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Keywords = linearized Poisson-Boltzmann equation

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20 pages, 3757 KiB  
Article
Analytical Solutions for Electroosmotic Flow and Heat Transfer Characteristics of Nanofluids in Circular Cylindrical Microchannels with Slip-Dependent Zeta Potential Considering Thermal Radiative Effects
by Zouqing Tan and Xiangcheng Ren
Micromachines 2025, 16(1), 63; https://doi.org/10.3390/mi16010063 - 5 Jan 2025
Viewed by 1374
Abstract
This study analyzes the impact of slip-dependent zeta potential on the heat transfer characteristics of nanofluids in cylindrical microchannels with consideration of thermal radiation effects. An analytical model is developed, accounting for the coupling between surface potential and interfacial slip. The linearized Poisson–Boltzmann [...] Read more.
This study analyzes the impact of slip-dependent zeta potential on the heat transfer characteristics of nanofluids in cylindrical microchannels with consideration of thermal radiation effects. An analytical model is developed, accounting for the coupling between surface potential and interfacial slip. The linearized Poisson–Boltzmann equation, along with the momentum and energy conservation equations, is solved analytically to obtain the electrical potential field, velocity field, temperature distribution, and Nusselt number for both slip-dependent (SD) and slip-independent (SI) zeta potentials. Subsequently, the effects of key parameters, including electric double-layer (EDL) thickness, slip length, nanoparticle volume fraction, thermal radiation parameters, and Brinkman number, on the velocity field, temperature field, and Nusselt number are discussed. The results show that the velocity is consistently higher for the SD zeta potential compared to the SI zeta potential. Meanwhile, the temperature for the SD case is higher than that for the SI case at lower Brinkman numbers, particularly for a thinner EDL. However, an inverse trend is observed at higher Brinkman numbers. Similar trends are observed for the Nusselt number under both SD and SI zeta potential conditions at different Brinkman numbers. Furthermore, for a thinner EDL, the differences in flow velocity, temperature, and Nusselt number between the SD and SI conditions are more pronounced. Full article
(This article belongs to the Section C1: Micro/Nanoscale Electrokinetics)
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32 pages, 5291 KiB  
Article
Analytical Investigation of Thermal Radiation Effects on Electroosmotic Propulsion of Electrically Conducting Ionic Nanofluid with Single-Walled Carbon Nanotube Interaction in Ciliated Channels
by Junaid Mehboob, Rahmat Ellahi and Sadiq Mohammad Sait
Symmetry 2024, 16(6), 717; https://doi.org/10.3390/sym16060717 - 9 Jun 2024
Cited by 21 | Viewed by 1140
Abstract
This study examines the behavior of single-walled carbon nanotubes (SWCNTs) suspended in a water-based ionic solution, driven by the combined mechanisms of electroosmosis and peristalsis through ciliated media. The inclusion of nanoparticles in ionic fluid expands the range of potential applications and allows [...] Read more.
This study examines the behavior of single-walled carbon nanotubes (SWCNTs) suspended in a water-based ionic solution, driven by the combined mechanisms of electroosmosis and peristalsis through ciliated media. The inclusion of nanoparticles in ionic fluid expands the range of potential applications and allows for the tailoring of properties to suit specific needs. This interaction between ionic fluids and nanomaterials results in advancements in various fields, including energy storage, electronics, biomedical engineering, and environmental remediation. The analysis investigates the influence of a transverse magnetic field, thermal radiation, and mixed convection acting on the channel walls. The novel physical outcomes include enhanced propulsion efficiency due to SWCNTs, understanding the influence of thermal radiation on fluid behavior and heat exchange, elucidation of the interactions between SWCNTs and the nanofluid, and recognizing implications for microfluidics and biomedical engineering. The Poisson–Boltzmann ionic distribution is linearized using the modified Debye–Hückel approximation. By employing real-world approximations, the governing equations are simplified using long-wavelength and low-Reynolds-number approximation. Conducting sensitivity analyses or exploring the impact of higher-order corrections on the model’s predictions in recent literature might alter the results significantly. This acknowledges the complexities of the modeling process and sets the groundwork for further enhancement and investigation. The resulting nonlinear system of equations is solved through regular perturbation techniques, and graphical representations showcase the variation in significant physical parameters. This study also discusses pumping and trapping phenomena in the context of relevant parameters. Full article
(This article belongs to the Section Mathematics)
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10 pages, 325 KiB  
Article
Analysis of Self-Gravitating Fluid Instabilities from the Post-Newtonian Boltzmann Equation
by Gilberto M. Kremer
Entropy 2024, 26(3), 246; https://doi.org/10.3390/e26030246 - 10 Mar 2024
Cited by 2 | Viewed by 1395
Abstract
Self-gravitating fluid instabilities are analysed within the framework of a post-Newtonian Boltzmann equation coupled with the Poisson equations for the gravitational potentials of the post-Newtonian theory. The Poisson equations are determined from the knowledge of the energy–momentum tensor calculated from a post-Newtonian Maxwell–Jüttner [...] Read more.
