A First-Passage Kinetic Monte Carlo algorithm for complex diffusion-reaction systems. - Aleksandar Donev; Vasily V. Bulatov; Tomas Oppelstrup; George H. Gilmer; Babak Sadigh; Malvin H. Kalos (J. Comput. Phys., 2010)

Poster: a highly efficient MGPT implementation for LAMMPS; with strong scaling. - Tomas Oppelstrup; Alexander Stukowski; Jaime Marian (SC Companion, 2011)

Toward real-time modeling of human heart ventricles at cellular resolution: simulation of drug-induced arrhythmias. - Arthur A. Mirin; David F. Richards; James N. Glosli; Erik W. Draeger; Bor Chan; Jean-Luc Fattebert; William D. Krauss; Tomas Oppelstrup; John Jeremy Rice; John A. Gunnels; Viatcheslav Gurev; Changhoan Kim; et al. (SC, 2012)

Science at LLNL with IBM Blue Gene/Q. - Brian Carnes; Bor Chan; Erik W. Draeger; Jean-Luc Fattebert; Larry Fried; James N. Glosli; William D. Krauss; Steve H. Langer; Rose McCallen; Arthur A. Mirin; Fady Najjar; Albert L. Nichols; et al. (IBM J. Res. Dev., 2013)

Matrix compression by common subexpression elimination. - Tomas Oppelstrup (J. Comput. Phys., 2013)

Reverse Code Generation for Parallel Discrete Event Simulation. - Markus Schordan; David R. Jefferson; Peter D. Barnes Jr.; Tomas Oppelstrup; Daniel J. Quinlan (RC, 2015)

Massively parallel models of the human circulatory system. - Amanda Randles; Erik W. Draeger; Tomas Oppelstrup; Liam Krauss; John A. Gunnels (SC, 2015)

SPOCK: Exact Parallel Kinetic Monte-Carlo on 1.5 Million Tasks. - Tomas Oppelstrup; David R. Jefferson; Vasily V. Bulatov; Luis A. Zepeda-Ruiz (SIGSIM-PADS, 2016)

Automatic Generation of Reversible C++ Code and Its Performance in a Scalable Kinetic Monte-Carlo Application. - Markus Schordan; Tomas Oppelstrup; David R. Jefferson; Peter D. Barnes Jr.; Daniel J. Quinlan (SIGSIM-PADS, 2016)

Exploratory Modeling and Simulation of the Evolutionary Dynamics of Single-Stranded RNA Virus Populations. - Jae-Seung Yeom; Tanya Kostova-Vassilevska; Peter D. Barnes Jr.; David R. Jefferson; Tomas Oppelstrup (IPDPS Workshops, 2017)

Generation of Reversible C++ Code for Optimistic Parallel Discrete Event Simulation. - Markus Schordan; Tomas Oppelstrup; David R. Jefferson; Peter D. Barnes Jr. (New Gener. Comput., 2018)

A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer. - Francesco Di Natale; Harsh Bhatia; Timothy S. Carpenter; Chris Neale; Sara Kokkila Schumacher; Tomas Oppelstrup; Liam Stanton; Xiaohua Zhang; Shiv Sundram; Thomas R. W. Scogland; Gautham Dharuman; Michael P. Surh; et al. (SC, 2019)

Reversible Languages and Incremental State Saving in Optimistic Parallel Discrete Event Simulation. - Markus Schordan; Tomas Oppelstrup; Michael Kirkedal Thomsen; Robert Glück (Selected Results of the COST Action IC1405, 2020)

Generalizable coordination of large multiscale workflows: challenges and learnings at scale. - Harsh Bhatia; Francesco Di Natale; Joseph Y. Moon; Xiaohua Zhang; Joseph R. Chavez; Fikret Aydin; Christopher B. Stanley; Tomas Oppelstrup; Chris Neale; Sara Kokkila Schumacher; Dong H. Ahn; Stephen Herbein; et al. (SC, 2021)

Machine-learning-based dynamic-importance sampling for adaptive multiscale simulations. - Harsh Bhatia; Timothy S. Carpenter; Helgi I. Ingólfsson; Gautham Dharuman; Piyush Karande; Shusen Liu 001; Tomas Oppelstrup; Chris Neale; Felice C. Lightstone; Brian Van Essen; James N. Glosli; Peer-Timo Bremer (Nat. Mach. Intell., 2021)

A biology-informed similarity metric for simulated patches of human cell membrane. - Harsh Bhatia; Jayaraman J. Thiagarajan; Rushil Anirudh; T. S. Jayram; Tomas Oppelstrup; Helgi I. Ingólfsson; Felice C. Lightstone; Peer-Timo Bremer (Mach. Learn. Sci. Technol., 2022)

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)

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)