Related papers: Mass-scaling replica-exchange molecular dynamics o…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
The reduction of the computational effort is desirable for the simulation of marine ecosystem models. Using a marine ecosystem model, the assessment and the validation of annual periodic solutions (i.e., steady annual cycles) against…
We present a distilled multi-time-step (DMTS) strategy to accelerate molecular dynamics simulations using foundation neural network models. DMTS uses a dual-level neural network where the target accurate potential is coupled to a simpler…
Replica exchange Monte Carlo (reMC), also known as parallel tempering, is an important technique for accelerating the convergence of the conventional Markov Chain Monte Carlo (MCMC) algorithms. However, such a method requires the evaluation…
Thermomechanical stress induced by through-silicon vias (TSVs) plays an important role in the performance and reliability analysis of 2.5D/3D ICs. While the finite element method (FEM) adopted by commercial software can provide accurate…
A systematic comparison was carried out to assess the influence of representative thermostat methods in constant-temperature molecular dynamics simulations. The thermostat schemes considered include the Nos\'e--Hoover thermostat and its…
We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different type…
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…
Kinetic transport equations are notoriously difficult to simulate because of their complex multiscale behaviors and the need to numerically resolve a high dimensional probability density function. Past literature has focused on building…
We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we…
Molecular Dynamic (MD) approach is applied to study the converging cylindrical shock waves in a dense Lennard-Jones (LJ) fluid. MD method is based on tracking of the atom motions and hence it has an fundamental advantages over hydrodynamic…
We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral…
We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of…
Fast and accurate sampling method is in high demand, in order to bridge the large gaps between molecular dynamic simulations and experimental observations. Recently, integrated tempering enhanced sampling method (ITS) has been proposed and…
A common way to simulate the transport and spread of pollutants in the atmosphere is via stochastic Lagrangian dispersion models. Mathematically, these models describe turbulent transport processes with stochastic differential equations…
We propose a class of subspace ascent methods for computing optimal approximate designs that covers both existing as well as new and more efficient algorithms. Within this class of methods, we construct a simple, randomized exchange…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…
Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD…