Danny Perez

29 papers A* 1A 2B 1Journal 24Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
LAMDA: Aiding Visual Exploration of Atomic Displacements in Molecular Dynamics Simulations.
CoRR
Rostyslav Hnatyshyn, Danny Perez, Gerik Scheuermann, Ross Maciejewski, Baldwin Nsonga
2026 J jnl
LAMDA: Aiding Visual Exploration of Atomic Displacements in Molecular Dynamics Simulations.
IEEE Trans. Vis. Comput. Graph.
Rostyslav Hnatyshyn, Danny Perez, Gerik Scheuermann, Ross Maciejewski, Baldwin Nsonga
2026 J jnl
Predicting Atomistic Transitions with Transformers.
CoRR
Henry Tischler, Wenting Li, Qi Tang, Danny Perez, Thomas Vogel
2025 J jnl
Accurate and Uncertainty-Aware Multi-Task Prediction of HEA Properties Using Prior-Guided Deep Gaussian Processes.
CoRR
Sk Md Ahnaf Akif Alvi, Mrinalini Mulukutla, Nicolas Flores, Danial Khatamsaz, Jan Janssen, Danny Perez, Douglas L. Allaire, Vahid Attari, Raymundo Arróyave
2025 J jnl
Best of both worlds: Enforcing detailed balance in machine learning models of transition rates.
Comput. Phys. Commun.
Anjana Anu Talapatra, Anup Pandey, Matthew S. Wilson, Ying Wai Li, Ghanshyam Pilania, Blas Pedro Uberuaga, Danny Perez
2025 J jnl
Deep Gaussian Process-based Cost-Aware Batch Bayesian Optimization for Complex Materials Design Campaigns.
CoRR
Sk Md Ahnaf Akif Alvi, Brent Vela, Vahid Attari, Jan Janssen, Danny Perez, Douglas L. Allaire, Raymundo Arróyave
2025 J jnl
Executorlib - Up-scaling Python workflows for hierarchical heterogenous high-performance computing.
J. Open Source Softw.
Jan Janssen, Michael Gilbert Taylor, Ping Yang, Jörg Neugebauer, Danny Perez
2025 J jnl
Parameter uncertainties for imperfect surrogate models in the low-noise regime.
Mach. Learn. Sci. Technol.
Thomas D. Swinburne, Danny Perez
2024 A conf
Breaking the Molecular Dynamics Timescale Barrier Using a Wafer-Scale System.
SC
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, Michael James, Sivasankaran Rajamanickam
2024 J jnl
Breaking the Molecular Dynamics Timescale Barrier Using a Wafer-Scale System.
CoRR
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, Michael James, Sivasankaran Rajamanickam
2024 J jnl
Breaking the mold: overcoming the time constraints of molecular dynamics on general-purpose hardware.
CoRR
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, Michael James, Sivasankaran Rajamanickam
2024 J jnl
Co-design for Particle Applications at Exascale.
Comput. Sci. Eng.
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, Anders M. N. Niklasson, James F. Belak, Susan M. Mniszewski, Danny Perez
2024 J jnl
Misspecification uncertainties in near-deterministic regression.
CoRR
Thomas D. Swinburne, Danny Perez
2024 J jnl
MolSieve: A Progressive Visual Analytics System for Molecular Dynamics Simulations.
IEEE Trans. Vis. Comput. Graph.
Rostyslav Hnatyshyn, Jieqiong Zhao, Danny Perez, James P. Ahrens, Ross Maciejewski
2023 A conf
Frontier: Exploring Exascale.
