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This review describes the theory and implementation of implicit solvation models based on continuum electrostatics. Within quantum chemistry this formalism is sometimes synonymous with the polarizable continuum model, a particular…
This paper proposes a new boundary integral equation (BIE) methodology based on the perfectly matched layer (PML) truncation technique for solving the electromagnetic scattering problems in a multi-layered medium. Instead of using the…
Cellular electrophysiology is often modeled using the cable equations. The cable model can only be used when ionic concentration effects and three dimensional geometry effects are negligible. The Poisson model, in which the electrostatic…
For multispecies ions, we study boundary layer solutions of charge conserving Poisson-Boltzmann (CCPB) equations [50] (with a small parameter \k{o}) over a finite one-dimensional (1D) spatial domain, subjected to Robin type boundary…
Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified…
Background: Models based on using perturbative polarization corrections and mean-field blocking approximation give conflicting results for masses of odd nuclei. Purpose: Systematically investigate the polarization and mean-field models,…
A new step-by-step diagonalization procedure for evaluating exact solutions of the nuclear deformed mean-field plus pairing interaction model is proposed via a simple Bethe ansatz in each step from which the eigenvalues and corresponding…
A method of deriving the Hamiltonian of the interacting boson model, that is based on the microscopic framework of the nuclear energy density functional, is presented. The constrained self-consistent mean-field calculation with a given…
The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into…
We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory but replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single…
Deep-HP is a scalable extension of the \TinkerHP\ multi-GPUs molecular dynamics (MD) package enabling the use of Pytorch/TensorFlow Deep Neural Networks (DNNs) models. Deep-HP increases DNNs MD capabilities by orders of magnitude offering…
We introduce a novel mesoscopic computational model based on a multiphase-multicomponent lattice Boltzmann method for the simulation of self-phoretic particles in the presence of liquid-liquid interfaces. Our model features fully resolved…
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes.…
We develop a double mean-field theory for charged macrogels immersed in electrolyte solutions in the spirit of the cell model approach. We first demonstrate that the equilibrium sampling of a single explicit coarse-grained charged polymer…
When ions are crowded, the effect of steric repulsion between ions (which can produce oscillations in charge density profiles) becomes significant and the conventional Poisson-Boltzmann (PB) equation should be modified. Several modified PB…
This paper tests a dielectric model for variation of hydration free energy with geometry of complex solutes in water. It works out some basic aspects of the theory of boundary integral methods for these problems. One aspect of the…
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions…
The properties of ionic solutions between charged surfaces are often studied within the Poisson-Boltzmann framework, by finding the electrostatic potential profile. For example, the osmotic pressure between two charged planar surfaces can…
Macromolecules, when immersed in a polar solvent like water, become charged by a fixed surface charge density which is compensated by ``counter-ions'' moving out of the surface. Such classical particle systems exhibit poor screening…
Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the…