Related papers: An implicit boundary integral method for computing…
We present a simple, yet general, end-to-end deep neural network representation of the potential energy surface for atomic and molecular systems. This methodology, which we call Deep Potential, is "first-principle" based, in the sense that…
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…
A statistical thermodynamic development is given of a new implicit solvent model that avoids the traditional system size limitations of computer simulation of macromolecular solutions with periodic boundary conditions. This implicit solvent…
A multiscale QM/classical approach is presented, that is able to model the optical properties of complex nanostructures composed of a molecular system adsorbed on metal nanoparticles. The latter are described by a combined…
The Immersed Boundary Method (IBM) is one of the popular one-fluid mixed Eulerian-Lagrangian methods to simulate motion of droplets. While the treatment of a moving complex boundary is an extremely time consuming and formidable task in a…
We develop an immersed boundary (IB) method for modeling flows around fixed or moving rigid bodies that is suitable for a broad range of Reynolds numbers, including steady Stokes flow. The spatio-temporal discretization of the fluid…
We describe a three-stage procedure to analyze the dependence of Poisson Boltzmann calculations on the shape, size and geometry of the boundary between solute and solvent. Our study is carried out within the boundary element formalism, but…
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…
We present a new multi-fluid, multi-temperature plasma solver with adaptive Cartesian mesh (ACM) based on a full-Newton (non-linear, implicit) scheme for collisional low-temperature plasma. The particle transport is described using the…
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic…
Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the…
The Immersed Boundary (IB) method is a widely-used numerical methodology for the simulation of fluid-structure interaction problems. The IB method utilizes an Eulerian discretization for the fluid equations of motion while maintaining a…
The paper presents a new method for shape and topology optimization based on an efficient and scalable boundary integral formulation for elasticity. To optimize topology, our approach uses iterative extraction of isosurfaces of a…
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. In this model the dielectric interface between the biomolecule and solvent is…
We develop a numerical method for solving a free boundary problem which describes shape relaxation, by surface tension, of a long and thin bubble of an inviscid fluid trapped inside a viscous fluid in a Hele-Shaw cell. The method of…
Modeling the chemical, electric, and thermal transport as well as phase transitions and the accompanying mesoscale microstructure evolution within a material in an electronic device setting involves the solution of partial differential…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of…
We show that classical molecular density functional theory (MDFT), here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a…
A unified framework to derive discrete time-marching schemes for coupling of immersed solid and elastic objects to the lattice Boltzmann method is presented. Based on operator splitting for the discrete Boltzmann equation, second-order…