexible tool for generation of pore network models which do not require any special information such as 2D SEM or 3D pore space images. In general, the networks generated by this method are irregular pore network models which are inherently closer to the complicated nature of the porous media rather than regular lattice networks. In this approach, the construction process is controlled only by the production rules that govern the development process of the network. In this study, genetic algorithm has been used to obtain the optimum values of the uncertain parameters of these production rules to build an appropriate irregular lattice network capable of the prediction of both static and hydraulic information of the target porous medium.

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Xiong, Qingrong; Baychev, Todor G.; Jivkov, Andrey P.

    2016-09-01

    Pore network models have been applied widely for simulating a variety of different physical and chemical processes, including phase exchange, non-Newtonian displacement, non-Darcy flow, reactive transport and thermodynamically consistent oil layers. The realism of such modelling, i.e. the credibility of their predictions, depends to a large extent on the quality of the correspondence between the pore space of a given medium and the pore network constructed as its representation. The main experimental techniques for pore space characterisation, including direct imaging, mercury intrusion porosimetry and gas adsorption, are firstly summarised. A review of the main pore network construction techniques is then presented. Particular focus is given on how such constructions are adapted to the data from experimentally characterised pore systems. Current applications of pore network models are considered, with special emphasis on the effects of adsorption, dissolution and precipitation, as well as biomass growth, on transport coefficients. Pore network models are found to be a valuable tool for understanding and predicting meso-scale phenomena, linking single pore processes, where other techniques are more accurate, and the homogenised continuum porous media, used by engineering community.

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

    PubMed

    Xiong, Qingrong; Baychev, Todor G; Jivkov, Andrey P

    2016-09-01

    Pore network models have been applied widely for simulating a variety of different physical and chemical processes, including phase exchange, non-Newtonian displacement, non-Darcy flow, reactive transport and thermodynamically consistent oil layers. The realism of such modelling, i.e. the credibility of their predictions, depends to a large extent on the quality of the correspondence between the pore space of a given medium and the pore network constructed as its representation. The main experimental techniques for pore space characterisation, including direct imaging, mercury intrusion porosimetry and gas adsorption, are firstly summarised. A review of the main pore network construction techniques is then presented. Particular focus is given on how such constructions are adapted to the data from experimentally characterised pore systems. Current applications of pore network models are considered, with special emphasis on the effects of adsorption, dissolution and precipitation, as well as biomass growth, on transport coefficients. Pore network models are found to be a valuable tool for understanding and predicting meso-scale phenomena, linking single pore processes, where other techniques are more accurate, and the homogenised continuum porous media, used by engineering community. PMID:27442725

  11. Molecular mechanism of pore formation by actinoporins.

    PubMed

    Kristan, Katarina Crnigoj; Viero, Gabriella; Dalla Serra, Mauro; Macek, Peter; Anderluh, Gregor

    2009-12-15

    Actinoporins are effective pore-forming toxins produced by sea anemones. These extremely potent, basic 20 kDa proteins readily form pores in membranes that contain sphingomyelin. Much has been learned about the molecular basis of their pore-forming mechanism in recent years. Pore formation is a multi-step process that involves recognition of membrane sphingomyelin, firm binding to the membrane accompanied by the transfer of the N-terminal region to the lipid-water interface and finally pore formation after oligomerisation of three to four monomers. The final conductive pathway is formed by amphipathic alpha-helices, hence actinoporins are an important example of so-called alpha-helical pore-forming toxins. Actinoporins have become useful model proteins to study protein-membrane interactions, specific recognition of lipids in the membrane, and protein oligomerisation in the lipid milieu. Recent sequence and structural data of proteins similar to actinoporins indicate that they are not a unique family restricted to sea anemones as was long believed. An AF domain superfamily (abbreviated from actinoporin-like proteins and fungal fruit-body lectins) was defined and shown to contain members from three animal and two plant phyla. On the basis of functional properties of some members we hypothesise that AF domain proteins are peripheral membrane proteins. Finally, ability of actinoporins to form transmembrane pores has been exploited in some novel biomedical applications. PMID:19268680

  12. Analytical applications for pore-forming proteins.

    PubMed

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

    2016-03-01

    Proteinaceous nanometer-scale pores are ubiquitous in biology. The canonical ionic channels (e.g., those that transport Na(+), K(+), Ca(2+), and Cl(-) across cell membranes) play key roles in many cellular processes, including nerve and muscle activity. Another class of channels includes bacterial pore-forming toxins, which disrupt cell function, and can lead to cell death. We describe here the recent development of these toxins for a wide range of biological sensing applications. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale. PMID:26431785

  13. High temperature ion channels and pores

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  14. Control of pore size in epoxy systems.

    SciTech Connect

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

    2009-01-01

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

  15. Enlarged facial pores: an update on treatments.

    PubMed

    Dong, Joanna; Lanoue, Julien; Goldenberg, Gary

    2016-07-01

    Enlarged facial pores remain a common dermatologic and cosmetic concern from acne and rosacea, among other conditions, that is difficult to treat due to the multifactorial nature of their pathogenesis and negative impact on patients' quality of life. Enlarged facial pores are primarily treated through addressing associative factors, such as increased sebum production and cutaneous aging. We review the current treatment modalities for enlarged or dense facial pores, including topical retinoids, chemical peels, oral antiandrogens, and lasers and devices, with a focus on newer therapies. PMID:27529707

  16. Nonlinear transport of soft droplets in pore networks

    NASA Astrophysics Data System (ADS)

    Vernerey, Franck; Benet Cerda, Eduard; Koo, Kanghyeon

    A large number of biological and technological processes depend on the transport of soft colloidal particles through porous media; this includes the transport and separation of cells, viruses or drugs through tissues, membranes and microfluidic devices. In these systems, the interactions between soft particles, background fluid and the surrounding pore space yield complex, nonlinear behaviors such as non-Darcy flows, localization and jamming. We devise a computational strategy to investigate the transport of non-wetting and deformable water droplets in a microfluidic device made of a random distribution of cylindrical obstacles. We first derive scaling laws for the entry of the droplet in a single pore and discuss the role of surface tension, contact angle and size in this process. This information is then used to study the transport of multiple droplets in an obstacle network. We find that when the droplet size is close to the pore size, fluid flow and droplet trafficking strongly interact, leading to local redistributions in pressure fields, intermittent clogging and jamming. Importantly, it is found that the overall droplet and fluid transport display three different scaling regimes depending on the forcing pressure, and that these regimes can be related to droplet properties.

  17. 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.

  18. The mitochondrial permeability transition pore and its role in cell death.

    PubMed Central

    Crompton, M

    1999-01-01

    This article reviews the involvement of the mitochondrial permeability transition pore in necrotic and apoptotic cell death. The pore is formed from a complex of the voltage-dependent anion channel (VDAC), the adenine nucleotide translocase and cyclophilin-D (CyP-D) at contact sites between the mitochondrial outer and inner membranes. In vitro, under pseudopathological conditions of oxidative stress, relatively high Ca2+ and low ATP, the complex flickers into an open-pore state allowing free diffusion of low-Mr solutes across the inner membrane. These conditions correspond to those that unfold during tissue ischaemia and reperfusion, suggesting that pore opening may be an important factor in the pathogenesis of necrotic cell death following ischaemia/reperfusion. Evidence that the pore does open during ischaemia/reperfusion is discussed. There are also strong indications that the VDAC-adenine nucleotide translocase-CyP-D complex can recruit a number of other proteins, including Bax, and that the complex is utilized in some capacity during apoptosis. The apoptotic pathway is amplified by the release of apoptogenic proteins from the mitochondrial intermembrane space, including cytochrome c, apoptosis-inducing factor and some procaspases. Current evidence that the pore complex is involved in outer-membrane rupture and release of these proteins during programmed cell death is reviewed, along with indications that transient pore opening may provoke 'accidental' apoptosis. PMID:10393078

  19. Nanofluidic Devices with Two Pores in Series for Resistive-Pulse Sensing of Single Virus Capsids

    PubMed Central

    Harms, Zachary D.; Mogensen, Klaus B.; Nunes, Pedro S.; Zhou, Kaimeng; Hildenbrand, Brett W.; Mitra, Indranil; Tan, Zhenning; Zlotnick, Adam; Kutter, Jörg P.; Jacobson, Stephen C.

    2011-01-01

    We report fabrication and characterization of nanochannel devices with two nanopores in series for resistive-pulse sensing of hepatitis B virus (HBV) capsids. The nanochannel and two pores are patterned by electron beam lithography between two microchannels and etched by reactive ion etching. The two nanopores are 50-nm wide, 50-nm deep, and 40-nm long and are spaced 2.0-μm apart. The nanochannel that brackets the two pores is 20x wider (1 μm) to reduce the electrical resistance adjacent to the two pores and to ensure the current returns to its baseline value between resistive-pulse events. Average pulse amplitudes differ by <2% between the two pores and demonstrate the fabrication technique is able to produce pores with nearly identical geometries. Because the two nanopores in series sense single particles at two discrete locations, particle properties, e.g., electrophoretic mobility, are determined from the pore-to-pore transit time. PMID:22029283

  20. A Unified Multi-Scale Model for Pore-Scale Flow Simulations in Soils

    SciTech Connect

    Yang, Xiaofan; Liu, Chongxuan; Shang, Jianying; Fang, Yilin; Bailey, Vanessa L.

    2014-01-30

    Pore-scale simulations have received increasing interest in subsurface sciences to provide mechanistic insights into the macroscopic phenomena of water flow and reactive transport processes. The application of the pore scale simulations to soils and sediments is, however, challenged because of the characterization limitation that often only allows partial resolution of pore structure and geometry. A significant proportion of the pore space in soils and sediments is below the spatial resolution, forming a mixed media of pore and porous domains. Here we reported a unified multi-scale model (UMSM) that can be used to simulate water flow and transport in mixed media of pore and porous domains under both saturated and unsaturated conditions. The approach modifies the classic Navier-Stokes equation by adding a Darcy term to describe fluid momentum and uses a generalized mass balance equation for saturated and unsaturated conditions. By properly defining physical parameters, the UMSM can be applied in both pore and porous domains. This paper describes the set of equations for the UMSM, a series of validation cases under saturated or unsaturated conditions, and a real soil case for the application of the approach.

  1. 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).

  2. The open pore conformation of potassium channels

    NASA Astrophysics Data System (ADS)

    Jiang, Youxing; Lee, Alice; Chen, Jiayun; Cadene, Martine; Chait, Brian T.; MacKinnon, Roderick

    2002-05-01

    Living cells regulate the activity of their ion channels through a process known as gating. To open the pore, protein conformational changes must occur within a channel's membrane-spanning ion pathway. KcsA and MthK, closed and opened K+ channels, respectively, reveal how such gating transitions occur. Pore-lining `inner' helices contain a `gating hinge' that bends by approximately 30°. In a straight conformation four inner helices form a bundle, closing the pore near its intracellular surface. In a bent configuration the inner helices splay open creating a wide (12Å) entryway. Amino-acid sequence conservation suggests a common structural basis for gating in a wide range of K+ channels, both ligand- and voltage-gated. The open conformation favours high conduction by compressing the membrane field to the selectivity filter, and also permits large organic cations and inactivation peptides to enter the pore from the intracellular solution.

  3. DESIGN MANUAL: FINE PORE AERATION SYSTEMS

    EPA Science Inventory

    This manual presents the best current practices for selecting, designing, operating, maintaining, and controlling fine pore aeration systems used in the treatment of municipal wastewater. It was prepared by the American Society of Civil Engineers Committee on Oxygen Transfer unde...

  4. Pore scale modeling of porosity-permeability relations in reacting porous media

    NASA Astrophysics Data System (ADS)

    Raoof, A.; Spiers, C. J.; Hassanizadeh, M.; Nick, H.

    2012-12-01

    The main objective of this research is to gain a better understanding of the relation between the progress of chemical reactions and porosity/permeability evolution in porous media, such as a reservoir rock in which CO2 is to be stored. The microscopic pore space is modeled using a Multi-Directional Pore Network (MDPN), which allows for a distribution of coordination number ranging between one and 26. This topological property, together with geometrical distributions of pore sizes are used to mimic the microstructure of real porous media at the mm to cm scale. In order to simulate transport of multi-component chemical species, mass balance equations are solved within each element of the network (i.e., pore body and pore throat) . We have considered both advective and diffusive transport processes within the pore spaces together with multi-component chemical reactions, allowing for both equilibrium and kinetic calculations. By averaging over the network domain, we calculate the evolution of porosity and permeability as well as of flux-averaged concentration breakthrough curves. We obtain constitutive relations linking porosity and permeability as they involve during dissolution of calcium carbonate within a calcite-cemented sandstone, under conditions relevant to geological storage of CO2. Effect of distribution of reactive minerals is evaluated and transition between advection- and diffusion- dominated transport is shown to play a key role in determining evolution of porosity and permeability in reservoir rocks.

  5. Pore scale modeling of porosity-permeability relations in reacting porous media

    NASA Astrophysics Data System (ADS)

    Raoof, A.; Spiers, C. J.; Hassanizadeh, S.; Nick, H. M.

    2013-12-01

    The main objective of this research is to gain a better understanding of the relation between the progress of chemical reactions and porosity/permeability evolution in porous media, such as a reservoir rock in which CO2 is to be stored. The microscopic pore space is modeled using a Multi-Directional Pore Network (MDPN), which allows for a distribution of coordination number. This topological property, together with geometrical distributions of pore sizes are used to mimic the microstructure of real porous media at the mm to cm scale. In order to simulate transport of multi-component chemical species, mass balance equations are solved within each element of the network (i.e., pore body and pore throat) . We have considered both advective and diffusive transport processes within the pore spaces together with multi-component chemical reactions, allowing for both equilibrium and kinetic calculations. By averaging over the network domain, we calculate the evolution of porosity and permeability as well as of flux-averaged concentration breakthrough curves. We obtain constitutive relations linking porosity and permeability as they involve during dissolution of calcium carbonate within a calcite-cemented sandstone as well as a carbonate rock, under conditions relevant to geological storage of CO2. Effect of distribution of reactive minerals is evaluated and transition between advection- and diffusion- dominated transport is shown to play a key role in determining evolution of porosity and permeability in reservoir rocks.

  6. Estimating Pore Properties from NMR Relaxation Time Measurements in Heterogeneous Media

    NASA Astrophysics Data System (ADS)

    Grunewald, E.; Knight, R.

    2008-12-01

    which heterogeneous pores are encountered in bimodal grain packs of pure quartz (long T2S) and hematite (short T2S). The scale of heterogeneity is varied by changing the mean grain size and relative mineral concentrations. When the mean grain size is small and the mineral concentrations are comparable, the T2-distribution is roughly monomodal indicating strong pore coupling. As the grain size is increased or the mineral concentrations are made increasingly uneven, the T2- distribution develops a bimodal character, more representative of the actual distribution of pore types. Numerical simulations of measurements in both experiment groups allow us to more closely investigate how the relaxing magnetization evolves in both time and space. Collectively, these experiments provide important insights into the effects of pore coupling on NMR measurements in heterogeneous systems and contribute to our ultimate goal of improving the interpretation of these data in complex near-surface sediments.

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

    SciTech Connect

    Satik, C.; Yortsos, Y.C.

    1996-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  9. Visualization of enzyme activities inside earthworm pores

    NASA Astrophysics Data System (ADS)

    Hoang, Duyen; Razavi, Bahar S.

    2015-04-01

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

  10. Investigation of Biogrout processes by numerical analysis at pore scale

    NASA Astrophysics Data System (ADS)

    Bergwerff, Luke; van Paassen, Leon A.; Picioreanu, Cristian; van Loosdrecht, Mark C. M.

    2013-04-01

    Biogrout is a soil improving process that aims to improve the strength of sandy soils. The process is based on microbially induced calcite precipitation (MICP). In this study the main process is based on denitrification facilitated by bacteria indigenous to the soil using substrates, which can be derived from pretreated waste streams containing calcium salts of fatty acids and calcium nitrate, making it a cost effective and environmentally friendly process. The goal of this research is to improve the understanding of the process by numerical analysis so that it may be improved and applied properly for varying applications, such as borehole stabilization, liquefaction prevention, levee fortification and mitigation of beach erosion. During the denitrification process there are many phases present in the pore space including a liquid phase containing solutes, crystals, bacteria forming biofilms and gas bubbles. Due to the amount of phases and their dynamic changes (multiphase flow with (non-linear) reactive transport), there are many interactions making the process very complex. To understand this complexity in the system, the interactions between these phases are studied in a reductionist approach, increasing the complexity of the system by one phase at a time. The model will initially include flow, solute transport, crystal nucleation and growth in 2D at pore scale. The flow will be described by Navier-Stokes equations. Initial study and simulations has revealed that describing crystal growth for this application on a fixed grid can introduce significant fundamental errors. Therefore a level set method will be employed to better describe the interface of developing crystals in between sand grains. Afterwards the model will be expanded to 3D to provide more realistic flow, nucleation and clogging behaviour at pore scale. Next biofilms and lastly gas bubbles may be added to the model. From the results of these pore scale models the behaviour of the system may be

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

    NASA Astrophysics Data System (ADS)

    Marcolli, C.

    2013-06-01

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

  12. Mechanical properties, pore size distribution, and pore solution of fly ash-belite cement mortars

    SciTech Connect

    Guerrero, A.; Goni, S.; Macias, A.; Luxan, M.P.

    1999-11-01

    The mechanical properties, pore size distribution, and extracted pore solution of fly ash-belite cement (FABC) mortars were studied for a period of 200 days. The influence of the calcination temperature, which ranged from 700 to 900 C, of the fly ash-belite cement was discussed. The evolution with hydration time of the pore size distribution was followed by mercury intrusion porosimetry, and the results correlated with those of flexural and compressive strength. The pore solution was expressed and analyzed at different times of hydration.

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

    NASA Astrophysics Data System (ADS)

    Moffett, Kevan B.; Gorelick, Steven M.

    2016-03-01

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

  14. Lagrangian Statistics and Modeling of Pore-Scale Dispersion in Heterogeneous Natural Porous Media

    NASA Astrophysics Data System (ADS)

    Meyer, D. W.; Bijeljic, B.; Blunt, M. J.

    2014-12-01

    Recent advances made in the area of micro-CT scanning of natural pore-space geometries enable detailed investigations of flow and transport processes at the pore-scale, e.g., [Bijeljic et al., Phys. Rev. E, 87, 2013]. A study is reported of Lagrangian statistics of fluid-particle velocity and acceleration in natural porous media of different rock type. The underlying 3d pore-space geometries were obtained by means of micro-CT scans of a beadpack, Bentheimer sandstone, and Ketton and Estaillades carbonates. Based on these statistics, we introduce a new Lagrangian model for transport that reproduces the aforementioned statistics. Our model is based on a spatio-temporal Markov process of the Lagrangian velocity of fluid particles, where the model parametrization is related to the medium characteristics. Transport predictions are validated against flow and transport results from pore-scale direct numerical simulation. The new model enables the detailed investigation of the transition between non-Fickian and Fickian dispersion in real porous media. Moreover, the model sheds light on the connection between geometrical pore-space characteristics and transport behavior.

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

    SciTech Connect

    W. Brent Lindquist

    2005-01-21

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

  16. Facial skin pores: a multiethnic study.

    PubMed

    Flament, Frederic; Francois, Ghislain; Qiu, Huixia; Ye, Chengda; Hanaya, Tomoo; Batisse, Dominique; Cointereau-Chardon, Suzy; Seixas, Mirela Donato Gianeti; Dal Belo, Susi Elaine; Bazin, Roland

    2015-01-01

    Skin pores (SP), as they are called by laymen, are common and benign features mostly located on the face (nose, cheeks, etc) that generate many aesthetic concerns or complaints. Despite the prevalence of skin pores, related literature is scarce. With the aim of describing the prevalence of skin pores and anatomic features among ethnic groups, a dermatoscopic instrument, using polarized lighting, coupled to a digital camera recorded the major features of skin pores (size, density, coverage) on the cheeks of 2,585 women in different countries and continents. A detection threshold of 250 μm, correlated to clinical scorings by experts, was input into a specific software to further allow for automatic counting of the SP density (N/cm(2)) and determination of their respective sizes in mm(2). Integrating both criteria also led to establishing the relative part of the skin surface (as a percentage) that is actually covered by SP on cheeks. The results showed that the values of respective sizes, densities, and skin coverage: 1) were recorded in all studied subjects; 2) varied greatly with ethnicity; 3) plateaued with age in most cases; and 4) globally refected self-assessment by subjects, in particular those who self-declare having "enlarged pores" like Brazilian women. Inversely, Chinese women were clearly distinct from other ethnicities in having very low density and sizes. Analyzing the present results suggests that facial skin pore's morphology as perceived by human eye less result from functional criteria of associated appendages such as sebaceous glands. To what extent skin pores may be viewed as additional criteria of a photo-altered skin is an issue to be further addressed. PMID:25733918

  17. The Arabidopsis Nuclear Pore and Nuclear Envelope

    PubMed Central

    Meier, Iris; Brkljacic, Jelena

    2010-01-01

    The nuclear envelope is a double membrane structure that separates the eukaryotic cytoplasm from the nucleoplasm. The nuclear pores embedded in the nuclear envelope are the sole gateways for macromolecular trafficking in and out of the nucleus. The nuclear pore complexes assembled at the nuclear pores are large protein conglomerates composed of multiple units of about 30 different nucleoporins. Proteins and RNAs traffic through the nuclear pore complexes, enabled by the interacting activities of nuclear transport receptors, nucleoporins, and elements of the Ran GTPase cycle. In addition to directional and possibly selective protein and RNA nuclear import and export, the nuclear pore gains increasing prominence as a spatial organizer of cellular processes, such as sumoylation and desumoylation. Individual nucleoporins and whole nuclear pore subcomplexes traffic to specific mitotic locations and have mitotic functions, for example at the kinetochores, in spindle assembly, and in conjunction with the checkpoints. Mutants of nucleoporin genes and genes of nuclear transport components lead to a wide array of defects from human diseases to compromised plant defense responses. The nuclear envelope acts as a repository of calcium, and its inner membrane is populated by functionally unique proteins connected to both chromatin and—through the nuclear envelope lumen—the cytoplasmic cytoskeleton. Plant nuclear pore and nuclear envelope research—predominantly focusing on Arabidopsis as a model—is discovering both similarities and surprisingly unique aspects compared to the more mature model systems. This chapter gives an overview of our current knowledge in the field and of exciting areas awaiting further exploration. PMID:22303264

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Takahashi, M.; Urushimatsu, Y.

    2008-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Daigle, H.; Thomas, B.

    2013-12-01

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

  1. Pore-Scale Simulation of Intragranular Diffusion: Effects of Incomplete Mixing on Macroscopic Manifestations

    SciTech Connect

    Scheibe, Timothy D.; Hou, Zhangshuan; Palmer, Bruce J.; Tartakovsky, Alexandre M.

    2013-07-01

    Diffusive mass transfer into and out of intragranular micropores ("intragranular diffusion") plays an important role in the large-scale transport of some groundwater contaminants. We are interested in understanding the combined effect of pore-scale advection and intragranular diffusion on solute transport at the effective porous medium scale. To study this problem, we have developed a three-dimensional pore-scale model of fluid flow and solute transport that incorporates diffusion into and out of intragranular pore spaces. Our model is based on the Smoothed Particle Hydrodynamics (SPH) simulation method, which represents fluid and solid phases by a mesh-free particle discretization. In the pore spaces, fluid flow is simulated by discretizing the Navier-Stokes equations using the SPH approach. Solute transport is represented by advection, diffusion within the fluid phase, and diffusion between the fluid and solid phases. Our model is implemented on large-scale parallel computing hardware, allowing us to simulate millions of computational particles and represent fully three-dimensional systems of pores and grains with arbitrarily complex physical geometry. We have used this model system to perform numerical experiments using various model porous media systems, which allows us to draw comparisons between macroscopic measures computed from the pore-scale simulations (such as breakthrough curves) and those predicted by macroscopic formulations that assume complete mixing over the representative volume. In this paper we present results of 3D simulations of pore-scale flow and transport, including cases with and without intragranular diffusion, in two model porous media, one with randomly-packed uniform spherical grains and a second with randomly-packed spheres drawn from a binary grain size distribution. Breakthrough curves were computed from the 3D simulations at various transport distances. Comparable breakthrough curves were computed using 1D macroscopic models with

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

    NASA Astrophysics Data System (ADS)

    McFarlane, Patrick; Semperlotti, Fabio; Sen, Mihir

    2013-10-01

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

  3. Hydrochromic Approaches to Mapping Human Sweat Pores.

    PubMed

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

    2016-06-21

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

  4. Mechanical properties of open-pore titanium foam.

    PubMed

    Imwinkelried, Thomas

    2007-06-15

    Open-pore titanium foams are produced using the so-called space holder method. The mechanical properties of titanium foams with porosities of 50-80% are studied. The stiffness and yield strength of the foams are found to encompass the property range between cancellous bone and cortical bone. The analyzed foams are found to be anisotropic due to the use of nonspherical space holder particles which rearrange during the compaction of the powder mixture. The titanium foams are stronger perpendicular to the compaction direction and weaker along the compaction axis. In view of the application as an implant material in the lumbar spine, an intermediate porosity of 60-65% is analyzed more in detail. The typical yield strength of titanium foam with 62.5% porosity is above 60 MPa in compression, bending, and tension. Stiffness values vary with the testing method from 7-14 GPa. PMID:17252551

  5. Analysis of a spatially deconvolved solar pore

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  6. Analysis of a spatially deconvolved solar pore

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  7. Performance of Small Pore Microchannel Plates

    NASA Technical Reports Server (NTRS)

    Siegmund, O. H. W.; Gummin, M. A.; Ravinett, T.; Jelinsky, S. R.; Edgar, M.

    1995-01-01

    Small pore size microchannel plates (MCP's) are needed to satisfy the requirements for future high resolution small and large format detectors for astronomy. MCP's with pore sizes in the range 5 micron to 8 micron are now being manufactured, but they are of limited availability and are of small size. We have obtained sets of Galileo 8 micron and 6.5 micron MCP's, and Philips 6 micron and 7 micron pore MCP's, and compared them to our larger pore MCP Z stacks. We have tested back to back MCP stacks of four of these MCP's and achieved gains greater than 2 x 1O(exp 7) with pulse height distributions of less than 40% FWHM, and background rates of less than 0.3 events sec(exp -1) cm(exp -2). Local counting rates up to approx. 100 events/pore/sec have been attained with little drop of the MCP gain. The bare MCP quantum efficiencies are somewhat lower than those expected, however. Flat field images are characterized by an absence of MCP fixed pattern noise.

  8. Modeling Tissue Growth Within Nonwoven Scaffolds Pores

    PubMed Central

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

    2011-01-01

    In this study we present a novel approach for predicting tissue growth within the pores of fibrous tissue engineering scaffolds. Thin nonwoven polyethylene terephthalate scaffolds were prepared to characterize tissue growth within scaffold pores, by mouse NR6 fibroblast cells. On the basis of measurements of tissue lengths at fiber crossovers and along fiber segments, mathematical models were determined during the proliferative phase of cell growth. Tissue growth at fiber crossovers decreased with increasing interfiber angle, with exponential relationships determined on day 6 and 10 of culture. Analysis of tissue growth along fiber segments determined two growth profiles, one with enhanced growth as a result of increased tissue lengths near the fiber crossover, achieved in the latter stage of culture. Derived mathematical models were used in the development of a software program to visualize predicted tissue growth within a pore. This study identifies key pore parameters that contribute toward tissue growth, and suggests models for predicting this growth, based on fibroblast cells. Such models may be used in aiding scaffold design, for optimum pore infiltration during the tissue engineering process. PMID:20687775

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

    NASA Astrophysics Data System (ADS)

    Wang, Gang

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

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

    NASA Astrophysics Data System (ADS)

    Fujikura, Yusuke; Oshita, Hideki

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

  11. Modeling Soil Pore Oxygen in Restored Wetlands

    NASA Astrophysics Data System (ADS)

    Rubol, S.; Loecke, T.; Burgin, A. J.; Franz, T.