Self-gravitating fluid instabilities are analysed within the framework of a post-Newtonian Boltzmann equation coupled with the Poisson equations for the gravitational potentials of the post-Newtonian theory. The Poisson equations are determined from the knowledge of the energy–momentum tensor calculated from a post-Newtonian Maxwell–Jüttner distribution function. The one-particle distribution function and the gravitational potentials are perturbed from their background states, and the perturbations are represented by plane waves characterised by a wave number vector and time-dependent small amplitudes. The time-dependent amplitude of the one-particle distribution function is supposed to be a linear combination of the summational invariants of the post-Newtonian kinetic theory. From the coupled system of differential equations for the time-dependent amplitudes of the one-particle distribution function and gravitational potentials, an evolution equation for the mass density contrast is obtained. It is shown that for perturbation wavelengths smaller than the Jeans wavelength, the mass density contrast propagates as harmonic waves in time. For perturbation wavelengths greater than the Jeans wavelength, the mass density contrast grows in time, and the instability growth in the post-Newtonian theory is more accentuated than the one of the Newtonian theory. Full article
(This article belongs to the Special Issue Statistical Mechanics of Self-Gravitating Systems)
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29 pages, 2445 KiB  
Article
Start-Up Multilayer Electro-Osmotic Flow of Maxwell Fluids through an Annular Microchannel under Hydrodynamic Slip Conditions
by Cesar A. Valencia, David A. Torres, Clara G. Hernández, Juan P. Escandón, Juan R. Gómez and René O. Vargas
Mathematics 2023, 11(20), 4231; https://doi.org/10.3390/math11204231 - 10 Oct 2023
Cited by 2 | Viewed by 2179
Abstract
The present investigation analyzes the transient multilayer electro-osmotic flow through an annular microchannel with hydrophobic walls. The fluids are considered immiscible and viscoelastic, following the Maxwell rheological model. In the problem examined, the linearized Poisson–Boltzmann and Cauchy momentum equations are used to determine [...] Read more.
The present investigation analyzes the transient multilayer electro-osmotic flow through an annular microchannel with hydrophobic walls. The fluids are considered immiscible and viscoelastic, following the Maxwell rheological model. In the problem examined, the linearized Poisson–Boltzmann and Cauchy momentum equations are used to determine the electric potential distribution and the flow field, respectively. Here, different interfacial phenomena are studied through the imposed boundary conditions, such as the hydrodynamic slip and specified zeta potentials at solid–liquid interfaces, the velocity continuity, the electroviscous stresses balance, the potential difference, and the continuity of electrical displacements at the interfaces between fluids. The semi-analytic solution uses the Laplace transform theory. In the results, the velocity profiles and velocity tracking show the oscillatory behavior of flow, which strongly depends on the dimensionless relaxation time. Furthermore, the hydrodynamic slip on the channel walls contributes to the release of energy stored in the fluids due to elastic effects at the start-up of the flow. Similarly, other dimensionless parameters are also investigated. This research aims to predict the parallel flow behavior in microfluidic devices under electro-osmotic effects. Full article
(This article belongs to the Special Issue Numerical and Analytical Study of Fluid Dynamics)
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13 pages, 1383 KiB  
Article
Solving Stochastic Nonlinear Poisson-Boltzmann Equations Using a Collocation Method Based on RBFs
by Samaneh Mokhtari, Ali Mesforush, Reza Mokhtari, Rahman Akbari and Clemens Heitzinger
Mathematics 2023, 11(9), 2118; https://doi.org/10.3390/math11092118 - 29 Apr 2023
Viewed by 1706
Abstract
In this paper, we present a numerical scheme based on a collocation method to solve stochastic non-linear Poisson–Boltzmann equations (PBE). This equation is a generalized version of the non-linear Poisson–Boltzmann equations arising from a form of biomolecular modeling to the stochastic case. Applying [...] Read more.
