Related papers: Implicit Solvation Using the Superposition Approxi…
Force field have for decades proven to be an indispensable tool for molecular simulations which are out of reach for ab-initio methods. Recent efforts to improve the accuracy of these simulations have focused on the inclusion of many-body…
In this work we present an efficient numerical algorithm for the solution of interfacial statistical associating fluid theory (iSAFT) in cylindrical geometry to facilitate the study of inhomogeneous fluids having curvatures. The new…
Numerical heating in particle-in-cell (PIC) codes currently precludes the accurate simulation of cold, relativistic plasma over long periods, severely limiting their applications in astrophysical environments. We present a spatially…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
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…
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…
Compositional simulation is challenging, because of highly nonlinear couplings between multi-component flow in porous media with thermodynamic phase behavior. The coupled nonlinear system is commonly solved by the fully-implicit scheme.…
We propose an enhanced approach to the extrapolation of mean potential forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends previous…
Computer simulation studies of aqueous solutions of argon are performed from ambient to supercritical conditions by using a recent polarizable potential model (BSV) and the non polarizable simple point charge extended (SPC/E) model. At…
We critically examine a broad class of explicitly polarisable soft solvent models aimed at applications in dissipative particle dynamics. We obtain the dielectric permittivity using the fluctuating box dipole method in linear response…
A self-consistent (SC) renormalization group approach of the effective medium kind has been developed and applied to the solution of the Ising model (IM). A renormalization group equation in the local potential approximation (LPA) derived…
The Immersed Boundary method is a simple, efficient, and robust numerical scheme for solving PDE in general domains, yet for fluid problems it only achieves first-order spatial accuracy near embedded boundaries for the velocity field and…
The fast Ewald methods are widely used to compute the point-charge electrostatic interactions in molecular simulations. The key step that introduces errors in the computation is the particle-mesh interpolation. In this work, the optimal…
We present an extension to the Poisson-Boltzmann model where the dipolar features of solvent molecules are taken explicitly into account. The formulation is derived at mean-field level and can be extended to any order in a systematic…
Recent experimental results by the Surface Force Apparatus (SFA) have identified a dramatic deviation from previously established theories of simple electrolytes. This deviation, referred to as anomalous underscreening, suggests that the…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
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…
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…
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…
Semi-implicit time-stepping schemes for atmosphere and ocean models require elliptic solvers that work efficiently on modern supercomputers. This paper reports our study of the potential computational savings when using mixed precision…