    2015-12-01

    Soil pore oxygen (O2) is usually modeled indirectly as a function of soil moisture. However, using soil moisture to describe the oxic /anoxic status of a soil may not be sufficient accurate, especially when soil pore O2 rapidly changes, as following hydrological forcing. As first step, we use the dataset collected in the constructed wetland near Dayton, OH, by Loecke and Burgin, to reconstruct the environmental functions and re-aeration status of the soil. The dataset consist of 24 Apogee sensors and 24 soil moisture and temperature sensors located at 10 cm depth in upland, transitional and submerged zone (see Figure 1). Data were recorded over two years at temporal interval of 30 minutes. Then, we explore the capability of existing biogeochemical models to predict metabolic activity and the soil pore O2. Figure1: Restored wetland field site with soil O2 sensors (yellow stars) in upland (red), transitional (green) and submerged (blue) zones.

  12. Optical detection of pores in adipocyte membrane

    NASA Astrophysics Data System (ADS)

    Yanina, I. Yu.; Doubrovski, V. A.; Tuchin, V. V.

    2013-08-01

    Structures that can be interpreted as cytoplasm droplets leaking through the membrane are experimentally detected on the membranes of adipocytes using optical digital microscopy. The effect of an aqueous alcohol solution of brilliant green on the amount and sizes of structures is studied. It is demonstrated that the optical irradiation of the adipocytes that are sensitized with the aid of the brilliant green leads to an increase in the amount of structures (pores) after the irradiation. The experimental results confirm the existence of an earlier-proposed effect of photochemical action on the sensitized cells of adipose tissue that involves additional formation of pores in the membrane of the sensitized cell under selective optical irradiation. The proposed method for the detection of micropores in the membrane of adipose tissue based on the detection of the cytoplasm droplets leaking from the cell can be considered as a method for the optical detection of nanosized pores.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  16. A dual pore carbon aerogel based air cathode for a highly rechargeable lithium-air battery

    NASA Astrophysics Data System (ADS)

    Wang, Fang; Xu, Yang-Hai; Luo, Zhong-Kuan; Pang, Yan; Wu, Qi-Xing; Liang, Chun-Sheng; Chen, Jing; Liu, Dong; Zhang, Xiang-hua

    2014-12-01

    Cathode structure plays a vital role in lithium-air battery for that it can provide space for discharged products accommodation and free path for oxygen, e- and Li+ transport. However, pore blockage, cathode passivation and degradation all result in low discharge rates and poor cycling capability. To get rid of these predicaments, a novel highly conductive dual pore carbon aerogel based air cathode is fabricated to construct a lithium-air battery, which exhibits 18 to 525 cycles in the LiTFSI/sulfolane electrolyte at a current density varying from 1.00 mA cm-2 to 0.05 mA cm-2, accompanied by a high energy efficiency of 78.32%. We postulate that the essence lies in that the as-prepared air cathode inventively create a suitable tri-phase boundary reaction zone, facilitating oxygen and Li+ diffusion in two independant pore channels, thus realizing a relative higher discharge rate capability, lower pore blockage and cathode passivation. Further, pore structure, carbon loading, rate capability, discharge depth and the air's effect are exploited and coordinated, targeting for a high power and reversible lithium-air battery. Such nano-porous carbon aerogel air cathode of novel dual pore structure and material design is expected to be an attractive alternative for lithium-air batteries and other lithium based batteries.

  17. The pore dimensions of gramicidin A.

    PubMed Central

    Smart, O S; Goodfellow, J M; Wallace, B A

    1993-01-01

    The ion channel forming peptide gramicidin A adopts a number of distinct conformations in different environments. We have developed a new method to analyze and display the pore dimensions of ion channels. The procedure is applied to two x-ray crystal structures of gramicidin that adopt distinct antiparallel double helical dimer conformations and a nuclear magnetic resonance (NMR) structure for the beta6.3 NH2-terminal to NH2-terminal dimer. The results are discussed with reference to ion conductance properties and dependence of pore dimensions on the environment. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 PMID:7508762

  18. The Pore Formation and Mobility Investigation: The Apparatus, Operations, Science Obtained, and Potential for Continued Usage

    NASA Technical Reports Server (NTRS)

    Gurgel, R. N.; Luz, P.; Smith, G. A.; Spivey, R.; Sen, S.; Anilkumar, A.

    2004-01-01

    The objective of the presentation is to provide an overview of the Pore Formation and Mobility Investigation (PFMI) hardware that is currently aboard the International Space Station and to identify European experiments could utilize it. The hardware, integration in the Glovebox, operations,-science results, and instrument performance assessment will be presented. The possibilities of adapting the optical observation system will also be reviewed.

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

    SciTech Connect

    Silin, Dmitriy; Patzek, Tad

    2009-02-01

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

  20. 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

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

    PubMed

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

    2015-01-01

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

  2. Using Microfluidics for Visualisation of Displacement Mechanisms on Pore Network Models

    NASA Astrophysics Data System (ADS)

    Gerami Kaviri Nejad, A.; Mostaghimi, P.; Armstrong, R. T.; Rafeie, M.; Ebrahimi Warkiani, M.

    2015-12-01

    We use microfluidic methods for studying displacement mechanisms of immiscible fluids including drainage and imbibition in porous media at the pore scale. We use soft lithography method to make 4' diameter silicon wafer to be used as a mould of our designs. We have fabricated a range of microfluidic chips based on a range of patterns including pore junction with unequal throats, junction of throats with different coordination numbers, and junction of tortuous throats. We also fabricate more complex networks as a combination of the mentioned simple patterns. Decane and water are used as the wetting and non-wetting phases, respectively. Using high-resolution microscopy, we visualise the displacement processes and the movement of the interface between two fluids at different saturations. We initially test to micromodel chip for modelling drainage into a pore junction and compare our results with the prediction by the Young-Laplace equations. Then we focus on the sequence of pore filling and effects of pore space geometry, tortuosity and the injection rate. We use plasma treating to vary the contact angle and then study the effects of wettability on interface movement. Using accurate pump and pressure controller, we measure pressure drop across the micromodels at different time. By image processing of fluids distribution in the microfluidic chip, saturation of both phases can be estimated. Then, we plot relative permeability versus saturation curves for different pore space geometries. Our results can be used for validation of numerical two phase flow simulation and also we provide novel suggestions for modifying the equations of motion in pore network models.

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

    NASA Astrophysics Data System (ADS)

    Jiang, Fei; Tsuji, Takeshi

    2014-11-01

    The C O2 behavior within the reservoirs of carbon capture and storage projects is usually predicted from large-scale simulations of the reservoir. A key parameter in reservoir simulation is relative permeability. However, mineral precipitation alters the pore structure over time, and leads correspondingly to permeability changing with time. In this study, we numerically investigate the influence of carbonate precipitation on relative permeability during C O2 storage. The pore spaces in rock samples were extracted by high-resolution microcomputed tomography (CT) scanned images. The fluid velocity field within the three-dimensional pore spaces was calculated by the lattice Boltzmann method, while reactive transport with calcite deposition was modeled by an advection-reaction formulation solved by the finite volume method. To increase the computational efficiency and reduce the processing time, we adopted a graphics processing unit parallel computing technique. The relative permeability of the sample rock was then calculated by a highly optimized two-phase lattice Boltzmann model. We also proposed two pore clogging models. In the first model, the clogging processes are modeled by transforming fluid nodes to solid nodes based on their precipitated mass level. In the second model, the porosity is artificially reduced by adjusting the gray scale threshold of the CT images. The developed method accurately simulates the mineralization process observed in laboratory experiment. Precipitation-induced evolution of pore structure significantly influenced the absolute permeability. The relative permeability, however, was much more influenced by pore reduction in the nonwetting phase than in the wetting phase. The output of the structural changes in pore geometry by this model could be input to C O2 reservoir simulators to investigate the outcome of sequestered C O2 .

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

    PubMed

    Jiang, Fei; Tsuji, Takeshi

    2014-11-01

    The CO_{2} behavior within the reservoirs of carbon capture and storage projects is usually predicted from large-scale simulations of the reservoir. A key parameter in reservoir simulation is relative permeability. However, mineral precipitation alters the pore structure over time, and leads correspondingly to permeability changing with time. In this study, we numerically investigate the influence of carbonate precipitation on relative permeability during CO_{2} storage. The pore spaces in rock samples were extracted by high-resolution microcomputed tomography (CT) scanned images. The fluid velocity field within the three-dimensional pore spaces was calculated by the lattice Boltzmann method, while reactive transport with calcite deposition was modeled by an advection-reaction formulation solved by the finite volume method. To increase the computational efficiency and reduce the processing time, we adopted a graphics processing unit parallel computing technique. The relative permeability of the sample rock was then calculated by a highly optimized two-phase lattice Boltzmann model. We also proposed two pore clogging models. In the first model, the clogging processes are modeled by transforming fluid nodes to solid nodes based on their precipitated mass level. In the second model, the porosity is artificially reduced by adjusting the gray scale threshold of the CT images. The developed method accurately simulates the mineralization process observed in laboratory experiment. Precipitation-induced evolution of pore structure significantly influenced the absolute permeability. The relative permeability, however, was much more influenced by pore reduction in the nonwetting phase than in the wetting phase. The output of the structural changes in pore geometry by this model could be input to CO_{2} reservoir simulators to investigate the outcome of sequestered CO_{2}. PMID:25493903

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

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

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

  6. Simple thermal treatment for the size control of pore arrays in a polystyrene colloidal crystal films

    NASA Astrophysics Data System (ADS)

    Jamiolkowski, Ryan M.; Fiorenza, Shane A.; Chen, Kevin; Tate, Alyssa M.; Pfeil, Shawn H.; Goldman, Yale E.

    Nanosphere Lithography (NSL) offers an attractive route to fabricating periodic structures with nanoscale features, without e-beam or deep UV lithography. In particular, it is uniquely suited to the low cost fabrication of large repeated arrays pores or pillars created by taking advantage of the interstitial spaces in close-packed monolayers of nano to micro-scale beads. However pore size, shape, and spacing cannot be controlled independently. We present both a robust method for producing large, approximately 1 cm2, hexagonally close packed monolayer films of 1 micron diameter polystyrene beads on glass substrates, and thermal treatment of these films near the glass temperature, Tg, of polystyrene to modify the pore size. This builds on earlier work showing that pore size can be modified for colloidal crystals formed at a liquid gas interface [2]. These processes promise a simple, reproducible, and low cost route to periodic pore arrays for nano-photonic applications such as zero mode waveguides (ZMWs) Funding: F30 AI114187 (RMJ), R01-GM080376 (YEG).

  7. 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.

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

    PubMed

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

    2015-04-01

    A theoretical and numerical study of the sound propagation in air-saturated porous media with straight main pores bearing lateral cavities (dead-ends) is presented. The lateral cavities are located at "nodes" periodically spaced along each main pore. The effect of periodicity in the distribution of the lateral cavities is studied, and the low frequency limit valid for the closely spaced dead-ends is considered separately. It is shown that the absorption coefficient and transmission loss are influenced by the viscous and thermal losses in the main pores as well as their perforation rate. The presence of long or short dead-ends significantly alters the acoustical properties of the material and can increase significantly the absorption at low frequencies (a few hundred hertz). These depend strongly on the geometry (diameter and length) of the dead-ends, on their number per node, and on the periodicity along the propagation axis. These effects are primarily due to low sound speed in the main pores and to thermal losses in the dead-end pores. The model predictions are compared with experimental results. Possible designs of materials of a few cm thicknesses displaying enhanced low frequency absorption at a few hundred hertz are proposed. PMID:25920830

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

    NASA Astrophysics Data System (ADS)

    Mehmani, Yashar; Oostrom, Mart; Balhoff, Matthew T.

    2014-03-01

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

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

    SciTech Connect

    Mehmani, Yashar; Oostrom, Martinus; Balhoff, Matthew

    2014-03-20

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

  11. Pore Topology Method: A General and Fast Pore-Scale Modeling Approach to Simulate Fluid Flow in Porous Media

    NASA Astrophysics Data System (ADS)

    Riasi, M. S.; Huang, G.; Montemagno, C.; Yeghiazarian, L.

    2014-12-01

    Micro-scale modeling of multiphase flow in porous media is critical to characterize porous materials. Several modeling techniques have been implemented to date, but none can be used as a general strategy for all porous media applications due to challenges presented by non-smooth high-curvature and deformable solid surfaces, and by a wide range of pore sizes and porosities. Finite approaches like the finite volume method require a high quality, problem-dependent mesh, while particle-based approaches like the lattice Boltzmann require too many particles to achieve a stable meaningful solution. Both come at a large computational cost. Other methods such as pore network modeling (PNM) have been developed to accelerate the solution process by simplifying the solution domain, but so far a unique and straightforward methodology to implement PNM is lacking. Pore topology method (PTM) is a new topologically consistent approach developed to simulate multiphase flow in porous media. The core of PTM is to reduce the complexity of the 3-D void space geometry by working with its medial surface as the solution domain. Medial surface is capable of capturing all the corners and surface curvatures in a porous structure, and therefore provides a topologically consistent representative geometry for porous structure. Despite the simplicity and low computational cost, PTM provides a fast and straightforward approach for micro-scale modeling of fluid flow in all types of porous media irrespective of their porosity and pore size distribution. In our previous work, we developed a non-iterative fast medial surface finder algorithm to determine a voxel-wide medial surface of the void space of porous media as well as a set of simple rules to determine the capillary pressure-saturation curves for a porous system assuming quasi-static two-phase flow with a planar w-nw interface. Our simulation results for a highly porous fibrous material and polygonal capillary tubes were in excellent agreement

  12. Influence of pore pressure and production-induced changes in pore pressure on in situ stress

    SciTech Connect

    Teufel, L.W.

    1996-02-01

    Knowledge of in situ stress and how stress changes with reservoir depletion and pore pressure drawdown is important in a multi-disciplinary approach to reservoir characterization, reservoir management, and improved oil recovery projects. This report summarizes a compilation of in situ stress data from six fields showing the effects of pore pressure and production-induced changes in pore pressure on the minimum horizontal stress. The in situ stress data and corresponding pore pressure data were obtained from field records of the operating companies and published reports. Horizontal stress was determined from closure pressure data of hydraulic fractures and leak-off tests. The stress measurements clearly demonstrate that the total minimum-horizontal stress is dependent on pore pressure. A decrease in pore pressure either by geologic processes or production of a reservoir will result in a decrease in the total minimum-horizontal stress. The magnitude of changes in stress state with net changes in pore pressure is dependent on local field conditions and cannot be accurately predicted by the uniaxial strain model that is commonly used by the petroleum industry.

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

    SciTech Connect

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

    2012-10-25

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

  14. Micro-CT Pore Scale Study Of Flow In Porous Media: Effect Of Voxel Resolution

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    In the last few years, pore scale studies have become the key to understanding the complex fluid flow processes in the fields of groundwater remediation, hydrocarbon recovery and environmental issues related to carbon storage and capture. A pore scale study is often comprised of two key procedures: 3D pore scale imaging and numerical modelling techniques. The essence of a pore scale study is to test the physics implemented in a model of complicated fluid flow processes at one scale (microscopic) and then apply the model to solve the problems associated with water resources and oil recovery at other scales (macroscopic and field). However, the process of up-scaling from the pore scale to the macroscopic scale has encountered many challenges due to both pore scale imaging and modelling techniques. Due to the technical limitations in the imaging method, there is always a compromise between the spatial (voxel) resolution and the physical volume of the sample (field of view, FOV) to be scanned by the imaging methods, specifically X-ray micro-CT (XMT) in our case In this study, a careful analysis was done to understand the effect of voxel size, using XMT to image the 3D pore space of a variety of porous media from sandstones to carbonates scanned at different voxel resolution (4.5 μm, 6.2 μm, 8.3 μm and 10.2 μm) but keeping the scanned FOV constant for all the samples. We systematically segment the micro-CT images into three phases, the macro-pore phase, an intermediate phase (unresolved micro-pores + grains) and the grain phase and then study the effect of voxel size on the structure of the macro-pore and the intermediate phases and the fluid flow properties using lattice-Boltzmann (LB) and pore network (PN) modelling methods. We have also applied a numerical coarsening algorithm (up-scale method) to reduce the computational power and time required to accurately predict the flow properties using the LB and PN method.

  15. Facial skin pores: a multiethnic study

    PubMed Central

    Flament, Frederic; Francois, Ghislain; Qiu, Huixia; Ye, Chengda; Hanaya, Tomoo; Batisse, Dominique; Cointereau-Chardon, Suzy; Seixas, Mirela Donato Gianeti; Dal Belo, Susi Elaine; Bazin, Roland

    2015-01-01

    Skin pores (SP), as they are called by laymen, are common and benign features mostly located on the face (nose, cheeks, etc) that generate many aesthetic concerns or complaints. Despite the prevalence of skin pores, related literature is scarce. With the aim of describing the prevalence of skin pores and anatomic features among ethnic groups, a dermatoscopic instrument, using polarized lighting, coupled to a digital camera recorded the major features of skin pores (size, density, coverage) on the cheeks of 2,585 women in different countries and continents. A detection threshold of 250 μm, correlated to clinical scorings by experts, was input into a specific software to further allow for automatic counting of the SP density (N/cm2) and determination of their respective sizes in mm2. Integrating both criteria also led to establishing the relative part of the skin surface (as a percentage) that is actually covered by SP on cheeks. The results showed that the values of respective sizes, densities, and skin coverage: 1) were recorded in all studied subjects; 2) varied greatly with ethnicity; 3) plateaued with age in most cases; and 4) globally refected self-assessment by subjects, in particular those who self-declare having “enlarged pores” like Brazilian women. Inversely, Chinese women were clearly distinct from other ethnicities in having very low density and sizes. Analyzing the present results suggests that facial skin pore’s morphology as perceived by human eye less result from functional criteria of associated appendages such as sebaceous glands. To what extent skin pores may be viewed as additional criteria of a photo-altered skin is an issue to be further addressed. PMID:25733918

  16. Assembly of the Bak Apoptotic Pore

    PubMed Central

    Ma, Stephen; Hockings, Colin; Anwari, Khatira; Kratina, Tobias; Fennell, Stephanie; Lazarou, Michael; Ryan, Michael T.; Kluck, Ruth M.; Dewson, Grant

    2013-01-01

    Bak and Bax are the essential effectors of the intrinsic pathway of apoptosis. Following an apoptotic stimulus, both undergo significant changes in conformation that facilitates their self-association to form pores in the mitochondrial outer membrane. However, the molecular structures of Bak and Bax oligomeric pores remain elusive. To characterize how Bak forms pores during apoptosis, we investigated its oligomerization under native conditions using blue native PAGE. We report that, in a healthy cell, inactive Bak is either monomeric or in a large complex involving VDAC2. Following an apoptotic stimulus, activated Bak forms BH3:groove homodimers that represent the basic stable oligomeric unit. These dimers multimerize to higher-order oligomers via a labile interface independent of both the BH3 domain and groove. Linkage of the α6:α6 interface is sufficient to stabilize higher-order Bak oligomers on native PAGE, suggesting an important role in the Bak oligomeric pore. Mutagenesis of the α6 helix disrupted apoptotic function because a chimera of Bak with the α6 derived from Bcl-2 could be activated by truncated Bid (tBid) and could form BH3:groove homodimers but could not form high molecular weight oligomers or mediate cell death. An α6 peptide could block Bak function but did so upstream of dimerization, potentially implicating α6 as a site for activation by BH3-only proteins. Our examination of native Bak oligomers indicates that the Bak apoptotic pore forms by the multimerization of BH3:groove homodimers and reveals that Bak α6 is not only important for Bak oligomerization and function but may also be involved in how Bak is activated by BH3-only proteins. PMID:23893415

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Technical Reports Server (NTRS)

    OKeeffe, James; Cozmuta, Ioana; Stolc, Viktor

    2003-01-01

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

  20. Estimating pore and cement volumes in thin section

    USGS Publications Warehouse

    Halley, R.B.

    1978-01-01

    Point count estimates of pore, grain and cement volumes from thin sections are inaccurate, often by more than 100 percent, even though they may be surprisingly precise (reproducibility + or - 3 percent). Errors are produced by: 1) inclusion of submicroscopic pore space within solid volume and 2) edge effects caused by grain curvature within a 30-micron thick thin section. Submicroscopic porosity may be measured by various physical tests or may be visually estimated from scanning electron micrographs. Edge error takes the form of an envelope around grains and increases with decreasing grain size and sorting, increasing grain irregularity and tighter grain packing. Cements are greatly involved in edge error because of their position at grain peripheries and their generally small grain size. Edge error is minimized by methods which reduce the thickness of the sample viewed during point counting. Methods which effectively reduce thickness include use of ultra-thin thin sections or acetate peels, point counting in reflected light, or carefully focusing and counting on the upper surface of the thin section.

  1. Pore size distribution and accessible pore size distribution in bituminous coals

    SciTech Connect

    Sakurovs, Richard; He, Lilin; Melnichenko, Yuri B; Radlinski, Andrzej Pawell; Blach, Tomasz P

    2012-01-01

    The porosity and pore size distribution of coals determine many of their properties, from gas release to their behavior on carbonization, and yet most methods of determining pore size distribution can only examine a restricted size range. Even then, only accessible pores can be investigated with these methods. Small-angle neutron scattering (SANS) and ultra small-angle neutron scattering (USANS) are increasingly used to characterize the size distribution of all of the pores non-destructively. Here we have used USANS/SANS to examine 24 well-characterized bituminous and subbituminous coals: three from the eastern US, two from Poland, one from New Zealand and the rest from the Sydney and Bowen Basins in Eastern Australia, and determined the relationships of the scattering intensity corresponding to different pore sizes with other coal properties. The range of pore radii examinable with these techniques is 2.5 nm to 7 {micro}m. We confirm that there is a wide range of pore sizes in coal. The pore size distribution was found to be strongly affected by both rank and type (expressed as either hydrogen or vitrinite content) in the size range 250 nm to 7 {micro}m and 5 to 10 nm, but weakly in intermediate regions. The results suggest that different mechanisms control coal porosity on different scales. Contrast-matching USANS and SANS were also used to determine the size distribution of the fraction of the pores in these coals that are inaccessible to deuterated methane, CD{sub 4}, at ambient temperature. In some coals most of the small ({approx} 10 nm) pores were found to be inaccessible to CD{sub 4} on the time scale of the measurement ({approx} 30 min - 16 h). This inaccessibility suggests that in these coals a considerable fraction of inherent methane may be trapped for extended periods of time, thus reducing the effectiveness of methane release from (or sorption by) these coals. Although the number of small pores was less in higher rank coals, the fraction of total

  2. Interactions between bedforms, turbulence and pore flow

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    A widespread occurrence of flow-form interaction in rivers is represented by subaqueous bedforms such as dunes. Many models have been proposed to explain how bedform generation and evolution are driven by turbulent flow structures that control the incipient motion of cohesionless sediments and later bedform development. However, most of these models have assumed such bedforms to be migrating over an impermeable bed, and that any surface-subsurface flow interaction is negligible. However, for some gravel-bed rivers the porosity can be high, up to 43%, which may result in significant flow both through the permeable bed (hyporheic flow) and across the surface-subsurface interface. The mass and momentum exchange occurring at the interface may have a strong impact on the structure of turbulent flow in the near-bed region. In the case of a dune, its topography induces a local pressure gradient that enhances flow across the interface. This results in a flow structure that may be radically different from that commonly proposed by past work. This paper presents results from a simplified laboratory model akin to a fine-grained bedform generated on top of a coarser sediment bed. Particle imaging velocimetry (PIV) measurements were conducted in order to characterise flow both over and underneath an idealised 2-dimensional dune (0.41 m long, 0.056 m high and having a leeside angle of 27°) overlaying a packed bed of uniform size spheres (D = 0.04 m diameter). Experiments were conducted in free surface flow conditions (Froude number = 0.1; Reynolds number = 25,000) for one bedform height: flow depth ratio (0.31). The flow above the dune was measured using a standard PIV technique while a novel endoscopic PIV (EPIV) system allowed collection of flow data within the pore spaces beneath the dune. The results show that topographically-induced subsurface flow significantly modifies the structure of flow in the leeside of the dune, resulting in a flow field that is radically different

  3. Pore-scale analysis of permeability reduction resulting from colloid deposition

    SciTech Connect

    Chen, C.; Packman, A.I.; Gaillard, J.-F.

    2008-06-20

    High-energy, synchrotron-based x-ray difference micro-tomography (XDMT) was combined with lattice Boltzmann simulations to assess changes in pore-scale flow patterns and bulk permeability resulting from colloid deposition in a granular porous medium. The detailed structural information obtained from XDMT was used to define internal boundary conditions for simulations of pore fluid flow both with and without colloidal deposits. As colloids accumulated in the pore space, the mean tortuosity increased and the tortuosity distribution became multi-modal, indicating the development of macro-scale heterogeneity. These structural changes also produced large reductions in bulk permeability that were not captured by empirical or semi-empirical estimators based on the first-order geometric properties of the porous medium. This work demonstrates that coupling between fluid flow and particle transport produces heterogeneities at the sub-millimeter scale that greatly affect the hydrogeologic properties of natural porous media.

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

    SciTech Connect

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

    1998-02-01

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

  5. Signal Transduction to the Permeability Transition Pore

    PubMed Central

    Rasola, Andrea; Sciacovelli, Marco; Pantic, Boris; Bernardi, Paolo

    2010-01-01

    The permeability transition pore (PTP) is an inner mitochondrial membrane channel that has been thoroughly characterized functionally, yet remains an elusive molecular entity. The best characterized PTP-regulatory component, cyclophilin (CyP) D, is a matrix protein that favors pore opening. CyP inhibitors, CyPD null animals, and in situ PTP readouts have established the role of PTP as an effector mechanism of cell death, and the growing definition of PTP signaling mechanisms. This review briefly covers the functional features of the PTP and the role played by its dysregulation in disease pathogenesis. Recent progress on PTP modulation by kinase/phosphatase signal transduction is discussed, with specific emphasis on hexokinase and on the Akt-ERK-GSK3 axis, which might modulate the PTP through CyPD phosphorylation. PMID:20153328

  6. Mineral dissolution kinetics at the pore scale

    SciTech Connect

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

    2007-05-24

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

  7. Pores and Void in Asclepiades' Physical Theory.

    PubMed

    Leith, David

    2012-01-01

    This paper examines a fundamental, though relatively understudied, aspect of the physical theory of the physician Asclepiades of Bithynia, namely his doctrine of pores. My principal thesis is that this doctrine is dependent on a conception of void taken directly from Epicurean physics. The paper falls into two parts: the first half addresses the evidence for the presence of void in Asclepiades' theory, and concludes that his conception of void was basically that of Epicurus; the second half focuses on the precise nature of Asclepiadean pores, and seeks to show that they represent void interstices between the primary particles of matter which are the constituents of the human body, and are thus exactly analogous to the void interstices between atoms within solid objects in Epicurus' theory. PMID:22984299

  8. Pores and Void in Asclepiades’ Physical Theory

    PubMed Central

    Leith, David

    2012-01-01

    This paper examines a fundamental, though relatively understudied, aspect of the physical theory of the physician Asclepiades of Bithynia, namely his doctrine of pores. My principal thesis is that this doctrine is dependent on a conception of void taken directly from Epicurean physics. The paper falls into two parts: the first half addresses the evidence for the presence of void in Asclepiades’ theory, and concludes that his conception of void was basically that of Epicurus; the second half focuses on the precise nature of Asclepiadean pores, and seeks to show that they represent void interstices between the primary particles of matter which are the constituents of the human body, and are thus exactly analogous to the void interstices between atoms within solid objects in Epicurus’ theory. PMID:22984299

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  10. Further characterization of Closed Pore Insulation (CPI)

    NASA Technical Reports Server (NTRS)

    Russak, M.; Feldman, C.