In this paper, we present a numerical scheme based on a collocation method to solve stochastic non-linear Poisson–Boltzmann equations (PBE). This equation is a generalized version of the non-linear Poisson–Boltzmann equations arising from a form of biomolecular modeling to the stochastic case. Applying the collocation method based on radial basis functions (RBFs) allows us to deal with the difficulties arising from the complexity of the domain. To indicate the accuracy of the RBF method, we present numerical results for two-dimensional models, we also study the stability of this method numerically. We examine our results with the RBF-reference value and the Chebyshev Spectral Collocation (CSC) method. Furthermore, we discuss finding the appropriate shape parameter to obtain an accurate numerical solution besides greatest stability. We have exerted the Newton–Raphson approach for solving the system of non-linear equations resulting from discretization by the RBF technique. Full article
(This article belongs to the Special Issue Stochastic Processes: Theory, Simulation and Applications)
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27 pages, 1543 KiB  
Article
Transient Analysis of the Electro-Osmotic Flow of Multilayer Immiscible Maxwell Fluids in an Annular Microchannel
by Juan P. Escandón, David A. Torres, Clara G. Hernández, Juan R. Gómez and René O. Vargas
Colloids Interfaces 2022, 6(4), 60; https://doi.org/10.3390/colloids6040060 - 24 Oct 2022
Cited by 4 | Viewed by 3014
Abstract
This work investigates the transient multilayer electro-osmotic flow of viscoelastic fluids through an annular microchannel. The dimensionless mathematical model of multilayer flow is integrated by the linearized Poisson-Boltzmann equation, the Cauchy momentum equation, the rheological Maxwell model, initial conditions, and the electrostatic and [...] Read more.
This work investigates the transient multilayer electro-osmotic flow of viscoelastic fluids through an annular microchannel. The dimensionless mathematical model of multilayer flow is integrated by the linearized Poisson-Boltzmann equation, the Cauchy momentum equation, the rheological Maxwell model, initial conditions, and the electrostatic and hydrodynamic boundary conditions at liquid-liquid and solid-liquid interfaces. Although the main force that drives the movement of fluids is due to electrokinetic effects, a pressure gradient can also be added to the flow. The semi-analytical solution for the electric potential distribution and velocity profiles considers analytical techniques as the Laplace transform method, with numerical procedures using the inverse matrix method for linear algebraic equations and the concentrated matrix exponential method for the inversion of the Laplace transform. The results presented for velocity profiles and velocity tracking at the transient regime reveal an interesting oscillatory behavior that depends on elastic fluid properties via relaxation times. The time required for the flow to reach steady-state is highly dependent on the viscosity ratios and the dimensionless relaxation times. In addition, the influence of other dimensionless parameters on the flow as the electrokinetic parameters, zeta potentials at the walls, permittivity ratios, ratio of pressure forces to electro-osmotic forces, number of fluid layers, and annular thickness are investigated. The findings of this study have significant implications for the precise control of parallel fluid transport in microfluidic devices for flow-focusing applications. Full article
(This article belongs to the Special Issue Rheology of Complex Fluids and Interfaces)
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110 pages, 1134 KiB  
Review
Quantum Current Algebra in Action: Linearization, Integrability of Classical and Factorization of Quantum Nonlinear Dynamical Systems
by Anatolij K. Prykarpatski
Universe 2022, 8(5), 288; https://doi.org/10.3390/universe8050288 - 20 May 2022
Cited by 6 | Viewed by 2450
Abstract
This review is devoted to the universal algebraic and geometric properties of the non-relativistic quantum current algebra symmetry and to their representations subject to applications in describing geometrical and analytical properties of quantum and classical integrable Hamiltonian systems of theoretical and mathematical physics. [...] Read more.
