Related papers: Implicit Solvation Using the Superposition Approxi…
Simulating liquid water to an accuracy that matches its wealth of available experimental data requires both precise electronic structure methods and reliable sampling of nuclear (quantum) motion. This is challenging because applying the…
Laguerre tessellations of macromolecules capture properties such as molecular interface surfaces, volumes and cavities. Explicit solvent molecular dynamics simulations of a macromolecule are slow as the number of solvent atoms considered…
Liquid structure at solid-liquid interfaces is critical for many natural and engineered processes ranging from biological signal transduction to electrochemical energy conversion. Advanced experimental and computational methods have…
Solvent can occupy up to ~70% of macromolecular crystals and hence having models that predict solvent distributions in periodic systems could improve in the interpretation of crystallographic data. Yet there are few implicit solvent models…
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like…
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…
Recent advances in stochastic optimization have yielded the interacting particle Langevin algorithm (IPLA), which leverages the notion of interacting particle systems (IPS) to efficiently sample from approximate posterior densities. This…
The surrogate process approximation (SPA) is applied to model the nonequilibrium dynamics of a reaction coordinate (RC) associated with the unfolding and refolding processes of a deca-alanine peptide at 300 K. The RC dynamics, which…
The AGBNP2 implicit solvent model, an evolution of the Analytical Generalized Born plus Non-Polar (AGBNP) model we have previously reported, is presented with the aim of modeling hydration effects beyond those described by conventional…
The association of ions in electrolyte solutions at very low concentration and low temperature is studied using computer simulations and quasi-chemical ion-pairing theory. The specific case of the restricted primitive model (charged hard…
We investigate the reliability of simulations of polyelectrolyte systems in aqueous environments, simulations that are performed using an efficient multi scale coarse grained polarizable pseudo-particle particle approach, denoted as pppl,…
The thesis focuses on the prediction of solvation thermodynamics using integral equation theories. Our main goal is to improve the approach using a rational correction. We achieve it by extending recently introduced pressure correction, and…
Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller…
Implicit solvent models are widely used to decrease the number of solvent degrees of freedom and enable the calculation of solvation energetics without water molecules. However, its accuracy often falls short compared to explicit models.…
Context. Simulating solar flares, which involve large-scale dynamics and small-scale magnetic reconnection, poses significant computational challenges. Aims. This study aims to develop an explicit Particle-In-Cell (PIC) solver within the…
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…
A new class of implicit-explicit (IMEX) methods combined with a p-adaptive mixed finite element formulation is proposed to simulate the diffusion of reacting species. Hierarchical polynomial functions are used to construct an…
We introduce a class of specially structured linear programming (LP) problems, which has favorable modeling capability for important application problems in different areas such as optimal transport, discrete tomography and economics. To…
Polarizable force fields are gradually becoming a common choice for ionic soft matter, in particular for molecular dynamics (MD) simulations of ionic liquids (ILs) and deep eutectic solvents (DESs). The CL&Pol force field introduced in 2019…
We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the…