    1973-01-01

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

  11. Paleo-hydrological history in pore water extracted from sedimentary rocks in the coastal area

    NASA Astrophysics Data System (ADS)

    Ikawa, R.; Machida, I.; Koshigai, M.; Nishizaki, S.; Marui, A.; Yoshizawa, T.; Ito, N.

    2010-12-01

    Over the past decade, new utilization methods of underground space development such as geological disposal of high level radioactive waste (HLW) and carbon capture and storage (CCS) have been important issues under discussion in Japan. Coastal areas have been identified as suitable candidate sites for such projects. A good understanding of the structure of seawater/freshwater interface and fault is important due to the fact that it serves as a preferential pathway through which radionuclide can be transported by means of groundwater. There is, however, little available information worldwide on deep groundwater studies in coastal areas. There is also virtually no study has been conducted on the behavior of groundwater and pore water in coastal impermeable sedimentary rocks. In this study, large scale core drilling (1000m depth) has been carried out in coastal area at Hamasato in the Horonobe area of Hokkaido, Japan in order to investigate the geological structure and deep groundwater flow system with the residence time. Pore water with various adsorptivity from drilling core samples was gradually collected by centrifugation and squeezing methods and analyzed for water chemistry. This is aimed at estimating the paleo-hydrological history of the coastal environment by geochemical information from the pore water. Lithoface in the study area consists of sandy r and alternate (sandy and silty) layers intercalations up to 250m deep. Below 250m, shows sand and silt layers. Pore water volume collected in the sand layers by centrifugation method was almost same, contrary to that in the silt layers which decreased with depth. On the other hand, the ratio of pore water with high adsorpivity in silt layers increased with depth. Except the surface layer (<50m), electric conductivity (EC) and Cl values in pore water samples increased with depth below 300m. In this study, we report on the characteristics of seawater/freshwater interface and deep groundwater flow system based on

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

    NASA Astrophysics Data System (ADS)

    Latief, Fourier Dzar Eljabbar

    2015-09-01

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

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

    DOE PAGESBeta

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

    2015-05-21

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

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

    SciTech Connect

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

    2015-05-21

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

  15. Transient pore pressure response to confining stress excursions in Berea sandstone flooded with an aqueous solution of CO2

    NASA Astrophysics Data System (ADS)

    Crews, Jackson B.; Cooper, Clay A.

    2014-06-01

    We measured the pore pressure response due to carbon dioxide (CO2) gas bubble nucleation and growth in a Berea sandstone core flooded with an initially subsaturated aqueous solution of CO2, in response to a rapid drop in confining stress, under conditions representative of a confined aquifer. A portion of the CO2 in the Earth's crust, derived from volcanic, magmatic, and biogenic sources, dissolves in groundwater. Sudden reductions in confining stress in the Earth's crust occur due to dilational strain generated by the propagation of seismic Rayleigh and P waves, or aseismic slip in the near field of earthquakes. A drop in confining stress produces a proportional drop in pore fluid pressure. When the pore fluid contains dissolved CO2, the pore pressure responds to a drop in confining stress like it does in the dissolved gas-free case, until the pore pressure falls below the bubble pressure. Gas bubble nucleation and diffusive growth in the pore space trigger spontaneous, transient buildup of the pore fluid pressure, and reduction of effective stress. We measured the rate of pore fluid pressure buildup in the 100 s immediately following the confining stress drop, as a function of the saturation with respect to CO2 at the lowest pore pressure realized during the confining stress drop, using five different CO2 partial pressures. The rate scales with the saturation with respect to dissolved CO2, from 10 kPa/min at 1.25 to 166 kPa/min at 1.8. The net pore pressure rise was as large as 0.7 MPa (100 psi) over 5 h.

  16. Pore destruction resulting from mechanical thermal expression

    SciTech Connect

    Clayton, S.A.; Wheeler, R.A.; Hoadley, A.F.A.

    2007-07-01

    Mechanical thermal expression (MTE) is a dewatering technology ideally suited for the dewatering of internally porous biomaterials. For such materials, the combined application of temperature and compressive force in the MTE process enhances the collapse of the porous structure, resulting in effective water removal. In this article, a comparison of the dewatering of titanium dioxide, which is an ideal incompressible, non-porous material, and lignite, which is a porous plant-based biomaterial, is presented. The comparison is based on the parameters critical to dewatering, namely the material compressibility and the permeability. With the aid of mercury porosimetry results, a detailed discussion of the pore destruction of lignite resulting from MTE processing is presented. It is illustrated that there is a well-defined relationship between the pore size distribution after MTE dewatering and the MTE temperature and pressure. The discussion is extended to an investigation of the effects of MTE processing conditions on the effective and noneffective porosity. The effective porosity is defined as the interconnected porosity, which contributes to flow through the compressed matrix, while the non-effective porosity is the remaining porosity, which does not contribute to flow. It is illustrated that there is a linear relationship in both the effective and non-effective porosity with the total porosity. The linear relationship is independent of the processing conditions. It is also shown that MTE processing collapses the effective and non-effective pores at roughly the same rate.

  17. Pore morphology study of silica aerogels

    SciTech Connect

    Hua, D.W.; Anderson, J.; Haereid, S.; Smith, D.M.

    1994-12-31

    Silica aerogels have numerous properties which suggest applications such as ultra high efficiency thermal insulation. These properties relate directly to the aerogel`s pore size distribution. The micro and meso pore size ranges can be investigated by normal small angle x-ray scattering and possibly, nitrogen adsorption. However, the measurement of larger pores (> 250 {angstrom}) is more difficult. Due to their limited mechanical strength, mercury porosimetry and nitrogen condensation can disrupt the gel structure and electron microscopy provides only limited large scale structure information. The use of small angle light scattering techniques seems to have promise, the only hurdle is that aerogels exhibit significant multiple scattering. This can be avoided if one observes the gels in the wet stage since the structure of the aerogel should be very similar to the wet gel (as the result of supercritical drying). Thus, if one can match the refractive index, the morphology can be probed. The combination of certain alcoholic solvents fit this index matching criteria. Preliminary results for the gel network (micron range) and primary particle structure (manometer) are reported by using small angle light scattering and ultra-small angle x-ray scattering. The effects on structure over the length scale range of <1 nm to >5 {mu}m under different conditions (precursors, pH, etc.) are presented. The change in structure of an aerogel during isostatic compaction to 228 MPa (to simulate drying from wetting solvents) are also discussed.

  18. Biomimetic collagen scaffolds with anisotropic pore architecture.

    PubMed

    Davidenko, N; Gibb, T; Schuster, C; Best, S M; Campbell, J J; Watson, C J; Cameron, R E

    2012-02-01

    Sponge-like matrices with a specific three-dimensional structural design resembling the actual extracellular matrix of a particular tissue show significant potential for the regeneration and repair of a broad range of damaged anisotropic tissues. The manipulation of the structure of collagen scaffolds using a freeze-drying technique was explored in this work as an intrinsically biocompatible way of tailoring the inner architecture of the scaffold. The research focused on the influence of temperature gradients, imposed during the phase of crystallisation of collagen suspensions, upon the degree of anisotropy in the microstructures of the scaffolds produced. Moulding technology was employed to achieve differences in heat transfer rates during the freezing processes. For this purpose various moulds with different configurations were developed with a view to producing uniaxial and multi-directional temperature gradients across the sample during this process. Scanning electron microscopy analysis of different cross-sections (longitudinal and horizontal) of scaffolds revealed that highly aligned matrices with axially directed pore architectures were obtained where single unidirectional temperature gradients were induced. Altering the freezing conditions by the introduction of multiple temperature gradients allowed collagen scaffolds to be produced with complex pore orientations, and anisotropy in pore size and alignment. PMID:22005330

  19. INVESTIGATION INTO BIOFOULING PHENOMENA IN FINE PORE AERATION DEVICES

    EPA Science Inventory

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

  20. INVESTIGATIONS INTO BIOFOULING PHENOMENA IN FINE PORE AERATION DEVICES

    EPA Science Inventory

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

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

    PubMed

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

    2016-01-01

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

  2. Disentangling the Complex Pore-Scale Dispersion Process in Natural Porous Media by Means of DNS

    NASA Astrophysics Data System (ADS)

    Medellin-Azuara, J.; Howitt, R. E.; MacEwan, D.; Lund, J. R.

    2014-12-01

    Over the recent past, important advances have been made in the area of micro-CT scanning of natural porous media. The acquired pore-space geometries enable detailed investigations of flow and transport via pore-scale direct numerical simulation (DNS). In this work, we utilize pore-scale DNS to investigate single-phase pore-scale dispersion. We focus on data stemming from beadpacks, Bentheimer sandstone, and Ketton and Estaillades carbonates. Our DNS results clearly show the transition from ballistic dispersion to the asymptotic Fickian regime (see figure a) at decimeter or meter scale depending on the medium type. We outline a universal Lagrangian model for tracer dispersion that is based on a low-dimensional parametrization of the complex three-dimensional motion of tracer particles (see figure b). We relate the process parameters to certain pore-geometry characteristics such as the tortuosity. Our model accurately captures the wide range of flow and transport dynamics observed in the samples considered. We establish the accuracy of the model by validating its limiting dispersion behavior, the resulting velocity statistics, and also, most challenging, snapshots of tracer plumes at travel times encompassing both ballistic and Fickian behavior.

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

    PubMed Central

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

    2016-01-01

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

  4. Frenkel-Halsey-Hill equation, dimensionality of adsorption, and pore anisotropy.

    PubMed

    Pomonis, Philippos J; Tsaousi, Eleni T

    2009-09-01

    The Frenkel-Halsey-Hill (FHH) equation V/V(m) approximately [log(P(0)/P)](-1/s) is revisited in relation to the meaning of its exponent in a specific intermediate range of pressure where capillary condensation occurs. It has been suggested in the past that plots of the form log V = constant - (D - 3)[loglog(P(0)/P)], or its equivalent log S = const - (D - 2) log r, can be used for the estimation of the dimensionality D of the adsorbing surface from those parts of the slopes at low pressure corresponding to straight lines. In the present study it is shown that, for pores of cylindrical geometry and at a specific range of pressure where those pores are filled-up during the process of capillary condensation, the local slopes d log V/d loglog[(P(0)/P)] or d log S/d log r, of plots similar to the above, may be used to estimate the pore anisotropy b of the adsorbing space from the relationships log b = [[d log V/d loglog[(P(0)/P)] - 3] log(0.5r) or log b = [[d log S/d log r] - 2] log(0.5r). These observations lead to the physicogeometrical conjunction that, during capillary condensation in cylindrical pores, usually assumed in nitrogen porosimetry, the scaling dimension of pore anisotropy b, scaled in units of radius r, is related to the dimensionality D of the process. PMID:19705894

  5. Pore Size Distribution Estimates Compared: Available software applied to soil CT and synthetic images.

    NASA Astrophysics Data System (ADS)

    Houston, Alasdair N.; Falconer, Ruth E.; Otten, Wilfred; Hapca, Simona M.

    2015-04-01

    The Pore Size Distribution (PSD) has been widely used as a means of characterising porous media and, in conjunction with knowledge of pore space connectivity, has been used to infer hydrological properties. There exist various strategies to estimate PSD from a segmented image and each strategy typically involves a sequence of algorithms that transform image information. Some of these algorithms may be explicitly parameterised, requiring decisions by a knowledgeable operator. As a result PSD estimates may be quite variable between software applications and operators. In order to better understand these differences, a constrained boolean model was used to construct synthetic images whose pore structure is without ambiguity and whose properties can be analytically determined. Applying to such images a selection of analysis procedures in the form of readily available software applications, reveals differences between PSD estimates and analytic information. In some cases it is possible to attribute these differences to artifacts visible within map images generated by the analysis procedures, permitting correction procedures to be devised. In the case of soil CT images which exhibit complex interconnected pore structure, differences in the PSD estimate between analysis procedures are very great in some cases. Inspection of map images can again help in identifying the cause of such problems, but this may result from a fundamental property of the procedure with respect to complex pore structure. Based on the evidence presented, we conclude that some readily available software will produce PSD estimates that can usefully characterise geomaterials.

  6. Sediment Core Sectioning and Extraction of Pore Waters under Anoxic Conditions.

    PubMed

    Keimowitz, Alison R; Zheng, Yan; Lee, Ming-Kuo; Natter, Michael; Keevan, Jeffrey

    2016-01-01

    We demonstrate a method for sectioning sediment cores and extracting pore waters while maintaining oxygen-free conditions. A simple, inexpensive system is built and can be transported to a temporary work space close to field sampling site(s) to facilitate rapid analysis. Cores are extruded into a portable glove bag, where they are sectioned and each 1-3 cm thick section (depending on core diameter) is sealed into 50 ml centrifuge tubes. Pore waters are separated with centrifugation outside of the glove bag and then returned to the glove bag for separation from the sediment. These extracted pore water samples can be analyzed immediately. Immediate analyses of redox sensitive species, such as sulfide, iron speciation, and arsenic speciation indicate that oxidation of pore waters is minimal; some samples show approximately 100% of the reduced species, e.g. 100% Fe(II) with no detectable Fe(III). Both sediment and pore water samples can be preserved to maintain chemical species for further analysis upon return to the laboratory. PMID:27023267

  7. Emergence of a large pore subpopulation during electroporating pulses.

    PubMed

    Smith, Kyle C; Son, Reuben S; Gowrishankar, T R; Weaver, James C

    2014-12-01

    Electroporation increases ionic and molecular transport through cell membranes by creating transient aqueous pores. These pores cannot be directly observed experimentally, but cell system modeling with dynamic electroporation predicts pore populations that produce cellular responses consistent with experiments. We show a cell system model's response that illustrates the life cycle of a pore population in response to a widely used 1 kV/cm, 100 μs trapezoidal pulse. Rapid pore creation occurs early in the pulse, followed by the gradual emergence of a subpopulation of large pores reaching ~30 nm radius. After the pulse, pores rapidly contract to form a single thermally broadened distribution of small pores (~1 nm radius) that slowly decays. We also show the response of the same model to pulses of 100 ns to 1 ms duration, each with an applied field strength adjusted such that a total of 10,000±100 pores are created. As pulse duration is increased, the pore size distributions vary dramatically and a distinct subpopulation of large pores emerges for pulses of microsecond and longer duration. This subpopulation of transient large pores is relevant to understanding rapid transport of macromolecules into and out of cells during a pulse. PMID:24290730

  8. Highly Porous NiTi with Isotropic Pore Morphology Fabricated by Self-Propagated High-Temperature Synthesis

    NASA Astrophysics Data System (ADS)

    Hosseini, S. A.; Alizadeh, M.; Ghasemi, A.; Meshkot, M. A.

    2013-02-01

    Highly porous NiTi with isotropic pore morphology has been successfully produced by self-propagating high-temperature synthesis of elemental Ni/Ti metallic powders. The effects of adding urea and NaCl as temporary pore fillers were investigated on pore morphology, microstructure, chemical composition, and the phase transformation temperatures of specimens. These parameters were studied by optical microscopy, scanning electron microscopy, x-ray diffraction, and differential scanning calorimetry (DSC). Highly porous specimens were obtained with up to 83% total porosity and pore sizes between 300 and 500 μm in diameter. Results show pore characteristics were improved from anisotropic to isotropic and pore morphology was changed from channel-like to irregular by adding pore filler powders. Furthermore, the highly porous specimens produced when using urea as a space holder, were of more uniform composition in comparison to NaCl. DSC results showed that a two-step martensitic phase transformation takes place during the cooling cycles and the austenite finish temperature ( A f) is close to human body temperature. Compression test results reveal that the compressive strength of highly porous NiTi is about 155 MPa and recoverable strain about 6% in superelasticity regime.

  9. Surface Energy Anisotropy Effects on Pore-Channel Stability:Rayleigh Instabilities in m-Plane Sapphire

    SciTech Connect

    Santala, Melissa K.; Glaeser, Andreas M.

    2005-09-07

    Internal, high-aspect-ratio pore channels with their long axes parallel to the m(10{bar 1}0) plane of sapphire were generated through sequential application of photolithography, ion-beam etching and solid-state diffusion bonding. The axial orientation of channels within the m plane was systematically varied to sample a range of bounding-surface crystallographies. The morphologic evolution of these pore channels during anneals at 1700 C was recorded by postanneal optical microscopy. The development and growth of periodic axial variations in the pore channel radius was observed, and ultimately led to the formation of discrete pores. The wavelength and average pore spacing, assumed to reflect the kinetically dominant perturbation wavelength, varied with the in-plane pore channel orientation, as did the time for complete channel breakup. Results are compared to those previously obtained when pore channels were etched into c(0001)-plane sapphire and annealed under similar conditions. The results indicate a strong effect of surface stability on the evolution behavior.

  10. Rock-physics-based carbonate pore type characterization and reservoir permeability heterogeneity evaluation, Upper San Andres reservoir, Permian Basin, west Texas

    NASA Astrophysics Data System (ADS)

    Dou, Qifeng; Sun, Yuefeng; Sullivan, Charlotte

    2011-05-01

    In addition to mineral composition and pore fluid, pore type variations play an important role in affecting the complexity of velocity-porosity relationship and permeability heterogeneity of carbonate reservoirs. Without consideration of pore type diversity, most rock physics models applicable to clastic rocks for explaining the rock acoustic properties and reservoir parameters relationship may not work well for carbonate reservoirs. A frame flexibility factor ( γ) defined in a new carbonate rock physics model can quantify the effect of pore structure changes on seismic wave velocity and permeability heterogeneity in carbonate reservoirs. Our study of an Upper San Andres carbonate reservoir, Permian Basin, shows that for core samples of given porosity, the lower the frame flexibility factor ( γ), the higher the sonic wave velocity. For the studied reservoir, samples with frame flexibility factor ( γ) < 3.85 represent either visible vuggy pore space in a dolopackstone or intercrystalline pore space in dolowackstone. On the other hand, samples with frame flexibility factor ( γ) > 3.85 indicate either dominant interparticle pore space in dolopackstone or microcrack pore space in dolowackstone or dolomudstone. Using the frame flexibility factor ( γ), different porosity-impedance and porosity-permeability trends can be classified with clear geologic interpretation such as pore type and rock texture variations to improve porosity and permeability prediction accuracy. New porosity-permeability relations with γ classification help delineate permeability heterogeneity in the Upper San Andres reservoir, and could be useful for other similar carbonate reservoir studies. In addition, results from analysis of amplitude variation with offset (AVO) and impedance modeling indicate that by combining rock physics model and pre-stack seismic inversion, simultaneous estimation of porosity and frame flexibility factor ( γ) is quite feasible because of the strong influence of

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

    PubMed Central

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

    2015-01-01

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

  12. Pattern curvature to control pore shape and its ordering

    NASA Astrophysics Data System (ADS)

    Yu, Guiduk; Shin, Kyusoon

    2013-03-01

    Triangular pore in inverse-hexagonal packing was fabricated by anodizing Al with convex pattern in hexagonal packing. The convexly patterned Al was prepared via replication of the concave structure formed in self-assembled anodized aluminum oxide (AAO). Self-assembled AAO without pre-patterning produces hexagonal packing circular pores. Exploitation of the inversed structure was found to create well-defined triangular pores in inverse-hexagonal packing. Anisotropic pore feature was discussed to come from the alternating distance between the pits and the curvature of the pattern. Also, by controlling the topography of the convex pattern around pits, we investigated the effect of pattern topography on pore initiation.

  13. Energy conversion device with support member having pore channels

    DOEpatents

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

    2014-01-07

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

  14. Displacement of soil pore water by trichloroethylene

    USGS Publications Warehouse

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

    1994-01-01

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

  15. Viral Subversion of the Nuclear Pore Complex

    PubMed Central

    Le Sage, Valerie; Mouland, Andrew J.

    2013-01-01

    The nuclear pore complex (NPC) acts as a selective barrier between the nucleus and the cytoplasm and is responsible for mediating communication by regulating the transport of RNA and proteins. Numerous viral pathogens have evolved different mechanisms to hijack the NPC in order to regulate trafficking of viral proteins, genomes and even capsids into and out of the nucleus thus promoting virus replication. The present review examines the different strategies and the specific nucleoporins utilized during viral infections as a means of promoting their life cycle and inhibiting host viral defenses. PMID:23959328

  16. Extreme accumulation of nucleotides in simulated hydrothermal pore systems

    PubMed Central

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

    2007-01-01

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

  17. Purification of the Vertebrate Nuclear Pore Complex by Biochemical Criteria

    PubMed Central

    Miller, Brian R.; Forbes, Douglass J.

    2015-01-01

    The nuclear pore is a large and complex biological machine, mediating all signal-directed transport between the nucleus and the cytoplasm. The vertebrate pore has a mass of ~120 million daltons or 30 times the size of a ribosome. The large size of the pore, coupled to its tight integration in the nuclear lamina, has hampered the isolation of pore complexes from vertebrate sources. We have now developed a strategy for the purification of nuclear pores from in vitro assembled annulate lamellae (AL), a cytoplasmic mimic of the nuclear envelope that lacks a lamina, nuclear matrix, and chromatin-associated proteins. We find that purified pore complexes from annulate lamellae contain every nuclear pore protein tested. In addition, immunoblotting reveals the presence of soluble transport receptors and factors known to play important roles in the transport of macromolecules through the pore. While transport factors such as Ran and NTF2 show only transient interaction with the pores, a number of soluble transport receptors, including importin β, show a tight association with the purified pores. In summary, we report that we have purified the vertebrate pore by biochemical criteria; silver staining reveals ~40–50 distinct protein bands. PMID:11208084

  18. Caterpillar regurgitant induces pore formation in plant membranes.

    PubMed

    Lühring, Hinrich; Nguyen, Van Dy; Schmidt, Lilian; Röse, Ursula S R

    2007-11-27

    Formation of channel-like pores in a plant membrane was induced within seconds after application of an aqueous solution containing regurgitant of the insect larvae Spodoptera littoralis. Gated pore currents recorded on the tonoplast of the Charophyte Chara corallina displayed conductances up to several hundred pS. A voltage-dependent gating reaction supports the assumption that pore-forming molecules have amphipathic properties. Regurgitant samples separated into masses smaller or larger than 3kDa were evaluated by patch-clamp and mass spectroscopy. Fractions containing peptides larger than 3kDa constituted pores of large conductances, peptides smaller than 3kDa constituted pores of small conductances. Peptide-free eluates did not constitute conducting pores, indicating that pore-forming components in regurgitant are membrane-spanning oligopeptides. PMID:17967419

  19. Effect of Pore Pressure on Slip Failure of an Impermeable Fault: A Coupled Micro Hydro-Geomechanical Model

    NASA Astrophysics Data System (ADS)

    Yang, Z.; Juanes, R.

    2015-12-01

    The geomechanical processes associated with subsurface fluid injection/extraction is of central importance for many industrial operations related to energy and water resources. However, the mechanisms controlling the stability and slip motion of a preexisting geologic fault remain poorly understood and are critical for the assessment of seismic risk. In this work, we develop a coupled hydro-geomechanical model to investigate the effect of fluid injection induced pressure perturbation on the slip behavior of a sealing fault. The model couples single-phase flow in the pores and mechanics of the solid phase. Granular packs (see example in Fig. 1a) are numerically generated where the grains can be either bonded or not, depending on the degree of cementation. A pore network is extracted for each granular pack with pore body volumes and pore throat conductivities calculated rigorously based on geometry of the local pore space. The pore fluid pressure is solved via an explicit scheme, taking into account the effect of deformation of the solid matrix. The mechanics part of the model is solved using the discrete element method (DEM). We first test the validity of the model with regard to the classical one-dimensional consolidation problem where an analytical solution exists. We then demonstrate the ability of the coupled model to reproduce rock deformation behavior measured in triaxial laboratory tests under the influence of pore pressure. We proceed to study the fault stability in presence of a pressure discontinuity across the impermeable fault which is implemented as a plane with its intersected pore throats being deactivated and thus obstructing fluid flow (Fig. 1b, c). We focus on the onset of shear failure along preexisting faults. We discuss the fault stability criterion in light of the numerical results obtained from the DEM simulations coupled with pore fluid flow. The implication on how should faults be treated in a large-scale continuum model is also presented.

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

    NASA Astrophysics Data System (ADS)

    Rodrigues, L. M.; Anwar, S.

    2013-12-01

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

  1. Interface engineering of synthetic pores: towards hypersensitive biosensors.

    PubMed

    Mora, Federico; Tran, Duy-Hien; Oudry, Natalie; Hopfgartner, Gerard; Jeannerat, Damien; Sakai, Naomi; Matile, Stefan

    2008-01-01

    Hydrophilic anchoring is introduced as a promising strategy to constructively control the various interactions of synthetic pore sensors with the surrounding biphasic environment. Artificial rigid-rod beta barrels are selected as classical synthetic multifunctional pores and random-coil tetralysines are attached as hydrophilic anchors. The synthesis of this advanced pore is accomplished in 32 steps from commercially available starting materials. With regard to pore activity as such, the key impact of hydrophilic anchoring is a change from a Hill coefficient n<1 to n=4. This change confirms successful suppression of the competing self-assembly with precipitation from the aqueous phase as the origin of the accomplished increase in pore activity. The hydrophilic anchors do not interfere with the blockage of the synthetic pore sensors by anionic analytes. In the case of stoichiometric binding of blockers (K(D)=EC(50) of the pore; EC(50)=concentration needed to observe 50 % pore activity), however, the increase in pore activity achieved by hydrophilic anchoring results in improved pore blockage under high dilution conditions. Controls confirm that this increase does not occur with analytes that do not exhibit stoichiometric binding (K(D)>EC(50)). These results not only reveal stoichiometric binding as the expected origin of the sensitivity limit of synthetic pore sensors, they also provide promising solutions for this problem. The combination of hydrophilic anchoring with targeted pore formation emerges as a particularly promising strategy to further reduce effective pore concentrations. The scope and limitations of this approach are exemplified with pertinent analyte pairs that are essential for the sensing of sucrose, lactose, acetate, and glutamate with synthetic pores in samples from the supermarket. PMID:18067110

  2. Amplitude blanking related to the pore-filling of gas hydrate in sediments

    USGS Publications Warehouse

    Lee, M.W.; Dillon, William P.

