Related papers: Multidimensional replica-exchange method for free-…
We discuss a method to calculate with quantum molecular dynamics simulations the rate of energy exchanges between electrons and ions in two-temperature plasmas, liquid metals and hot solids. Promising results from this method were recently…
We propose a free-energy-perturbation approach accelerated by machine-learning potentials to efficiently compute transition temperatures and entropies for all rungs of Jacob's ladder. We apply the approach to the dynamically stabilized…
In engineering, it is a common desire to couple existing simulation tools together into one big system by passing information from subsystems as parameters into the subsystems under influence. As executed at fixed time points, this data…
How accurate is pair additivity in describing interactions between soft polymer-based nanoparticles? Using numerical simulations we compute the free energy cost required to overlap multiple chains in the same region of space, and provide a…
Transition interface sampling (TIS) and replica exchange TIS (RETIS) are powerful methods for computing rates of rare events inaccessible to straightforward molecular dynamics (MD) simulations. Path reweighting extends their output,…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
We introduce an algorithm to systematically improve the efficiency of parallel tempering Monte Carlo simulations by optimizing the simulated temperature set. Our approach is closely related to a recently introduced adaptive algorithm that…
Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed…
We report a novel Monte Carlo scheme that greatly enhances the power of parallel-tempering simulations. In this method, we boost the accumulation of statistical averages by including information about all potential parallel tempering trial…
We propose a new global optimization method ({\em Simulated Tempering}) for simulating effectively a system with a rough free energy landscape (i.e. many coexisting states) at finite non-zero temperature. This method is related to simulated…
A recently developed quasi two-dimensional exact-exchange formalism within the framework of Density Functional Theory has been applied to a strongly inhomogeneous interacting electron gas, and the results were compared with state-of-the-art…
We present extensive Monte Carlo simulations on a two-dimensional XY model with a modified form of interaction potential. Thermodynamic quantities other than energy, specific heat etc (such as magnetization, susceptibility, fourth order…
The proposed method of the free energy calculation is based on the approximation of the energy distribution in the microcanonical ensemble by the Gaussian distribution. We hope that our approach will be effective for the systems with…
We estimated the residual entropy of ice Ih by the recently developed simulation protocol, namely, the combination of Replica-Exchange Wang-Landau algorithm and Multicanonical Replica-Exchange Method. We employed a model with the nearest…
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…
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…
In this paper, I investigate more closely the recently proposed Free Energy Monte Carlo algorithm that is devised in particular for calculations where conventional Monte Carlo simulations struggle with ergodicity problems. The simplest…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…