Related papers: The AGBNP2 Implicit Solvation Model
We describe an implicit general relativistic hydrodynamics code. The evolution equations are formulated in comoving coordinates. A conservative finite differencing of the Einstein equations is outlined, and artificial viscosity and…
Generalized hydrodynamics (GHD) is a recent theoretical approach that is becoming a go-to tool for characterizing out-of-equilibrium phenomena in integrable and near-integrable quantum many-body systems. Here, we benchmark its performance…
We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The…
In the present study, we propose a modified version of the Nonlinear Shallow Water Equations (Saint-Venant or NSWE) for irrotational surface waves in the case when the bottom undergoes some significant variations in space and time. The…
The present work demonstrates a robust protocol for probing localized electronic structure in condensed-phase systems, operating in terms of a recently proposed theory for decomposing the results of Kohn-Sham density functional theory in a…
A recent version of statistical associating fluid theory (SAFT), namely SAFT2, is coupled with the van der Waals and Platteeuw theory to study the alkane hydrate phase equilibrium conditions. The model is found to provide an accurate…
A statistical thermodynamic development is given of a new implicit solvent model that avoids the traditional system size limitations of computer simulation of macromolecular solutions with periodic boundary conditions. This implicit solvent…
From paints to food products, solvent evaporation is ubiquitous and critically impacts product rheological properties. It affects Newtonian fluids by concentrating any non-volatile components and viscoelastic materials, which hardens up. In…
Recent molecular simulation and integral equation results alkali-halide ion pair potentials-of-mean-force in water are discussed. Dielectric model calculations are implemented to check that these models produce that characteristic structure…
Recent advances in constructing stellar evolution models of hydrogen-deficient post-asymptotic giant branch (AGB) stars are presented. Hydrogen-deficiency can originate from mixing and subsequent convective burning of protons in the deeper…
We introduce a second-order numerical scheme for compressible atmospheric motions at small to planetary scales. The collocated finite volume method treats the advection of mass, momentum, and mass-weighted potential temperature in…
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…
Accurate simulations are essential for engineering applications, and intricate continuum mechanical material models are constructed to achieve this goal. However, the increasing complexity of the material models and geometrical properties…
We address the investigation of the solvation properties of the minimal orientational model for water, originally proposed by Bell and Lavis. The model presents two liquid phases separated by a critical line. The difference between the two…
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…
In this work, we develop a framework for atomistic modeling of electronic polarizability to predict the Raman spectra of hydrogen-bonded clusters and liquids from molecular dynamics (MD) simulations. The total polarizability of the system…
The structural properties of liquid GeSe$_2$ are studied by using first-principles molecular dynamics in conjuncton with the Becke, Lee, Yang and Parr (BLYP) generalized gradient approximation for the exchange and correlation energy. The…
Predicting the asymmetric structure and dynamics of solvated hydroxide and hydronium in water has been a challenging task from ab initio molecular dynamics (AIMD). The difficulty mainly comes from a lack of accurate and efficient…
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…
Non-local electrostatic interactions associated with the finite solvent size and ion polarizability are investigated within the mean-field linear response theory. To this end, we introduce a field theoretic model of a polar liquid composed…