Deep learning techniques for solving elliptic interface problems have gained significant attentions.In this paper,we introduce a hybrid residual and weak form(HRW)loss aimed at mitigating the challenge of model traini...Deep learning techniques for solving elliptic interface problems have gained significant attentions.In this paper,we introduce a hybrid residual and weak form(HRW)loss aimed at mitigating the challenge of model training.HRW utilizes the functions residual loss and Ritz method in an adversary-system,which enhances the probability of jumping out of the local optimum even when the loss landscape comprises multiple soft constraints(regularization terms),thus improving model’s capability and robustness.For the problem with interface conditions,unlike existing methods that use the domain decomposition,we design a Pre-activated ResNet of ResNet(PRoR)network structure employing a single network to feed both coordinates and corresponding subdomain indicators,thus reduces the number of parameters.The effectiveness and improvements of the PRoR with HRW are verified on two-dimensional interface problems with regular or irregular interfaces.We then apply the PRoR with HRW to solve the size-modified Poisson-Boltzmann equation,an improved dielectric continuum model for predicting the electrostatic potentials in an ionic solvent by considering the steric effects.Our findings demonstrate that the PRoR with HRW accurately approximates solvation free-energies of three proteins with irregular interfaces,showing the competitive results compared to the ones obtained using the finite element method.展开更多
Generalized Poisson l3oltzmann equation which takes into account both ionic interaction in bulk solution and steric effects of adsorbed ions has been suggested. We found that, for inorganic cations adsorption on negat...Generalized Poisson l3oltzmann equation which takes into account both ionic interaction in bulk solution and steric effects of adsorbed ions has been suggested. We found that, for inorganic cations adsorption on negatively charged surface, the steric effect is not significant for surface charge density 〈 0.0032 C/dm2, while the ionic interaction is an important effect for electrolyte concentration 〉 0.15 tool/1 in bulk solution. We conclude that for most actual cases the original PB equation can give reliable result in describing inorganic cation adsorption.展开更多
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model describe...Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson- Boltzmann （PB）/Poisson-Nernst-Planck （PNP） equations has made great contributions towards simulation of these pro- cesses. However, the model has shortcomings in its commonly used form and cannot capture （or cannot accurately capture） some important physical properties of the biological systems. Considerable efforts have been made to improve the con- tinuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecu- lar systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.展开更多
The effects of the Electrical Double Layer （EDL） on the liquid mean flow and the flow stability in microchannels are investigated by solving the Poisson-Boltzmann equation. The models of the traditional streaming El...The effects of the Electrical Double Layer （EDL） on the liquid mean flow and the flow stability in microchannels are investigated by solving the Poisson-Boltzmann equation. The models of the traditional streaming Electrical Current Balance （ECB） and the newly introduced streaming Electrical Current Density Balance （ECDB） are applied to determine the electrical streaming current. The numerical results show that the electrical streaming current backflow in the ECB model near the wall can be removed by using the ECDB model, which is suitable to study the effects of the EDL on the mean flow and the flow stability in microchannels. The flow is found more unstable if the ECDB model is applied.展开更多
We consider the problem of measuring the electric charge of nanoparticles immersed in a fluid electrolyte. We develop a mathematical framework based on the solution of the nonlinear Poisson-Boltzmann equation to obtai...We consider the problem of measuring the electric charge of nanoparticles immersed in a fluid electrolyte. We develop a mathematical framework based on the solution of the nonlinear Poisson-Boltzmann equation to obtain interaction forces between nanoparticles immersed in a fluid electrolyte and an Atomic Force Microscopy micro spherical probe. This force-separation information is shown explicitly to depend on the charge of the nanoparticle.? This method overcomes the statistical nature of extant methods and renders a charge value for an individual single nanoparticle.展开更多
