Aaron R. Dinner

19 papers Journal 19
YearRankTypeTitle / Venue / Authors
2026 J jnl
Quantum statistics from classical simulations via generative Gibbs sampling.
CoRR
Weizhou Wang, Xuanxi Zhang, Jonathan Weare, Aaron R. Dinner
2025 J jnl
An exact multiple-time-step variational formulation for the committor and the transition rate.
CoRR
Chatipat Lorpaiboon, Jonathan Weare, Aaron R. Dinner
2025 J jnl
Hierarchical geometric deep learning enables scalable analysis of molecular dynamics.
CoRR
Zihan Pengmei, Spencer C. Guo, Chatipat Lorpaiboon, Aaron R. Dinner
2025 J jnl
Mitigating mode collapse in normalizing flows by annealing with an adaptive schedule: Application to parameter estimation.
CoRR
Yihang Wang, Chris Chi, Aaron R. Dinner
2025 J jnl
Sampling Parameters of Ordinary Differential Equations with Constrained Langevin Dynamics.
SIAM/ASA J. Uncertain. Quantification
Chris Chi, Jonathan Weare, Aaron R. Dinner
2024 J jnl
geom2vec: pretrained GNNs as geometric featurizers for conformational dynamics.
CoRR
Zihan Pengmei, Chatipat Lorpaiboon, Spencer C. Guo, Jonathan Weare, Aaron R. Dinner
2023 J jnl
Pervasive, conserved secondary structure in highly charged protein regions.
PLoS Comput. Biol.
Catherine G. Triandafillou, Rosalind Wenshan Pan, Aaron R. Dinner, D. Allan Drummond
2023 J jnl
Predicting rare events using neural networks and short-trajectory data.
J. Comput. Phys.
John Strahan, Justin Finkel, Aaron R. Dinner, Jonathan Weare
2023 J jnl
Transformers are efficient hierarchical chemical graph learners.
CoRR
Zihan Pengmei, Zimu Li, Chih-chan Tien, Risi Kondor, Aaron R. Dinner
2021 J jnl
Error Bounds for Dynamical Spectral Estimation.
SIAM J. Math. Data Sci.
Robert J. Webber, Erik H. Thiede, Douglas Dow, Aaron R. Dinner, Jonathan Weare
2020 J jnl
Error bounds for dynamical spectral estimation.
CoRR
Robert J. Webber, Erik H. Thiede, Douglas Dow, Aaron R. Dinner, Jonathan Weare
2020 J jnl
Stratification as a General Variance Reduction Method for Markov Chain Monte Carlo.
SIAM/ASA J. Uncertain. Quantification
Aaron R. Dinner, Erik H. Thiede, Brian Van Koten, Jonathan Weare
2018 J jnl
Trajectory Stratification of Stochastic Dynamics.
SIAM Rev.
Aaron R. Dinner, Jonathan C. Mattingly, Jeremy O. B. Tempkin, Brian Van Koten, Jonathan Weare
2015 J jnl
Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data.
PLoS Comput. Biol.
Alan L. Hutchison, Mark Maienschein-Cline, Andrew H. Chiang, S. M. Ali Tabei, Herman Gudjonson, Neil Bahroos, Ravi Allada, Aaron R. Dinner
2012 J jnl
Discovering transcription factor regulatory targets using gene expression and binding data.
Bioinform.
Mark Maienschein-Cline, Jie Zhou, Kevin P. White, Roger Sciammas, Aaron R. Dinner
2012 J jnl
Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle.
PLoS Comput. Biol.
Yihan Lin, Ying Li, Sean Crosson, Aaron R. Dinner, Norbert F. Scherer
2009 J jnl
CHARMM: The biomolecular simulation program.
J. Comput. Chem.
Bernard R. Brooks, Charles L. Brooks III, Alexander D. MacKerell Jr., Lennart Nilsson, Robert J. Petrella, Benoît Roux, Y. Won, G. Archontis, Christian Bartels, Stefan Boresch, Amedeo Caflisch, Leo S. D. Caves, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, Victor Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus
2006 J jnl
Monte Carlo simulations of biomolecules: The MC module in CHARMM.
J. Comput. Chem.
Jie Hu, Ao Ma, Aaron R. Dinner
2000 J jnl
Local deformations of polymers with nonplanar rigid main-chain internal coordinates.
J. Comput. Chem.
Aaron R. Dinner