    2001-01-01

    Seismic indicators of gas-hydrate-bearing sediments include elevated interval velocities and amplitude reduction of seismic reflections owing to the presence of gas hydrate in the sediment's pore spaces. However, large amplitude blanking with relatively low interval velocities observed at the Blake Ridge has been enigmatic because realistic seismic models were absent to explain the observation. This study proposes models in which the gas hydrate concentrations vary in proportion to the porosity. Where gas hydrate concentrations are greater in more porous media, a significant amplitude blanking can be achieved with relatively low interval velocity. Depending on the amount of gas hydrate concentration in the pore space, reflection amplitudes from hydrate-bearing sediments can be much less, less or greater than those from corresponding non-hydrate-bearing sediments.

  3. Strain localization driven by co-seismic pore fluid pressurization

    NASA Astrophysics Data System (ADS)

    Rice, James; Platt, John; Brantut, Nicolas; Rudnicki, John

    2015-04-01

    The absence of a thermal anomaly associated with the San Andreas fault, and low driving stress resolved on it, suggest that such mature faults weaken dramatically during seismic slip. Thermal pressurization (TP) and thermal decomposition (TD) are two mechanisms to explain this co-seismic weakening. Both rely on elevated pore pressures in a fluid-saturated gouge, with TP achieving this through thermal expansion of native pore fluid and TD by releasing additional pore fluid (e.g., H2O or CO2) during a reaction. We use a one-dimensional model for a fluid-saturated gouge layer sheared between two undeforming half-spaces to study how TP (Rice et al., Platt et al., JGR-B, 2014) and TD (Platt et al., submitted JGR-B) drive seismic strain localization. A linear stability analysis is first used to predict the localized zone thickness for each of the weakening mechanisms. Using representative parameters for fault gouge we predict localized zone thicknesses of a few tens of microns, in line with laboratory (Kitajima et al., 2010) and field (Chester and Chester, 1998) observations. Next we use numerical simulations to study how the localized zone develops once nonlinear effects become important. These show that the final localized zone thickness is very similar to the linear stability prediction. In the simulations, the onset of localization accelerates fault weakening, making co-seismic strain localization an important consideration, apparently neglected in all current earthquake simulations. Finally we show how a secondary instability can lead to migration of the deforming zone across the gouge layer. This instability is driven by hydrothermal diffusion for TP, and by reactant depletion for TD. Our results show that migration must be taken into account when inferring the width of the deforming zone from field observations. Even when the zone of localized straining is only a few tens of microns wide, migration can lead to a final strain profile with a zone of roughly uniform

  4. Strain localization driven by co-seismic pore fluid pressurization

    NASA Astrophysics Data System (ADS)

    Platt, J. D.; Brantut, N.; Rice, J. R.; Rudnicki, J. W.

    2014-12-01

    The absence of a thermal anomaly associated with the San Andreas fault, and low driving stress resolved on it, suggest that such mature faults weaken dramatically during seismic slip. Thermal pressurization (TP) and thermal decomposition (TD) are two mechanisms to explain this co-seismic weakening. Both rely on elevated pore pressures in a fluid-saturated gouge, with TP achieving this through thermal expansion of native pore fluid and TD by releasing additional pore fluid (e.g., H2O or CO2) during a reaction. We use a one-dimensional model for a fluid-saturated gouge layer sheared between two undeforming half-spaces to study how TP (Rice et al., Platt et al., JGR-B, 2014) and TD (Platt et al., submitted JGR-B) drive seismic strain localization. A linear stability analysis is first used to predict the localized zone thickness for each of the weakening mechanisms. Using representative parameters for fault gouge we predict localized zone thicknesses of a few tens of microns, in line with laboratory (Kitajima et al., 2010) and field (Chester and Chester, 1998) observations. Next we use numerical simulations to study how the localized zone develops once nonlinear effects become important. These show that the final localized zone thickness is very similar to the linear stability prediction. In the simulations, the onset of localization accelerates fault weakening, making co-seismic strain localization an important consideration, apparently neglected in all current earthquake simulations. Finally we show how a secondary instability can lead to migration of the deforming zone across the gouge layer. This instability is driven by hydrothermal diffusion for TP, and by reactant depletion for TD. Our results show that migration must be taken into account when inferring the width of the deforming zone from field observations. Even when the zone of localized straining is only a few tens of microns wide, migration can lead to a final strain profile with a zone of roughly uniform

  5. Derivation of Permeability-Pore Relationship for Fractal Porous Reservoirs Using Series-Parallel Flow Resistance Model and Lattice Boltzmann Method

    NASA Astrophysics Data System (ADS)

    Wang, Baoyu; Jin, Yi; Chen, Qing; Zheng, Junling; Zhu, Yibo; Zhang, Xiaobing

    2014-09-01

    Permeability of porous reservoirs plays a significant role in engineering and scientific applications. In this study, we investigated the relationship between pore size fractal dimension (Df) and its porosity, as well as that between Df and the pore structure parameters, and consequentially developed an algorithm to generate pore spaces with arbitrary fractal dimension characterizing the pore size distribution. Using the series-parallel flow resistance model and lattice Boltzmann method (LBM) in combination, we then systematically analyzed the effects of physical properties on the fluid flows in two-dimensional (2D) context, and quantitatively derived a permeability-pore relationship for fractal porous media. The new relationship shows that: (i) the permeability of a fractal porous medium is proportional to the square of its maximum pore size λmax; (ii) the larger the fractal dimension Df of a pore space, the smaller the flow resistance of the porous medium; (iii) porosity φ to the power of (4 - Df)/(2 - Df) is proportional to the permeability of a porous medium; (iv) similar to the Kozeny-Carman (KC) equation, the tortuosity τ has its square inversely proportional to the permeability; more importantly, it is found to be a function of porosity approximately satisfying the relationship τ = φDf-2 in a fractal porous medium. Moreover, we demonstrated that the newly derived fractal permeability-pore relationship is equivalent to KC equation and Poiseuille's law respectively, at Df = 1 and Df = 2.

  6. Pores in the epidermis: aquaporins and tight junctions.

    PubMed

    Brandner, J M

    2007-12-01

    Water homeostasis of the epidermis is important for the appearance and physical properties of the skin, as well as for water balance in the body. It depends on several factors, e.g. barrier quality, uptake of water into the epidermis, concentration of water-retaining humectants, and external humidity. Aquaporins (AQPs) are pores in the plasmamembranes of cells. Monomeric AQPs form barrel-like structures that are primarily water selective, some AQPs also transport glycerol and possibly other small solutes. In the epidermis, AQP3 is the predominant AQP. It is localized mainly in basal but also in suprabasal layers of the epidermis and is permeable for water as well as for glycerol, a humectant. Mice deficient in AQP3 exhibit reduced stratum corneum (SC) hydration and impaired SC barrier recovery after SC removal. In skin diseases associated with elevated transepidermal water loss (TEWL) and reduced SC hydration, altered expression of AQP3 was shown. Tight junctions (TJ) are cell-cell junctions, which play a central role in sealing the intercellular space of cell sheets and thereby establishing a paracellular barrier. Within the TJ, pores are postulated to exist, which allow the controlled diffusion of water and solutes via the paracellular pathway. In the epidermis, TJ structures were demonstrated in the stratum granulosum whereas TJ proteins were found in all viable layers. Mice which overexpress or are deficient of key-proteins of TJ die soon after birth because of a tremendous TEWL. In various skin diseases that are accompanied by elevated TEWL and reduced skin hydration, staining patterns of TJ proteins are altered. This review will summarize our current knowledge of the involvement of AQPs and TJ in the water homeostasis of the epidermis. PMID:18489380

  7. Size of diffusion pore of Alcaligenes faecalis.

    PubMed

    Ishii, J; Nakae, T

    1988-03-01

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

  8. Size of diffusion pore of Alcaligenes faecalis.

    PubMed Central

    Ishii, J; Nakae, T

    1988-01-01

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

  9. Bimodal mesoporous silica with bottleneck pores.

    PubMed

    Reber, M J; Brühwiler, D

    2015-11-01

    Bimodal mesoporous silica consisting of two sets of well-defined mesopores is synthesized by a partial pseudomorphic transformation of an ordered mesoporous starting material (SBA-15 type). The introduction of a second set of smaller mesopores (MCM-41 type) establishes a pore system with bottlenecks that restricts the access to the core of the bimodal mesoporous silica particles. The particle size and shape of the starting material are retained, but micropores present in the starting material disappear during the transformation, leading to a true bimodal mesoporous product. A varying degree of transformation allows the adjustment of the pore volume contribution of the two mesopore domains. Information on the accessibility of the mesopores is obtained by the adsorption of fluorescence-labeled poly(amidoamine) dendrimers and imaging by confocal laser scanning microscopy. This information is correlated with nitrogen sorption data to provide insights regarding the spatial distribution of the two mesopore domains. The bimodal mesoporous materials are excellent model systems for the investigation of cavitation effects in nitrogen desorption isotherms. PMID:26399172

  10. Deformation by pore collapse in the Shu'aiba limestone: An experimental study

    NASA Astrophysics Data System (ADS)

    Al-Ghamdi, Mohammed A.

    The mechanical properties of the Shu'aiba limestone, the main reservoir in Shaybah field, Saudi Arabia, are investigated in this study. Stresses at failure are measured in the laboratory for cylindrical rock samples taken from the Shu'aiba reservoir. A failure envelope is constructed, from the critical stress states at failure, which shows that this reservoir material is mechanically weak. Experiments are carried out in the conventional uniaxial, triaxial, and hydrostatic compression modes to examine the different failure characteristics of this limestone. Two main hypotheses concerning the deformation behavior of the Shu'aiba limestone are tested in this study. The first hypothesis deals with failure by a mechanism known as "pore collapse" in which the rock deforms by reduction of pore space. Pore collapse is found to be the dominant mechanism of deformation in this limestone under triaxial and hydrostatic compression loading. The effect of initial porosity on the critical effective pressure at the onset of pore collapse is examined. A linear relationship exists by which the critical effective pressure at the onset of pore collapse can be predicted from initial porosities in the range 20% to 30%. The second hypothesis states that an increase in temperature should lower the critical effective pressure values that we measure in room temperature experiments for the same material. Conducting experiments at 90°C and 150°C on essentially the same samples used in room temperature experiments shows a considerable drop in critical effective pressures at the onset of pore collapse. Initial porosities are found to be linearly related to the critical effective pressures for the porosity range of 20% to 31%.

  11. The effect of a variable pore radius on formation resistivity factor

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    Formation resistivity factor F was introduced as the ratio of the resistivity of a rock fully saturated with conductive water to the resistivity of the conductive water based on results of laboratory measurements. It was also found that the formation factor is a function of the type and character of a formation and is related to porosity by a relationship including an exponent m. For model calculations of the formation factor, capillary channel models describing a straight tube with a constant circular cross-sectional area are frequently used. However, the pore channel radius is not constant in natural rocks. A modified capillary model that describes a straight pore channel with a radius varying between its two extreme values rt (pore throat) and rb (pore body) is presented. The proposed model can therefore explain the effect of pore shape upon formation factor and porosity. In this case, exponent m is controlled by the porosity itself and the ratio rb/rt. Different rock types have a specific position in a plot of formation factor versus porosity including a forward calculated grid for varying ratio rb/rt. Sand and gravel are characterized by low ratios rb/rt of 2.5 to 4.5, while sandstones possess intermediate rb/rt of 5.0 to 20.0. Carbonates show the greatest variability with ratios of 1.0 to 40.0. This new approach can be used to derive the ratio rb/rt from a determination of porosity and formation factor and thus enhances the understanding of pore space geometries in different formation types, which is also of importance for hydraulic conductivity.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    SciTech Connect

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

    2015-04-08

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

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

    DOE PAGESBeta

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

    2015-04-08

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

  15. A new view of the lethal apoptotic pore.

    PubMed

    Basañez, Gorka; Soane, Lucian; Hardwick, J Marie

    2012-01-01

    Cell death by apoptosis is indispensable for proper development and tissue homeostasis in all multicellular organisms, and its deregulation plays a key role in cancer and many other diseases. A crucial event in apoptosis is the formation of protein-permeable pores in the outer mitochondrial membrane that release cytochrome c and other apoptosis-promoting factors into the cytosol. Research efforts over the past two decades have established that apoptotic pores require BCL-2 family proteins, with the proapoptotic BAX-type proteins being direct effectors of pore formation. Accumulating evidence indicates that other cellular components also cooperate with BCL-2 family members to regulate the apoptotic pore. Despite this knowledge, the molecular pathway leading to apoptotic pore formation at the outer mitochondrial membrane and the precise nature of this outer membrane pore remain enigmatic. In this issue of PLOS Biology, Kushnareva and colleagues describe a novel kinetic analysis of the dynamics of BAX-dependent apoptotic pore formation recapitulated in native mitochondrial outer membranes. Their study reveals the existence of a hitherto unknown outer mitochondrial membrane factor that is critical for BAX-mediated apoptotic pore formation, and challenges the currently popular view that the apoptotic pore is a purely proteinaceous multimeric assembly of BAX proteins. It also supports the notion that membrane remodeling events are implicated in the formation of a lipid-containing apoptotic pore. PMID:23049484

  16. Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

    PubMed Central

    Bennett, W. F. Drew; Sapay, Nicolas; Tieleman, D. Peter

    2014-01-01

    Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes. PMID:24411253

  17. Membrane mechanics can account for fusion pore dilation in stages.

    PubMed Central

    Chizmadzhev, Y A; Cohen, F S; Shcherbakov, A; Zimmerberg, J

    1995-01-01

    Once formed, fusion pores rapidly enlarge to semi-stable conductance values. The membranes lining the fusion pore are continuous bilayer structures, so variations of conductance in time reflect bending and stretching of membranes. We therefore modeled the evolution of fusion pores using the theory of the mechanics of deforming homogeneous membranes. We calculated the changes in length and width of theoretical fusion pores according to standard dynamical equations of motion. Theoretical fusion pores quickly achieve semi-stable dimensions, which correspond to energy minima located in a canyon between energy barriers. The height of the barrier preventing pore expansion diminishes along the dimensions of length and width. The bottom of the canyon slopes gently downward along increasing length. As a consequence, theoretical fusion pores slowly lengthen and widen as the dimensions migrate along the bottom of the canyon, until the barrier vanishes and the pore rapidly enlarges. The dynamics of growth is sensitive to tension, spontaneous curvature, bending elasticity, and mobilities. This sensitivity can account for the quantitative differences in pore evolution observed in two experimental systems: HA-expressing cells fusing to planar bilayer membranes and beige mouse mast cell degranulation. We conclude that the mechanics of membranes could cause the phenomenon of stagewise growth of fusion pores. Images FIGURE 9 PMID:8599655

  18. Change of pore properties during carbonization of coking coal

    SciTech Connect

    Miura, S.; Silveston, P.L.

    1980-01-01

    Porosimetry, sorption and density measurements are reported on two caking bituminous coals. West Virginia Jewel No. 2 medium volatile and a Pennsylvania Pittsburgh seam high volatile C, for final carbonization temperatures between 400 and 1000/sup 0/C. Samples were not confined and heating rates of 3 and 8.2%/min were employed. The medium volatile samples exhibit pronounced maxima in pore volume, pore surface area and porosity between 600 and 800/sup 0/C. These temperatures are unexpectedly greater than those at which maximum particle dilation and maximum rate of devolatilization occur. An explanation for this observation is that closed pores are created during carbonization below 600/sup 0/C which are opened when carbonization is carried to higher temperatures. Shape of the pore volume curves suggest new pore initiation, pore growth and pore shrinkage are the dominant processes operating, although collapse of the ultra micro pore structure seems to occur above 800/sup 0/C. A pore development model employing simple expressions for the three dominant processes successfully predicts the pore volume and surface area changes. Apparent activation energies derived from the model indicate that the rates of these dominant steps are controled by basicaly physical, not chemical, changes.

  19. Electrokinetic induced solute dispersion in porous media; pore network modeling

    NASA Astrophysics Data System (ADS)

    Li, Shuai; Schotting, Ruud; Raoof, Amir

    2013-04-01

    Electrokinetic flow plays an important role in remediation process, separation technique, and chromatography. The solute dispersion is a key parameter to determine transport efficiency. In this study, we present the electrokinetic effects on solute dispersion in porous media at the pore scale, using a pore network model. The analytical solution of the electrokinetic coupling coefficient was obtained to quantity the fluid flow velocity in a cylinder capillary. The effect of electrical double layer on the electrokinetic coupling coefficient was investigated by applying different ionic concentration. By averaging the velocity over cross section within a single pore, the average flux was obtained. Applying such single pore relationships, in the thin electrical double layer limit, to each and every pore within the pore network, potential distribution and the induced fluid flow was calculated for the whole domain. The resulting pore velocities were used to simulate solute transport within the pore network. By averaging the results, we obtained the breakthrough curve (BTC) of the average concentration at the outlet of the pore network. Optimizing the solution of continuum scale advection-dispersion equation to such a BTC, solute dispersion coefficient was estimated. We have compared the dispersion caused by electrokinetic flow and pure pressure driven flow under different Peclet number values. In addition, the effect of microstructure and topological properties of porous media on fluid flow and solute dispersion is presented, mainly based on different pore coordination numbers.

  20. Modelling multiphase dynamics during infiltration using a pore network model

    NASA Astrophysics Data System (ADS)

    Tzavaras, Jannis; Arns, Ji-Youns; Max, Koehne; Hans-Joerg, Vogel

    2013-04-01

    We present an implementation of water infiltration into a pore network model where the local water pressures is continuously updated during the transient process. The network geometry is designed to represent structured soil which is different from simple granular porous media in some respect: Pores are more elongated and less isometric and the pore size distribution is much wider and structured hierarchically. To reproduce these properties, the classical concept of pore-bodies and throats is replaced by direct measurements of pore topology and the pores below the minimal pore size of the network model are represented by a continuous network of water saturated micro pores. The latter ensures that the water phase is always continuous which affects the propagation of the water potential during infiltration. The network model is based on cylindrical pores and considers capillary and gravitational forces. The propagation of interfaces is calculated for each time step by repeatedly solving the complete set of linear equation arising from Kirchhoff's law based on mass balance at each node of the network. This is done using the public domain package ITPack. The successive overrelaxation (SOR) and the Jacobi conjugate gradient (JCG) method proved to be more robust and faster than other solvers tested for the complex topology. The model accounts for entrapped air which is assumed to be incompressible. We present first results demonstrating the impact of external forcing (i.e infiltration rate) and pore topology on the dynamics of water-gas interfaces, the volume of entrapped air and hysteresis.

  1. A model for determining inaccessible pore volume in polymer flooding

    SciTech Connect

    Jensen, T.B. ); Satchwell, R.M. )

    1992-01-01

    Until now, only imprecise approximation of inaccessible pore volume have been employed in mathematical models of polymer flooding, causing these reservoir models to yield inaccurate results. This paper reports a new model to precisely describe inaccessible pore volume in polymer flow through porous media. The model can also be applied as a screening tool for determining candidate reservoirs for polymer flooding given a typical polymer, or it can be used to screen different polymer types once a candidate reservoir has been chosen. This new model is based on theoretical and actual pore throat entry and polymer molecule size distributions. Both pore throat and polymer size distributions are thoroughly reviewed. Inaccessible pore volume, in this model, is defined as the probability of randomly selected polymer molecules being larger than randomly selected pore throats, and is determined by statistically describing the polymer and pore throats as continuous distributions. Examples of the inaccessible pore volume model employing Uniform, Triangular, and Gamma distributions are included. Results obtained show an adequate match between experimental data and theoretical results. A nomograph for determining inaccessible pore volume in polymer flow through porous media based on pore throat and polymer molecule sizes is presented.

  2. Bovine Serum Albumin Adsorption in Mesoporous Titanium Dioxide: Pore Size and Pore Chemistry Effect.

    PubMed

    Liu, Chang; Guo, Yanhua; Hong, Qiliang; Rao, Chao; Zhang, Haijuan; Dong, Yihui; Huang, Liangliang; Lu, Xiaohua; Bao, Ningzhong

    2016-04-26

    Understanding the mechanism of protein adsorption and designing materials with high sensitivity, high specificity and fast response are critical to develop the next-generation biosensing and diagnostic platforms. Mesoporous materials with high surface area, tunable pores, and good thermal/hydrostatic stabilities are promising candidates in this field. Because of the excellent biocompatibility, titanium dioxide has received an increasing interest in the past decade for biomedical applications. In this work, we synthesized mesoporous titanium dioxide with controlled pore sizes (7.2-28.0 nm) and explored their application for bovine serum albumin (BSA) adsorption. Scanning electron microscopy (SEM), X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and nitrogen adsorption/desorption experiments were performed to characterize the mesoporous TiO2 samples before and after BSA adsorption. Isothermal microcalorimetry was applied to measure both the adsorption heat and conformation rearrangement heat of BSA in those mesopores. We also carried out thermogravimetry measurements to qualitatively estimate the concentration of hydroxyl groups, which plays an important role in stabilizing BSA in-pore adsorption. The adsorption stability was also examined by leaching experiments. The results showed that TiO2 mesopores can host BSA adsorption when their diameters are larger than the hydrodynamic size of BSA (∼9.5 nm). In larger mesopores studied, two BSA molecules were adsorbed in the same pores. In contrast to the general understanding that large mesopores demonstrate poor stabilities for protein adsorptions, the synthesized mesoporous TiO2 samples demonstrated good leaching stabilities for BSA adsorption. This is probably due to the combination of the mesoporous confinement and the in-pore hydroxyl groups. PMID:27048991

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

  5. 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

  6. Silicon pore optics development for ATHENA

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  7. Distributed Pore Chemistry in Porous Organic Polymers

    NASA Technical Reports Server (NTRS)

    Koontz, Steven L. (Inventor)

    1998-01-01

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

  8. Distributed Pore Chemistry in Porous Organic Polymers

    NASA Technical Reports Server (NTRS)

    Koontz, Steven L. (Inventor)

    1999-01-01

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

  9. P2X7R large pore is partially blocked by pore forming proteins antagonists in astrocytes.

    PubMed

    Faria, Robson X; Reis, Ricardo A M; Ferreira, Leonardo G B; Cezar-de-Mello, Paula F T; Moraes, Milton O

    2016-06-01

    The ATP-gated P2X7R (P2X7R) is a channel, which is involved in events, such as inflammation, cell death, and pain. The most intriguing event concerning P2X7R functions is the phenomenon of pore dilation. Once P2X7R is activated, the permeability of the plasma membrane becomes higher, leading to the permeation of 1000 Da-weight solutes. The mechanisms involved in this process remain unclear. Nevertheless, this event is not exclusively through P2X7R, as other proteins may form large pores in the plasma membrane. Recent evidence concerning pore formation reveals putative P2X7R and other pores-associated protein complexes, revealing cross-interactive pharmacological and biophysical issues. In this work, we showed results that corroborated with cross-interactive aspects with P2X7R and pores in astrocytes. These cells expressed most of the pores, including P2X7R. We discovered that different pore types open with peculiar characteristics, as both anionic and cationic charged solutes permeate the plasma membrane, following P2X7R activation. Moreover, we showed that both synergic and additive relationships are found within P2X7, cationic, and anionic large pores. Therefore, our data suggest that other protein-related pores are assembled following the formation of P2X7R pore. PMID:26830892

  10. Morphological instability of whiskers, pores, and tubules

    NASA Astrophysics Data System (ADS)

    Kirill, Dimitri Jay

    1999-11-01

    A thin, stressed solid cylinder, a whisker, is subject to mass transport by curvature and elastic-stress-driven surface diffusion. The stability of the cylindrical surface is examined using linear stability theory. It is found that the applied stress leads to a greater range of unstable wavenumbers, and hence is destabilizing. The presence of elastic strains can excite non-axisymmetric modes, which, under certain conditions, are preferred and can give rise to helical surfaces. In addition, asymptotic formulas for growth rate in the limit of long and short wavelengths are found. A possible experiment is proposed which, if undertaken, should reveal the helical instability. The linear stability analysis is then extended to the case of cylindrical pore channels and hollow cylindrical tubules. In both cases, results similar to the whisker are found---increased applied stress leads to a greater range of unstable wavenumbers. For both the pore and tubule geometries, the dominant modes are axisymmetric for any value of applied stress; this contrasts with the solid whisker results. Since the tubule geometry consists of an inner and outer surface, there is a phase relationship between the two surface perturbations. The most dangerous eigenmode can exhibit either in-phase (sinuous) or 180° out-of-phase (varicose) perturbations, depending on the value of applied stress. Furthermore, there is a critical value of applied stress below which the most dangerous mode is varicose, and above which it is sinuous. Lastly, asymptotic formulas for growth rate are obtained in the limit of a thin-walled tubule. These results compare favorably to work done on stressed lamellar composites.

  11. 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

  12. Quantified Pore-Scale Nanoparticle Transport in Porous Media and the Implications for Colloid Filtration Theory.

    PubMed

    Molnar, Ian L; Sanematsu, Paula C; Gerhard, Jason I; Willson, Clinton S; O'Carroll, Denis M

    2016-08-01

    This study evaluates the pore-scale distribution of silver nanoparticles during transport through a sandy porous medium via quantitative synchrotron X-ray computed microtomography (qSXCMT). The associated distributions of nanoparticle flow velocities and mass flow rates were obtained by coupling these images with computational fluid dynamic (CFD) simulations. This allowed, for the first time, the comparison of nanoparticle mass flow with that assumed by the standard colloid filtration theory (CFT) modeling approach. It was found that (i) 25% of the pore space was further from the grain than assumed by the CFT model; (ii) the average pore velocity agreed well between results of the coupled qSXCMT/CFD approach and the CFT model within the model fluid envelope, although the former were 2 times larger than the latter in the centers of the larger pores and individual velocities were upwards of 20 times those in the CFT model at identical distances from grain surfaces ; and (iii) approximately 30% of all nanoparticle mass and 38% of all nanoparticle mass flow occurred further away from the grain surface than expected by the CFT model. This work suggests that a significantly smaller fraction of nanoparticles than expected will contact a grain surface by diffusion via CFT models, likely contributing to inadequate CFT model nanoparticle transport predictions. PMID:27385389

  13. 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.

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

    SciTech Connect

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

    1995-12-31

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

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

    SciTech Connect

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

    2015-11-01

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

  16. Improving sensitivity and accuracy of pore structural characterisation using scanning curves in integrated gas sorption and mercury porosimetry experiments.

    PubMed

    Hitchcock, Iain; Lunel, Marie; Bakalis, Serafim; Fletcher, Robin S; Holt, Elizabeth M; Rigby, Sean P

    2014-03-01

    Gas sorption scanning curves are increasingly used as a means to supplement the pore structural information implicit in boundary adsorption and desorption isotherms to obtain more detailed pore space descriptors for disordered solids. However, co-operative adsorption phenomena set fundamental limits to the level of information that conventional scanning curve experiments can deliver. In this work, we use the novel integrated gas sorption and mercury porosimetry technique to show that crossing scanning curves are obtained for some through ink-bottle pores within a disordered solid, thence demonstrating that their shielded pore bodies are undetectable using conventional scanning experiments. While gas sorption alone was not sensitive enough to detect these pore features, the integrated technique was, and, thence, this synergistic method is more powerful than the two individual techniques applied separately. The integrated method also showed how the appropriate filling mechanism equation (e.g. meniscus geometry for capillary condensation equations), to use to convert filling pressure to pore size, varied with position along the adsorption branch, thereby enabling avoidance of the further systematic error introduced into PSDs by assuming a single filling mechanism for disordered solids. PMID:24407663

  17. 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.

