Related papers: Adaptive Equilibration of Molecular Dynamics Simul…

The efficient calculation of rare-event kinetics in complex dynamical systems, such as the rate and pathways of ligand dissociation from a protein, is a generally unsolved problem. Markov state models can systematically integrate ensembles…

The recent improvement in experimental capabilities for interrogating and controlling molecular systems with ultrafast coherent light sources calls for the development of theoretical approaches that can accurately and efficiently treat…

We introduce a novel approach for the simultaneous optimization of plasma physics and coil engineering objectives using fixed-boundary equilibria that is computationally efficient and applicable to a broad range of vacuum and finite plasma…

We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss…

We propose an algorithm for molecular dynamics or Monte Carlo simulations that uses an interpolation procedure to estimate potential energy values from energies and gradients evaluated previously at points of a simplicial mesh. We chose an…

In dusty (complex) plasmas, containing mesoscopic charged grains, the grain-grain interaction in many cases can be well described through a Yukawa potential. In this Review we summarize the basics of the computational and theoretical…

It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…

Molecular dynamics algorithms are subject to some amount of error dependent on the size of the time step that is used. This error can be corrected by periodically updating the system with a Metropolis criteria, where the integration step is…

Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…

A comprehensive study is presented on the short-time dynamics in suspensions of charged colloidal spheres. The explored parameter space covers the major part of the fluid-state regime, with colloid concentrations extending up to the…

Thermodynamic and flash equilibrium calculations are the cornerstones of simulation process calculations. The iterative approach, a widely used nonlinear problem-solving technique, relies on derivative calculations throughout the procedure…

The Milestoning method has achieved great success in the calculation of equilibrium kinetic properties such as rate constants from molecular dynamics simulations. The goal of this work is to advance Milestoning into the realm of…

We show that optimal control of the electron dynamics is able to prepare molecular ground states, within chemical accuracy, with evolution times approaching the bounds imposed by quantum mechanics. We propose a specific parameterization of…

Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…

Different advanced bridge function closures are utilized to investigate the structural and thermodynamic properties of dense Yukawa one-component plasma liquids within the framework of integral equation theory. The isomorph-based…

The uncertainty in the equilibration in heavy ion collisions due to the choice of the value of the coupling is examined. The results of the equilibration are indeed affected by this choice. In particular, a variation of $\a_s$ from 0.3 to…

We present a new method of conducting molecular dynamics simulation in isothermal-isobaric ensemble based on Langevin equations of motion. The stochastic coupling to all particle and cell degrees of freedoms is introduced in a correct way,…

This paper describes an algorithm for selecting parameter values (e.g. temperature values) at which to measure equilibrium properties with Parallel Tempering Monte Carlo simulation. Simple approaches to choosing parameter values can lead to…

Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization…

We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…