Related papers: Force Fields for Deep Eutectic Mixtures: Applicati…
The interaction of phosphate groups with ions in an aqueous environment has a strong impact on the structure and folding processes of DNA and RNA. The dynamic variety of ionic arrangements, including both contact pairs and water separated…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…
We use functional, Fr\'echet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities…
We present an ab initio molecular dynamics (MD) investigation of the tautomeric equilibrium for aqueous solutions of glycine and acetone at realistic experimental conditions. Metadynamics is used to accelerate proton migration among…
We formulate and study computationally the low Mach number fluctuating hydrodynamic equations for electrolyte solutions. We are interested in studying transport in mixtures of charged species at the mesoscale, down to scales below the Debye…
The solvation structure of protons in aqueous media is highly relevant to electric properties and to proton transport in liquids and membranes. At ambient temperature, polar liquids display structural fluctuations on femto- to picosecond…
The pressure- and anion-dependent electronic structure of EuX (X=Te, Se, S, O) monochalcogenides is probed with element- and orbital-specific X-ray absorption spectroscopy in a diamond anvil cell. An isotropic lattice contraction enhances…
In fractured natural formations, the equations governing fluid flow and geomechanics are strongly coupled. Hydrodynamical properties depend on the mechanical configuration, and they are therefore difficult to accurately resolve using…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
The influences of water molecules surrounding biological molecules during irradiation with heavy particles (atoms,ions) are currently a major subject in radiation science on a molecular level. In order to elucidate the underlying complex…
In the frame of collective dynamics in water, models built on elementary excitations and long-range electromagnetic interactions in the cell and bulk liquid are presented. Making use of the low effective mass of water coherence domains…
We report a multiscale modeling study for charged cylindrical nanopores using three modeling levels that include (1) an all-atom explicit-water model studied with molecular dynamics (MD), and reduced models with implicit water containing…
Deep eutectic solvents (DESs) have gained attention in recent years as attractive alternatives to traditional solvents. There is a growing number of publications dealing with the thermodynamic modeling of DESs highlighting the importance of…
The study of the modification of interfacial properties between an organic solvent and aqueous electrolyte solutions is presented by using electrostatic Dissipative Particle Dynamics (DPD) simulations. In this article the parametrization…
The accurate description of iron oxides/water interfaces requires reliable force field parameters that can be developed through the comparison with sophisticated quantum mechanical calculations. Here a set of CLASS2 force field parameters…
In this work, we consider the problem of training a generator from evaluations of energy functions or unnormalized densities. This is a fundamental problem in probabilistic inference, which is crucial for scientific applications such as…
Treating water as a linearly responding dielectric continuum on molecular length scales allows very simple estimates of solvation structure and thermodynamics for charged and polar solutes. While this approach can successfully account for…
In this work we present the dielectric behavior of water with a novel flexible model that improved all three sites water models Different concentrations of the ionic liquid 1- butyl-3-methylimidazolium [bmim]…
The Phase-Field Method (PFM) is employed to simulate two-phase flows with the fully-coupled Cahn-Hilliard-Navier-Stokes (CHNS) equations governing the temporal evolution. The methodology minimizes the total energy functional, accounting for…
Water is perhaps the most simulated liquid. Recently three water models have been developed following the adaptive force matching (AFM) method that provides excellent predictions of water properties with only electronic structure…