Related papers: Linear scaling computation of forces for the domai…
In this paper, a diffuse-interface lattice Boltzmann method (DI-LBM) is developed for fluid-particle interaction problems. In this method, the sharp interface between the fluid and solid is replaced by a thin but nonzero thickness…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
The simplified lattice Boltzmann method (SLBM) is a recent development in the lattice Boltzmann method (LBM) community, addressing the intrinsic limitations of the traditional LBM by directly evolving macroscopic quantities and maintaining…
The distribution of forces on the surface of complex, deforming geometries is an invaluable output of flow simulations. One particular example of such geometries involves self-propelled swimmers. Surface forces can provide significant…
We prove global existence of smooth solutions near Maxwellians for the non-cutoff Vlasov-Poisson-Boltzmann system in the weakly collisional regime. To address the weak dissipation of the non-cutoff linearized Boltzmann operator, we develop…
We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling of molecules using the pre-calculated statistical libraries…
We study the ionic distribution near a charged surface. A new method for performing Monte Carlo simulations in this geometry is discussed. A theory is then presented that allows us to accurately reproduce the density profiles obtained in…
Optimal exploitation of supercomputing resources for the evaluation of electrostatic forces remains a challenge in molecular dynamics simulations of very large systems. The most efficient methods are currently based on particle-mesh Ewald…
We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation, for molecules represented as non-overlapping spherical cavities.…
We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving…
Two non-overlapping domain decomposition methods are presented for the mixed finite element formulation of linear elasticity with weakly enforced stress symmetry. The methods utilize either displacement or normal stress Lagrange multiplier…
In the framework of a recently reported linear-scaling method for density-functional-pseudopotential calculations, we investigate the use of localized basis functions for such work. We propose a basis set in which each local orbital is…
Wereportonanewmultiscalemethodapproachforthestudyofsystemswith 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…
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…
Discretization of non-linear Poisson-Boltzmann Equation equations results in a system of non-linear equations with symmetric Jacobian. The Newton algorithm is the most useful tool for solving non-linear equations. It consists of solving a…
A hybrid computational method coupling the lattice-Boltzmann (LB) method and a Langevin-dynamics (LD) method is developed to simulate nanoscale particle and polymer (NPP) suspensions in the presence of both thermal fluctuation and…
A upscaled lattice Boltzmann method (LBM) for flow simulations in heterogeneous porous media, at both pore and Darcy scales, is proposed in this paper. In the micro-scale simulations, we model flows using LBM with the modified Guo et al.…
The Poisson-Boltzmann model is an effective and popular approach for modeling solvated biomolecules in continuum solvent with dissolved electrolytes. In this paper, we report our recent work in developing a Galerkin boundary integral method…
We develop a Monte Carlo wave function algorithm for the quantum linear Boltzmann equation, a Markovian master equation describing the quantum motion of a test particle interacting with the particles of an environmental background gas. The…
In this paper we propose and analyze a new Multiscale Method for solving semi-linear elliptic problems with heterogeneous and highly variable coefficient functions. For this purpose we construct a generalized finite element basis that spans…