Related papers: Exact electrostatic energy calculation for charged…
An accurate force calculation with the Poisson-Boltzmann equation is challenging, as it requires the electric field on the molecular surface. Here, we present a calculation of the electric field on the solute-solvent interface that is exact…
Solvation in 1-ethyl-3-methylmidazolium chloride and in 1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is investigated via molecular dynamics computer simulations with diatomic and benzenelike molecules employed as probe…
The full-dimensional time-dependent Schrodinger equation for the electronic dynamics of single-electron systems in intense external fields is solved directly using a discrete method. Our approach combines the finite-difference and Lagrange…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
Can we avoid molecular dynamics simulations to estimate the electrostatic interaction between charged objects separated by a nanometric distance in water? To answer this question, we develop a continuous model for the dielectric properties…
This paper mainly considers three iterations based on charge-conservative finite element approximation in Lipschitz domain for the stationary thermally coupled inductionless MHD equations. Based on the hybrid finite element method, the…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
We present an accurate equation of state for water based on a simple microscopic Hamiltonian, with only four parameters that are well-constrained by bulk experimental data. With one additional parameter for the range of interaction, this…
We propose a method of free energy calculation for a system of interacting particles arranged in a Bravais lattice. It will be shown how to treat divergences for infinite unbounded systems with "catastrophic" potetntials like Coulomb and…
Within the framework of a functional integral formalism incorporating ionic charge and hard-core (HC) interactions on an equal footing, we formulate a unified theory of equilibrium thermodynamics and ion association in charged solutions.…
Electrostatic interactions make a large contribution to solvation free energy in ionic fluids such as electrolytes and colloidal dispersions. The electrostatic contribution to solvation free energy has been ascribed to the self-energy of a…
Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach,…
We propose a new model for estimating the free energy of forming a molecular cavity in a solvent, by assuming this energy is dominated by the electrostatic energy associated with creating the static (interface) potential inside the cavity.…
We present a broad family of high-order finite element algorithms for simulating the flow of electroneutral electrolytes. The governing partial differential equations that we solve are the electroneutral…
Complexation in symmetric solutions of oppositely charged polyelectrolytes is studied theoretically. We include polyion crosslinking due to formation of thermoreversible ionic pairs. The electrostatic free energy is calculated within the…
For charged systems in heterogeneous dielectric media, a key obstacle for molecular dynamics (MD) simulations is the need to solve the Poisson equation in the media. This obstacle can be bypassed using MD methods that treat the local…
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…
In a recent Letter we introduced Hellmann-Feynman operator sampling in diffusion Monte Carlo calculations. Here we derive, by evaluating the second derivative of the total energy, an efficient method for the calculation of the static…
We used a thermodynamic integration scheme, which is specifically designed for disordered systems, to compute the interfacial free energy of the solid-liquid interface in the hard-sphere model. We separated the bulk contribution to the…
Chemically-active colloids modify the concentration of chemical solutes surrounding them in order to self-propel. In doing so, they generate long-ranged hydrodynamic flows and chemical gradients that modify the trajectories of other…