Related papers: Polarizable Multipolar Molecular Dynamics Using Di…
We present a new method to couple the Direct Simulation Monte Carlo (DSMC) algorithm with molecular dynamics (MD). The coupling approach generalizes prior coupling methods using a cell-based decision. The approach is supported by a lifting…
We present a promising coarse-graining strategy for linking micro- and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD)…
Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using…
The Many-Body Expansion (MBE) is a useful tool to simulate condensed phase chemical systems, often avoiding the steep computational cost of usual electronic structure methods. However, it often requires higher than 2-body terms to achieve…
Chemically-active colloids modify the concentration of chemical solutes surrounding them in order to self-propel. In doing so, they generate long-ranged hydrodynamic flows and chemical gradients that modify the trajectories of other…
The material point method (MPM) has been increasingly used for the simulation of large deformation processes in fluid-infiltrated porous materials. For undrained poromechanical problems, however, standard MPMs are numerically unstable…
Distributed model predictive control (DMPC) is a flexible and scalable feedback control method applicable to a wide range of systems. While the stability analysis of DMPC is quite well understood, there exist only limited implementation…
One important development in interaction potential models, or atomistic force fields, for molecular simulation is the inclusion of explicit polarisation, which represents the induction effects of charged or polar molecules on polarisable…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
A mesoscopic colloid model is developed in which a spherical colloid is represented by many interacting sites on its surface. The hydrodynamic interactions with thermal fluctuations are taken accounts in full using Dissipative Particle…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
A new kinetic model for multiphase flow was presented under the framework of the discrete Boltzmann method (DBM). Significantly different from the previous DBM, a bottom-up approach was adopted in this model. The effects of molecular size…
Earlier, using phenomenological approach, we showed that in some cases polarizable models of condensed phase systems can be reduced to nonpolarizable equivalent models with scaled charges. Examples of such systems include ionic liquids,…
In this study, a fast multipole method (FMM) is used to decrease the computational time of a fully-coupled poroelastic hydraulic fracture model with a controllable effect on its accuracy. The hydraulic fracture model is based on the…
An adpative integration technique for time advancement of particle motion in the context of coupled computational fluid dynamics (CFD) - discrete element method (DEM) simulations is presented in this work. CFD-DEM models provide an accurate…
Large thermal fluctuations of the liquid phase obscure the weak macroscopic electric field that drives electrochemical reactions, rendering the extraction of reliable interfacial charge distributions from ab initio molecular dynamics…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
Fluctuating-charge models are computationally efficient methods of treating polarization and charge-transfer phenomena in molecular mechanics and classical molecular dynamics simulations. They are also theoretically appealing as they are…
A micro-hydromechanical model for granular materials is presented. It combines the discrete element method (DEM) for the modeling of the solid phase and a pore-scale finite volume (PFV) formulation for the flow of an incompressible pore…
Quantum-mechanically-driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically-driven structural…