A mathematical formalization of the parallel replica dynamics. - Claude Le Bris; Tony Lelièvre; Mitchell Luskin; Danny Perez (Monte Carlo Methods Appl., 2012)

Analysis of Transition State Theory Rates upon Spatial Coarse-Graining. - Andrew Binder; Mitchell Luskin; Danny Perez; Arthur F. Voter (Multiscale Model. Simul., 2015)

TADSim: Discrete Event-Based Performance Prediction for Temperature-Accelerated Dynamics. - Susan M. Mniszewski; Christoph Junghans; Arthur F. Voter; Danny Perez; Stephan J. Eidenbenz (ACM Trans. Model. Comput. Simul., 2015)

Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics. - Richard J. Zamora; Arthur F. Voter; Danny Perez; Nandakishore Santhi; Susan M. Mniszewski; Sunil Thulasidasan; Stephan J. Eidenbenz (Simul., 2016)

Programmable Caches with a Data Management Language and Policy Engine. - Michael A. Sevilla; Carlos Maltzahn; Peter Alvaro; Reza Nasirigerdeh; Bradley W. Settlemyer; Danny Perez; David Rich; Galen M. Shipman (CCGrid, 2018)

Testing Research Software: A Case Study. - Nasir U. Eisty; Danny Perez; Jeffrey C. Carver; J. David Moulton; Hai Ah Nam (ICCS (7), 2020)

Rapid Exploration of Optimization Strategies on Advanced Architectures using TestSNAP and LAMMPS. - Rahulkumar Gayatri; Stan G. Moore; Evan Weinberg; Nicholas Lubbers; Sarah Anderson; Jack Deslippe; Danny Perez; Aidan P. Thompson (CoRR, 2020)

Pairwise Difference Regression: A Machine Learning Meta-algorithm for Improved Prediction and Uncertainty Quantification in Chemical Search. - Michael Tynes; Wenhao Gao 001; Daniel J. Burrill; Enrique R. Batista; Danny Perez; Ping Yang; Nicholas Lubbers (J. Chem. Inf. Model., 2021)

MDZ: An Efficient Error-bounded Lossy Compressor for Molecular Dynamics. - Kai Zhao 008; Sheng Di; Danny Perez; Xin Liang 001; Zizhong Chen; Franck Cappello (ICDE, 2022)

Combining machine-learned and empirical force fields with the parareal algorithm: application to the diffusion of atomistic defects. - Olga Gorynina; Frédéric Legoll; Tony Lelièvre; Danny Perez (CoRR, 2022)

Resource allocation for task-level speculative scientific applications: A proof of concept using Parallel Trajectory Splicing. - Andrew Garmon; Vinay Ramakrishnaiah; Danny Perez (Parallel Comput., 2022)

Frontier: Exploring Exascale. - Scott Atchley; Christopher Zimmer 001; John Lange; David E. Bernholdt; Verónica G. Melesse Vergara; Thomas Beck; Michael J. Brim; Reuben D. Budiardja; Sunita Chandrasekaran; Markus Eisenbach 002; Thomas M. Evans 001; Matthew Ezell; et al. (SC, 2023)

Regression-Based Projection for Learning Mori-Zwanzig Operators. - Yen Ting Lin; Yifeng Tian; Danny Perez; Daniel Livescu (SIAM J. Appl. Dyn. Syst., 2023)

Breaking the Molecular Dynamics Timescale Barrier Using a Wafer-Scale System. - Kylee Santos; Stan G. Moore; Tomas Oppelstrup; Amirali Sharifian; Ilya Sharapov; Aidan P. Thompson; Delyan Z. Kalchev; Danny Perez; Robert Schreiber; Scott Pakin; Edgar A. Leon; James H. Laros III; et al. (SC, 2024)

Misspecification uncertainties in near-deterministic regression. - Thomas D. Swinburne; Danny Perez (CoRR, 2024)

Breaking the mold: overcoming the time constraints of molecular dynamics on general-purpose hardware. - Danny Perez; Aidan P. Thompson; Stan G. Moore; Tomas Oppelstrup; Ilya Sharapov; Kylee Santos; Amirali Sharifian; Delyan Z. Kalchev; Robert Schreiber; Scott Pakin; Edgar A. Leon; James H. Laros III; et al. (CoRR, 2024)

Co-design for Particle Applications at Exascale. - Samuel Temple Reeve; Jean-Luc Fattebert; Stephen Dewitt; Pablo Seleson; David Joy; Stuart R. Slattery; Aaron Scheinberg; Rene Halver; Christoph Junghans; Christian F. A. Negre; Michael E. Wall; Yu Zhang 010; et al. (Comput. Sci. Eng., 2024)

MolSieve: A Progressive Visual Analytics System for Molecular Dynamics Simulations. - Rostyslav Hnatyshyn; Jieqiong Zhao; Danny Perez; James P. Ahrens; Ross Maciejewski (IEEE Trans. Vis. Comput. Graph., 2024)

Best of both worlds: Enforcing detailed balance in machine learning models of transition rates. - Anjana Anu Talapatra; Anup Pandey; Matthew S. Wilson; Ying Wai Li; Ghanshyam Pilania; Blas Pedro Uberuaga; Danny Perez (Comput. Phys. Commun., 2025)

Parameter uncertainties for imperfect surrogate models in the low-noise regime. - Thomas D. Swinburne; Danny Perez (Mach. Learn. Sci. Technol., 2025)

Executorlib - Up-scaling Python workflows for hierarchical heterogenous high-performance computing. - Jan Janssen; Michael Gilbert Taylor; Ping Yang; Jörg Neugebauer; Danny Perez (J. Open Source Softw., 2025)

Accurate and Uncertainty-Aware Multi-Task Prediction of HEA Properties Using Prior-Guided Deep Gaussian Processes. - Sk Md Ahnaf Akif Alvi; Mrinalini Mulukutla; Nicolas Flores; Danial Khatamsaz; Jan Janssen; Danny Perez; Douglas L. Allaire; Vahid Attari; Raymundo Arróyave (CoRR, 2025)