Related papers: Mass-scaling replica-exchange molecular dynamics o…
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral…
Despite the increasing prevalence of vector observations, computation of optimal experimental design for multi-response models has received limited attention. To address this problem within the framework of approximate designs, we introduce…
Replica exchange (RE) is one of the most popular enhanced-sampling simulations technique in use today. Despite widespread successes, RE simulations can sometimes fail to converge in practical amounts of time, e.g., when sampling around…
Synthetic molecular dynamics (synMD) trajectories from learned generative models have been proposed as a useful addition to the biomolecular simulation toolbox. The computational expense of explicitly integrating the equations of motion in…
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…
Radiative transfer calculations are essential for modeling planetary atmospheres. However, standard methods are computationally demanding and impose accuracy-speed trade-offs. High computational costs force numerical simplifications in…
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…
This work provides an efficient sampling method for the covariance matrix adaptation evolution strategy (CMA-ES) in large-scale settings. In contract to the Gaussian sampling in CMA-ES, the proposed method generates mutation vectors from a…
Atomistic simulations of heat transport in complex materials are costly and hard to converge. This has led to the development of several noise-reduction techniques applicable to equilibrium molecular-dynamics (MD) simulations. We analyze…
In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some…
This paper proposes a computationally efficient simulation strategy for cold thermal energy storage (TES) systems based on phase change material (PCM). Taking as a starting point the recent design of a TES system based on PCM, designed to…
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian Dynamics (BD) or…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
Designing an effective move-generation function for Simulated Annealing (SA) in complex models remains a significant challenge. In this work, we present a combination of theoretical analysis and numerical experiments to examine the impact…
In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…
Two-dimensional Raman and hybrid terahertz/Raman spectroscopic techniques provide invaluable insight into molecular structure and dynamics of condensed-phase systems. However, corroborating experimental results with theory is difficult due…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
The dynamics of a polydisperse model glassformer are investigated by augmenting molecular dynamics (MD) simulation with swap Monte Carlo (SMC). Three variants of the SMC algorithm are analyzed with regard to convergence and performance. We…
The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano-/micro- scale. The method shows great potential to solve the computational bottleneck of long-range…
We develop an online optimisation algorithm for in situ calibration of collision models in simulations of rarefied gas flows. The online optimised collision models are able to achieve similar accuracy to Direct Molecular Simulation (DMS) at…