The Experts below are selected from a list of 309 Experts worldwide ranked by ideXlab platform

Alexander M Berezhkovskii - One of the best experts on this subject based on the ideXlab platform.

  • two site versus continuum diffusion model of blocker dynamics in a Membrane Channel comparative analysis of escape kinetics
    Journal of Chemical Physics, 2019
    Co-Authors: Leonardo Dagdug, Alexander M Berezhkovskii, Sergey M Bezrukov
    Abstract:

    This paper deals with the escape of a charged blocker molecule from a voltage-biased Membrane Channel with a constriction zone which the molecule cannot pass through. Recently, we developed a two-site model of the blocker dynamics in such a system and applied it to analyze the escape kinetics. Here, we compare the decay of the blocker survival probability predicted by the two-site model with that for the survival probability given by a more accurate model which assumes continuum diffusion of the blocker molecule inside the Channel. The main finding of the present work is that both models predict the same decay of the survival probability at long times. This result is of practical importance since only the long-time tail of the survival probability can be studied in single-Channel experiments in which, due to a limited time resolution, only long-lasting individual events of Channel blockades can be measured.This paper deals with the escape of a charged blocker molecule from a voltage-biased Membrane Channel with a constriction zone which the molecule cannot pass through. Recently, we developed a two-site model of the blocker dynamics in such a system and applied it to analyze the escape kinetics. Here, we compare the decay of the blocker survival probability predicted by the two-site model with that for the survival probability given by a more accurate model which assumes continuum diffusion of the blocker molecule inside the Channel. The main finding of the present work is that both models predict the same decay of the survival probability at long times. This result is of practical importance since only the long-time tail of the survival probability can be studied in single-Channel experiments in which, due to a limited time resolution, only long-lasting individual events of Channel blockades can be measured.

  • blocker escape kinetics from a Membrane Channel analyzed by mapping blocker diffusive dynamics onto a two site model
    Journal of Chemical Physics, 2019
    Co-Authors: Alexander M Berezhkovskii, Sergey M Bezrukov
    Abstract:

    : When a large solute molecule enters a Membrane Channel from the Membrane-bathing electrolyte solution, it blocks the small-ion current flowing through the Channel. If the molecule spends in the Channel sufficiently long time, individual blockades can be resolved in single-Channel experiments. In this paper, we develop an analytical theory of the blocker escape kinetics from the Channel, assuming that a charged blocking molecule cannot pass through a constriction region (bottleneck). We focus on the effect of the external voltage bias on the blocker survival probability in the Channel. The bias creates a potential well for the charged blocker in the Channel with the minimum located near the bottleneck. When the bias is strong, the well is deep, and escape from the Channel is a slow process that allows for time-resolved observation of individual blocking events. Our analysis is performed in the framework of a two-site model of the blocker dynamics in the Channel. Importantly, the rate constants, fully determining this model, are derived from a more realistic continuum diffusion model. This is done by mapping the latter onto its two-site counterpart which, while being much simpler, captures the main features of the blocker escape kinetics at high biases.

  • Relaxation and fluctuations of the number of particles in a Membrane Channel at arbitrary particle-Channel interaction
    Journal of Chemical Physics, 2008
    Co-Authors: Vladimir Yu. Zitserman, Alexander M Berezhkovskii, Mark A. Pustovoit, Sergey M Bezrukov
    Abstract:

    We analyze the relaxation of the particle number fluctuations in a Membrane Channel at arbitrary particle-Channel interaction and derive general expressions for the relaxation time and low-frequency limit of the power spectral density. These expressions simplify significantly when the Channel is symmetric. For a square-well potential of mean force that occupies the entire Channel, we verify the accuracy of the analytical predictions by Brownian dynamics simulations. For such a Channel we show that as the depth of the well increases, the familiar scaling of the relaxation time with the Channel length squared is transformed into a linear dependence on the length.

  • Counting translocations of strongly repelling particles through single Channels: Fluctuation theorem for Membrane transport
    Physical Review Letters, 2008
    Co-Authors: Alexander M Berezhkovskii, Sergey M Bezrukov
    Abstract:

    Transport of strongly repelling particles through a single Membrane Channel is analyzed assuming that the Channel cannot be occupied by more than one particle. An exact solution is found for the Laplace transform of the probability P_{n}(t) that n particles have been transported in time t. This transform is used to find the flux through the Channel and to show that P_{n}(t) and P_{-n}(t) are related by the fluctuation theorem. The solution is obtained using an observation that P_{n}(t) is the propagator for a non-Markovian random walk, which can be found by solving a set of integral equations.

