Related papers: Optimizing Replica Exchange Moves For Molecular Dy…
Because of growing interest in temperature-based sampling methods like replica exchange, this note aims to make some observations and raise some potentially important questions which we have not seen addressed sufficiently in the…
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is…
A new concept of the molecular structure optimization method based on quantum dynamics computations is presented. Nuclei are treated as quantum mechanical particles, as are electrons, and the many-body wave function of the system is…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that…
Techniques for simulating molecules whose conformations satisfy constraints are presented. A method for selecting appropriate moves in Monte Carlo simulations is given. The resulting moves not only obey the constraints but also maintain…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
We combine replica exchange (parallel tempering) with normalizing flows, a class of deep generative models. These two sampling strategies complement each other, resulting in an efficient strategy for sampling molecular systems characterized…
Replica exchange (REX) is one of the most widely used enhanced sampling methodologies, yet its efficiency is limited by the requirement for a large number of intermediate temperature replicas. Here we present Generative Replica Exchange…
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…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
The miniaturization of gears towards the nanoscale is a formidable task posing a variety of challenges to current fabrication technologies. In context, the understanding, via computer simulations, of the mechanisms mediating the transfer of…
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…
Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of so-called rare events that are characterized by transitions between metastable states separated by sizeable free energy barriers. Their…
I give an overview of rare event simulation techniques to generate dynamical pathways across high free energy barriers. The methods on which I will concentrate are the reactive flux approach, transition path sampling, (replica-exchange)…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
This paper explores the connection between dynamical system properties and statistical physics of ensembles of such systems. Simple models are used to give novel phase transitions; particularly for finite N particle systems with many…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…