相关论文: Integral equation models for solvent in macromolec…
An integral equation method is presented for the 1D steady-state Poisson-Nernst-Planck equations modeling ion transport through membrane channels. The differential equations are recast as integral equations using Green's 3rd identity…
This work aims to extend the residual distribution (RD) framework to stiff relaxation problems. The RD is a class of schemes which is used to solve hyperbolic system of partial differential equations. Up to our knowledge, it was used only…
Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial…
A new computational method is presented for study suspensions of charged soft particles undergoing fluctuating hydrodynamic and electrostatic interactions. The proposed model is appropriate for polymers, proteins and porous particles…
We derive and analyze a broad class of finite element methods for numerically simulating the stationary, low Reynolds number flow of concentrated mixtures of several distinct chemical species in a common thermodynamic phase. The underlying…
Particle-In-Cell (PIC) methods are frequently used for kinetic, high-fidelity simulations of plasmas. Implicit formulations of PIC algorithms feature strong conservation properties, up to numerical round-off errors, and are not subject to…
[ This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in The Journal of Chemical Physics, 157, 024504 (2022) and may be found at:…
The selection of suitable ionic liquids (ILs) is critical for CO2 capture and electrocatalytic conversion into valuable chemical products. The screening process can be enhanced with theoretical simulations that reveal the…
This paper introduces a new method for discretizing and solving integral equation formulations of Maxwell's equations which achieves spectral accuracy for smooth surfaces. The approach is based on a hybrid Nystr\"om-collocation method using…
A variety of problems in device and materials design require the rapid forward modeling of Maxwell's equations in complex micro-structured materials. By combining high-order accurate integral equation methods with classical multiple…
Small-angle X-ray or neutron scattering (SAXS/SANS/SAS) is widely used to obtain structural information on biomolecules or soft-matter complexes in solution. Deriving a molecular interpretation of the scattering signals requires methods for…
Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
In this work, a systematic protocol is proposed to automatically parametrize implicit solvent models with polar and nonpolar components. The proposed protocol utilizes the classical Poisson model or the Kohn-Sham density functional theory…
We use molecular dynamics simulations to test integral equation theory predictions for the structure of fluids of spherical particles with eight different piecewise-constant pair interaction forms comprising a hard core and a combination of…
We present a three-dimensional (3D) common-refinement method for non-matching meshes between discrete non-overlapping subdomains of incompressible fluid and nonlinear hyperelastic structure. To begin, we first investigate the accuracy of…
In the paper a new method to solve the tree-dimensional reference interaction site model (3DRISM) integral equations is proposed. The algorithm uses the multi-grid technique which allows to decrease the computational expanses. 3DRISM…
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural features, and that are suitable to model either…
Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent…
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…