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

    PubMed

    Welch, William R W; Piri, Mohammad

    2016-01-01

    Molecular dynamics (MD) simulations were performed on a hydrocarbon mixture representing a typical gas condensate composed mostly of methane and other small molecules with small fractions of heavier hydrocarbons, representative of mixtures found in tight shale reservoirs. The fluid was examined both in bulk and confined to graphitic nano-scale slits and pores. Numerous widths and diameters of slits and pores respectively were examined under variable pressures at 300 K in order to find conditions in which the fluid at the center of the apertures would not be affected by capillary condensation due to the oil-wet walls. For the bulk fluid, retrograde phase behavior was verified by liquid volumes obtained from Voronoi tessellations. In cases of both one and two-dimensional confinement, for the smallest apertures, heavy molecules aggregated inside the pore space and compression of the gas outside the solid structure lead to decreases in density of the confined fluid. Normal density/pressure relationships were observed for slits having gaps of above 3 nm and pores having diameters above 6 nm. At 70 bar, the minimum gap width at which the fluid could pass through the center of slits without condensation effects was predicted to be 6 nm and the corresponding diameter in pores was predicted to be 8 nm. The models suggest that in nanoscale networks involving pores smaller than these limiting dimensions, capillary condensation should significantly impede transmission of natural gases with similar composition. PMID:26733485

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

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

  1. Fouling Study of Silicon Oxide Pores Exposed to Tap Water

    SciTech Connect

    Nilsson, J.; Bourcier, W.L.; Lee, J.R.I.; Letant, S.E.; /LLNL, Livermore

    2007-07-12

    We report on the fouling of Focused Ion Beam (FIB)-fabricated silicon oxide nanopores after exposure to tap water for two weeks. Pore clogging was monitored by Scanning Electron Microscopy (SEM) on both bare silicon oxide and chemically functionalized nanopores. While fouling occurred on hydrophilic silicon oxide pore walls, the hydrophobic nature of alkane chains prevented clogging on the chemically functionalized pore walls. These results have implications for nanopore sensing platform design.

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

    SciTech Connect

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

    2007-03-15

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

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

    NASA Astrophysics Data System (ADS)

    Or, D.; Ebrahimi, A.

    2014-12-01

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

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

    SciTech Connect

    Kremer, M.; Prausnitz, J.M.

    1992-06-01

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

  5. Pore-size-distribution of cationic polyacrylamide hydrogels

    SciTech Connect

    Kremer, M.; Prausnitz, J.M.

    1992-06-01

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

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

    PubMed

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

    2008-05-15

    We demonstrate rapid fabrication of submicrometer-diameter pores in borosilicate glass using femtosecond laser machining and subsequent wet-etch techniques. This approach allows direct and repeatable fabrication of high-quality pores with diameters of 400-800 nm. Such small pores coupled with the desirable electrical and chemical properties of glass enable sensitive resistive-pulse analysis to determine the size and concentration of macromolecules and nanoparticles. Plasma-enhanced chemical vapor deposition allows further reduction of pore diameters to below 300 nm. PMID:18483543

  7. Pore volume accessibility of particulate and monolithic stationary phases.

    PubMed

    Urban, Jiří

    2015-05-29

    A chromatographic characterization of pore volume accessibility for both particulate and monolithic stationary phases is presented. Size-exclusion calibration curves have been used to determine the pore volume fraction that is accessible for six alkylbenzenes and twelve polystyrene standards in tetrahydrofuran as the mobile phase. Accessible porosity has been then correlated with the size of the pores from which individual compounds are just excluded. I have determined pore volume accessibility of commercially available columns packed with fully and superficially porous particles, as well as with silica-based monolithic stationary phase. I also have investigated pore accessibility of polymer-based monolithic stationary phases. Suggested protocol is used to characterize pore formation at the early stage of the polymerization, to evaluate an extent of hypercrosslinking during modification of pore surface, and to characterize the pore accessibility of monolithic stationary phases hypercrosslinked after an early termination of polymerization reaction. Pore volume accessibility was also correlated to column efficiency of both particulate and monolithic stationary phases. PMID:25892635

  8. Enhanced membrane pore formation by multimeric/oligomeric antimicrobial peptides.

    PubMed

    Arnusch, Christopher J; Branderhorst, Hilbert; de Kruijff, Ben; Liskamp, Rob M J; Breukink, Eefjan; Pieters, Roland J

    2007-11-20

    The pore-forming antibacterial peptide magainin 2 was made divalent, tetravalent, and octavalent via a copper(I)-mediated 1-3 dipolar cycloaddition reaction ("click" chemistry). This series of pore-forming compounds was tested in vitro for their ability to form pores in large unilamillar vesicles (LUVs). A large increase in the pore-forming capability was especially observed with the tetravalent and octavalent magainin compounds in the LUVs consisting of DOPC, and the octavalent magainin compound showed a marked increase with the DOPC/DOPG LUVs. Activity was observed in the low nanomolar range for these compounds. PMID:17944489

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

    NASA Astrophysics Data System (ADS)

    Garner, Allen L.; Bogdan Neculaes, V.

    2012-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    PubMed Central

    Hu, Yuan; Sinha, Sudipta Kumar

    2015-01-01

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

  13. Process of inducing pores in membranes by melittin

    PubMed Central

    Lee, Ming-Tao; Sun, Tzu-Lin; Hung, Wei-Chin; Huang, Huey W.

    2013-01-01

    Melittin is a prototype of the ubiquitous antimicrobial peptides that induce pores in membranes. It is commonly used as a molecular device for membrane permeabilization. Even at concentrations in the nanomolar range, melittin can induce transient pores that allow transmembrane conduction of atomic ions but not leakage of glucose or larger molecules. At micromolar concentrations, melittin induces stable pores allowing transmembrane leakage of molecules up to tens of kilodaltons, corresponding to its antimicrobial activities. Despite extensive studies, aspects of the molecular mechanism for pore formation remain unclear. To clarify the mechanism, one must know the states of the melittin-bound membrane before and after the process. By correlating experiments using giant unilamellar vesicles with those of peptide-lipid multilayers, we found that melittin bound on the vesicle translocated and redistributed to both sides of the membrane before the formation of stable pores. Furthermore, stable pores are formed only above a critical peptide-to-lipid ratio. The initial states for transient and stable pores are different, which implies different mechanisms at low and high peptide concentrations. To determine the lipidic structure of the pore, the pores in peptide–lipid multilayers were induced to form a lattice and examined by anomalous X-ray diffraction. The electron density distribution of lipid labels shows that the pore is formed by merging of two interfaces through a hole. The molecular property of melittin is such that it adsorbs strongly to the bilayer interface. Pore formation can be viewed as the bilayer adopting a lipid configuration to accommodate its excessive interfacial area. PMID:23940362

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

    SciTech Connect

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

    2011-10-29

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

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

    SciTech Connect

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

    2015-08-01

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

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

    EPA Science Inventory

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

  17. FINE PORE DIFFUSER FOULING: THE LOS ANGELES STUDIES

    EPA Science Inventory

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

  18. Secondary pores in carbonate reservoirs on Arabian Peninsula

    SciTech Connect

    Nurmi, R.; Waterhouse, M.; Watfa, M.

    1987-05-01

    Nearly all of the giant carbonate reservoirs on the Arabian Peninsula have both primary and secondary pore systems. There are, however, significant stratigraphic and geographic variations of origin, volume, and reservoir importance of secondary pores. The Permian Khuff reservoir zones generally has more secondary porosity than any younger, or shallower, reservoir formations. Highly permeable idiotopic (sucrosic) dolomites are commonly developed in zones which originally contained primary pores. The zones with the highest porosity often contain secondary pores, with calcite-free oomoldic dolomites having higher permeability than oomoldic limestones. Fractures resulting from halokinetics and/or salt dissolution are generally the most important secondary pores in Khuff reservoirs. The prolific Jurassic Arab reservoir zones, generally have lesser amounts of secondary pores than Khuff reservoirs, but a variety of secondary pores are present. Commonly the Arab C zone contains the greatest volume of secondary pores, generally of a moldic (grain and/or skeletal) nature. Secondary porosity associated with dolomitization is regionally more common in the eastern Gulf. Cretaceous (rudist) reefal and chalk reservoirs often contain zones of secondary porosity with enhanced permeability resulting from the leaching of aragonitic and high-magnesium calcite skeletal material. Secondary porosity is present in the western gulf in both the Minagish grainstones and dolomitized Shuaiba Formation, whereas the grainstones of the eastern gulf have little secondary porosity. Large fracture systems are present everywhere in low-permeability chalks and wackestones. An unusually high degree of porosity heterogeneity appears to be ubiquitous in Cretaceous sequences.

  19. FINE PORE DIFFUSER FOULING: THE LOS ANGELES STUDIES

    EPA Science Inventory

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

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

    EPA Science Inventory

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

  1. Gating Immunity and Death at the Nuclear Pore Complex.

    PubMed

    Dasso, Mary; Fontoura, Beatriz M A

    2016-09-01

    The nuclear pore complex is the primary conduit for nuclear import and export of molecules. In this issue, Gu et al. uncover a novel mechanism in which immune signaling and programmed cell death require nuclear pore rearrangement and release of sequestered cyclin-dependent kinase inhibitors to elicit immunity and death. PMID:27610561

  2. Influence of Pore Size on Fracture Strength of Porous Ceramics

    NASA Astrophysics Data System (ADS)

    Yoshida, Keigo; Tsukidate, Hironori; Murakami, Akira; Miyata, Hiroshi

    Porous ceramics possess the excellent penetration and adiabatic characteristics, etc., and are used as heatproof filter materials for environmental equipments, etc. Moreover, porous ceramics controlled with porosity and pore size in the wide range have been actively developed. However, how the strength characteristics of porous ceramics are influenced by porosity and pore size of the material are not understood still enough. In this research, the evaluation tests on fracture strength, fracture energy and fracture toughness of porous alumina ceramics which porosity are almost equal, while pore sizes are different mutually were performed, and the relation between the pore size and the fracture strength was studied. The tests results show that the dispersion of fracture strength data is few though fracture strength of porous ceramics is lower than that of high-density ceramics. The relation based on linear fracture mechanics between the defect size and the fracture strength is valid when the one that a pore accompanies with the peculiar defect of the material was regarded as a defect size. In addition, fracture energy increases with the increase of pore size, and this seems based on a crooked propagation path of a crack. Finally, the process zone fracture model with considering the effect of the pore and grain size of the material is proposed. According to this model, for all pore size and crack length, it was shown that the fracture strengths of cracked specimens are evaluated.

  3. Porous Boron Nitride with Tunable Pore Size.

    PubMed

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

    2014-01-16

    On the basis of a global structural search and first-principles calculations, we predict two types of porous boron-nitride (BN) networks that can be built up with zigzag BN nanoribbons (BNNRs). The BNNRs are either directly connected with puckered B (N) atoms at the edge (type I) or connected with sp(3)-bonded BN chains (type II). Besides mechanical stability, these materials are predicted to be thermally stable at 1000 K. The porous BN materials entail large surface areas, ranging from 2800 to 4800 m(2)/g. In particular, type-II BN material with relatively large pores is highly favorable for hydrogen storage because the computed hydrogen adsorption energy (-0.18 eV) is very close to the optimal adsorption energy (-0.15 eV) suggested for reversible hydrogen storage at room temperature. Moreover, the type-II materials are semiconductors with width-dependent direct bandgaps, rendering the type-II BN materials promising not only for hydrogen storage but also for optoelectronic and photonic applications. PMID:26270717

  4. Two interacting particles in a spherical pore

    NASA Astrophysics Data System (ADS)

    Urrutia, Ignacio; Castelletti, Gabriela

    2011-02-01

    In this work we analytically evaluate, for the first time, the exact canonical partition function for two interacting spherical particles into a spherical pore. The interaction with the spherical substrate and between particles is described by an attractive square-well and a square-shoulder potential. In addition, we obtain exact expressions for both the one particle and an averaged two particle density distribution. We develop a thermodynamic approach to few-body systems by introducing a method based on thermodynamic measures [I. Urrutia, J. Chem. Phys. 134, 104503 (2010)] for nonhard interaction potentials. This analysis enables us to obtain expressions for the pressure, the surface tension, and the equivalent magnitudes for the total and Gaussian curvatures. As a by-product, we solve systems composed of two particles outside a fixed spherical obstacle. We study the low density limit for a many-body system confined to a spherical cavity and a many-body system surrounding a spherical obstacle. From this analysis we derive the exact first order dependence of the surface tension and Tolman length. Our findings show that the Tolman length goes to zero in the case of a purely hard wall spherical substrate, but contains a zero order term in density for square-well and square-shoulder wall-fluid potentials. This suggests that any nonhard wall-fluid potential should produce a non-null zero order term in the Tolman length.

  5. Silicon pore optics developments and status

    NASA Astrophysics Data System (ADS)

    Bavdaz, Marcos; Wille, Eric; Wallace, Kotska; Shortt, Brian; Collon, Maximilien; Ackermann, Marcelo; Olde Riekerink, Mark; Haneveld, Jeroen; van Baren, Coen; Erhard, Markus; Christensen, Finn; Krumrey, Michael; Burwitz, Vadim

    2012-09-01

    Silicon Pore Optics (SPO) is a lightweight high performance X-ray optics technology being developed in Europe, driven by applications in observatory class high energy astrophysics missions. An example of such application is the former ESA science mission candidate ATHENA (Advanced Telescope for High Energy Astrophysics), which uses the SPO technology for its two telescopes, in order to provide an effective area exceeding 1 m2 at 1 keV, and 0.5 m2 at 6 keV, featuring an angular resolution of 10” or better [1 to 24]. This paper reports on the development activities led by ESA, and the status of the SPO technology. The technology development programme has succeeded in maturing the SPO further and achieving important milestones, in each of the main activity streams: environmental compatibility, industrial production and optical performance. In order to accurately characterise the increasing performance of this innovative optical technology, the associated X-ray test facilities and beam-lines have been refined and upgraded.

  6. Physical modelling of the nuclear pore complex

    PubMed Central

    Fassati, Ariberto; Ford, Ian J.; Hoogenboom, Bart W.

    2013-01-01

    Physically interesting behaviour can arise when soft matter is confined to nanoscale dimensions. A highly relevant biological example of such a phenomenon is the Nuclear Pore Complex (NPC) found perforating the nuclear envelope of eukaryotic cells. In the central conduit of the NPC, of ∼30–60 nm diameter, a disordered network of proteins regulates all macromolecular transport between the nucleus and the cytoplasm. In spite of a wealth of experimental data, the selectivity barrier of the NPC has yet to be explained fully. Experimental and theoretical approaches are complicated by the disordered and heterogeneous nature of the NPC conduit. Modelling approaches have focused on the behaviour of the partially unfolded protein domains in the confined geometry of the NPC conduit, and have demonstrated that within the range of parameters thought relevant for the NPC, widely varying behaviour can be observed. In this review, we summarise recent efforts to physically model the NPC barrier and function. We illustrate how attempts to understand NPC barrier function have employed many different modelling techniques, each of which have contributed to our understanding of the NPC.

  7. Bacterial pore-forming proteins as anthelmintics

    PubMed Central

    2013-01-01

    Crystal (Cry) proteins are made by the Gram-positive bacterium Bacillus thuringiensis (Bt). Cry proteins are pore-forming proteins and are the most widely used biological insecticides in the world. Our laboratory found some Cry proteins are highly effective against a broad range of nematodes (roundworms). Here, we discuss our results of Cry protein activity against intestinal roundworms. Both Cry5B and Cry21A have therapeutic activities against infections of the roundworm Heligmosomoides polygyrus bakeri in mice. Cry5B also shows highly therapeutic activity against Ancylostoma ceylanicum infection in hamsters. A. ceylanicum is a minor hookworm parasite of humans, and it is closely related to the more prevalent Ancylostoma duodenale. In addition, Cry proteins show excellent combinatorial therapeutic properties with nicotinic acetylcholine receptor (nAChR) agonists, one of the two classes of compounds approved by the World Health Organization for the treatment for intestinal roundworms in humans. Given their non-toxicity to humans and their broad spectrum of nematicidal action, Cry proteins show great potential as next-generation anthelmintics. PMID:22562659

  8. Impact cratering in sandstone: The MEMIN pilot study on the effect of pore water

    NASA Astrophysics Data System (ADS)

    Kenkmann, Thomas; Wünnemann, Kai; Deutsch, Alexander; Poelchau, Michael H.; Schäfer, Frank; Thoma, Klaus

    2011-06-01

    Planetary surfaces are subjected to meteorite bombardment and crater formation. Rocks forming these surfaces are often porous and contain fluids. To understand the role of both parameters on impact cratering, we conducted laboratory experiments with dry and wet sandstone blocks impacted by centimeter-sized steel spheres. We utilized a 40 m two-stage light-gas gun to achieve impact velocities of up to 5.4 km s-1. Cratering efficiency, ejection velocities, and spall volume are enhanced if the pore space of the sandstone is filled with water. In addition, the crater morphologies differ substantially from wet to dry targets, i.e., craters in wet targets are larger, but shallower. We report on the effects of pore water on the excavation flow field and the degree of target damage. We suggest that vaporization of water upon pressure release significantly contributes to the impact process.

  9. Three-dimensional morphology of pores and cracks in intact and mechanically deformed sandstones

    NASA Astrophysics Data System (ADS)

    Menendez, B.; David, C.; Wong, T.-F.; Martinez-Nistal, A.

    2003-04-01

    We have studied four different sandstones under confocal laser scanning microscopy (CLSM). In order to discriminate the void space from the grains, the samples were impregnated with a fluorescent dyed (Rhodamine B) resin and thin-sections with a thickness larger than usual were prepared and studied with CSLM. Two different kinds of samples have been studied: mechanically deformed samples of Darley Dale and Berea sandstones and intact samples of Rothbach and Bentheim sandstones. On each sample several three dimensional blocks have been investigated with size 228 by 152 microns and depths ranging from 35 to 100 microns. From each block a series of tens of parallel "virtual sections" has been recorded, separated by 1 or 2 microns in depth. First we show some examples on Darley Dale and Berea sandstone samples deformed in triaxial experiments. Rotating animations are built from series of 3D views of reconstructed crack networks taken step by step for different block orientations. When put together these 3D views nicely simulate a rotation of the 3D block. To create and run the animations we used the Confocal Assistant free software on a PC. Spectacular 3D animations representing crack networks in mechanically deformed samples are obtained this way in a very short time: some examples will be shown on the screen. Secondly we show on a poster some static 3D reconstructions of the pore and/or crack networks obtained using the Slicer Dicer software. For the intact samples we observe that pore (or grain) walls are smoother in Bentheim sandstone whereas in Rothbach sandstone the presence of a significant amount of coating clay minerals results in a visible surface roughness. Some differences in pore size and pore shape were also observed, with a more homogeneous distribution in Bentheim sandstone than in Rothbach sandstone. In both sandstones we observe the classical pore-to-throats junctions. Complex contact geometry between adjacent grains are sometimes observed. In the

  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. PMID:24757414

  11. Open–closed switching of synthetic tubular pores

    PubMed Central

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

    2015-01-01

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

  12. Respiratory Pores on Ostrich Struthio camelus (Aves: Struthionidae) Eggshells.

    PubMed

    Koyama, T; Tennyson, A J D

    2016-01-01

    Respiratory pores are essential for the survival of the embryo within the eggshell. Distribution patterns of such pores on ostrich (Struthio camelus) eggshells show remarkable variations in bird group. Eggshells preserved in the museum of New Zealand have long, superficial, winding grooves and ridges, with pores distributed densely in the bottom of grooves. Both the grooves and ridges that separate them are twisted. By contrast, the surfaces of eggs from farmed ostriches are mostly smooth, with only occasional, short grooves, and respiratory pores distributed more evenly. The cause of ridging and grooving of the surface of eggs from wild birds is unclear but may be due to the need for stronger shells and effects of environmental stresses. It appears that the arrangement of respiratory pores on ostrich eggshells seems to be changeable by surrounding stresses. PMID:27526124

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

    NASA Technical Reports Server (NTRS)

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

    1982-01-01

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

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

    SciTech Connect

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

    2012-01-01

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

  15. Surface and pore properties of ANL and PETC coals

    SciTech Connect

    Bartholomew, C.H.; White, W.E.; Thornock, D.; Wells, W.F.; Hecker, W.C.; Smoot, L.D.; Smith, D.M.; Williams, F.L.

    1988-01-01

    Surface areas, pore volumes, pore size distribution, and solid densities were measured for three ANL coals (Pittsburgh No. 8, Wyodak, and Beulah Zap Lignite), two PETC coals (Lower Wilcox, and Dietz) and a Utah Scofield coal and for chars derived from these coals. Surface areas were measured using nitrogen and carbon dioxide adsorptions; pore volumes were determined using nitrogen adsorption, mercury porosimetry, and NMR spin-lattice relaxation measurements of samples saturated with water. Solid densities were obtained using helium displacement. The results indicate that chars have larger surface areas and pores relative to coals; large fractions of the internal surfaces of coals are not penetrated by nitrogen molecules but are penetrated by carbon dioxide suggesting that the pores are mostly smaller than 1 nm.

  16. Cation-halide transport through peptide pores containing aminopicolinic acid.

    PubMed

    Basak, Debajyoti; Sridhar, Sucheta; Bera, Amal K; Madhavan, Nandita

    2016-05-18

    Synthetic pores that selectively transport ions of biological significance through membranes could be potentially used in medical diagnostics or therapeutics. Herein, we report cation-selective octapeptide pores derived from alanine and aminopicolinic acid. The ion transport mechanism through the pores has been established to be a cation-chloride symport. The cation-chloride co-transport is biologically essential for the efficient functioning of the central nervous system and has been implicated in diseases such as epilepsy. The pores formed in synthetic lipid bilayers do not exhibit any closing events. The ease of synthesis as well as infinite lifetimes of these pores provides scope for modifying their transport behaviour to develop sensors. PMID:27137995

  17. Electroosmotic Flow Rectification in Pyramidal-Pore Mica Membranes

    SciTech Connect

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

    2010-02-01

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

  18. Small pores in soils: Is the physico-chemical environment accurately reflected in biogeochemical models ?

    NASA Astrophysics Data System (ADS)

    Weber, Tobias K. D.; Riedel, Thomas

    2015-04-01

    Free water is a prerequesite to chemical reactions and biological activity in earth's upper crust essential to life. The void volume between the solid compounds provides space for water, air, and organisms that thrive on the consumption of minerals and organic matter thereby regulating soil carbon turnover. However, not all water in the pore space in soils and sediments is in its liquid state. This is a result of the adhesive forces which reduce the water activity in small pores and charged mineral surfaces. This water has a lower tendency to react chemically in solution as this additional binding energy lowers its activity. In this work, we estimated the amount of soil pore water that is thermodynamically different from a simple aqueous solution. The quantity of soil pore water with properties different to liquid water was found to systematically increase with increasing clay content. The significance of this is that the grain size and surface area apparently affects the thermodynamic state of water. This implies that current methods to determine the amount of water content, traditionally determined from bulk density or gravimetric water content after drying at 105°C overestimates the amount of free water in a soil especially at higher clay content. Our findings have consequences for biogeochemical processes in soils, e.g. nutrients may be contained in water which is not free which could enhance preservation. From water activity measurements on a set of various soils with 0 to 100 wt-% clay, we can show that 5 to 130 mg H2O per g of soil can generally be considered as unsuitable for microbial respiration. These results may therefore provide a unifying explanation for the grain size dependency of organic matter preservation in sedimentary environments and call for a revised view on the biogeochemical environment in soils and sediments. This could allow a different type of process oriented modelling.

  19. Effect of Pore-scale Velocity on the Biodegradation of Contaminants during Transport in Porous Media

    NASA Astrophysics Data System (ADS)

    Mendoza-Sanchez, I.; Autenrieth, R. L.; McDonald, T. J.; Cunningham, J. A.

    2007-12-01

    Column experiments were conducted to evaluate the effect of pore velocity on the extent of biodegradation of cis- dichloroethene (cis-DCE) during transport in porous media. The columns were filled with homogeneous glass beads and inoculated with the KB-1 culture (provided by SiREM, Guelph, Ontario, Canada), which is capable of complete dechlorination of perchloroethene to ethene. The columns were fed continuously with a synthetic groundwater containing a constant concentration of cis-DCE. Three different pore flow velocities (0.03, 0.08, and 0.51 m/day) were tested in duplicate, subjecting each column to a constant velocity for the entire experiment. Dechlorination of cis-DCE to vinyl chloride and ethene was monitored over time and space within the columns. Protein concentrations, also measured over time and space, were used to relate cell growth to biodegradation efficiency. At the end of the experiment, microbial DNA was harvested from the columns, and denaturing gradient gel electrophoresis (DGGE) was used to determine differences in the microbial communities that had developed in the columns subjected to different flow rates. The results show that the pore velocity has a strong influence on the microbial population and the degree of dechlorination. At high flow velocity (0.51 m/day), the degradation of cis-DCE to ethene was complete, and the organism capable of cis-DCE dechlorination ({Dehalococcoides sp.}) was present at the end of the experiment. In contrast, at medium and low flow velocities (0.08 and 0.03 m/day), incomplete dechlorination was observed with an absence or low concentration of {Dehalococcoides sp}. These results suggest that it is important for field-scale groundwater remediation to understand the interaction between physical and biological processes on the scale of single pores.

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

    PubMed Central

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

    2014-01-01

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

  1. MRI and PGSE NMR Studies of Long-range, Pore-pore Interaction Effects in Gas Adsorption

    NASA Astrophysics Data System (ADS)

    Hitchcock, Iain; Rigby, Sean; Chudek, John; Holt, Liz; Lowe, John

    2011-03-01

    In this work MRI and PGSE NMR have been used to directly study the advanced condensation effect during water adsorption in a macroscopically heterogeneous sol-gel silica pellet. It has been found that capillary condensation will occur at unexpectedly lower pressures in regions of much larger pores that lie in close proximity to smaller pores.

  2. Pore Scale Dynamics of Microemulsion Formation.

    PubMed

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

    2016-07-19

    consequences on the pore scale mixing behavior and resulting microemulsion properties. PMID:27336294

  3. Influence of pore morphology and topology on capillary trapping in geological carbon dioxide sequestration

    NASA Astrophysics Data System (ADS)

    Andersson, L.; Harper, E.; Herring, A. L.; Wildenschild, D.

    2012-12-01

    Current carbon capture and storage (CCS) techniques could reduce the release of anthropogenic CO2 into the atmosphere by subsurface sequestration of CO2 in saline aquifers. In geological storage CO2 is injected into deep underground porous formations where CO2 is in the supercritical state. Deep saline aquifers are particularly attractive because of their abundance and potentially large storage volumes. Despite very broad research efforts there are still substantial uncertainties related to the effectiveness of the trapping, dissolution, and precipitation processes controlling the permanent storage of CO2. After injection of CO2 the saline water (brine) will imbibe back and reoccupy the pore space as the CO2 moves upwards, trapping a large part of the CO2. This trapping mechanism is known as capillary trapping and occurs as isolated CO2 bubbles are locked in the brine inside the pores of the porous rock. The large-scale movement of CO2 within the brine is thereby prevented. This mechanism thus constitutes an important storage mechanism after the CO2 injection until the subsequent dissolution trapping and precipitation of carbonate mineral. The capillary trapping of CO2 depends largely on the shape and interconnectivity of the pore space and it is therefore important to study the influence of pore scale morphology and topology to understand and optimize large scale capillary trapping. We use a high pressure set-up, designed for supercritical CO2 conditions, with a flow cell compatible with synchrotron-based X-ray computed micro-tomography (CMT) to generate high-resolution images to study capillary trapping. We use sintered glass bead columns as an approximation for unconsolidated reservoir systems. The smooth surface glass bead data allow us to separate the chemistry and surface roughness effects of the porous medium from the effect of the morphology and topology on the capillary trapping. We will relate these aspects of the pore space to the distribution of the

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

    SciTech Connect

    Luo, P.; Machel, H. G.

