Related papers: Solv-eze: Automated Placement of Explicit Water Mo…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Understanding concentrated electrolytes requires a theory that spans local hydration and mesoscale interfacial assembly. We present an integrated workflow-SCOPE-that combines (i) enhanced sampling focused on a single Li+ ion, (ii)…
This paper collects the efforts done in our previous works [P. Degond, S. Jin, L. Mieussens, A Smooth Transition Between Kinetic and Hydrodynamic Equations, J. Comp. Phys., 209 (2005) 665--694.],[P.Degond, G. Dimarco, L. Mieussens, A Moving…
Accurately simulating the properties of liquid water remains a central challenge in molecular simulations. In this work, we use machine learning potentials to investigate how the convergence settings of electronic structure calculations…
In this work, we present a solution to the challenging problem of reconstructing liquids from image data. The challenges in reconstructing liquids, which is not faced in previous reconstruction works on rigid and deforming surfaces, lies in…
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems namely,…
Modelling micro- and meso-scopic scale thermodynamic and transport properties of soft condensed matter hinges upon its representation. This is especially relevant for polar solvents such as water, since these require effective…
Implicit neural representations have emerged as a powerful approach for encoding complex geometries as continuous functions. These implicit models are widely used in computer vision and 3D content creation, but their integration into…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
Ligands entering a protein binding pocket essentially compete with water molecules for binding to the protein. Hence, the location and thermodynamic properties of water molecules in protein structures have gained increased attention in the…
An effective computer program for three dimensional relativistic hydrodynamical model has been developed. It implements a new approach to the early hot phase of relativistic heavy-ion collisions. The computer program simulates time-space…
Recently, a family of models that couple multifluid systems to the full Maxwell equations draw a lot of attention in laboratory, space, and astrophysical plasma modeling. These models are more complete descriptions of the plasma than…
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…
We report applications of analytical formalisms and Molecular Dynamics (MD) simulations to the calculation of redox entropy of plastocyanin metalloprotein in aqueous solution. The goal of our analysis is to establish critical components of…
Our paper proposes an innovative approach for modeling Fluid-Structure Interaction (FSI). Our method combines both traditional monolithic and partitioned approaches, creating a hybrid solution that facilitates FSI. At each time iteration,…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Using fluorescence microscopy we study the adsorption of single latex microparticles at a water/water interface between demixing aqueous solutions of polymers, generally known as a water-in-water emulsion. Similar microparticles at the…
We generalize to three dimensions (3D) a recently developed improved multi-component pseudopotential lattice Boltzmann method and analyze its applicability to simulate flows through realistic porous media. The model is validated and…
The magnetohydrodynamics (MHD) equations are continuum models used in the study of a wide range of plasma physics systems, including the evolution of complex plasma dynamics in tokamak disruptions. However, efficient numerical solution…