  • Diffusion-limited binding to a site on the wall of a Membrane Channel.
    Journal of Chemical Physics, 2006
    Co-Authors: Leonardo Dagdug, Alexander M Berezhkovskii
    Abstract:

    The authors develop a theory of diffusion-controlled reactions with a site located on the wall of a cylindrical Membrane Channel that connects two reservoirs containing diffusing particles which are trapped by the site at the first contact. An expression for the Laplace transform of the rate coefficient, k(t), is derived assuming that the size of the site is small compared to the Channel radius. The expression is used to find the stationary value of the rate coefficient, k(∞), as a function of the length and radius of the Channel, the radius of the site, and its position inside the Channel (distances from the two ends of the Channel) as well as the particle diffusion constants in the bulk and in the Channel. Their derivation is based on the one-dimensional description of the particle motion in the Channel, which is generalized to include binding to the site into consideration. The validity of the approximate one-dimensional description of diffusion and binding was checked by three-dimensional Brownian dyn...

Sergey M Bezrukov - One of the best experts on this subject based on the ideXlab platform.

  • two site versus continuum diffusion model of blocker dynamics in a Membrane Channel comparative analysis of escape kinetics
    Journal of Chemical Physics, 2019
    Co-Authors: Leonardo Dagdug, Alexander M Berezhkovskii, Sergey M Bezrukov
    Abstract:

    This paper deals with the escape of a charged blocker molecule from a voltage-biased Membrane Channel with a constriction zone which the molecule cannot pass through. Recently, we developed a two-site model of the blocker dynamics in such a system and applied it to analyze the escape kinetics. Here, we compare the decay of the blocker survival probability predicted by the two-site model with that for the survival probability given by a more accurate model which assumes continuum diffusion of the blocker molecule inside the Channel. The main finding of the present work is that both models predict the same decay of the survival probability at long times. This result is of practical importance since only the long-time tail of the survival probability can be studied in single-Channel experiments in which, due to a limited time resolution, only long-lasting individual events of Channel blockades can be measured.This paper deals with the escape of a charged blocker molecule from a voltage-biased Membrane Channel with a constriction zone which the molecule cannot pass through. Recently, we developed a two-site model of the blocker dynamics in such a system and applied it to analyze the escape kinetics. Here, we compare the decay of the blocker survival probability predicted by the two-site model with that for the survival probability given by a more accurate model which assumes continuum diffusion of the blocker molecule inside the Channel. The main finding of the present work is that both models predict the same decay of the survival probability at long times. This result is of practical importance since only the long-time tail of the survival probability can be studied in single-Channel experiments in which, due to a limited time resolution, only long-lasting individual events of Channel blockades can be measured.

  • blocker escape kinetics from a Membrane Channel analyzed by mapping blocker diffusive dynamics onto a two site model
    Journal of Chemical Physics, 2019
    Co-Authors: Alexander M Berezhkovskii, Sergey M Bezrukov
    Abstract:

    : When a large solute molecule enters a Membrane Channel from the Membrane-bathing electrolyte solution, it blocks the small-ion current flowing through the Channel. If the molecule spends in the Channel sufficiently long time, individual blockades can be resolved in single-Channel experiments. In this paper, we develop an analytical theory of the blocker escape kinetics from the Channel, assuming that a charged blocking molecule cannot pass through a constriction region (bottleneck). We focus on the effect of the external voltage bias on the blocker survival probability in the Channel. The bias creates a potential well for the charged blocker in the Channel with the minimum located near the bottleneck. When the bias is strong, the well is deep, and escape from the Channel is a slow process that allows for time-resolved observation of individual blocking events. Our analysis is performed in the framework of a two-site model of the blocker dynamics in the Channel. Importantly, the rate constants, fully determining this model, are derived from a more realistic continuum diffusion model. This is done by mapping the latter onto its two-site counterpart which, while being much simpler, captures the main features of the blocker escape kinetics at high biases.

  • Relaxation and fluctuations of the number of particles in a Membrane Channel at arbitrary particle-Channel interaction
    Journal of Chemical Physics, 2008
    Co-Authors: Vladimir Yu. Zitserman, Alexander M Berezhkovskii, Mark A. Pustovoit, Sergey M Bezrukov
    Abstract:

    We analyze the relaxation of the particle number fluctuations in a Membrane Channel at arbitrary particle-Channel interaction and derive general expressions for the relaxation time and low-frequency limit of the power spectral density. These expressions simplify significantly when the Channel is symmetric. For a square-well potential of mean force that occupies the entire Channel, we verify the accuracy of the analytical predictions by Brownian dynamics simulations. For such a Channel we show that as the depth of the well increases, the familiar scaling of the relaxation time with the Channel length squared is transformed into a linear dependence on the length.