    1995-11-01

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

  5. The Type III Secretion Translocation Pore Senses Host Cell Contact

    PubMed Central

    Armentrout, Erin I.; Rietsch, Arne

    2016-01-01

    Type III secretion systems (T3SS) are nano-syringes used by a wide range of Gram-negative pathogens to promote infection by directly injecting effector proteins into targeted host cells. Translocation of effectors is triggered by host-cell contact and requires assembly of a pore in the host-cell plasma membrane, which consists of two translocator proteins. Our understanding of the translocation pore, how it is assembled in the host cell membrane and its precise role in effector translocation, is extremely limited. Here we use a genetic technique to identify protein-protein contacts between pore-forming translocator proteins, as well as the T3SS needle-tip, that are critical for translocon function. The data help establish the orientation of the translocator proteins in the host cell membrane. Analysis of translocon function in mutants that break these contacts demonstrates that an interaction between the pore-forming translocator PopD and the needle-tip is required for sensing host cell contact. Moreover, tethering PopD at a dimer interface also specifically prevents host-cell sensing, arguing that the translocation pore is actively involved in detecting host cell contact. The work presented here therefore establishes a signal transduction pathway for sensing host cell contact that is initiated by a conformational change in the translocation pore, and is subsequently transmitted to the base of the apparatus via a specific contact between the pore and the T3SS needle-tip. PMID:27022930

  6. Hetero-oligomeric MspA pores in Mycobacterium smegmatis.

    PubMed

    Pavlenok, Mikhail; Niederweis, Michael

    2016-04-01

    The porin MspA of Mycobacterium smegmatis is a biological nanopore used for DNA sequencing. The octameric MspA pore can be isolated from M. smegmatis in milligram quantities, is extremely stable against denaturation and rapidly inserts into lipid membranes. Here, we show that MspA pores composed of different Msp subunits are formed in M. smegmatis and that hetero-oligomers of different Msp monomers increase the heterogeneity of MspA pores designed for DNA sequencing. To improve the quality of preparations of mutant MspA proteins, all four msp genes were deleted from the M. smegmatis genome after insertion of an inducible porin gene from M. tuberculosis. In the msp quadruple mutant M. smegmatis ML712 no Msp porins were detected and mutant MspA proteins were produced at wild-type levels. Lipid bilayer experiments demonstrated that MspA pores isolated from ML712 formed functional channels and had a narrower conductance distribution than pores purified from M. smegmatis with background msp expression. Thus, the M. smegmatis msp quadruple mutant improves the homogeneity of MspA pores designed for DNA sequencing and might also facilitate the identification and functional characterization of other mycobacterial pore proteins. PMID:26912121

  7. The dielectric properties of water within model transbilayer pores.

    PubMed Central

    Sansom, M S; Smith, G R; Adcock, C; Biggin, P C

    1997-01-01

    Ion channels contain extended columns of water molecules within their transbilayer pores. The dynamic properties of such intrapore water have been shown to differ from those of water in its bulk state. In previous molecular dynamics simulations of two classes of model pore (parallel bundles of Ala20 alpha-helices and antiparallel barrels of Ala10 beta-strands), a substantially reduced translational and rotational mobility of waters was observed within the pore relative to bulk water. Molecular dynamics simulations in the presence of a transpore electrostatic field (i.e., a voltage drop along the pore axis) have been used to estimate the resultant polarization (due to reorientation) of the intrapore water, and hence to determine the local dielectric behavior within the pore. It is shown that the local dielectric constant of water within a pore is reduced for models formed by parallel alpha-helix bundles, but not by those formed by beta-barrels. This result is discussed in the context of electrostatics calculations of ion permeation through channels, and the effect of the local dielectric of water within a helix bundle pore is illustrated with a simple Poisson-Boltzmann calculation. Images FIGURE 1 PMID:9370434

  8. Pore formation by actinoporins, cytolysins from sea anemones.

    PubMed

    Rojko, Nejc; Dalla Serra, Mauro; Maček, Peter; Anderluh, Gregor

    2016-03-01

    Actinoporins (APs) from sea anemones are ~20kDa pore forming toxins with a β-sandwich structure flanked by two α-helices. The molecular mechanism of APs pore formation is composed of several well-defined steps. APs bind to membrane by interfacial binding site composed of several aromatic amino acid residues that allow binding to phosphatidylcholine and specific recognition of sphingomyelin. Subsequently, the N-terminal α-helix from the β-sandwich has to be inserted into the lipid/water interphase in order to form a functional pore. Functional studies and single molecule imaging revealed that only several monomers, 3-4, oligomerise to form a functional pore. In this model the α-helices and surrounding lipid molecules build toroidal pore. In agreement, AP pores are transient and electrically heterogeneous. On the contrary, crystallized oligomers of actinoporin fragaceatoxin C were found to be composed of eight monomers with no lipids present between the adjacent α-helices. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Maur Dalla Serra and Franco Gambale. PMID:26351738

  9. EFFECT OF PORE SIZE ON TRAPPING ZINC VAPORS

    SciTech Connect

    Korinko, P.

    2010-12-17

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

  10. Assembly and stability of nisin-lipid II pores.

    PubMed

    Hasper, Hester Emilie; de Kruijff, Ben; Breukink, Eefjan

    2004-09-14

    The peptide antibiotic nisin was the first reported example of an antibiotic that kills bacteria via targeted pore formation. The specific target of nisin is Lipid II, an essential intermediate in the bacterial cell-wall synthesis. High-affinity binding of the antibiotic to Lipid II is followed by rapid permeabilization of the membrane. Here, we investigated the assembly and stability of nisin-Lipid II pore complexes by means of pyrene fluorescence and circular dichroism. We demonstrated that nisin uses all available Lipid II molecules in the membrane to form pore complexes. The pore complexes have a uniform structure and consist of 8 nisin and 4 Lipid II molecules. Moreover, the pores displayed a remarkable stability, because they were able to resist the solubilization of the membrane environment by mild detergents. Similar experiments with [N20P/M21P]nisin showed that the hinge region is essential for the assembly into stable pore complexes. The new insights were used to propose a refined model for nisin pore formation. PMID:15350143

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

    PubMed Central

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

    2012-01-01

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

  12. Connecting Wastewater Injection and Seismicity through Pore Pressure

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  13. Inkjet-printed lines with well-defined morphologies and low electrical resistance on repellent pore-structured polyimide films.

    PubMed

    Kim, Changjae; Nogi, Masaya; Suganuma, Katsuaki; Yamato, Yo

    2012-04-01

    Polyimide films are the most promising substrates for use in printed electronics because of their high thermal stability. However, the high wettability of polyimide films by conductive inks often produces thin inkjet-printed lines with splashed and wavy boundaries, resulting in high electrical resistance of the lines. To overcome these disadvantages, we fabricated repellent pore structures composed of polyamideimide with high thermal stability on a polyimide film. Using this film, the inkjet-printed line thickness was increased without penetration of silver nanoparticles into the pore structures, thus resulting in very sharp edges without any splashing. This was because the repellent treatment restricted the spreading of the silver nanoparticles into the pore structures and the pore structures prevented ink splashing upon impact on the film. As a result, the electrical resistance of these lines decreased to one-fifth that of the lines on the pristine polyimide film. The inkjet printing of conductive inks onto repellent pore structures would contribute to the future of printed electronics because this technique enables printing closely packed line patterns while maintaining high conductivity within a limited space. PMID:22452572

  14. The effect of microscale pore structure on matrix diffusion—a site-specific study on tonalite

    NASA Astrophysics Data System (ADS)

    Siitari-Kauppi, M.; Lindberg, A.; Hellmuth, K. H.; Timonen, J.; Väätäinen, K.; Hartikainen, J.; Hartikainen, K.

    1997-04-01

    The matrix diffusion of non-sorbing tracers was studied in rocks from the Syyry area, Central Finland (SY1). The effect of alteration and weathering on rock matrix porosity and on the available pore space, which affects diffusivity, are discussed. The main rock type in the crystalline bedrock of Syyry is a slightly foliated, gray tonalite with mica gneiss inclusions as well as minor, more mafic inclusions. The total porosity and the spatial porosity distribution and microstructure of the rocks were investigated using infiltration of carbon- 14-methylmethacrylate, electron microscopy and Hg-porosimetry. The laboratory-scale diffusion experiments were performed using (1) the out-leaching technique of methylmethacrylate (MMA), (2) the through-diffusion of tritiated water (HTO) and chloride in the liquid phase and (3) the through-diffusion of helium in the gas phase. The results of structure investigations indicate that alteration and weathering create micrometric-scale pore apertures, visible as fissures and cracks. These migration pathways dominate in laboratory-scale diffusion experiments and result in high effective porosities and effective diffusivities. Alteration also creates spherical pores, smaller than 1 μm, especially in heavily altered biotite and plagioclase minerals. The altered mineral phases act as quasi dead-end pores hindering the diffusion of non-sorbing tracers. The heterogeneity of the matrix is increased. The heterogeneous spatial pore structure of altered and weathered rock samples causes uncertainty in the diffusion coefficients owing to an assumed homogeneous matrix in Fickian diffusion models.

  15. Managing Free-energy Barriers in Nuclear Pore Transport

    PubMed Central

    Nielsen, Brian; Jeppesen, Claus

    2006-01-01

    The Nuclear Pore Complexes (NPC) facilitate highly selective gateways for transport of macromolecules across the Nuclear Envelope (NE). Based on the current accumulated knowledge of the architecture of NPC we have established a minimal physical model of the pore and the transport mechanism. The barrier properties of the NPC model are analyzed by the recently established Wang–Landau Monte Carlo computer simulation technique and the transport properties are extracted by employing Kramers’ theory of reaction rates. We show that our physical model can account for a range of characteristics observed for nuclear pore transport. PMID:19669451

  16. Metal oxide porous ceramic membranes with small pore sizes

    DOEpatents

    Anderson, Marc A.; Xu, Qunyin

    1991-01-01

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

  17. Metal oxide porous ceramic membranes with small pore sizes

    DOEpatents

    Anderson, Marc A.; Xu, Qunyin

    1992-01-01

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

  18. The effect of pore water pressure on debris flow dynamics

    NASA Astrophysics Data System (ADS)

    Okura, Y.; Parker, G.; Marr, J. G.; Yu, B.; Ochiai, H.

    2003-12-01

    Pore-water likely plays an important role to reduce shear force in debris flow. In experiments, we observed pore-water pressure during flow to clarify the relationship between the flow speed and pore water pressure which would be affected by flow depth and particle size distribution. Soil materials were prepared with mixing materials of sand, silt and clay. Pore-water pressure on the flume bed, flow depth, velocity and run out distance was observed, and the following results were quantitatively obtained in this series of experiments. 1. A positive relation was observed between strain rate and pore-water pressure ratio in the flow. The strain rate and pressure ratio were dimensionless parameters of the ratios of surface velocity to flow depth and pore-water pressure head to flow depth, respectively. This relationship indicated that shear resistance decreased as the pressure potential leading to acceleration of flow velocity increased. 2. A positive relation was also observed between flow depth and pore-water pressure ratio. This indicated that the pore pressure diffusion became increasingly obstructed as the flow depth increased. 3. The pore-water pressure ratio tended to increase with the uniformity coefficient of debris flow materials. The reason for this might have been that smaller particles suspended in the flow increased pore-water pressure, and the wider range of particle distribution effectively prevented pore-water pressure diffusion. 4. There was an apparently negative correlation between the equivalent coefficient of frictions and the pressure ratios. Equivalent friction is apparent friction during flow. The most likely reason for this is that shear resistance would decrease and run out distance increase as the pressure ratio increased. These results indicated that the effect of pore water fluctuations should be one of the most important factors affecting the shear resistance in debris flows. This work was supported by the National Science Foundation

  19. 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

  20. 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.

  1. 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.

  2. Diffusion Pore Imaging by Hyperpolarized Xenon-129 Nuclear Magnetic Resonance

    NASA Astrophysics Data System (ADS)

    Kuder, Tristan Anselm; Bachert, Peter; Windschuh, Johannes; Laun, Frederik Bernd

    2013-07-01

    While NMR diffusion measurements are widely used to derive parameters indirectly related to the microstructure of biological tissues and porous media, direct imaging of pore shapes would be of high interest. Here we demonstrate experimentally that complexly shaped closed pores can be imaged by diffusion acquisitions. Collecting the signal from the whole sample eliminates the problem of vanishing signal at increasing resolution of conventional NMR imaging. This approach may be used to noninvasively obtain structural information inaccessible so far such as pore or cell shapes, cell density, or axon integrity.

  3. Evolution of pore-geometry and relative-permeability due to carbonate precipitation within natural rock sample: Insights from a coupled FVM-LBM method

    NASA Astrophysics Data System (ADS)

    Tsuji, T.; Jiang, F.

    2013-12-01

    To predict long-term CO2 behavior within the reservoir in Carbon Capture and Storage (CCS) projects, we usually use reservoir simulation. A key parameter in the reservoir simulation is 'relative permeability'. However, since the relative permeability is significantly influenced by mineral precipitation (e.g., change of pore space), we should consider the time evolution of relative permeability in reservoir simulation. To investigate the influence of carbonate precipitation to the relative permeability during CO2 storage, we develop numerical calculation method. Pore spaces of Berea sandstone were extracted by high-resolution micro-CT scanned images. The fluid velocity field within the 3D pore spaces was then calculated using the two-phase lattice Boltzmann method (LBM). The calcite deposition within the pore space was calculated by using an advection-reaction formulation solved by finite volume method; we modeled the precipitated rock by transferring the fluid node to solid node according to the calcium concentration level. To increase the computation efficiency, we applied the graphics processor unit (GPU) parallel computing technique. The relative permeability of the rock sample is finally calculated separately by a highly optimized two-phase LB model. The calculated permeability variation due to the carbonate precipitation demonstrates that evolution of pore structure significantly influences the absolute permeability, while it only affects the relative permeability of non-wettable phase at low water saturation conditions.

  4. Topology of a percolating soil pore network

    NASA Astrophysics Data System (ADS)

    Capa-Morocho, M.; Ruiz-Ramos, M.; Hapca, S. M.; Houston, A.; Tarquis, A. M.

    2012-04-01

    A connectivity function defined by the 3D-Euler number, is a topological indicator and can be related to hydraulic properties (Vogel and Roth, 2001). This study aims to develop connectivity Euler indexes as indicators of the ability of soils for fluid percolation. The starting point was a 3D grey image acquired by X-ray computed tomography of a soil at bulk density of 1.2 mg cm-3. This image was used in the simulation of 40000 particles following a directed random walk algorithms with 7 binarization thresholds. These data consisted of 7 files containing the simulated end points of the 40000 random walks, obtained in Ruiz-Ramos et al. (2010). MATLAB software was used for computing the frequency matrix of the number of particles arriving at every end point of the random walks and their 3D representation. In a former work (Capa et al., 2011) a criteria for choosing the optimal threshold of grey value was identified: Final positions were divided in two subgroups, cg1 (positions with frequency of the number of particles received greater than the median) and cg2 (frequency lower or equal to median). Images with maximum difference between the Z coordinate of the center of gravity of both subgroups were selected as those with optimal threshold that reflects the major internal differences in soil structure that are relevant to percolation. According to this criterion, the optimal threshold for the soil with density 1.2 mg cm-3 was 24.Thresholds above and below the optimal (23 and 25) were also considered to confirm this selection; therefore the analysis were conducted for three files (1 image with 3 grey threshold values, which have different porosity). Additionally, three random matrix simulations with the same porosity than the selected binaries images were used to test the existence of pore connectivity as a consequence of a non-random soil structure. Therefore, 6 matrix were considered (three structured and three random) for this study. Random matrix presented a normal

  5. A level set method for materials with texturally equilibrated pores

    NASA Astrophysics Data System (ADS)

    Ghanbarzadeh, Soheil; Hesse, Marc A.; Prodanović, Maša

    2015-09-01

    Textural equilibrium controls the distribution of the liquid phase in many naturally occurring porous materials such as partially molten rocks and alloys, salt-brine and ice-water systems. In these materials, pore geometry evolves to minimize the solid-liquid interfacial energy while maintaining a constant dihedral angle, θ, at solid-liquid contact lines. We present a level set method to compute an implicit representation of the liquid-solid interface in textural equilibrium with space-filling tessellations of multiple solid grains in three dimensions. Each grain is represented by a separate level set function and interfacial energy minimization is achieved by evolving the solid-liquid interface under surface diffusion to constant mean curvature surface. The liquid volume and dihedral angle constraints are added to the formulation using virtual convective and normal velocity terms. This results in an initial value problem for a system of non-linear coupled PDEs governing the evolution of the level sets for each grain, using the implicit representation of the solid grains as initial condition. A domain decomposition scheme is devised to restrict the computational domain of each grain to few grid points around the grain. The coupling between the interfaces is achieved in a higher level on the original computational domain. The spatial resolution of the discretization is improved through high-order spatial differentiation schemes and localization of computations through domain composition. Examples of three-dimensional solutions are also obtained for different grain distributions networks that illustrate the geometric flexibility of the method.

  6. Modeling of nanoparticle transport and deposition in a porous medium: Effects of pore surface heterogeneity

    NASA Astrophysics Data System (ADS)

    Pham, Ngoc; Papavassiliou, Dimitrios

    2014-11-01

    Pore surface charge heterogeneity has been found to affect particle retention in flow through porous media. In this study, retention of nanoparticles under different surface blocking conditions is numerically investigated. Micro-CT scanning is used to reconstruct the 3D geometry of sandstone and image-based analysis is used to characterize the pore space and the mineral composition of the rock. Flow of water through the sample is simulated with the lattice Boltzmann method. The motion of nanoparticles is modeled by injection of particles moving under convection and molecular diffusion and recording their trajectories in time. When interacting with the pore surface, particles can be retained onto the surface with a particular deposition rate. As deposited particles hinder the retention of other particles by blocking occupied sites, the deposition is considered to be a second order process. Particle breakthrough under different modeled and real distributions of surface heterogeneity as a function of various surface blocking conditions is investigated. The effect is stronger when parts of the surface are much more favorable for deposition than others. Acknowledgements: Advanced Energy Consortium (AEC BEG08-022) & XSEDE (CTS090017).

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

    PubMed

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

    2005-01-01

    Designing a reliable plant growth system for crop production in space requires the understanding of pore fluid distribution in porous media under microgravity. The objective of this experimental investigation, which was conducted aboard NASA KC-135 reduced gravity flight, is to study possible particle separation and the distribution of discontinuous wetting fluid in porous media under microgravity. KC-135 aircraft provided gravity conditions of 1, 1.8, and 10(-2) g. Glass beads of a known size distribution were used as porous media; and Hexadecane, a petroleum compound immiscible with and lighter than water, was used as wetting fluid at residual saturation. Nitrogen freezer was used to solidify the discontinuous Hexadecane ganglia in glass beads to preserve the ganglia size changes during different gravity conditions, so that the blob-size distributions (BSDs) could be measured after flight. It was concluded from this study that microgravity has little effect on the size distribution of pore fluid blobs corresponding to residual saturation of wetting fluids in porous media. The blobs showed no noticeable breakup or coalescence during microgravity. However, based on the increase in bulk volume of samples due to particle separation under microgravity, groups of particles, within which pore fluid blobs were encapsulated, appeared to have rearranged themselves under microgravity. PMID:16052743

  8. Systematic Design of Pore Size and Functionality in Isoreticular MOFs and Their Application in Methane Storage

    NASA Astrophysics Data System (ADS)

    Eddaoudi, Mohamed; Kim, Jaheon; Rosi, Nathaniel; Vodak, David; Wachter, Joseph; O'Keeffe, Michael; Yaghi, Omar M.

    2002-01-01

    A strategy based on reticulating metal ions and organic carboxylate links into extended networks has been advanced to a point that allowed the design of porous structures in which pore size and functionality could be varied systematically. Metal-organic framework (MOF-5), a prototype of a new class of porous materials and one that is constructed from octahedral Zn-O-C clusters and benzene links, was used to demonstrate that its three-dimensional porous system can be functionalized with the organic groups -Br, -NH2, -OC3H7, -OC5H11, -C2H4, and -C4H4 and that its pore size can be expanded with the long molecular struts biphenyl, tetrahydropyrene, pyrene, and terphenyl. We synthesized an isoreticular series (one that has the same framework topology) of 16 highly crystalline materials whose open space represented up to 91.1% of the crystal volume, as well as homogeneous periodic pores that can be incrementally varied from 3.8 to 28.8 angstroms. One member of this series exhibited a high capacity for methane storage (240 cubic centimeters at standard temperature and pressure per gram at 36 atmospheres and ambient temperature), and others the lowest densities (0.41 to 0.21 gram per cubic centimeter) for a crystalline material at room temperature.

  9. Systematic design of pore size and functionality in isoreticular MOFs and their application in methane storage.

    PubMed

    Eddaoudi, Mohamed; Kim, Jaheon; Rosi, Nathaniel; Vodak, David; Wachter, Joseph; O'Keeffe, Michael; Yaghi, Omar M

    2002-01-18

    A strategy based on reticulating metal ions and organic carboxylate links into extended networks has been advanced to a point that allowed the design of porous structures in which pore size and functionality could be varied systematically. Metal-organic framework (MOF-5), a prototype of a new class of porous materials and one that is constructed from octahedral Zn-O-C clusters and benzene links, was used to demonstrate that its three-dimensional porous system can be functionalized with the organic groups -Br, -NH2, -OC3H7, -OC5H11, -C2H4, and -C4H4 and that its pore size can be expanded with the long molecular struts biphenyl, tetrahydropyrene, pyrene, and terphenyl. We synthesized an isoreticular series (one that has the same framework topology) of 16 highly crystalline materials whose open space represented up to 91.1% of the crystal volume, as well as homogeneous periodic pores that can be incrementally varied from 3.8 to 28.8 angstroms. One member of this series exhibited a high capacity for methane storage (240 cubic centimeters at standard temperature and pressure per gram at 36 atmospheres and ambient temperature), and others the lowest densities (0.41 to 0.21 gram per cubic centimeter) for a crystalline material at room temperature. PMID:11799235

  10. Varied pore organization in mesostructured semiconductors based on the [SnSe4](4-) anion.

    PubMed

    Trikalitis, P N; Rangan, K K; Bakas, T; Kanatzidis, M G

    2001-04-01

    Open framework metal chalcogenide solids, with pore sizes in the nano- and mesoscale, are of potentially broad technological and fundamental interest in research areas ranging from optoelectronics to the physics of quantum confinement. Although there have been significant advances in the design and synthesis of mesostructured silicas, the construction of their non-oxidic analogues still remains a challenge. Here we describe a synthetic strategy that allows the preparation of a large class of mesoporous materials based on supramolecular assembly of tetrahedral Zintl anions [SnSe4]4- with transition metals in the presence of cetylpyridinium (CP) surfactant molecules. These mesostructured semiconducting selenide materials are of the general formulae (CP)4-2xMxSnSe4 (where 1.0 < x < 1.3; M=Mn, Fe, Co, Zn, Cd, Hg). The resulting materials are open framework chalcogenides and form mesophases with uniform pore size (with spacings between 35 and 40 A). The pore arrangement depends on the synthetic conditions and metal used, and include disordered wormhole, hexagonal and even cubic phases. All compounds are medium bandgap semiconductors (varying between 1.4 and 2.5 eV). We expect that such semiconducting porous networks could be used for optoelectronic, photosynthetic and photocatalytic applications. PMID:11287949

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

    NASA Technical Reports Server (NTRS)

    Donovan, S. S.

    1978-01-01

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

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

    SciTech Connect

    Tomutsa, Liviu; Silin, Dmitriy; Radmilovich, Velimir

    2005-08-23

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

  13. Investigating axial diffusion in cylindrical pores using confocal single-particle fluorescence correlation spectroscopy.

    PubMed

    Chen, Fang; Neupane, Bhanu; Li, Peiyuan; Su, Wei; Wang, Gufeng

    2016-08-01

    We explored the feasibility of using confocal fluorescence correlation spectroscopy to study small nanoparticle diffusion in hundred-nanometer-sized cylindrical pores. By modeling single particle diffusion in tube-like confined three-dimensional space aligned parallel to the confocal optical axis, we showed that two diffusion dynamics can be observed in both original intensity traces and the autocorrelation functions (ACFs): the confined two-dimensional lateral diffusion and the unconfined one-dimensional (1D) axial diffusion. The separation of the axial and confined lateral diffusion dynamics provides an opportunity to study diffusions in different dimensions separately. We further experimentally studied 45 nm carboxylated polystyrene particles diffusing in 300 nm alumina pores. The experimental data showed consistency with the simulation. To extract the accurate axial diffusion coefficient, we found that a 1D diffusion model with a Lorentzian axial collection profile needs to be used to analyze the experimental ACFs. The diffusion of the 45 nm nanoparticles in polyethyleneglycol-passivated 300 nm pores slowed down by a factor of ∼2, which can be satisfactorily explained by hydrodynamic frictions. PMID:27196052

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

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

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

    SciTech Connect

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

    2013-11-11

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

  16. Estimating three phase relative permeability based on realistic pore scale configurations

    NASA Astrophysics Data System (ADS)

    Verma, R.; Prodanovic, M.; Wildenschild, D.

    2013-12-01

    Multiphase (water, oil, gas) flow in porous media is commonly encountered in subsurface. Study of multiphase flows is important in applications such as hydrocarbon recovery, carbon capture and storage, groundwater flow modeling, flow of non-aqueous phase liquids (NAPL), and many others. The problem is notoriously difficult to study, and much effort has gone into understanding the physics of the multiphase flow on the pore scale. In particular, imaging techniques such as x-ray microtomography can now provide 3D microstructure as well as fluid phase configurations at a very high resolution. Using these images, one can validate simulations done by various techniques, such as pore network modeling, the Lattice-Boltzmann method or computational fluid dynamics to name a few. In this work, we present an analysis of several pore-scale images of multiphase flow as well as comparable multiphase flow simulations and show the distribution of various phases in three phase flow situations. We are particularly interested in quantifying spatial configurations, connectivity and relative permeability of the intermediate wetting phase. The rock wettability is one of the key parameters that determines positioning of the phases within the pore space. The wetting phase sticks closer to the wall, while the non-wetting phase is at the center of the pores. In three phase flow, the intermediate wetting phase exists as a layer between the two phases, and this is often the oil phase that we are trying to drain from the system. At the macro scale, this means that the relative permeability is a function of more than one saturation as well as its often complicated spatial configuration. One of the key observations from experiment is high oil relative permeability even at low oil saturations. It is hypothesized that the oil exists as a very thin layer throughout the core sample, and one of the goals of this work is to validate this hypothesis. This layer is rather difficult to observe even with

  17. Dilatancy and pore pressure effects during fracture and shear of antigorite-rich serpentinite

    NASA Astrophysics Data System (ADS)

    French, M. E.; Zhu, W.