This review is devoted to the universal algebraic and geometric properties of the non-relativistic quantum current algebra symmetry and to their representations subject to applications in describing geometrical and analytical properties of quantum and classical integrable Hamiltonian systems of theoretical and mathematical physics. The Fock space, the non-relativistic quantum current algebra symmetry and its cyclic representations on separable Hilbert spaces are reviewed and described in detail. The unitary current algebra family of operators and generating functional equations are described. A generating functional method to constructing irreducible current algebra representations is reviewed, and the ergodicity of the corresponding representation Hilbert space measure is mentioned. The algebraic properties of the so called coherent states are also reviewed, generated by cyclic representations of the Heisenberg algebra on Hilbert spaces. Unbelievable and impressive applications of coherent states to the theory of nonlinear dynamical systems on Hilbert spaces are described, along with their linearization and integrability. Moreover, we present a further development of these results within the modern Lie-algebraic approach to nonlinear dynamical systems on Poissonian functional manifolds, which proved to be both unexpected and important for the classification of integrable Hamiltonian flows on Hilbert spaces. The quantum current Lie algebra symmetry properties and their functional representations, interpreted as a universal algebraic structure of symmetries of completely integrable nonlinear dynamical systems of theoretical and mathematical physics on functional manifolds, are analyzed in detail. Based on the current algebra symmetry structure and their functional representations, an effective integrability criterion is formulated for a wide class of completely integrable Hamiltonian systems on functional manifolds. The related algebraic structure of the Poissonian operators and an effective algorithm of their analytical construction are described. The current algebra representations in separable Hilbert spaces and the factorized structure of quantum integrable many-particle Hamiltonian systems are reviewed. The related current algebra-based Hamiltonian reconstruction of the many-particle oscillatory and Calogero–Moser–Sutherland quantum models are reviewed and discussed in detail. The related quasi-classical quantum current algebra density representations and the collective variable approach in equilibrium statistical physics are reviewed. In addition, the classical Wigner type current algebra representation and its application to non-equilibrium classical statistical mechanics are described, and the construction of the Lie–Poisson structure on the phase space of the infinite hierarchy of distribution functions is presented. The related Boltzmann–Bogolubov type kinetic equation for the generating functional of many-particle distribution functions is constructed, and the invariant reduction scheme, compatible with imposed correlation functions constraints, is suggested and analyzed in detail. We also review current algebra functional representations and their geometric structure subject to the analytical description of quasi-stationary hydrodynamic flows and their magneto-hydrodynamic generalizations. A unified geometric description of the ideal idiabatic liquid dynamics is presented, and its Hamiltonian structure is analyzed. A special chapter of the review is devoted to recent results on the description of modified current Lie algebra symmetries on torus and their Lie-algebraic structures, related to integrable so-called heavenly type spatially many-dimensional dynamical systems on functional manifolds. Full article
(This article belongs to the Special Issue Selected Topics in Gravity, Field Theory and Quantum Mechanics)
14 pages, 3155 KiB  
Article
Electrophoretic Mobility and Electric Conductivity of Salt-Free Suspensions of Charged Soft Particles
by Wei C. Lin and Huan J. Keh
Colloids Interfaces 2021, 5(4), 45; https://doi.org/10.3390/colloids5040045 - 17 Oct 2021
Cited by 1 | Viewed by 2806
Abstract
A unit cell model is employed to analyze the electrophoresis and electric conduction in a concentrated suspension of spherical charged soft particles (each is a hard core coated with a porous polyelectrolyte layer) in a salt-free medium. The linearized Poisson–Boltzmann equation applicable to [...] Read more.
