Related papers: Adaptively accelerating reactive molecular dynamic…
A popular way to accelerate the sampling of rare events in molecular dynamics simulations is to introduce a potential that increases the fluctuations of selected collective variables. For this strategy to be successful, it is critical to…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
The Scintillating Bubble Chamber collaboration is searching for Weakly Interacting Massive Particles using a novel bubble chamber with intended thresholds as low as 100eV. Existing molecular dynamics simulations of bubble formation in…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
We introduce a new method to accurately and efficiently estimate the effective dynamics of collective variables in molecular simulations. Such reduced dynamics play an essential role in the study of a broad class of processes, ranging from…
We present an accelerated algorithm that samples correctly the thermodynamic ensemble in complex systems where the dynamics is controlled by activation barriers. The efficiency of the thermodynamically-weighted activation-relaxation…
A novel particle merging algorithm for rarefied gas dynamics simulations is proposed that can conserve arbitrary velocity and spatial moments of the particle distribution via solving a non-negative least squares problem. An extension that…
Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using…
In this paper, we introduce a new algorithm for rare event estimation based on adaptive importance sampling. We consider a smoothed version of the optimal importance sampling density, which is approximated by an ensemble of interacting…
In this paper we consider a biased velocity jump process with excluded-volume interactions for chemotaxis, where we account for the size of each particle. Starting with a system of N individual hard rod particles in one dimension, we derive…
In the last few decades, several novel algorithms have been designed for finding critical points on PES and the minimum energy paths connecting them. This has led to considerably improve our understanding of reaction mechanisms and kinetics…
Estimating rare event kinetics from molecular dynamics simulations is a non-trivial task despite the great advances in enhanced sampling methods. Weighted Ensemble (WE) simulation, a special class of enhanced sampling techniques, offers a…
The dynamics of complex systems often involve thermally activated barrier crossing events that allow these systems to move from one basin of attraction on the high dimensional energy surface to another. Such events are ubiquitous, but…
We develop a biased Monte Carlo algorithm to measure probabilities of rare events in cluster-cluster aggregation for arbitrary collision kernels. Given a trajectory with a fixed number of collisions, the algorithm modifies both the waiting…
Rare events are processes that occur upon the emergence of unlikely fluctuations. Unlike what their name suggests, rare events are fairly ubiquitous in nature, as the occurrence of many structural transformations in biology and material…
We introduce a framework to investigate ab-initio the dynamics of rare thermally activated reactions. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear…
The next generation of force fields for molecular dynamics will be developed using a wealth of data. Training systematically with experimental data remains a challenge, however, especially for machine learning potentials. Differentiable…
We study the effects of fast spatial movement of molecules on the dynamics of chemical species in a spatially heterogeneous chemical reaction network using a compartment model. The reaction networks we consider are either single- or…