    2015-12-01

    Geophysical observations show evidence of near-lithostatic pore pressure in fault zones that experience episodic slow slip events. In addition, dilatancy hardening is one of several hypotheses proposed to explain the transient self-sustaining nature of slow slip. Thus, pore pressure evolution is possibly an important control on slow slip behavior. Phyllosilicates are abundant in regions of subduction zones and along the deep San Andreas Fault where slow slip is observed, yet previous work on phyllosilicate-bearing rocks indicates that fracture and frictional sliding occur with little dilation of the pore space. We present experimental results of pore pressure effects during fracture and frictional shear of antigorite-rich serpentinite. Triaxial deformation experiments were conducted on intact cores 25.4 mm in diameter and 53.0 mm in length and ~1.5 mm thick gouge zones sandwiched between porous sandstone or steel sawcut forcing blocks. Experiments were conducted at room temperature, confining pressures from 50 to 100 MPa, pore pressure from 0 to 95 MPa, and axial displacement rates from 0.016 to 4.0 μm/s (shear rates from 0.02 to 5 μm/s). Foliated and macroscopically isotropic intact serpentinite samples were tested; fabric orientation is strongly correlated with both strength and dilatancy. When foliation is oriented parallel to σ1, strength and dilatancy are greatest and similar to those for crystalline rocks. When foliation is oriented 45 ° to σ1, however, dilatancy and strength are both greatly reduced. During frictional shear we observe a transition from rate-strengthening to rate-weakening behavior at ~0.5 μm/s, which is within range of typical slow slip rates and consistent with previous studies. This transition occurs concurrently with a transition from slip-induced compaction to dilation. Higher pore pressure correlates with overall higher friction coefficient, and also with lower compaction rates and higher dilation rates in the rate

  18. 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.

  19. 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.

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

    PubMed

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

    2008-11-01

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

  1. Ion transport and dehydration in sub-nanoscale pores

    NASA Astrophysics Data System (ADS)

    Sahu, Subin; di Ventra, Massimiliano; Zwolak, Michael

    Ions in solution develop tightly bound layers of water - hydration layers - which stabilize disassociation and enable ionic currents to flow. Sub-nanometer pores in a membrane enable ions to pass provided that they shed their hydration shell. This process has an associated large energy penalty that is predicted to give rise to ''quantized'' steps in the ionic conductance. Using all-atom molecular dynamics simulation, we demonstrate that the ionic current begins to show nonlinear behavior as the radius of the pore is reduced to the sub-nanometer scale. This nonlinear behavior is seen as a sharp rise in the pore resistance and excess noise in the current. Our work sheds light on basic mechanism of ion transport through sub-nanoscale pores. S. Sahu acknowledges support by UMD/CNST Cooperative Research Agreement, Award 70NANB10H193 through University of Maryland.

  2. Hydrochromic conjugated polymers for human sweat pore mapping

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  3. The perforin pore facilitates the delivery of cationic cargos.

    PubMed

    Stewart, Sarah E; Kondos, Stephanie C; Matthews, Antony Y; D'Angelo, Michael E; Dunstone, Michelle A; Whisstock, James C; Trapani, Joseph A; Bird, Phillip I

    2014-03-28

    Cytotoxic lymphocytes eliminate virally infected or neoplastic cells through the action of cytotoxic proteases (granzymes). The pore-forming protein perforin is essential for delivery of granzymes into the cytoplasm of target cells; however the mechanism of this delivery is incompletely understood. Perforin contains a membrane attack complex/perforin (MACPF) domain and oligomerizes to form an aqueous pore in the plasma membrane; therefore the simplest (and best supported) model suggests that granzymes passively diffuse through the perforin pore into the cytoplasm of the target cell. Here we demonstrate that perforin preferentially delivers cationic molecules while anionic and neutral cargoes are delivered inefficiently. Furthermore, another distantly related pore-forming MACPF protein, pleurotolysin (from the oyster mushroom), also favors the delivery of cationic molecules, and efficiently delivers human granzyme B. We propose that this facilitated diffusion is due to conserved features of oligomerized MACPF proteins, which may include an anionic lumen. PMID:24558045

  4. Porosity, pore size distribution and in situ strength of concrete

    SciTech Connect

    Kumar, Rakesh; Bhattacharjee, B

    2003-01-01

    In this study, in situ strength of concrete was determined through compression test of cores drilled out from laboratory cast beams. The apparent porosity and pore size distribution of the same concrete were determined through mercury intrusion porosimetry, performed on small-drilled cores. The normal-strength concrete mixes used in the experimental investigation were designed to exhibit a wide variation in their strengths. To ensure further variation in porosity, pore size distribution and strength, two modes of compaction, two varieties of coarse aggregates, different levels of age, curing period and exposure condition of concrete were also introduced in experimental scheme. With the data so generated, an appraisal of the most frequently referred relationships involving strength, porosity and pore size of cement-based materials was carried out. Finally, a new empirical model relating the in situ strength of concrete with porosity, pore size characteristics, cement content, aggregate type, exposure conditions, etc., is presented.

  5. Pore-scale simulation of laminar flow through porous media

    NASA Astrophysics Data System (ADS)

    Piller, M.; Casagrande, D.; Schena, G.; Santini, M.

    2014-04-01

    The experimental investigation of flow through porous media is inherently difficult due to the lack of optical access. The recent developments in the fields of X-ray micro-tomography (micro-CT hereafter), digital sample reconstruction by image-processing techniques and fluid-dynamics simulation, together with the increasing power of super-computers, allow to carry out pore-scale simulations through digitally-reconstructed porous samples. The scientific relevance of pore-scale simulations lies in the possibility of upscaling the pore-level data, yielding volume-averaged quantities useful for practical purposes. One of the best-known examples of upscaling is the calculation of absolute and relative permeability of reservoir rocks. This contribution presents a complete work-flow for setting up pore-scale simulations, starting from the micro-CT of a (in general small) porous sample. Relevant applications are discussed in order to reveal the potential of the proposed methodology.

  6. Membrane pore formation at protein-lipid interfaces.

    PubMed

    Gilbert, Robert J C; Dalla Serra, Mauro; Froelich, Christopher J; Wallace, Mark I; Anderluh, Gregor

    2014-11-01

    Pore-forming proteins (PFPs) interact with lipid bilayers to compromise membrane integrity. Many PFPs function by inserting a ring of oligomerized subunits into the bilayer to form a protein-lined hydrophilic channel. However, mounting evidence suggests that PFPs can also generate 'proteolipidic' pores by contributing to the fusion of inner and outer bilayer leaflets to form a toroidal structure. We discuss here toroidal pore formation by peptides including melittin, protegrin, and Alzheimer's Aβ1-41, as well as by PFPs from several evolutionarily unrelated families: the colicin/Bcl-2 grouping including the pro-apoptotic protein Bax, actinoporins derived from sea anemones, and the membrane attack complex-perforin/cholesterol dependent cytolysin (MACPF/CDC) set of proteins. We also explore how the structure and biological role of toroidal pores might be investigated further. PMID:25440714

  7. Pores with longitudinal irregularities distinguish objects by shape.

    PubMed

    Qiu, Yinghua; Hinkle, Preston; Yang, Crystal; Bakker, Henriette E; Schiel, Matthew; Wang, Hong; Melnikov, Dmitriy; Gracheva, Maria; Toimil-Molares, Maria Eugenia; Imhof, Arnout; Siwy, Zuzanna S

    2015-04-28

    The resistive-pulse technique has been used to detect and size objects which pass through a single pore. The amplitude of the ion current change observed when a particle is in the pore is correlated with the particle volume. Up to date, however, the resistive-pulse approach has not been able to distinguish between objects of similar volume but different shapes. In this manuscript, we propose using pores with longitudinal irregularities as a sensitive tool capable of distinguishing spherical and rod-shaped particles with different lengths. The ion current modulations within resulting resistive pulses carry information on the length of passing objects. The performed experiments also indicate the rods rotate while translocating, and displace an effective volume that is larger than their geometrical volume, and which also depends on the pore diameter. PMID:25787224

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  11. Numerical simulation of pore size dependent anhydrite precipitation in geothermal reservoirs

    NASA Astrophysics Data System (ADS)

    Mürmann, Mario; Kühn, Michael; Pape, Hansgeorg; Clauser, Christoph

    2013-04-01

    cementation in a 2D hypothetical core flooding experiment. With this new approach cementation patterns observed in the Allermöhe core samples can be explained now. The obtained results show that the variation of fluid supersaturation within a pore governs spatially heterogeneous anhydrite cementation. This variation and the fluid velocity determine the precipitation. Our numerical simulation results clearly emphasize the necessity to consider the spatial variation of supersaturation on the pore scale. References Baermann A., Kroeger J., Taugs R., Wuestenhagen K., Zarth M. (2000) Anhydrite cementation in Rhaetian Sandstone in Hamburg - Morphology and Structures, Zeitschrift für Angewandte Geologie, 46(3), 138-143 (in German). Clauser C. (2003) Numerical Simulation of Reactive Flow in Hot Aquifers. SHEMAT and processing SHEMAT, Springer Publishers, Heidelberg. Emmanuel S., Berkowitz B. (2007) Effects of pore size controlled solubility on reactive transport in heterogeneous rock, Geophysical Research Letters, 34, L06404. Putnis A., Mauthe G. (2001) The effect of pore size on cementation in porous rocks, Geofluids, 1, 37-41. Wagner R., Kühn M., Meyn V., Pape H., Vath U., Clauser C. (2005) Numerical simulation of pore space clogging in geothermal reservoirs by precipitation of anhydrite. International Journal of Rock Mechanics and Mining Sciences 42, 1070-1081, doi: 10.1016/ j.ijrmms.2005.05.008.

  12. Reactive Transport in Porous Media: Pore-scale Mass Exchange between Aqueous Phase and Biofilms

    NASA Astrophysics Data System (ADS)

    Hassanizadeh, S.; Qin, C.

    2013-12-01

    In the presence of water and necessary nutrients, biofilms can grow on soil grain surfaces. They occupy void pore spaces blocking water flow. As a result, some hydrodynamic properties of porous media like porosity and permeability will be reduced. This ultimately leads to a condition known as bioclogging. Also, biofilms can degrade certain compounds. So, the features of bioclogging and biodegradation in porous media with biofilms have given rise to a broad range of environmental and engineering applications, such as bioremediation, biobarriers, microbial enhanced oil recovery, and protection of steel corrosion. To date, a number of macroscale and pore-scale models for describing biodegradation in porous media with biofilms are available in the literature. At the macro scale, to simplify numerical implementation, a ';one-equation' model is normally preferred. In this approach, only the solute concentration in aqueous phase is modeled associated with the consumption of solute in biofilms. Because the solute concentration in biofilms is different from that in aqueous phase, an effectiveness factor may be used in Monod kinetics for relating reaction rate within biofilms to the solute concentration in aqueous phase. Notice that this approach has its validity domains like local equilibrium and reaction-rate limited consumption. Another approach to modeling biodegradation is referred to as a ';two-equation' model, in which one needs to simultaneously track the solute concentrations in both aqueous phase and biofilms. In addition, the two concentrations may be related by a first-order kinetic mass exchange model. This first-rate exchange model is normally represented by a constant mas exchange coefficient multiplied by the concentration difference in the two domains. Here, one may question if complex advection-diffusion-reaction processes can be represented just by a constant mass exchange coefficient. In addition, the kinetic model of mass exchange between aqueous phase

  13. Dynamic pore-pressure fluctuations in rapidly shearing granular materials

    USGS Publications Warehouse

    Iverson, R.M.; LaHusen, R.G.

    1989-01-01

    Results from two types of experiments show that intergranular pore pressures fluctuated dynamically during rapid, steady shear deformation of water-saturated granular materials. During some fluctuations, the pore water locally supported all normal and shear stresses, while grain-contact stresses transiently fell to zero. Fluctuations also propagated outward from the shear zone; this process modifies grain-contact stresses in adjacent areas and potentially instigates shear-zone growth.

  14. 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.

  15. Comparative squamation of the lateral line canal pores in sharks.

    PubMed

    McKenzie, R W; Motta, P J; Rohr, J R

    2014-05-01

    The current study collected the first quantitative data on lateral line pore squamation patterns in sharks and assessed whether divergent squamation patterns are similar to experimental models that cause reduction in boundary layer turbulence. In addition, the hypothesis that divergent orientation angles are exclusively found in fast-swimming shark species was tested. The posterior lateral line and supraorbital lateral line pore squamation of the fast-swimming pelagic shortfin mako shark Isurus oxyrinchus and the slow-swimming epi-benthic spiny dogfish shark Squalus acanthias was examined. Pore scale morphology and pore coverage were qualitatively analysed and compared. In addition, pore squamation orientation patterns were quantified for four regions along the posterior lateral line and compared for both species. Isurus oxyrinchus possessed consistent pore scale coverage among sampled regions and had a divergent squamation pattern with multiple scale rows directed dorsally and ventrally away from the anterior margin of the pore with an average divergent angle of 13° for the first row of scales. Squalus acanthias possessed variable amounts of scale coverage among the sampled regions and had a divergent squamation pattern with multiple scale rows directed ventrally away from the anterior margin of the pore with an average angle of 19° for the first row of scales. Overall, the squamation pattern measured in I. oxyrinchus fell within the parameters used in the fluid flow analysis, which suggests that this pattern may reduce boundary layer turbulence and affect lateral line sensitivity. The exclusively ventral oriented scale pattern seen in S. acanthias possessed a high degree of divergence but the pattern did not match that of the fluid flow models. Given current knowledge, it is unclear how this would affect boundary layer flow. By studying the relationship between squamation patterns and the lateral line, new insights are provided into sensory biology that warrant

  16. Phase-Field Modeling of Lipid Vesicles With Pores

    NASA Astrophysics Data System (ADS)

    Seifi, Saman; Salac, David

    2013-11-01

    The formation and annihilation of pores in a lipid vesicle membrane is critical to a number of biotechnologies, such as drug delivery. Previous models of vesicle behavior have ignored the influence of topological changes in the vesicle membrane. Here the entire Helfrich model of a vesicle membrane is considered. Topological changes in the vesicle membrane, such as the formation of a pore, are captured through the use of an embedded phase-field model. The numerical method and sample results will be presented.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  18. Pore size and the lab-field reaction rate riddle

    NASA Astrophysics Data System (ADS)

    Emmanuel, S.; Ague, J. J.; Walderhaug, O.

    2009-12-01

    Pore size is usually thought to influence the rate of crystal growth during diagenesis and metamorphism by controlling the ratio of surface area to fluid volume. However, theory suggests that in micron-scale to nanometer-scale pores, interfacial energy effects can also become important. We used mercury porosimetry to investigate the pore-size distributions in naturally cemented sandstone adjacent to stylolites and found that quartz precipitation was inhibited in pores smaller than 10 microns in diameter. We demonstrate that standard kinetic models cannot reproduce the observed pore-size patterns in mineralized samples; by contrast, excellent fits with the data are obtained when interfacial energy effects are taken into account. Moreover, as such micron-scale pores comprise the overwhelming majority of surface area in the sandstone, average reaction rates for the rock are significantly reduced. Reaction rates in geological media determined in field studies can be orders of magnitude lower than those measured in laboratory experiments, and we propose that reduced reaction rates in rocks with micron-scale porosity could account for the apparent paradox.

  19. Smooth DNA transport through a narrowed pore geometry.

    PubMed

    Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Wanunu, Meni

    2014-11-18

    Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35-20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics. PMID:25418307

  20. Membrane pore formation in atomistic and coarse-grained simulations.

    PubMed

    Kirsch, Sonja A; Böckmann, Rainer A

    2016-10-01

    Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26748016

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

    SciTech Connect

    Das, Chandan K.; Singh, Jayant K.

    2014-05-28

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

  2. Smooth DNA Transport through a Narrowed Pore Geometry

    PubMed Central

    Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Wanunu, Meni

    2014-01-01

    Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35–20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics. PMID:25418307

  3. Local membrane mechanics of pore-spanning bilayers.

    PubMed

    Mey, Ingo; Stephan, Milena; Schmitt, Eva K; Müller, Martin Michael; Ben Amar, Martine; Steinem, Claudia; Janshoff, Andreas

    2009-05-27

    The mechanical behavior of lipid bilayers spanning the pores of highly ordered porous silicon substrates was scrutinized by local indentation experiments as a function of surface functionalization, lipid composition, solvent content, indentation velocity, and pore radius. Solvent-containing nano black lipid membranes (nano-BLMs) as well as solvent-free pore-spanning bilayers were imaged by fluorescence and atomic force microscopy prior to force curve acquisition, which allows distinguishing between membrane-covered and uncovered pores. Force indentation curves on pore-spanning bilayers attached to functionalized hydrophobic porous silicon substrates reveal a predominately linear response that is mainly attributed to prestress in the membranes. This is in agreement with the observation that indentation leads to membrane lysis well below 5% area dilatation. However, membrane bending and lateral tension dominate over prestress and stretching if solvent-free supported membranes obtained from spreading giant liposomes on hydrophilic porous silicon are indented. An elastic regime diagram is presented that readily allows determining the dominant contribution to the mechanical response upon indentation as a function of load and pore radius. PMID:19453196

  4. Pore growth in U-Mo/Al dispersion fuel

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  5. Regulation of landslide motion by dilatancy and pore pressure feedback

    USGS Publications Warehouse

    Iverson, R.M.

    2005-01-01

    A new mathematical model clarifies how diverse styles and rates of landslide motion can result from regulation of Coulomb friction by dilation or contraction of water-saturated basal shear zones. Normalization of the model equations shows that feedback due to coupling between landslide motion, shear zone volume change, and pore pressure change depends on a single dimensionless parameter ??, which, in turn, depends on the dilatancy angle ?? and the intrinsic timescales for pore pressure generation and dissipation. If shear zone soil contracts during slope failure, then ?? 0, and negative feedback permits slow, steady landslide motion to occur while positive pore pressure is supplied by rain infiltration. Steady state slip velocities v0 obey v0 = -(K/??) p*e, where K is the hydraulic conductivity and p*e is the normalized (dimensionless) negative pore pressure generated by dilation. If rain infiltration and attendant pore pressure growth continue unabated, however, their influence ultimately overwhelms the stabilizing influence of negative p*e. Then, unbounded landslide acceleration occurs, accentuated by an instability that develops if ?? diminishes as landslide motion proceeds. Nonetheless, numerical solutions of the model equations show that slow, nearly steady motion of a clay-rich landslide may persist for many months as a result of negative pore pressure feedback that regulates basal Coulomb friction. Similarly stabilized motion is less likely to occur in sand-rich landslides that are characterized by weaker negative feedback.

  6. Determinants of pore folding in potassium channel biogenesis

    PubMed Central

    Delaney, Erin; Khanna, Pooja; Tu, LiWei; Robinson, John M.; Deutsch, Carol

    2014-01-01

    Many ion channels, both selective and nonselective, have reentrant pore loops that contribute to the architecture of the permeation pathway. It is a fundamental feature of these diverse channels, regardless of whether they are gated by changes of membrane potential or by neurotransmitters, and is critical to function of the channel. Misfolding of the pore loop leads to loss of trafficking and expression of these channels on the cell surface. Mature tetrameric potassium channels contain an α-helix within the pore loop. We systematically mutated the “pore helix” residues of the channel Kv1.3 and assessed the ability of the monomer to fold into a tertiary reentrant loop. Our results show that pore loop residues form a canonical α-helix in the monomer early in biogenesis and that disruption of tertiary folding is caused by hydrophilic substitutions only along one face of this α-helix. These results provide insight into the determinants of the reentrant pore conformation, which is essential for ion channel function. PMID:24616516

  7. Do conservative solutes migrate at average pore-water velocity?

    PubMed

    Rovey, Charles W; Niemann, William L

    2005-01-01

    According to common understanding, the advective velocity of a conservative solute equals the average linear pore-water velocity. Yet direct monitoring indicates that the two velocities may be different in heterogeneous media. For example, at the Camp Dodge, Iowa, site the advective velocity of discrete Cl- plumes was less than one tenth of the average pore-water velocity calculated from Darcy's law using the measured hydraulic gradient, effective porosity, and hydraulic conductivity (K) from large-scale three-dimensional (3D) techniques, e.g., pumping tests. Possibly, this difference reflects the influence of different pore systems, if the K relevant to transient solute flux is influenced more by lower-K heterogeneity than a steady or quasi-steady water flux. To test this idea, tracer tests were conducted under controlled laboratory conditions. Under one-dimensional flow conditions, the advective velocity of discrete conservative solutes equaled the average pore-water velocity determined from volumetric flow rates and Darcy's law. In a larger 3D flow system, however, the same solutes migrated at approximately 65% of the average pore-water velocity. These results, coupled with direct observation of dye tracers and their velocities as they migrated through both homogeneous and heterogeneous sections of the same model, demonstrate that heterogeneity can slow the advective velocity of discrete solute plumes relative to the average pore-water velocity within heterogeneous 3D flow sytems. PMID:15726924

  8. 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

  9. On the Minimum Energy Path to Membrane Pore Formation

    NASA Astrophysics Data System (ADS)

    Ting, Christina; Wang, Zhen-Gang

    2011-03-01

    Several experimental methods have been developed to study the mechanical response of vesicles under an applied tension. Of particular note are the micropipette aspiration techniques and the use of a viscous solution to extend the lifetime of pores. MD simulations have also been used to study the energetic and structural properties of these transient pores on a molecular level. However, they often require extremely high tensions beyond the regime where pore formation is a thermally-activated event. We approach the nucleation problem by combining the string method with dynamic self-consistent field (DSCF) theory to obtain the full minimum energy path (MEP) to pore formation for a range of surface tensions γ . We compare our results with classical nucleation theory (CNT). Near the coexistence (γ --> 0) the rim of the pore is well-defined and the line tension is well approximated by the macroscopic definition given by CNT. However, when the free energy barrier is within ~ 10 kT , the transition state is somewhere between a stalk-like structure and a thinned membrane leading to a hole that is partially exposed to solvents. These molecular rearrangements involved in the formation of a pore are not captured by CNT.

  10. Properties of Aqueous Electrolytes within Narrow Slit-Shaped Pores

    NASA Astrophysics Data System (ADS)

    Ho, Tuan A.; Argyris, Dimitrios; Striolo, Alberto

    2011-03-01

    We report equilibrium molecular dynamics simulation results for structural and dynamic properties of aqueous electrolyte solutions confined within narrow pores. The slit-shaped pores are carved from cristobalite silica, corundum alumina, magnesium oxide, and other materials. The pore width is in the range 0.8 -- 2.0 nm. The aqueous solutions contain NaCl, CsCl, CaCl 2 , and SrCl 2 electrolytes at 1M concentration or larger. Equilibrium simulations are performed at ambient conditions within the NVT ensemble. The data suggest the formation of layered structures, which are consistent with results obtained for thin films of solution supported on free-standing surfaces. However, confinement enhances the differences in transport properties observed between those ions that are near the solid and those at the pore center. Because the self-diffusion coefficient is faster as the distance from the solid increases, the ions that are at the pore center diffuse more quickly through the pore than those adsorbed closer to the wall. Thus our results could be used to design membranes to separate, e.g., aqueous NaCl from CsCl solutions. Research supported by the Department of Energy and, in part, by the National Science Foundation.

  11. Mangrove pore water exchange across a latitudinal gradient

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    We combined observations of the natural tracer radon (222Rn) with hydrodynamic models across a broad latitudinal gradient covering several climate zones to estimate pore water exchange rates in mangroves. Pore water exchange ranged from 2.1 to 35.5 cm d-1 from temperate to tropical regions and averaged 16.3 ± 5.1 cm d-1. If upscaled to the global weighted mangrove area, pore water exchange in mangroves would recirculate the entire volume of water overlying the continental shelf in less than 153 years. Although pore water exchange (recirculated seawater) and river discharge represent different pathways for water entering the coastal ocean, the estimated global mangrove pore water exchange would be equal to approximately one third of annual global river discharge to the ocean (3.84 × 1013 m3 yr-1). Because biogeochemical processes in mangroves are largely dependent on pore water exchange, these large exchange rates have major implications for coastal nutrient, carbon, and greenhouse gas cycling in tropical marine systems.

  12. Pore scale definition and computation from tomography data

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

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

    PubMed

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

    2016-04-19

    Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007)Proc Natl Acad Sci USA104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of[Formula: see text]wt % that is typical for concentrations in shallow lakes on early Earth. PMID:27044100

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

    PubMed

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

    2015-05-28

    Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (Φ)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed. PMID:25778700

  15. Impact of pore fluid composition changes on soil filter clogging

    SciTech Connect

    Reddi, L.N.; Bonala, M.V.S.

    1997-12-31

    Current design criteria for soil filters in geotechnical engineering are based on mechanical principles of straining alone without any physico-chemical considerations. Transport and deposition of colloid-size particles in the subsurface are influenced by pore fluid composition. It is essential to design filters in contaminated environment, such as those for leachate collection systems, with due considerations of the pore fluid composition. In this paper, the impact of changes in pore fluid composition on sod filter clogging is assessed with the help of a mathematical model. The role of pore fluid composition in soil filter clogging is studied by evaluating its effect on the erodibility of base soils, size of the migrating particles, and on the likelihood of particle deposition. The results suggest that pore fluid composition influences the deposition to the extent it can cause significant changes in pore clogging. In the cases where particles are generated from base soils, filter clogging increased at low salt concentrations but was limited by reduced erodibilities at high salt concentrations.

  16. Quantification of subsurface pore pressure through IODP drilling

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    It is critical to understand the magnitude and distribution of subsurface pore fluid pressure: it controls effective stress and thus mechanical strength, slope stability, and sediment compaction. Elevated pore pressures also drive fluid flows that serve as agents of mass, solute, and heat fluxes. The Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) have provided important avenues to quantify pore pressure in a range of geologic and tectonic settings. These approaches include 1) analysis of continuous downhole logs and shipboard physical properties data to infer compaction state and in situ pressure and stress, 2) laboratory consolidation testing of core samples collected by drilling, 3) direct downhole measurements using pore pressure probes, 3) pore pressure and stress measurements using downhole tools that can be deployed in wide diameter pipe recently acquired for riser drilling, and 4) long-term monitoring of formation pore pressure in sealed boreholes within hydraulically isolated intervals. Here, we summarize key advances in quantification of subsurface pore pressure rooted in scientific drilling, highlighting with examples from subduction zones, the Gulf of Mexico, and the New Jersey continental shelf. At the Nankai, Costa Rican, and Barbados subduction zones, consolidation testing of cores samples, combined with analysis of physical properties data, indicates that even within a few km landward of the trench, pore pressures in and below plate boundary décollement zones reach a significant fraction of the lithostatic load (λ*=0.25-0.91). These results document a viable and quantifiable mechanism to explain the mechanical weakness of subduction décollements, and are corroborated by a small number of direct measurements in sealed boreholes and by inferences from seismic reflection data. Recent downhole measurements conducted during riser drilling using the modular formation dynamics tester wireline tool (MDT) in a forearc basin ~50

  17. Modeling of seismic field in porous medium:Simulation study of single pore and pore ensemble effects

    NASA Astrophysics Data System (ADS)

    Shatskaya, A. A.; Nemirovich-Danchenko, M. M.; Terre, D. A.

