Related papers: Implicit solvation model for density-functional st…
Implicit solvation is an effective, highly coarse-grained approach in atomic-scale simulations to account for a surrounding liquid electrolyte on the level of a continuous polarizable medium. Originating in molecular chemistry with finite…
The ab-initio computational treatment of electrochemical systems requires an appropriate treatment of the solid/liquid interfaces. A fully quantum mechanical treatment of the interface is computationally demanding due to the large number of…
Recent studies on the solvation of atomistic and nanoscale solutes indicate that a strong coupling exists between the hydrophobic, dispersion, and electrostatic contributions to the solvation free energy, a facet not considered in current…
A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104},…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
We have developed and implemented an implicit electrolyte model in the Vienna Ab initio Simulation Package (VASP) that includes nonlinear dielectric and ionic responses as well as a nonlocal definition of the cavities defining the spatial…
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…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
In this work we study and contrast implicit solvation models against explicit atomistic, quantum mechanical models in the description of the band alignment of semiconductors in aqueous environment, using simulations based on density…
The implicit solvent approach offers a computationally efficient framework to model solvation effects in molecular simulations. However, its accuracy often falls short compared to explicit solvent models, limiting its use in precise…
In the past decade, variational implicit solvation models (VISM) have achieved great success in solvation energy predictions. However, all existing VISMs in literature lack the uniqueness of an energy minimizing solute-solvent interface and…
In this article, we apply the binary level set method to the Variational Implicit Solvent Model (VISM), which is a theoretical and computational tool to study biomolecular systems with complex topology. Central in VISM is an effective free…
Molecular dynamics (MD) simulations enable the study of the motion of small and large (bio)molecules and the estimation of their conformational ensembles. The description of the environment (solvent) has thereby a large impact. Implicit…
Implicit electron-density solvation models based on joint density-functional theory offer a computationally efficient solution to the problem of calculating thermodynamic quantities of solvated systems from firstprinciples quantum…
For many chemical processes the accurate description of solvent effects are vitally important. Here, we describe a hybrid ansatz for the explicit quantum mechanical description of solute-solvent and solvent-solvent interactions based on…
Dispersion of low-density rigid particles with complex geometries is ubiquitous in both natural and industrial environments. We show that while explicit methods for coupling the incompressible Navier-Stokes equations and Newton's equations…
We present a novel implicit porous flow solver using SPH, which maintains fluid incompressibility and is able to model a wide range of scenarios, driven by strongly coupled solid-fluid interaction forces. Many previous SPH porous flow…
Liquids in contact with solids are submitted to intermolecular forces making liquids heterogeneous and stress tensors are not any more spherical as in homogeneous bulks. The aim of this article is to show that a square-gradient functional…
In this paper we propose a novel and general approach to design semi-implicit methods for the simulation of fluid-structure interaction problems in a fully Eulerian framework. In order to properly present the new method, we focus on the…
Within a dipolar Poisson-Boltzmann theory including electrostatic correlations, we consider the effect of explicit solvent structure on solvent and ion partition confined to charged nanopores. We develop a relaxation scheme for the solution…