  • Counting translocations of strongly repelling particles through single Channels: Fluctuation theorem for Membrane transport
    Physical Review Letters, 2008
    Co-Authors: Alexander M Berezhkovskii, Sergey M Bezrukov
    Abstract:

    Transport of strongly repelling particles through a single Membrane Channel is analyzed assuming that the Channel cannot be occupied by more than one particle. An exact solution is found for the Laplace transform of the probability P_{n}(t) that n particles have been transported in time t. This transform is used to find the flux through the Channel and to show that P_{n}(t) and P_{-n}(t) are related by the fluctuation theorem. The solution is obtained using an observation that P_{n}(t) is the propagator for a non-Markovian random walk, which can be found by solving a set of integral equations.

  • Effect of binding on particle number fluctuations in a Membrane Channel
    Journal of Chemical Physics, 2002
    Co-Authors: Alexander M Berezhkovskii, Mark A. Pustovoit, Sergey M Bezrukov
    Abstract:

    Transport of solutes through Membrane Channels produces additional noise in the Channel ion current because the number of solute molecules in the Channel fluctuates. We obtain a general expression for the power spectral density of these fluctuations in a cylindrical Channel in the presence of a binding site of arbitrary strength. The expression shows how the spectral density transforms from that in the case of no-binding to the Lorentzian spectral density corresponding to the strong-binding limit. Brownian dynamics simulations confirm our analytical results.

R Benzl - One of the best experts on this subject based on the ideXlab platform.

  • The sugar-specific outer Membrane Channel ScrY contains functional characteristics of general diffusion pores and substrate-specific porins.
    Molecular microbiology, 1991
    Co-Authors: K Schülein, K. Schmid, R Benzl
    Abstract:

    Escherichia coli K-12 strain PS1-28-37 carries the multicopy plasmid pPSO28-37 containing a DNA fragment coding for two of the proteins that enable bacteria to utilize sucrose as sole carbon source. One of the different gene products of the plasmid is the outer Membrane protein, ScrY. This protein was isolated and purified by chromatography across a gel filtration column. Reconstitution experiments with lipid bilayer Membrane demonstrated that ScrY formed ion-permeable Channels with properties very similar to those of general diffusion pores of enteric bacteria. The presence of sugars in the aqueous phase led to a dose-dependent block of ion transport through the Channel, like the situation found with LamB (maltoporin) of Escherichia coli and Salmonella typhimurium. The binding constants of a variety of different sugars were determined. The stability constant for malto-oligosaccharide binding increased with increasing numbers of glucose residues. Disaccharides generally had a larger binding constant than monosaccharides. The binding of different sugars to ScrY and LamB of E. coli is discussed with respect to the kinetics of sugar movement through the Channel.

Abdul Latif Ahmad - One of the best experts on this subject based on the ideXlab platform.

  • Modified Boundary Condition for Membrane Wall Concentration Prediction in Narrow Membrane Channel
    Journal of Applied Membrane Science & Technology, 2017
    Co-Authors: Abdul Latif Ahmad, M.z. Abu Bakar, S.r. Abd Shukor
    Abstract:

    The efforts of CFD simulation study to reveal the Membrane wall concentration in the Membrane Channel which consider hydrodynamics and permeation properties are found to be inadequate. Hence, the ultimate objective of this paper is focusing on the employment of modified boundary condition to model the Membrane interface in the Membrane Channel. Permeation properties such as permeation flux and concentration have been integrated in this modified boundary condition. Commercial CFD simulation package has been utilized to predict the Membrane wall concentration for different transMembrane pressure and feed Reynolds number in the Membrane Channel. The simulated results were validated and compared with the published data from literature, showing a satisfactory agreement. This study has proven the increment in feed Reynolds number can enhance the mass transfer rate and suppress the formation Membrane wall concentration. The utilization of modified boundary condition has promoted the accuracy and capability of commercial CFD simulation package to model and predict the hydrodynamics and permeation phenomenon in the Membrane Channel.

  • Modeling, simulation, and experimental validation for aqueous solutions flowing in nanofiltration Membrane Channel
    Industrial & Engineering Chemistry Research, 2007
    Co-Authors: Abdul Latif Ahmad
    Abstract:

    Detailed investigation on the influence of hydrodynamics, pressure, and transport properties toward a concentration polarization phenomenon in a Membrane Channel is crucial for Membrane module design purposes. Hence, a computational fluid dynamics (CFD) simulation and modeling approach has been conducted to reveal and anticipate the Membrane transport properties and concentration polarization phenomenon. The current CFD model has been validated by experimental data, which exhibited excellent accordance between simulated and experimental values. The current study has also demonstrated that physical transport properties and boundary conditions should be modeled as variables in the solution of governing equations, since these parameters potentially affect the predicted values.

