相关论文: Towards Open Boundary Molecular Dynamics Simulatio…
Lithium chloride LiCl is widely used as a prototype system to study the strongly dissociated 1-1 electrolyte solution. Here, we combined experimental measurements and classical molecular dynamics simulations to study the ion conduction in…
We present a generalized form of open boundary conditions, and an associated numerical algorithm, for simulating incompressible flows involving open or outflow boundaries. The generalized form represents a family of open boundary…
Lubricated friction is a multiscale problem where molecular processes dictate the macroscopic response of the system. Traditional lubrication models rely on semi-empirical constitutive relations, which become unreliable under extreme…
In recent years, several particle-based stochastic simulation algorithms (PSSA) have been developed to study the spatially resolved dynamics of biochemical networks at a molecular scale. A challenge all these approaches have to address is…
We present a highly accurate and transferable parameterization of water using the atomic cluster expansion (ACE). To efficiently sample liquid water, we propose a novel approach that involves sampling static calculations of various ice…
In a recently proposed computational model of open molecular systems out of equilibrium [Ebrahimi Viand et al. J.Chem.Phys. 153, 101102 (2020)], the action of different reservoirs enters as a linear sum into the Liouville-type evolution…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Atomic diffusion affects the properties of various engineering materials, which predominantly occur in the polycrystalline state. A rigorous description of polycrystalline diffusion must therefore account for crystallographic defects,…
We present numerical simulations of active fluid droplets immersed in an external fluid in 2-dimensions { using} an Immersed Boundary method to simulate the fluid droplet interface as a Lagrangian mesh. We present results from two example…
In this work, a coarse-graining method previously proposed by the authors in a companion paper based on solving diffusion equations is applied to CFD-DEM simulations, where coarse graining is used to obtain solid volume fraction, particle…
Active colloids constitute a novel class of materials composed of colloidal-scale particles locally converting chemical energy into motility, mimicking micro-organisms. Evolving far from equilibrium, these systems display structural…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon…
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…
An analytical solution of the equations describing impurity diffusion due to the migration of nonequilibrium impurity interstitial atoms was obtained for the case of the Robin boundary condition on the surface of a semiconductor. The…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
We use molecular simulations of an ionic liquid in contact with a range of nanoporous carbons to investigate correlations between ion size, pore size, pore topology and properties of the adsorbed ions. We show that diffusion coefficients…
We derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables we…
We present a high-order implicit large-eddy simulation (ILES) approach for simulating transitional turbulent flows. The approach consists of an Interior Embedded Discontinuous Galerkin (IEDG) method for the discretization of the…