Related papers: The AGBNP2 Implicit Solvation Model
We modelled the aqueous solvation of a nonpolar solute as a function of the radius, temperature and pressure. In this study a simple two-dimensional Mercedes-Benz (MB) water model was used in NPT Monte Carlo simulations. This model has…
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…
Shallow Water Moment Equations are reduced-order models for free-surface flows that employ a vertical velocity expansion and derive additional so-called moment equations for the expansion coefficients. Among desirable analytical properties…
In this paper the full and exhaustive algorithm of formation of a smooth molecular Solvent Excluded Surface- SES, and also Solvent Accessible Surface- SAS is presented. These surfaces are a boundary between molecule and solvent. The basis…
The hydration free energy of a macromolecule is the central property of interest for understanding its distribution over conformations and its state of aggregation. Calculating the hydration free energy of a macromolecule in all-atom…
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 novel hyperbolic reformulation of the Serre-Green-Naghdi (SGN) model for the description of dispersive water waves. Contrarily to the classical Boussinesq-type models, it contains only first order derivatives, thus allowing to…
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio…
In this paper we study two multidimensional nonlinear dispersive systems: the Serre-Green-Naghdi (SGN) equations describing dispersive shallow water flows, and Iordanskii-Kogarko-Wijngaarden (IKW) equations describing fluids containing…
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…
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…
Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…
Recent studies of the hydration of micro- and nanoscale solutes have demonstrated a strong {\it coupling} between hydrophobic, dispersion and electrostatic contributions, a fact not accounted for in current implicit solvent models. We…
Most organic and inorganic surfaces (e.g., glass, nucleic acids or lipid membranes) become charged in aqueous solutions. The resulting ionic distribution induces effective interactions between the charged surfaces. Stacks of like-charged…
Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key…
We present an overview of the recent progress that has been made in understanding the origin of hydrophobic interactions. We discuss the different character of the solvation behavior of apolar solutes at small and large length scales. We…
Simulating water accurately has been a challenge due to the complexity of describing polarization and intermolecular charge transfer. Quantum mechanical (QM) electronic structures provide an accurate description of polarization in response…
Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the…
Non-adiabatic molecular dynamics simulations are used to analyze the role of different solvent degrees of freedom in the non-radiative relaxation of the first excited state of the hydrated electron. The relaxation occurs through a…
A simple, dual-site model of bolaamphiphiles (bolaforms or bipolar amphiphiles) is developed based on an earlier single-site model of (monopolar) amphiphiles [S. Dey, J. Saha, Phys. Rev. E 95, 023315 (2017)]. The model incorporates aqueous…