155,412 research outputs found
Yield stress fluids method to determine the pore size distribution of a porous medium
No full textIn this paper a new method is presented in order to determine the pore size distribution in a porous medium. This original technique uses the rheological properties of some non-Newtonian yield stress fluids flowing through the porous sample. This technique is based on the capillary bundle model (like the other classical methods) which, despite its apparent simplicity, is capable of properly characterizing the percolating pore size distribution. Then this distribution can be simply obtained from the measurement of the total flow rate as a function of the imposed pressure gradient. The present technique is successfully tested analytically and numerically for usual pore size distributions such as the Gaussian mono and multimodal distributions, using Bingham and Casson fluids. The technique can also be extended to any yield stress fluid and any kind of distribution
What have we learned from two-pore potassium channels? Their molecular configuration and function in the human heart
No full textTwo-pore domain potassium channels (K2P) control excitability, stabilize the resting
membrane potential below firing threshold, and accelerate repolarisation in different cells. Until
now, fifteen different genes for the six K2P channel subfamily were cloned. The pore-forming
part is translated from two genes and they are built up from a dimer of two two-unit transmembrane
domains functioning with a wide spectrum of physiological profiles. K2P ion channels
were discovered in the last two decades and gave novel opportunity to recognize the complex
molecular mechanism of the potassium ion flux, and may lead to the design of individual drug
targeting in the future. In this review, we summarise the structure, function, channelopathies
and pharmacological silhouette of the two-pore potassium channels in the human tissues. In
addition, we present the computer model of the partially reconstructed wild type K2P1/TWIK1
lacking the intracellular C and N terminal loop
Pore structure characterization of low permeability rocks
No full textTese (doutorado) - Universidade Federal de Santa Catarina, Centro Tecnológico, Programa de Pós-Graduação em Ciência e Engenharia de Materiais, Florianópolis, 2014.Hoje as pesquisas em rochas de baixa permeabilidade (grande tendência no mundo e em breve na indústria petrolífera brasileira) se voltam à escala de poros seja para investigação petrofísica, morfológica, de distribuição de tamanhos de grãos ou poros ou escoamento de fluidos, prática descrita pelos valores de permeabilidade. A avaliação destas propriedades por sua vez, é essencial ao desenvolvimento e exploração de reservas de hidrocarbonetos. No entanto, a determinação de parâmetros do sistema poroso nessas rochas, arenitos de baixa permeabilidade (TGS) e rochas selantes (SR), continua a ser um grande desafio devido à extrema variabilidade de ambientes deposicionais e complexa microestrutura composta por argilas e tamanhos de poros de submícrons a ångströms. Nesta tese empregou-se um conjunto de técnicas experimentais para a caracterização da estrutura porosa de TGS e SR. De tal modo, o trabalho foi dividido em dois tópicos principais: (i) Caracterização do sistema poroso e propriedades petrofísicas em TGS utilizando-se as técnicas de permeabilidade por decaimento de pulso (PDP), NMR de baixo campo, adsorção gasosa N2 (N2GA), porosimetria por intrusão Hg (MICP), nano- e microtomografia de raios X (res. Abstract : Nowadays, significant research effort in low-permeability rocks (a wide tendency elsewhere and soon in the Brazilian petroleum industry) has been focused on pore-scale petrophysics, morphologies and distributions, as well as fluid flow circulation described by the values of permeability. The evaluation of these properties in turn is essential for the assessment and exploitation of hydrocarbon reserves; however, determining pore system parameters in such rocks as tight gas sandstones (TGS) and seal rocks (SR) remains challenging because of the extreme variability in depositional environments resulting in complex pore structures comprised by clays and length scales from sub-microns to Angstroms. In this work we applied a set of techniques to characterize submicron-pore structures in TGS and SR. Therefore it was divided into two main topics of interest: (i) Characterization of petrophysical properties and pore systems in very low permeability TGS using Pulse-Decay Permeability (PDP), Low Field Nuclear Magnetic Resonance (LFNMR), Nitrogen Gas Adsorption (N2GA), Mercury Intrusion Capillary Pressure (MICP) and Multi-scale 3D X-ray Nano- and MicroCT (down to 0.7 µm resolution) techniques; (ii) Study of Photoacoustic Spectrometry (PAS) for determining thermal diffusivity (TD) and porosity in three seal rocks originating from dissimilar fields as a key issue for safe exploration, storage purposes (CO2 sequestration) and developments in shale characterization. The values obtained for TD were between 0.01667 and 0.09298 (cm2/s) while porosity ranged from 1.42 to 9%. For the analyzed TGS the 3D pore-structure characterization lead to pore tortuosity and shape factors ranges of 2.19-5.47 and 3.2-8.5, respectively, and pore size distributions tended to be bimodal for MICP, trimodal for 3D multi-scale and tetramodal for LFNMR measurements. The porosity values ranged from 1.94 to 11.96% obtained by the combination of N2GA and MICP techniques and permeability from 0.036 to 0.00066 mD by PDP technique. The measured pore-structure parameters were also used to predict empirical permeability in TGS (using e.g. Carman-Kozeny (Dullien, 1992) and Coates (1999) models). The set of applied methods has shown to be a useful tool for the unconventional reservoir characterization since it allows obtaining pore morphological and quantitative parameters which account for the permeability values
The selectivity, voltage-dependence and acid sensitivity of the tandem pore potassium channel TASK-1 : contributions of the pore domains
No full textWe have investigated the contribution to ionic
selectivity of residues in the selectivity filter and pore
helices of the P1 and P2 domains in the acid sensitive
potassium channel TASK-1. We used site directed mutagenesis
and electrophysiological studies, assisted by structural
models built through computational methods. We have
measured selectivity in channels expressed in Xenopus
oocytes, using voltage clamp to measure shifts in reversal
potential and current amplitudes when Rb+ or Na+ replaced
extracellular K+. Both P1 and P2 contribute to selectivity,
and most mutations, including mutation of residues in the
triplets GYG and GFG in P1 and P2, made channels nonselective.