  • Impact of different spacer filaments geometries on 2D unsteady hydrodynamics and concentration polarization in spiral wound Membrane Channel
    Journal of Membrane Science, 2006
    Co-Authors: Abdul Latif Ahmad
    Abstract:

    Abstract Detail study on the hydrodynamics and concentration polarization phenomenon in the spacer-filled Membrane is important to ensure concentration polarization phenomenon can be minimized at minimum energy consumption. The primary goal of this paper mainly focusing on the integration of the permeation properties in commercial CFD codes FLUENT 6 to study the impact of different spacer filaments on unsteady hydrodynamics and concentration polarization in the spacer-filled Membrane Channel. Based on the velocity contour plot, unsteady vortices emerge, move and dissipate in different spacer-filled Membrane Channel. Besides, the unsteady hydrodynamic is constrained by the entrance transition effect and only presents at the downstream region of spacer-filled Channel. Triangular spacer exhibits the shortest transition length followed by cylindrical and rectangular spacer. Within desirable operating Reynolds number ( Re f

  • Impact of different spacer filament geometries on concentration polarization control in narrow Membrane Channel
    Journal of Membrane Science, 2005
    Co-Authors: Abdul Latif Ahmad, M.z. Abu Bakar
    Abstract:

    Fluid flow condition adjacent to the Membrane interface plays a vital role in controlling mass transfer and concentration polarization mechanism across the Membrane. Thus, optimized design of spacer is crucial to deter the formation of concentration polarization layer while maintaining certain degree of pressure drop. The main objective of this paper is to integrate the permeation properties in commercial CFD codes FLUENT 6 for simulating flow conditions and permeation properties in the spacer-filled narrow Membrane Channel. Turbulence model have been integrated in the solution of time averaged incompressible flow equations. Different types of spacer filament geometries have been analyzed and evaluated to determine their ability in controlling concentration polarization and pressure drop. This study has also demonstrated the dependency of filament geometries performance on feed Reynolds number. This method potentially offers faster approach to determine the optimum geometries of spacer filament in the narrow Membrane Channel if compared with experimental methods.

  • Integrated CFD simulation of concentration polarization in narrow Membrane Channel
    Computers & Chemical Engineering, 2005
    Co-Authors: Abdul Latif Ahmad, M.z. Abu Bakar, S.r. Abd Shukor
    Abstract:

    Numerous analyses on the mass transfer phenomena and hydrodynamics for the fluid adjacent to the Membrane have been studied and visualized by computational fluid dynamics (CFD) mathematical modeling and simulation. The availability of CFD simulation study to reveal the concentration polarization profile in the Membrane Channel, which considering hydrodynamics and Membrane transport properties is found to be limited. The main goal of this paper is targeted to the utilization of CFD simulation using commercial CFD package FLUENT to predict the concentration polarization profile, mass transfer coefficient and wall shear stress under different types of conditions in the empty narrow Membrane Channel. The permeation conditions such as permeation flux and mass fraction have been taken into account in the solution of the governing equations. Simulation results show that the concentration polarization phenomena can be reduced by increasing feed Reynolds number. The decrease of wall shear stress also contributes to the formation of the concentration polarization layer along the Membrane surface. The simulated results were validated and compared with the literature data, showing a satisfactory agreement.

Demetrius Tsernoglou - One of the best experts on this subject based on the ideXlab platform.

  • structure of the aeromonas toxin proaerolysin in its water soluble and Membrane Channel states
    Nature, 1994
    Co-Authors: Michael W Parker, J T Buckley, J P M Postma, Alec D Tucker, Kevin Leonard, Franc Pattus, Demetrius Tsernoglou
    Abstract:

    AEROLYSIN is chiefly responsible for the pathogenicity of Aeromonas hydrophila, a bacterium associated with diarrhoeal diseases and deep wound infections1. Like many other microbial toxins, the protein changes in a multistep process from a completely water-soluble form to produce a transMembrane Channel that destroys sensitive cells by breaking their permeability barriers2. Here we describe the structure of proaerolysin determined by X-ray crystallography at 2.8 A resolution. The protoxin (Mr 52,000) adopts a novel protein fold. Images of an aerolysin oligomer derived from electron microscopy have assisted in constructing a model of the Membrane Channel and have led to the proposal of a scheme to account for insertion of the protein into lipid bilayers to form ion Channels.