Computing equilibrium free energies using non-equilibrium molecular dynamics

C Dellago, G Hummer - Entropy, 2013 - mdpi.com
As shown by Jarzynski, free energy differences between equilibrium states can be
expressed in terms of the statistics of work carried out on a system during non-equilibrium …

First-principles study of point defects in an fcc Fe-10Ni-20Cr model alloy

JB Piochaud, TPC Klaver, G Adjanor, P Olsson… - Physical Review B …, 2014 - APS
The influence of the local environment on vacancy and self-interstitial formation energies
has been investigated in a face-centered-cubic (fcc) Fe-10Ni-20Cr model alloy by analyzing …

Calculation of excess free energies of precipitates via direct thermodynamic integration across phase boundaries

B Sadigh, P Erhart - Physical Review B—Condensed Matter and Materials …, 2012 - APS
We describe a technique for constraining macroscopic fluctuations in thermodynamic
variables well-suited for Monte Carlo (MC) simulations of multiphase equilibria. In particular …

Molecular monte carlo simulations using graphics processing units: To waste recycle or not?

J Kim, JM Rodgers, M Athenes… - Journal of Chemical Theory …, 2011 - ACS Publications
In the waste recycling Monte Carlo (WRMC) algorithm, multiple trial states may be
simultaneously generated and utilized during Monte Carlo moves to improve the statistical …

Estimating linear mass transport coefficients in solid solutions via correlation splitting and a law of total diffusion

M Athènes, G Adjanor, J Creuze - Physical Review Materials, 2022 - APS
Directly computing linear mass transport coefficients in stochastic models entails integrating
over time the equilibrium correlations between atomic displacements. Here, we show how to …

[PDF][PDF] Conditioning and enhanced sampling schemes for simulating thermodynamic and kinetic properties of condensed matter

M Athènes - 2018 - cea.hal.science
Abstract The Monte Carlo method is a stochastic simulation approach essentially used to
estimate multi-dimensional integrals. This is traditionally achieved by generating a sample of …

Using Bayes formula to estimate rates of rare events in transition path sampling simulations

P Terrier, MC Marinica, M Athènes - The Journal of Chemical Physics, 2015 - pubs.aip.org
Transition path sampling is a method for estimating the rates of rare events in molecular
systems based on the gradual transformation of a path distribution containing a small …

Estimating time-correlation functions by sampling and unbiasing dynamically activated events

M Athènes, MC Marinica, T Jourdan - The Journal of chemical physics, 2012 - pubs.aip.org
Transition path sampling is a rare-event method that estimates state-to-state time-correlation
functions in many-body systems from samples of short trajectories. In this framework, it is …

Etude à l'échelle atomique de la plasticité et de la sur-stœchiométrie dans le dioxyde d'uranium

A Soulié - 2018 - theses.hal.science
L'objectif de ce travail consiste d'une part à étudier la plasticité dans le dioxyde d'uranium en
décrivant à l'échelle atomique le mécanisme de glissement des dislocations, et d'autre part …

Mass transport computations via correlation splitting and a law of total diffusion

M Athènes, G Adjanor, J Creuze - arXiv preprint arXiv:2112.01978, 2021 - arxiv.org
Directly computing mass transport coefficients in stochastic models requires integrating over
time the equilibrium correlations between atomic displacements. Here, we show how to …