47 citations · 211 across the 12 of their papers we have counts for
7 papers · 1 filter
Estimating thermodynamic expectations and free energies in expanded ensemble simulations: systematic variance reduction through conditioning
Manuel Athènes, Pierre Terrier
Markov chain Monte Carlo methods are primarily used for sampling from a given probability distribution and estimating multi-dimensional integrals based on the information contained…
Using Bayes formula to estimate rates of rare events in transition path sampling simulations
Pierre Terrier, Mihai-Cosmin Marinica, Manuel Athènes
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 frac…
Path Factorization Approach to Stochastic Simulations
Manuel Athènes, Vasily V. Bulatov
The computational efficiency of stochastic simulation algorithms is notoriously limited by the kinetic trapping of the simulated trajectories within low energy basins. Here we pres…
Free energy calculations from adaptive molecular dynamics simulations with adiabatic reweighting
Lingling Cao, Gabriel Stoltz, Tony Lelièvre +2
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated…
Waste-recycling Monte Carlo with optimal estimates: application to free energy calculations in alloys
Gilles Adjanor, Manuel Athènes, Jocelyn M. Rodgers
The estimator proposed recently by Delmas and Jourdain for waste-recycling Monte Carlo achieves variance reduction optimally with respect to a control variate that is evaluated dir…
Simulating structural transitions by direct transition current sampling: the example of LJ38
Massimiliano Picciani, Manuel Athenes, Jorge Kurchan +1
Reaction paths and probabilities are inferred, in a usual Monte Carlo or Molecular Dynamic simulation, directly from the evolution of the positions of the particles. The process be…
Free energy reconstruction from steered dynamics without post-processing
Manuel Athènes, Mihai-Cosmin Marinica
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to…