403 citations · 957 across the 25 of their papers we have counts for
26 papers
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…
Improving Estimation of the Koopman Operator with Kolmogorov-Smirnov Indicator Functions
Van A. Ngo, Yen Ting Lin, Danny Perez
It has become common to perform kinetic analysis using approximate Koopman operators that transforms high-dimensional time series of observables into ranked dynamical modes. Key to…
Arbitrarily accurate, nonparametric coarse graining with Markov renewal processes and the Mori-Zwanzig formulation
David Aristoff, Mats Johnson, Danny Perez
Stochastic dynamics, such as molecular dynamics, are important in many scientific applications. However, summarizing and analyzing the results of such simulations is often challeng…
Combining machine-learned and empirical force fields with the parareal algorithm: application to the diffusion of atomistic defects
Olga Gorynina, Frederic Legoll, Tony Lelievre +1
We numerically investigate an adaptive version of the parareal algorithm in the context of molecular dynamics. This adaptive variant has been originally introduced in [F. Legoll, T…
Roadmap on Electronic Structure Codes in the Exascale Era
Vikram Gavini, Stefano Baroni, Volker Blum +38
Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state…
Regression-based projection for learning Mori-Zwanzig operators
Yen Ting Lin, Yifeng Tian, Danny Perez +1
We propose to adopt statistical regression as the projection operator to enable data-driven learning of the operators in the Mori--Zwanzig formalism. We present a principled method…