Related papers: Multidimensional Replica Exchange simulations for …
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval of replicas and their exchange probabilities. Here, we…
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…
Generalized ensemble methods such as Hamiltonian replica exchange (HREX) and expanded ensemble (EE) have been shown effective in free energy calculations for various contexts, given their ability to circumvent free energy barriers via…
Ring polymer molecular dynamics (RPMD) is an accurate method for calculating thermal chemical reaction rates. It has recently been discovered that low-temperature calculations are strongly affected by the simulation parameters. Here, for…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
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…
Markov Chain Monte Carlo (MCMC) excels at sampling complex posteriors but traditionally lags behind nested sampling in accurate evidence estimation, which is crucial for model comparison in astrophysical problems. We introduce reddemcee, an…
Redox potentials of electron transfer reactions are of fundamental importance for the performance and description of electrochemical devices. Despite decades of research, accurate computational predictions for the redox potential of even…
Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving…
Space plasma simulations have seen an increase in the use of magnetohydrodynamic (MHD) with embedded Particle-in-Cell (PIC) models. This combined MHD-EPIC algorithm simulates some regions of interest using the kinetic PIC method while…
Obtainable computational efficiency is evaluated when using an Adaptive Mesh Refinement (AMR) strategy in time accurate simulations governed by sets of conservation laws. For a variety of 1D, 2D, and 3D hydro- and magnetohydrodynamic…
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…
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…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic…
Emulation has been successfully applied across a wide variety of scientific disciplines for efficiently analysing computationally intensive models. We develop known boundary emulation strategies which utilise the fact that, for many…