SC
Scott Atchley, Christopher Zimmer, John Lange, David E. Bernholdt, Verónica G. Melesse Vergara, Thomas Beck, Michael J. Brim, Reuben D. Budiardja, Sunita Chandrasekaran, Markus Eisenbach, Thomas M. Evans, Matthew Ezell, Nicholas Frontiere, Antigoni Georgiadou, Joe Glenski, Philipp Grete, Steven P. Hamilton, John K. Holmen, Axel Huebl, Daniel A. Jacobson, Wayne Joubert, Kim H. McMahon, Elia Merzari, Stan G. Moore, Andrew Myers, Stephen Nichols, Sarp Oral, Thomas Papatheodore, Danny Perez, David M. Rogers, Evan Schneider, Jean-Luc Vay, P. K. Yeung
2023 J jnl
MolSieve: A Progressive Visual Analytics System for Molecular Dynamics Simulations.
CoRR
Rostyslav Hnatyshyn, Jieqiong Zhao, Danny Perez, James P. Ahrens, Ross Maciejewski
2023 J jnl
Regression-Based Projection for Learning Mori-Zwanzig Operators.
SIAM J. Appl. Dyn. Syst.
Yen Ting Lin, Yifeng Tian, Danny Perez, Daniel Livescu
2022 J jnl
Combining machine-learned and empirical force fields with the parareal algorithm: application to the diffusion of atomistic defects.
CoRR
Olga Gorynina, Frédéric Legoll, Tony Lelièvre, Danny Perez
2022 A* conf
MDZ: An Efficient Error-bounded Lossy Compressor for Molecular Dynamics.
ICDE
Kai Zhao, Sheng Di, Danny Perez, Xin Liang, Zizhong Chen, Franck Cappello
2022 J jnl
Resource allocation for task-level speculative scientific applications: A proof of concept using Parallel Trajectory Splicing.
Parallel Comput.
Andrew Garmon, Vinay Ramakrishnaiah, Danny Perez
2021 J jnl
Pairwise Difference Regression: A Machine Learning Meta-algorithm for Improved Prediction and Uncertainty Quantification in Chemical Search.
J. Chem. Inf. Model.
Michael Tynes, Wenhao Gao, Daniel J. Burrill, Enrique R. Batista, Danny Perez, Ping Yang, Nicholas Lubbers
2020 J jnl
Rapid Exploration of Optimization Strategies on Advanced Architectures using TestSNAP and LAMMPS.
CoRR
Rahulkumar Gayatri, Stan G. Moore, Evan Weinberg, Nicholas Lubbers, Sarah Anderson, Jack Deslippe, Danny Perez, Aidan P. Thompson
2020 J jnl
Resource allocation for task-level speculative scientific applications: a proof of concept using Parallel Trajectory Splicing.
CoRR
Andrew Garmon, Vinay Ramakrishnaiah, Danny Perez
2020 — conf
Testing Research Software: A Case Study.
ICCS (7)
Nasir U. Eisty, Danny Perez, Jeffrey C. Carver, J. David Moulton, Hai Ah Nam
2018 B conf
Programmable Caches with a Data Management Language and Policy Engine.
CCGrid
Michael A. Sevilla, Carlos Maltzahn, Peter Alvaro, Reza Nasirigerdeh, Bradley W. Settlemyer, Danny Perez, David Rich, Galen M. Shipman
2016 J jnl
Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics.
Simul.
Richard J. Zamora, Arthur F. Voter, Danny Perez, Nandakishore Santhi, Susan M. Mniszewski, Sunil Thulasidasan, Stephan J. Eidenbenz
2015 J jnl
Analysis of Transition State Theory Rates upon Spatial Coarse-Graining.
Multiscale Model. Simul.
Andrew Binder, Mitchell Luskin, Danny Perez, Arthur F. Voter
2015 J jnl
TADSim: Discrete Event-Based Performance Prediction for Temperature-Accelerated Dynamics.
ACM Trans. Model. Comput. Simul.
Susan M. Mniszewski, Christoph Junghans, Arthur F. Voter, Danny Perez, Stephan J. Eidenbenz
2012 J jnl
A mathematical formalization of the parallel replica dynamics.
Monte Carlo Methods Appl.
Claude Le Bris, Tony Lelièvre, Mitchell Luskin, Danny Perez