403 citations · 957 across the 25 of their papers we have counts for
6 papers · 1 filter
MolSieve: A Progressive Visual Analytics System for Molecular Dynamics Simulations
Rostyslav Hnatyshyn, Jieqiong Zhao, Danny Perez +2
Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a mod…
Training Data Selection for Accuracy and Transferability of Interatomic Potentials
David Montes de Oca Zapiain, Mitchell A. Wood, Nicholas Lubbers +3
Advances in machine learning (ML) techniques have enabled the development of interatomic potentials that promise both the accuracy of first principles methods and the low-cost, lin…
Automated calculation and convergence of defect transport tensors
Thomas D Swinburne, Danny Perez
Defect transport is a key process in materials science and catalysis, but as migration mechanisms are often too complex to enumerate a priori, calculation of transport tensors typi…
An Entropy-Maximization Approach to Automated Training Set Generation for Interatomic Potentials
Mariia Karabin, Danny Perez
Machine learning (ML)-based interatomic potentials are currently garnering a lot of attention as they strive to achieve the accuracy of electronic structure methods at the computat…
Self-optimized construction of transition rate matrices from accelerated atomistic simulations with Bayesian uncertainty quantification
Thomas D Swinburne, Danny Perez
A massively parallel method to build large transition rate matrices from temperature accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is use…
Accelerating the convergence of replica exchange simulations using Gibbs sampling and adaptive temperature sets
Thomas Vogel, Danny Perez
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 c…