A unit cell model is employed to analyze the electrophoresis and electric conduction in a concentrated suspension of spherical charged soft particles (each is a hard core coated with a porous polyelectrolyte layer) in a salt-free medium. The linearized Poisson–Boltzmann equation applicable to a unit cell is solved for the equilibrium electrostatic potential distribution in the liquid solution containing the counterions only surrounding a soft particle. The counterionic continuity equation and modified Stokes/Brinkman equations are solved for the ionic electrochemical potential energy and fluid velocity distributions, respectively. Closed-form formulas for the electrophoretic mobility of the soft particles and effective electric conductivity of the suspension are derived, and the effect of particle interactions on these transport characteristics is interesting and significant. Same as the case in a suspension containing added electrolytes under the Debye–Hückel approximation, the scaled electrophoretic mobility in a salt-free suspension is an increasing function of the fixed charge density of the soft particles and decreases with increases in the core-to-particle radius ratio, ratio of the particle radius to the permeation length in the porous layer, and particle volume fraction, keeping the other parameters unchanged. The normalized effective electric conductivity of the salt-free suspension also increases with an increase in the fixed charge density and with a decrease in the core-to-particle radius ratio, but is not a monotonic function of the particle volume fraction. Full article
(This article belongs to the Special Issue Locomotion of Colloidal Particles)
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20 pages, 825 KiB  
Article
The Casimir Interaction between Spheres Immersed in Electrolytes
by Renan O. Nunes, Benjamin Spreng, Reinaldo de Melo e Souza, Gert-Ludwig Ingold, Paulo A. Maia Neto and Felipe S. S. Rosa
Universe 2021, 7(5), 156; https://doi.org/10.3390/universe7050156 - 18 May 2021
Cited by 15 | Viewed by 3165
Abstract
We investigate the Casimir interaction between two dielectric spheres immersed in an electrolyte solution. Since ionized solutions typically correspond to a plasma frequency much smaller than kBT/ħ at room temperature, only the contribution of the zeroth Matsubara frequency is [...] Read more.
We investigate the Casimir interaction between two dielectric spheres immersed in an electrolyte solution. Since ionized solutions typically correspond to a plasma frequency much smaller than kBT/ħ at room temperature, only the contribution of the zeroth Matsubara frequency is affected by ionic screening. We follow the electrostatic fluctuational approach and derive the zero-frequency contribution from the linear Poisson-Boltzmann (Debye-Hückel) equation for the geometry of two spherical surfaces of arbitrary radii. We show that a contribution from monopole fluctuations, which is reminiscent of the Kirkwood-Shumaker interaction, arises from the exclusion of ionic charge in the volume occupied by the spheres. Alongside the contribution from dipole fluctuations, such monopolar term provides the leading-order Casimir energy for very small spheres. Finally, we also investigate the large sphere limit and the conditions for validity of the proximity force (Derjaguin) approximation. Altogether, our results represent the first step towards a full scattering approach to the screening of the Casimir interaction between spheres that takes into account the nonlocal response of the electrolyte solution. Full article
(This article belongs to the Special Issue The Casimir Effect: From a Laboratory Table to the Universe)
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16 pages, 1954 KiB  
Article
Transient Pressure-Driven Electroosmotic Flow through Elliptic Cross-Sectional Microchannels with Various Eccentricities
by Nattakarn Numpanviwat and Pearanat Chuchard
Computation 2021, 9(3), 27; https://doi.org/10.3390/computation9030027 - 1 Mar 2021
Cited by 2 | Viewed by 2640
Abstract
The semi-analytical solution for transient electroosmotic flow through elliptic cylindrical microchannels is derived from the Navier-Stokes equations using the Laplace transform. The electroosmotic force expressed by the linearized Poisson-Boltzmann equation is considered the external force in the Navier-Stokes equations. The velocity field solution [...] Read more.