    2015-11-01

    The article considers the effect of porous media on elastic wave field. Based on numerical modeling, diffraction pattern of the wave propagating through a single pore in carbonates has been produced. Matrix properties (calcite and dolomite) and fluid (water) are modeled based on thin core section image. The qualitative comparison with the available computational data has been performed. Provided that ensemble of pores is involved, the effect of porous medium on seismic field has been studied. For comparison with experimental data the model of porous sintered aluminum Al-6061 has been considered. The processing of numerical modeling results made it possible to estimate average velocities in the model of porous aluminum and compare them with physical modeling data. The provided estimates have indicated qualitative (single pore) and quantitative (ensemble of pores) correlation of simulation and experiment results.

  18. Neutrons measure phase behavior in pores at Angstrom size

    SciTech Connect

    Bardoel, Agatha A; Melnichenko, Yuri B

    2012-01-01

    Researchers have measured the phase behavior of green house gases in pores at the Angstrom-level, using small angle neutron scattering (SANS) at the Oak Ridge National Laboratory's High Flux Isotope Reactor. Yuri Melnichenko, an instrument scientist on the General Purpose Small Angle Neutron Scattering (GP SANS) Diffractometer at ORNL's High Flux Isotope Reactor, his postdoctoral associate Lilin He and collaborators Nidia Gallego and Cristian Contescu from the Material Sciences Division (ORNL) were engaged in the work. They were studying nanoporous carbons to assess their attractiveness as storage media for hydrogen, with a view to potential use for on-board hydrogen storage for transportation applications. Nanoporous carbons can also serve as electrode material for supercapacitors and batteries. The researchers successfully determined that the most efficiently condensing pore size in a carbon nanoporous material for hydrogen storage is less than one nanometer. In a paper recently published by the Journal of the American Chemical Society, the collaborators used small angle neutron scattering to study how hydrogen condenses in small pores at ambient temperature. They discovered that the surface-molecule interactions create internal pressures in pores that may exceed the external gas pressure by a factor of up to 50. 'This is an exciting result,' Melnichenko said, 'as you achieve extreme densification in pores 'for free', i.e. without spending any energy. These results can be used to guide the development of new carbon adsorbents tailored to maximize hydrogen storage capacities.' Another important factor that defines the adsorption capacity of sub-nanometer pores is their shape. In order to get accurate structural information and maximize sorption capacity, it is important that pores are small and of approximately uniform size. In collaboration with Drexel University's Yury Gogotsi who supplied the samples, Melnichenko and his collaborators used the GP SANS

  19. 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. PMID:25603366

  20. Pore-scale mechanisms of gas flow in tight sand reservoirs

    SciTech Connect

    Silin, D.; Kneafsey, T.J.; Ajo-Franklin, J.B.; Nico, P.

    2010-11-30

    Tight gas sands are unconventional hydrocarbon energy resource storing large volume of natural gas. Microscopy and 3D imaging of reservoir samples at different scales and resolutions provide insights into the coaredo not significantly smaller in size than conventional sandstones, the extremely dense grain packing makes the pore space tortuous, and the porosity is small. In some cases the inter-granular void space is presented by micron-scale slits, whose geometry requires imaging at submicron resolutions. Maximal Inscribed Spheres computations simulate different scenarios of capillary-equilibrium two-phase fluid displacement. For tight sands, the simulations predict an unusually low wetting fluid saturation threshold, at which the non-wetting phase becomes disconnected. Flow simulations in combination with Maximal Inscribed Spheres computations evaluate relative permeability curves. The computations show that at the threshold saturation, when the nonwetting fluid becomes disconnected, the flow of both fluids is practically blocked. The nonwetting phase is immobile due to the disconnectedness, while the permeability to the wetting phase remains essentially equal to zero due to the pore space geometry. This observation explains the Permeability Jail, which was defined earlier by others. The gas is trapped by capillarity, and the brine is immobile due to the dynamic effects. At the same time, in drainage, simulations predict that the mobility of at least one of the fluids is greater than zero at all saturations. A pore-scale model of gas condensate dropout predicts the rate to be proportional to the scalar product of the fluid velocity and pressure gradient. The narrowest constriction in the flow path is subject to the highest rate of condensation. The pore-scale model naturally upscales to the Panfilov's Darcy-scale model, which implies that the condensate dropout rate is proportional to the pressure gradient squared. Pressure gradient is the greatest near the matrix

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  2. Pore-pressure gradients, stresses, and induced earthquakes

    SciTech Connect

    Segall, P. . Geophysics Dept. Geological Survey, Menlo Park, CA )

    1992-01-01

    In the theory of poroelasticity, spatial gradients in pore-pressure enter the equilibrium equations in the same way as distributed body forces. Pore-pressure gradients are thus associated with poroelastic stresses in the same way that temperature gradients associated with thermoelastic stresses. The author has suggested that pore-pressure gradients caused by pumping are responsible for earthquakes near some oil and gas fields. Seismic data from a number of active oil and gas fields in California, Texas, Alberta, and elsewhere clearly show that earthquakes are occurring near fields where pore pressures have declined by several 10's of MPa. These observations can not be explained by changes in effective stress alone, which predicts that decreasing pore-fluid pressures tend to stabilize faults. He believes that poro-elastic stresses resulting from pore-fluid extraction are responsible for earthquakes in these situations. Fluid injection also induces poro-elastic stresses, however it is difficult to separate this effect from the destabilizing effect of increased pore-pressure within fault zones. To test the poroelastic model for induced seismicity, theoretical predictions are compared to data from a deep gas field in the Pyrenean foreland. Hundreds of shallow, small to moderate earthquakes have occurred there since 1969. The earthquakes are tightly clustered near the gas field. Reservoir pressure had declined by 30 MPa at the onset of seismicity. The relationship between average reservoir pressure decline and subsidence is remarkably linear, lending support to the linear poroelastic model. Using laboratory derived material parameters and in situ reservoir pressure measurements, it is possible to predict the surface deformations and the change in stress field without adjustable parameters. The computed vertical displacements are in good agreement with the observed subsidence. The poroelastic stress changes at the onset of seismicity are of the order of a few bars.

  3. A robust model for pore-water chemistry of clayrock

    NASA Astrophysics Data System (ADS)

    Gaucher, E. C.; Tournassat, C.; Pearson, F. J.; Blanc, P.; Crouzet, C.; Lerouge, C.; Altmann, S.

    2009-11-01

    The chemistry of pore water is an important property of clayrocks being considered as host rocks for long-term storage of radioactive waste. It may be difficult, if not impossible, to obtain water samples for chemical analysis from such rocks because of their low hydraulic conductivity. This paper presents an approach for calculating the pore-water compositions of clayrocks from laboratory-measured properties of core samples, including their leachable Cl and SO 4 concentrations and analysed exchangeable cations, and from mineral and cation exchange equilibria based on the formation mineralogy. New core sampling and analysis procedures are presented that reduce or quantify side reactions such as sample oxidation (e.g. pyrite) and soluble mineral dissolution (celestite, SrSO 4) that affect measured SO 4 concentrations and exchangeable cation distributions. The model considers phase equilibria only with minerals that are observed in the formation including the principal clay phases. The model has been used to calculate the composition of mobile pore water in the Callovo-Oxfordian clayrock and validated against measurements of water chemistry made in an underground research laboratory in that formation. The model reproduces the measured, in situ pore-water composition without any estimated parameters. All required parameters can be obtained from core sample analysis. We highlight the need to consider only those mineral phases which can be shown to be in equilibrium with contacting pore water. The consequence of this is that some conceptual models available in the literature appear not to be appropriate for modelling clayrocks, particularly those considering high temperature and/or high pressure detrital phases as chemical buffers of pore water. The robustness of our model with respect to uncertainties in the log K values of clay phases is also demonstrated. Large uncertainties in log K values for clay minerals have relatively small effects on modelled pore

  4. Detecting pore-lining regions in transmembrane protein sequences

    PubMed Central

    2012-01-01

    Background Alpha-helical transmembrane channel and transporter proteins play vital roles in a diverse range of essential biological processes and are crucial in facilitating the passage of ions and molecules across the lipid bilayer. However, the experimental difficulties associated with obtaining high quality crystals has led to their significant under-representation in structural databases. Computational methods that can identify structural features from sequence alone are therefore of high importance. Results We present a method capable of automatically identifying pore-lining regions in transmembrane proteins from sequence information alone, which can then be used to determine the pore stoichiometry. By labelling pore-lining residues in crystal structures using geometric criteria, we have trained a support vector machine classifier to predict the likelihood of a transmembrane helix being involved in pore formation. Results from testing this approach under stringent cross-validation indicate that prediction accuracy of 72% is possible, while a support vector regression model is able to predict the number of subunits participating in the pore with 62% accuracy. Conclusion To our knowledge, this is the first tool capable of identifying pore-lining regions in proteins and we present the results of applying it to a data set of sequences with available crystal structures. Our method provides a way to characterise pores in transmembrane proteins and may even provide a starting point for discovering novel routes of therapeutic intervention in a number of important diseases. This software is freely available as source code from: http://bioinf.cs.ucl.ac.uk/downloads/memsat-svm/. PMID:22805427

  5. Extending electromagnetic methods to map coastal pore water salinities

    USGS Publications Warehouse

    Greenwood, Wm. J.; Kruse, S.; Swarzenski, P.

    2006-01-01

    The feasibility of mapping pore water salinity based on surface electromagnetic (EM) methods over land and shallow marine water is examined in a coastal wetland on Tampa Bay, Florida. Forward models predict that useful information on seabed conductivity can be obtained through <1.5 m of saline water, using floating EM-31 and EM-34 instruments from Geonics Ltd. The EM-31 functioned as predicted when compared against resistivity soundings and pore water samples and proved valuable for profiling in otherwise inaccessible terrain due to its relatively small size. Experiments with the EM-34 in marine water, however, did not reproduce the theoretical instrument response. The most effective technique for predicting pore water conductivities based on EM data entailed (1) computing formation factors from resistivity surveys and pore water samples at representative sites and (2) combining these formation factors with onshore and offshore EM-31 readings for broader spatial coverage. This method proved successful for imaging zones of elevated pore water conductivities/ salinities associated with mangrove forests, presumably caused by salt water exclusion by mangrove roots. These zones extend 5 to 10 m seaward from mangrove trunks fringing Tampa Bay. Modeling indicates that EM-31 measurements lack the resolution necessary to image the subtle pore water conductivity variations expected in association with diffuse submarine ground water discharge of fresher water in the marine water of Tampa Bay. The technique has potential for locating high-contrast zones and other pore water salinity anomalies in areas not accessible to conventional marine- or land-based resistivity arrays and hence may be useful for studies of coastal-wetland ecosystems. Copyright ?? 2005 National Ground Water Association.

  6. Reservoir condition pore-scale imaging of multiple fluid phases using X-ray microtomography.

    PubMed

    Andrew, Matthew; Bijeljic, Branko; Blunt, Martin

    2015-01-01

    X-ray microtomography was used to image, at a resolution of 6.6 µm, the pore-scale arrangement of residual carbon dioxide ganglia in the pore-space of a carbonate rock at pressures and temperatures representative of typical formations used for CO2 storage. Chemical equilibrium between the CO2, brine and rock phases was maintained using a high pressure high temperature reactor, replicating conditions far away from the injection site. Fluid flow was controlled using high pressure high temperature syringe pumps. To maintain representative in-situ conditions within the micro-CT scanner a carbon fiber high pressure micro-CT coreholder was used. Diffusive CO2 exchange across the confining sleeve from the pore-space of the rock to the confining fluid was prevented by surrounding the core with a triple wrap of aluminum foil. Reconstructed brine contrast was modeled using a polychromatic x-ray source, and brine composition was chosen to maximize the three phase contrast between the two fluids and the rock. Flexible flow lines were used to reduce forces on the sample during image acquisition, potentially causing unwanted sample motion, a major shortcoming in previous techniques. An internal thermocouple, placed directly adjacent to the rock core, coupled with an external flexible heating wrap and a PID controller was used to maintain a constant temperature within the flow cell. Substantial amounts of CO2 were trapped, with a residual saturation of 0.203±0.013, and the sizes of larger volume ganglia obey power law distributions, consistent with percolation theory. PMID:25741751

  7. Reservoir Condition Pore-scale Imaging of Multiple Fluid Phases Using X-ray Microtomography

    PubMed Central

    Andrew, Matthew; Bijeljic, Branko; Blunt, Martin

    2015-01-01

    X-ray microtomography was used to image, at a resolution of 6.6 µm, the pore-scale arrangement of residual carbon dioxide ganglia in the pore-space of a carbonate rock at pressures and temperatures representative of typical formations used for CO2 storage. Chemical equilibrium between the CO2, brine and rock phases was maintained using a high pressure high temperature reactor, replicating conditions far away from the injection site. Fluid flow was controlled using high pressure high temperature syringe pumps. To maintain representative in-situ conditions within the micro-CT scanner a carbon fiber high pressure micro-CT coreholder was used. Diffusive CO2 exchange across the confining sleeve from the pore-space of the rock to the confining fluid was prevented by surrounding the core with a triple wrap of aluminum foil. Reconstructed brine contrast was modeled using a polychromatic x-ray source, and brine composition was chosen to maximize the three phase contrast between the two fluids and the rock. Flexible flow lines were used to reduce forces on the sample during image acquisition, potentially causing unwanted sample motion, a major shortcoming in previous techniques. An internal thermocouple, placed directly adjacent to the rock core, coupled with an external flexible heating wrap and a PID controller was used to maintain a constant temperature within the flow cell. Substantial amounts of CO2 were trapped, with a residual saturation of 0.203 ± 0.013, and the sizes of larger volume ganglia obey power law distributions, consistent with percolation theory. PMID:25741751

  8. Pore networks in continental and marine mudstones: Characteristics and controls on sealing behavior

    USGS Publications Warehouse

    Heath, J.E.; Dewers, T.A.; McPherson, B.J.O.L.; Petrusak, R.; Chidsey, T.C.; Rinehart, A.J.; Mozley, P.S.

    2011-01-01

    Mudstone pore networks are strong modifiers of sedimentary basin fluid dynamics and have a critical role in the distribution of hydrocarbons and containment of injected fluids. Using core samples from continental and marine mudstones, we investigate properties of pore types and networks from a variety of geologic environments, together with estimates of capillary beam- scanning electron microscopy, suggest seven dominant mudstone pore types distinguished by geometry and connectivity. A dominant planar pore type occurs in all investigated mudstones and generally has high coordination numbers (i.e., number of neighboring connected pores). Connected networks of pores of this type contribute to high mercury capillary pressures due to small pore throats at the junctions of connected pores and likely control most matrix transport in these mudstones. Other pore types are related to authigenic (e.g., replacement or pore-lining precipitation) clay minerals and pyrite nodules; pores in clay packets adjacent to larger, more competent clastic grains; pores in organic phases; and stylolitic and microfracture-related pores. Pores within regions of authigenic clay minerals often form small isolated networks (<3 ??m). Pores in stringers of organic phases occur as tubular pores or slit- and/or sheet-like pores. These form short, connected lengths in 3D reconstructions, but appear to form networks no larger than a few microns in size. Sealing efficiency of the studied mudstones increases with greater distal depositional environments and greater maximum depth of burial. ?? 2011 Geological Society of America.

  9. Idealized Shale Sorption Isotherm Measurements to Determine Pore Volume, Pore Size Distribution, and Surface Area

    NASA Astrophysics Data System (ADS)

    Holmes, R.; Wang, B.; Aljama, H.; Rupp, E.; Wilcox, J.

    2014-12-01

    One method for mitigating the impacts of anthropogenic CO2-related climate change is the sequestration of CO2 in depleted gas and oil reservoirs, including shale. The accurate characterization of the heterogeneous material properties of shale, including pore volume, surface area, pore size distributions (PSDs) and composition is needed to understand the interaction of CO2 with shale. Idealized powdered shale sorption isotherms were created by varying incremental amounts of four essential components by weight. The first two components, organic carbon and clay, have been shown to be the most important components for CO2 uptake in shales. Organic carbon was represented by kerogen isolated from a Silurian shale, and clay groups were represented by illite from the Green River shale formation. The rest of the idealized shale was composed of equal parts by weight of SiO2 to represent quartz and CaCO3 to represent carbonate components. Baltic, Eagle Ford, and Barnett shale sorption measurements were used to validate the idealized samples. The idealized and validation shale sorption isotherms were measured volumetrically using low pressure N2 (77K) and CO2 (273K) adsorbates on a Quantachrome Autosorb IQ2. Gravimetric isotherms were also produced for a subset of these samples using CO2 and CH4adsorbates under subsurface temperature and pressure conditions using a Rubotherm magnetic suspension balance. Preliminary analyses were inconclusive in validating the idealized samples. This could be a result of conflicting reports of total organic carbon (TOC) content in each sample, a problem stemming from the heterogeneity of the samples and different techniques used for measuring TOC content. The TOC content of the validation samples (Eagle Ford and Barnett) was measured by Rock-Eval pyrolysis at Weatherford Laboratories, while the TOC content in the Baltic validation samples was determined by LECO TOC. Development of a uniform process for measuring TOC in the validation samples is

  10. Final Report for Subcontract B541028, Pore-Scale Modeling to Support "Pore Connectivity" Research Work

    SciTech Connect

    Ewing, R P

    2009-02-25

    This report covers modeling aspects of a combined experimental and modeling task in support of the DOE Science and Technology Program (formerly OSTI) within the Office of Civilian Radioactive Waste Management (OCRWM). Research Objectives The research for this project dealt with diffusive retardation: solute moving through a fracture diffuses into and out of the rock matrix. This diffusive exchange retards overall solute movement, and retardation both dilutes waste being released, and allows additional decay. Diffusive retardation involves not only fracture conductivity and matrix diffusion, but also other issues and processes: contaminants may sorb to the rock matrix, fracture flow may be episodic, a given fracture may or may not flow depending on the volume of flow and the fracture's connection to the overall fracture network, the matrix imbibes water during flow episodes and dries between episodes, and so on. The objective of the project was to improve understanding of diffusive retardation of radionuclides due to fracture / matrix interactions. Results from combined experimental/modeling work were to (1) determine whether the current understanding and model representation of matrix diffusion is valid, (2) provide insights into the upscaling of laboratory-scale diffusion experiments, and (3) help in evaluating the impact on diffusive retardation of episodic fracture flow and pore connectivity in Yucca Mountain tuffs. Questions explored included the following: (1) What is the relationship between the diffusion coefficient measured at one scale, to that measured or observed at a different scale? In classical materials this relationship is trivial; in low-connectivity materials it is not. (2) Is the measured diffusivity insensitive to the shape of the sample? Again, in classical materials there should be no sample shape effect. (3) Does sorption affect diffusive exchange in low-connectivity media differently than in classical media? (4) What is the effect of matrix

  11. Assessment of Image Processing and Resolution on Permeability and Drainage Simulations Through 3D Pore-networks Obtained Using X-ray Computed Tomography

    NASA Astrophysics Data System (ADS)

    Mills, G.; Willson, C. S.; Thompson, K. E.; Rivers, M. L.

    2013-12-01

    Typically, continuum-scale flow parameters are obtained through laboratory experiments. Over the past several years, image-based modeling, which is a direct simulation of flow through the structural arrangements of the voids and solids obtained using X-ray computed tomography (XCT) in a sample porous medium, has become a reliable technique for predicting certain flow parameters. Even though XCT is capable of resolving micron-level details, the voxel resolution of the reconstructed image is still dependent upon a number of factors, including the sample size, X-ray energy and XCT beamline setup. Thus, each imaging experiment requires a tradeoff between the sample size that can be imaged, the voxel resolution, and the length scale of the pore space that can be extracted. In addition, the geometric and topological properties of the void space and 3D pore network structure are dictated by the image processing and the choice of pore network generation method. In this research, image-based pore network models are used to quantitatively assess the impact of image resolution, image processing and the choice of pore network generation methods on simulated parameters. A 5 mm diameter and ~15 mm in length Berea sandstone core was scanned two times. First, a ~12 mm long section of the entire cross-section was scanned at 4.1 micron voxel resolution; next, a ~1.4 mm diameter and ~4.12 mm length section within the 1st domain was scanned at 1 micron voxel resolution. The resulting 3D datasets were filtered and segmented into solid and void space. The low resolution image was filtered and segmented using two different approaches in order to evaluate the potential of each approach in identifying the different solid phases in the original 16 bit dataset. A set of networks were created by varying the pore density on both the high and low resolution datasets in order to assess the impact of these factors on flow simulations. Single-phase permeability and a two-phase drainage pore

  12. The mitochondrial permeability transition pore in AD 2016: An update.

    PubMed

    Biasutto, Lucia; Azzolini, Michele; Szabò, Ildikò; Zoratti, Mario

    2016-10-01

    Over the past 30years the mitochondrial permeability transition - the permeabilization of the inner mitochondrial membrane due to the opening of a wide pore - has progressed from being considered a curious artifact induced in isolated mitochondria by Ca(2+) and phosphate to a key cell-death-inducing process in several major pathologies. Its relevance is by now universally acknowledged and a pharmacology targeting the phenomenon is being developed. The molecular nature of the pore remains to this day uncertain, but progress has recently been made with the identification of the FOF1 ATP synthase as the probable proteic substrate. Researchers sharing this conviction are however divided into two camps: these believing that only the ATP synthase dimers or oligomers can form the pore, presumably in the contact region between monomers, and those who consider that the ring-forming c subunits in the FO sector actually constitute the walls of the pore. The latest development is the emergence of a new candidate: Spastic Paraplegia 7 (SPG7), a mitochondrial AAA-type membrane protease which forms a 6-stave barrel. This review summarizes recent developments of research on the pathophysiological relevance and on the molecular nature of the mitochondrial permeability transition pore. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou. PMID:26902508

  13. Regulation of soil organic C mineralisation at the pore scale.

    PubMed

    Ruamps, Léo S; Nunan, Naoise; Pouteau, Valérie; Leloup, Julie; Raynaud, Xavier; Roy, Virginie; Chenu, Claire

    2013-10-01

    Little is known about the factors that regulate C mineralisation at the soil pore scale or how these factors vary throughout the pore network. This study sought to understand how the decomposition of organic carbon varies within the soil pore network and to determine the relative importance of local environmental properties relative to biological properties as controlling factors. This was achieved by sterilising samples of soil and reinoculating them with axenic bacterial suspensions using the matric potential to target different locations in the pore network. Carbon mineralisation curves were described with two-compartment first-order models to distinguish CO2 derived from the labile organic carbon released during sterilisation from CO2 derived from organic C unaffected by sterilisation. The data indicated that the size of the labile pool of organic C, possibly of microbial origin, varied as a function of location in the pore network but that the organic carbon unaffected by sterilisation did not. The mineralisation rate of the labile C varied with the bacterial type inoculated, but the mineralisation rate of the organic C unaffected by sterilisation was insensitive to bacterial type. Taken together, the results suggest that microbial metabolism is a less significant regulator of soil organic carbon decomposition than are microbial habitat properties. PMID:23346944

  14. Statistical geometry of pores and statistics of porous nanofibrous assemblies

    PubMed Central

    Eichhorn, Stephen J; Sampson, William W

    2005-01-01

    The application of theoretical models to describe the structure of the types of fibrous network produced by the electrospinning of polymers for use in tissue engineering and a number of other applications is presented. Emphasis is placed on formal analyses of the pore size distribution and porosities that one would encounter with such structures and the nature of their relationships with other structural characteristics likely to be important for the performance of nanofibrous materials. The theoretical structures considered result from interactions between randomly placed straight rods that represent fibres with nanoscale dimensions. The dominant role of fibre diameter in controlling the pore diameter of the networks is shown and we discuss the perhaps counter-intuitive finding that at a given network mass per unit area and porosity, increasing fibre diameter results in an increase in mean pore radius. Larger pores may be required for ingrowth of cells to nanofibrous networks, hence this study clarifies that simply making the diameters of the fibres smaller might not be the way to improve cell proliferation on such substrates. An extensive review of structural features of the network such as the distribution of mass, inter-fibre contacts and available surface for cell attachment, fibre contact distributions for integrity of the networks and the porosity and pore size distributions is given, with emphasis placed on nanofibre dimensions for the first time. PMID:16849188

  15. Pore Water Collection, Analysis and Evolution: The Need for Standardization.

    PubMed

    Gruzalski, Jacob G; Markwiese, James T; Carriker, Neil E; Rogers, William J; Vitale, Rock J; Thal, David I

    2016-01-01

    Investigating the ecological impacts of contaminants released into the environment requires integration of multiple lines of evidence. Collection and analysis of interstitial water is an often-used line of evidence for developing benthic exposure estimates in aquatic ecosystems. It is a well-established principle that chemical and toxicity data on interstitial water samples should represent in-situ conditions; i.e., sample integrity must be maintained throughout the sample collection process to avoid alteration of the in-situ geochemical conditions. Unfortunately, collection and processing of pore water is not standardized to address possible geochemical transformations introduced by atmospheric exposure. Furthermore, there are no suitable benchmarks (ecological or human health) against which to evaluate adverse effects from chemicals in pore water; i.e., empirical data is lacking on the toxicity of inorganic contaminants in sediment interstitial water. It is clear that pore water data is best evaluated by considering the bioavailability of trace elements and the partitioning of contaminants between the aqueous and solid phases. It is also evident that there is a need for sediment researchers and regulatory agencies to collaborate in developing a standardized approach for sediment/pore water collection and data evaluation. Without such guidelines, the number of different pore water collection and extraction techniques will continue to expand, and investigators will continue to evaluate potentially questionable data by comparison to inappropriate criteria. PMID:26613987

  16. The role of pore geometry in single nanoparticle detection

    SciTech Connect

    Davenport, Matthew; Healy, Ken; Pevarnik, Matthew; Teslich, Nick; Cabrini, Stefano; Morrison, Alan P.; Siwy, Zuzanna S.; Letant, Sonia E.

    2012-08-22

    In this study, we observe single nanoparticle translocation events via resistive pulse sensing using silicon nitride pores described by a range of lengths and diameters. Pores are prepared by focused ion beam milling in 50 nm-, 100 nm-, and 500 nm-thick silicon nitride membranes with diameters fabricated to accommodate spherical silica nanoparticles with sizes chosen to mimic that of virus particles. In this manner, we are able to characterize the role of pore geometry in three key components of the detection scheme, namely, event magnitude, event duration, and event frequency. We find that the electric field created by the applied voltage and the pore’s geometry is a critical factor. We develop approximations to describe this field, which are verified with computer simulations, and interactions between particles and this field. In so doing, we formulate what we believe to be the first approximation for the magnitude of ionic current blockage that explicitly addresses the invariance of access resistance of solid-state pores during particle translocation. These approximations also provide a suitable foundation for estimating the zeta potential of the particles and/or pore surface when studied in conjunction with event durations. We also verify that translocation achieved by electro-osmostic transport is an effective means of slowing translocation velocities of highly charged particles without compromising particle capture rate as compared to more traditional approaches based on electrophoretic transport.

  17. The role of pore geometry in single nanoparticle detection

    DOE PAGESBeta

    Davenport, Matthew; Healy, Ken; Pevarnik, Matthew; Teslich, Nick; Cabrini, Stefano; Morrison, Alan P.; Siwy, Zuzanna S.; Letant, Sonia E.

    2012-08-22

    In this study, we observe single nanoparticle translocation events via resistive pulse sensing using silicon nitride pores described by a range of lengths and diameters. Pores are prepared by focused ion beam milling in 50 nm-, 100 nm-, and 500 nm-thick silicon nitride membranes with diameters fabricated to accommodate spherical silica nanoparticles with sizes chosen to mimic that of virus particles. In this manner, we are able to characterize the role of pore geometry in three key components of the detection scheme, namely, event magnitude, event duration, an