A new method, i.e. the iterative method in functional theory, was introduced to solve analytically the nonlinear Poisson-Boltzmann （PB） equation under general potential ψ condition for the electric double layer of ...A new method, i.e. the iterative method in functional theory, was introduced to solve analytically the nonlinear Poisson-Boltzmann （PB） equation under general potential ψ condition for the electric double layer of a charged cylindrical colloid particle in a symmetrical electrolyte solution. The iterative solutions of ψ are expressed as functions of the distance from the axis of the particle with solution parameters： the concentration of ions c, the aggregation number of ions in a unit length m, the dielectric constant e, the system temperature T and so on. The relative errors show that generally only the first and the second iterative solutions can give accuracy higher than 97%. From the second iterative solution the radius and the surface potential of a cylinder have been defined and the corresponding values have been estimated with the solution parameters, Furthermore, the charge density, the activity coefficient of ions and the osmotic coefficient of solvent were also discussed,展开更多
With the help of the method of separation of variables and the Debye-Hüchel approximation, the Poisson-Boltzmann equation that describes the distribution of the potential in the electrical double layer of a cylin...With the help of the method of separation of variables and the Debye-Hüchel approximation, the Poisson-Boltzmann equation that describes the distribution of the potential in the electrical double layer of a cylindrical particle with a limited length has been firstly solved under a very low potential condition. Then with the help of the functional analysis theory this equation has been further analytically solved under general potential conditions and consequently, the corresponding surface charge densities have been obtained. Both the potential and the surface charge densities cointide with those results obtained from the Debye-Hüchel approximation when the very low potential of zeψ〈〈kT is introduced.展开更多
The applicability of the Poisson-Boltzmann model for micro-and nanoscale electroosmotic flows is a very important theoretical and engineering problem.In this contribution we investigate this problem at two aspects:fir...The applicability of the Poisson-Boltzmann model for micro-and nanoscale electroosmotic flows is a very important theoretical and engineering problem.In this contribution we investigate this problem at two aspects:first the high ionic concentration effect on the Boltzmann distribution assumption in the diffusion layer is studied by comparisons with the molecular dynamics(MD)simulation results;then the electrical double layer(EDL)interaction effect caused by low ionic concentrations in small channels is discussed by comparing with the dynamic model described by the coupled Poisson-Nernst-Planck(PNP)and Navier-Stokes(NS)equations.The results show that the Poisson-Boltzmann(PB)model is applicable in a very wide range:(i)the PB model can still provide good predictions of the ions density profiles up to a very high ionic concentration(∼1 M)in the diffusion layer;(ii)the PB model predicts the net charge density accurately as long as the EDL thickness is smaller than the channel width and then overrates the net charge density profile as the EDL thickness increasing,and the predicted electric potential profile is still very accurate up to a very strong EDL interaction(λ/W∼10).展开更多
文摘Deep learning techniques for solving elliptic interface problems have gained significant attentions.In this paper,we introduce a hybrid residual and weak form(HRW)loss aimed at mitigating the challenge of model training.HRW utilizes the functions residual loss and Ritz method in an adversary-system,which enhances the probability of jumping out of the local optimum even when the loss landscape comprises multiple soft constraints(regularization terms),thus improving model’s capability and robustness.For the problem with interface conditions,unlike existing methods that use the domain decomposition,we design a Pre-activated ResNet of ResNet(PRoR)network structure employing a single network to feed both coordinates and corresponding subdomain indicators,thus reduces the number of parameters.The effectiveness and improvements of the PRoR with HRW are verified on two-dimensional interface problems with regular or irregular interfaces.We then apply the PRoR with HRW to solve the size-modified Poisson-Boltzmann equation,an improved dielectric continuum model for predicting the electrostatic potentials in an ionic solvent by considering the steric effects.Our findings demonstrate that the PRoR with HRW accurately approximates solvation free-energies of three proteins with irregular interfaces,showing the competitive results compared to the ones obtained using the finite element method.
基金Supported by the National Natural Science Foundation of China under Grant Nos.40971146 and 40740420660the National Basic Research Program of China under Grant No.2010CB134511Scientific and Technological Innovation Foundation of Southwest University for Graduates under Grant No.kb2010013
文摘Generalized Poisson l3oltzmann equation which takes into account both ionic interaction in bulk solution and steric effects of adsorbed ions has been suggested. We found that, for inorganic cations adsorption on negatively charged surface, the steric effect is not significant for surface charge density 〈 0.0032 C/dm2, while the ionic interaction is an important effect for electrolyte concentration 〉 0.15 tool/1 in bulk solution. We conclude that for most actual cases the original PB equation can give reliable result in describing inorganic cation adsorption.