We interpret the effects of these—and of other
mutations—in terms of the way the pore is likely to be
stabilised structurally. We show also that residues in the
outer pore mouth contribute to selectivity in TASK-1.
Mutations resulting in loss of selectivity (e.g. I94S, G95A)
were associated with slowing of the response of channels to
depolarisation. More important physiologically, pH sensitivity
is also lost or altered by such mutations. Mutations
that retained selectivity (e.g. I94L, I94V) also retained their
response to acidification. It is likely that responses both to
voltage and pH changes involve gating at the selectivity filter
Structural insights into Clostridium perfringens delta toxin pore formation
No full textClostridium perfringens Delta toxin is one of the three hemolysin-like proteins produced by C. perfringens type C and possibly type B strains. One of the others, NetB, has been shown to be the major cause of Avian Nectrotic Enteritis, which following the reduction in use of antibiotics as growth promoters, has become an emerging disease of industrial poultry. Delta toxin itself is cytotoxic to the wide range of human and animal macrophages and platelets that present GM2 ganglioside on their membranes. It has sequence similarity with Staphylococcus aureus β-pore forming toxins and is expected to heptamerize and form pores in the lipid bilayer of host cell membranes. Nevertheless, its exact mode of action remains undetermined. Here we report the 2.4 Å crystal structure of monomeric Delta toxin. The superposition of this structure with the structure of the phospholipid-bound F component of S. aureus leucocidin (LukF) revealed that the glycerol molecules bound to Delta toxin and the phospholipids in LukF are accommodated in the same hydrophobic clefts, corresponding to where the toxin is expected to latch onto the membrane, though the binding sites show significant differences. From structure-based sequence alignment with the known structure of staphylococcal α-hemolysin, a model of the Delta toxin pore form has been built. Using electron microscopy, we have validated our model and characterized the Delta toxin pore on liposomes. These results highlight both similarities and differences in the mechanism of Delta toxin (and by extension NetB) cytotoxicity from that of the staphylococcal pore-forming toxins
The response of the tandem pore potassium channel TASK-3 (K2P9.1) to voltage : gating at the cytoplasmic mouth
No full textAlthough the tandem pore potassium channel TASK-3 is thought to open and shut at its
selectivity filter in response to changes of extracellular pH, it is currently unknown whether the
channel also shows gating at its inner, cytoplasmic mouth through movements of membrane
helices M2 and M4.We used two electrode voltage clamp and single channel recording to show
that TASK-3 responds to voltage in a way that reveals such gating. In wild-type channels, Popen
was very low at negative voltages, but increased with depolarisation. The effect of voltage was
relatively weak and the gating charge small, ∼0.17.Mutants A237T (in M4) and N133A (in M2)
increased Popen at a given voltage, increasing mean open time and the number of openings per
burst. In addition, the relationship between Popen andvoltagewas shifted to lesspositive voltages.