The semi-analytical solution for transient electroosmotic flow through elliptic cylindrical microchannels is derived from the Navier-Stokes equations using the Laplace transform. The electroosmotic force expressed by the linearized Poisson-Boltzmann equation is considered the external force in the Navier-Stokes equations. The velocity field solution is obtained in the form of the Mathieu and modified Mathieu functions and it is capable of describing the flow behavior in the system when the boundary condition is either constant or varied. The fluid velocity is calculated numerically using the inverse Laplace transform in order to describe the transient behavior. Moreover, the flow rates and the relative errors on the flow rates are presented to investigate the effect of eccentricity of the elliptic cross-section. The investigation shows that, when the area of the channel cross-sections is fixed, the relative errors are less than 1% if the eccentricity is not greater than 0.5. As a result, an elliptic channel with the eccentricity not greater than 0.5 can be assumed to be circular when the solution is written in the form of trigonometric functions in order to avoid the difficulty in computing the Mathieu and modified Mathieu functions. Full article
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17 pages, 1610 KiB  
Article
Implicit Temporal Discretization and Exact Energy Conservation for Particle Methods Applied to the Poisson–Boltzmann Equation
by Giovanni Lapenta and Wei Jiang
Plasma 2018, 1(2), 242-258; https://doi.org/10.3390/plasma1020021 - 9 Oct 2018
Cited by 5 | Viewed by 3260
Abstract
We report on a new multiscale method approach for the study of systems with wide separation of short-range forces acting on short time scales and long-range forces acting on much slower scales. We consider the case of the Poisson–Boltzmann equation that describes the [...] Read more.
We report on a new multiscale method approach for the study of systems with wide separation of short-range forces acting on short time scales and long-range forces acting on much slower scales. We consider the case of the Poisson–Boltzmann equation that describes the long-range forces using the Boltzmann formula (i.e., we assume the medium to be in quasi local thermal equilibrium). We develop a new approach where fields and particle information (mediated by the equations for their moments) are solved self-consistently. The new approach is implicit and numerically stable, providing exact energy conservation. We test different implementations that all lead to exact energy conservation. The new method requires the solution of a large set of non-linear equations. We consider three solution strategies: Jacobian Free Newton Krylov, an alternative, called field hiding which is based on hiding part of the residual calculation and replacing them with direct solutions and a Direct Newton Schwarz solver that considers a simplified, single, particle-based Jacobian. The field hiding strategy proves to be the most efficient approach. Full article
(This article belongs to the Special Issue Multiscale Methods in Plasma Physics)
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12 pages, 3488 KiB  
Article
An Exact Solution for Power-Law Fluids in a Slit Microchannel with Different Zeta Potentials under Electroosmotic Forces
by Du-Soon Choi, Sungchan Yun and WooSeok Choi
Micromachines 2018, 9(10), 504; https://doi.org/10.3390/mi9100504 - 5 Oct 2018
Cited by 10 | Viewed by 3380
Abstract
Electroosmotic flow (EOF) is one of the most important techniques in a microfluidic system. Many microfluidic devices are made from a combination of different materials, and thus asymmetric electrochemical boundary conditions should be applied for the reasonable analysis of the EOF. In this [...] Read more.
Electroosmotic flow (EOF) is one of the most important techniques in a microfluidic system. Many microfluidic devices are made from a combination of different materials, and thus asymmetric electrochemical boundary conditions should be applied for the reasonable analysis of the EOF. In this study, the EOF of power-law fluids in a slit microchannel with different zeta potentials at the top and bottom walls are studied analytically. The flow is assumed to be steady, fully developed, and unidirectional with no applied pressure. The continuity equation, the Cauchy momentum equation, and the linearized Poisson-Boltzmann equation are solved for the velocity field. The exact solutions of the velocity distribution are obtained in terms of the Appell’s first hypergeometric functions. The velocity distributions are investigated and discussed as a function of the fluid behavior index, Debye length, and the difference in the zeta potential between the top and bottom. Full article
(This article belongs to the Special Issue Micro/Nano-Chip Electrokinetics, Volume III)
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23 pages, 2695 KiB  
Article
A Unified Gas Kinetic Scheme for Transport and Collision Effects in Plasma
by Dongxin Pan, Chengwen Zhong, Congshan Zhuo and Wei Tan
Appl. Sci. 2018, 8(5), 746; https://doi.org/10.3390/app8050746 - 9 May 2018
Cited by 18 | Viewed by 4124
Abstract
In this study, the Boltzmann equation with electric acceleration term is discretized and solved by the unified gas-kinetic scheme (UGKS). The charged particle transport driven by electric field is included in the electric acceleration term. To capture non-equilibrium distribution function, the probability distribution [...] Read more.