基金supported by the National Natural Science Foundation of China(Grant No.91230106)the Chinese Academy of Sciences Program for Cross&Cooperative Team of the Science&Technology Innovation
文摘Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson- Boltzmann （PB）/Poisson-Nernst-Planck （PNP） equations has made great contributions towards simulation of these pro- cesses. However, the model has shortcomings in its commonly used form and cannot capture （or cannot accurately capture） some important physical properties of the biological systems. Considerable efforts have been made to improve the con- tinuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecu- lar systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.
基金Project supported by the National Natural Science Foundation of China (Grant No. 20676093)
文摘The effects of the Electrical Double Layer （EDL） on the liquid mean flow and the flow stability in microchannels are investigated by solving the Poisson-Boltzmann equation. The models of the traditional streaming Electrical Current Balance （ECB） and the newly introduced streaming Electrical Current Density Balance （ECDB） are applied to determine the electrical streaming current. The numerical results show that the electrical streaming current backflow in the ECB model near the wall can be removed by using the ECDB model, which is suitable to study the effects of the EDL on the mean flow and the flow stability in microchannels. The flow is found more unstable if the ECDB model is applied.
文摘We consider the problem of measuring the electric charge of nanoparticles immersed in a fluid electrolyte. We develop a mathematical framework based on the solution of the nonlinear Poisson-Boltzmann equation to obtain interaction forces between nanoparticles immersed in a fluid electrolyte and an Atomic Force Microscopy micro spherical probe. This force-separation information is shown explicitly to depend on the charge of the nanoparticle.? This method overcomes the statistical nature of extant methods and renders a charge value for an individual single nanoparticle.
基金Project supported by the National Natural Science Foundation of China （Nos. 20676051, 20573048 and 20473034） and the 0pen Project Program of the Key Laboratory of Industrial Biotechnology, Ministry of Education （No. KLIB-KF200504）.
文摘A new method, i.e. the iterative method in functional theory, was introduced to solve analytically the nonlinear Poisson-Boltzmann （PB） equation under general potential ψ condition for the electric double layer of a charged cylindrical colloid particle in a symmetrical electrolyte solution. The iterative solutions of ψ are expressed as functions of the distance from the axis of the particle with solution parameters： the concentration of ions c, the aggregation number of ions in a unit length m, the dielectric constant e, the system temperature T and so on. The relative errors show that generally only the first and the second iterative solutions can give accuracy higher than 97%. From the second iterative solution the radius and the surface potential of a cylinder have been defined and the corresponding values have been estimated with the solution parameters, Furthermore, the charge density, the activity coefficient of ions and the osmotic coefficient of solvent were also discussed,
基金Supported by the National Natural Science Foundation of China(No.20473034) the Taihu Scholar Foundation of SouthernYangtze University(2003).
文摘With the help of the method of separation of variables and the Debye-Hüchel approximation, the Poisson-Boltzmann equation that describes the distribution of the potential in the electrical double layer of a cylindrical particle with a limited length has been firstly solved under a very low potential condition. Then with the help of the functional analysis theory this equation has been further analytically solved under general potential conditions and consequently, the corresponding surface charge densities have been obtained. Both the potential and the surface charge densities cointide with those results obtained from the Debye-Hüchel approximation when the very low potential of zeψ〈〈kT is introduced.
文摘The applicability of the Poisson-Boltzmann model for micro-and nanoscale electroosmotic flows is a very important theoretical and engineering problem.In this contribution we investigate this problem at two aspects:first the high ionic concentration effect on the Boltzmann distribution assumption in the diffusion layer is studied by comparisons with the molecular dynamics(MD)simulation results;then the electrical double layer(EDL)interaction effect caused by low ionic concentrations in small channels is discussed by comparing with the dynamic model described by the coupled Poisson-Nernst-Planck(PNP)and Navier-Stokes(NS)equations.The results show that the Poisson-Boltzmann(PB)model is applicable in a very wide range:(i)the PB model can still provide good predictions of the ions density profiles up to a very high ionic concentration(∼1 M)in the diffusion layer;(ii)the PB model predicts the net charge density accurately as long as the EDL thickness is smaller than the channel width and then overrates the net charge density profile as the EDL thickness increasing,and the predicted electric potential profile is still very accurate up to a very strong EDL interaction(λ/W∼10).