Mutation of putative hinge glycines (G117A, G231A), residues that are conserved throughout
the tandem pore channel family, reduced Popen at a given voltage, shifting the relationship
with voltage to a more positive potential range. None of these mutants substantially affected
the response of the channel to extracellular acidification. We have used the results from single
channel recording to develop a simple kinetic model to show how gating occurs through two
classes of conformation change, with two routes out of the open state, as expected if gating
occurs both at the selectivity filter and at its cytoplasmic mouth
Identification of a key residue for Oligomerisation and pore-formation of Clostridium perfringens NetB
No full textNecrotic enteritis toxin B (NetB) is a β-pore-forming toxin produced by Clostridium perfringens and has been identified as a key virulence factor in the pathogenesis of avian necrotic enteritis, a disease causing significant economic damage to the poultry industry worldwide. In this study, site-directed mutagenesis was used to identify amino acids that play a role in NetB oligomerisation and pore-formation. NetB K41H showed significantly reduced toxicity towards LMH cells and human red blood cells relative to wild type toxin. NetB K41H was unable to oligomerise and form pores in liposomes. These findings suggest that NetB K41H could be developed as a genetic toxoid vaccine to protect against necrotic enteritis
Gas hydrate growth and dissociation in narrow pore networks: capillary inhibition and hysteresis phenomena
No full textMarine sediments hosting gas hydrates are commonly fine-grained (silts, muds, clays)
with very narrow mean pore diameters (0.1 mm). This has led to speculation that capillary
phenomena could play an important role in controlling hydrate distribution in the seafloor, and
may be in part responsible for discrepancies between observed and predicted (from bulk phase
equilibria) hydrate stability zone (HSZ) thicknesses. Numerous recent laboratory studies have confirmed
a close relationship between hydrate inhibition and pore size, stability being reduced in
narrow pores; however, to date the focus has been hydrate dissociation conditions in porous
media, with capillary controls on the equally important process of hydrate growth being largely
neglected. Here, we present experimental methane hydrate growth and dissociation conditions
for synthetic mesoporous silicas over a range of pressure–temperature (PT) conditions (273–
293 K, to 20 MPa) and pore size distributions. Results demonstrate that hydrate formation and
decomposition in narrow pore networks is characterized by a distinct hysteresis: solid growth
occurs at significantly lower temperatures (or higher pressures) than dissociation. Hysteresis
takes the form of repeatable, irreversible closed primary growth and dissociation PT loops,
within which various characteristic secondary ‘scanning’ curve pathways may be followed.
Similar behaviour has recently been observed for ice–water systems in porous media, and is
characteristic of liquid–vapour transitions in mesoporous materials. The causes of such hysteresis
are still not fully understood; our results suggest pore blocking during hydrate growth as a
primary cause
Cohesiveness tunes assembly and morphology of FG nucleoporin domain meshworks – Implications for nuclear pore permeability
No full textNuclear pore complexes control the exchange of macromolecules between the cytoplasm and the nucleus. A selective permeability barrier that arises from a supramolecular assembly of intrinsically unfolded nucleoporin domains rich in phenylalanine-glycine dipeptides (FG domains) fills the nuclear pore. There is increasing evidence that selective transport requires cohesive FG domain interactions. To understand the functional roles of cohesive interactions, we studied monolayers of end-grafted FG domains as a bottom-up nanoscale model system of the permeability barrier. Based on detailed physicochemical analysis of the model films and comparison of the data with polymer theory, we propose that cohesiveness is tuned to promote rapid assembly of the permeability barrier and to generate a stable and compact pore-filling meshwork with a small mesh size. Our results highlight the functional importance of weak interactions, typically a few kBT per chain, and contribute important information to understand the mechanism of size-selective transport
Virus-sized colloid transport in a single pore: Model development and sensitivity analysis
No full textA mathematical model is developed to simulate the transport and deposition of virus-sized colloids in a cylindrical pore throat considering various processes such as advection, diffusion, colloid–collector surface interactions and hydrodynamic wall effects. The pore space is divided into three different regions, namely, bulk, diffusion and potential regions, based on the dominant processes acting in each of these regions. In the bulk region, colloid transport is governed by advection and diffusion whereas in the diffusion region, colloid mobility due to diffusion is retarded by hydrodynamic wall effects. Colloid–collector interaction forces dominate the transport in the potential region where colloid deposition occurs. The governing equations are non-dimensionalized and solved numerically. A sensitivity analysis indicates that the virus-sized colloid transport and deposition is significantly affected by various pore-scale parameters such as the surface potentials on colloid and collector, ionic strength of the solution, flow velocity, pore size and colloid size. The adsorbed concentration and hence, the favorability of the surface for adsorption increases with: (i) decreasing magnitude and ratio of surface potentials on colloid and collector, (ii) increasing ionic strength and (iii) increasing pore radius. The adsorbed concentration increases with increasing Pe, reaching a maximum value at Pe = 0.1 and then decreases thereafter. Also, the colloid size significantly affects particle deposition with the adsorbed concentration increasing with increasing particle radius, reaching a maximum value at a particle radius of 100 nm and then decreasing with increasing radius. System hydrodynamics is found to have a greater effect on larger particles than on smaller ones. The secondary minimum contribution to particle deposition has been found to increase as the favorability of the surface for adsorption decreases. The sensitivity of the model to a given parameter will be high if the conditions are favorable for adsorption. The results agree qualitatively with the column-scale experimental observations available in the literature. The current model forms the building block in upscaling colloid transport from pore scale to Darcy scale using Pore-Network Modeling
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