In this study, the Boltzmann equation with electric acceleration term is discretized and solved by the unified gas-kinetic scheme (UGKS). The charged particle transport driven by electric field is included in the electric acceleration term. To capture non-equilibrium distribution function, the probability distribution functions of gas is discretized in a discrete velocity space. After discretization, the numerical flux for distribution function is computed to update the microscopic and macroscopic states. The flux is decided by an integral solution of Boltzmann equation based on characteristic problem. An electron-ion collision model is introduced in the Boltzmann Bhatnagar-Gross-Krook (BGK) equation. This finite volume method for the UGKS couples the free transport and long-range interaction between particles. For simplicity, the electric field induced by charged particles is controlled by the Poisson’s equation, which is solved using the Green’s function for two dimensional plasma system subjected to the symmetry or periodic boundary conditions. Two numerical cases, linear Landau damping and Gaussian beam, are carried out to validate the proposed method. The linear electron plasma wave damping is simulated based on electron-ion collision operator. Comparison results show good accuracy and higher efficiency than particle based methods. Difference between Poisson’s equation and complete electromagnetic Maxwell equation is presented by numerical results based on the two models. Highly non-equilibrium and rarefied plasma flows, such as electron flows driven by electromagnetic field, can be simulated easily. The UGKS-Poisson model is proved to be promising in plasma flow simulation. Full article
(This article belongs to the Special Issue Development and Applications of Kinetic Solvers for Complex Flows)
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17 pages, 1810 KiB  
Article
A Finite Element Solution of Lateral Periodic Poisson–Boltzmann Model for Membrane Channel Proteins
by Nan Ji, Tiantian Liu, Jingjie Xu, Longzhu Q. Shen and Benzhuo Lu
Int. J. Mol. Sci. 2018, 19(3), 695; https://doi.org/10.3390/ijms19030695 - 28 Feb 2018
Cited by 11 | Viewed by 4502
Abstract
Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of [...] Read more.
Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of the Poisson–Boltzmann (PB) equation to handle membrane proteins. The use of lateral periodic boundary conditions can properly simulate the discrete distribution of membrane proteins on the membrane plane and avoid boundary effects, which are caused by the finite box size in the traditional PB calculations. In this work, we: (1) develop a first finite element solver (FEPB) to solve the PB equation with a two-dimensional periodicity for membrane channel proteins, with different numerical treatments of the singular charges distributions in the channel protein; (2) add the membrane as a dielectric slab in the PB model, and use an improved mesh construction method to automatically identify the membrane channel/pore region even with a tilt angle relative to the z-axis; and (3) add a non-polar solvation energy term to complete the estimation of the total solvation energy of a membrane protein. A mesh resolution of about 0.25 Å (cubic grid space)/0.36 Å (tetrahedron edge length) is found to be most accurate in linear finite element calculation of the PB solvation energy. Computational studies are performed on a few exemplary molecules. The results indicate that all factors, the membrane thickness, the length of periodic box, membrane dielectric constant, pore region dielectric constant, and ionic strength, have individually considerable influence on the solvation energy of a channel protein. This demonstrates the necessity to treat all of those effects in the PB model for membrane protein simulations. Full article
(This article belongs to the Special Issue Ion Transporters and Channels in Physiology and Pathophysiology)
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