Aaron R. Dinner

According to our database, Aaron R. Dinner authored at least 13 papers between 2000 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

geom2vec: pretrained GNNs as geometric featurizers for conformational dynamics.

Zihan Pengmei, Chatipat Lorpaiboon, Spencer C. Guo, Jonathan Weare, Aaron R. Dinner

CoRR, 2024

2023

Pervasive, conserved secondary structure in highly charged protein regions.

Catherine G. Triandafillou, Rosalind Wenshan Pan, Aaron R. Dinner, D. Allan Drummond

PLoS Comput. Biol., October, 2023

Predicting rare events using neural networks and short-trajectory data.

John Strahan, Justin Finkel, Aaron R. Dinner, Jonathan Weare

J. Comput. Phys., September, 2023

Transformers are efficient hierarchical chemical graph learners.

Zihan Pengmei, Zimu Li, Chih-chan Tien, Risi Kondor, Aaron R. Dinner

CoRR, 2023

2021

Error Bounds for Dynamical Spectral Estimation.

Robert J. Webber, Erik H. Thiede, Douglas Dow, Aaron R. Dinner, Jonathan Weare

SIAM J. Math. Data Sci., 2021

2020

Stratification as a General Variance Reduction Method for Markov Chain Monte Carlo.

Aaron R. Dinner, Erik H. Thiede, Brian Van Koten, Jonathan Weare

SIAM/ASA J. Uncertain. Quantification, 2020

2018

Trajectory Stratification of Stochastic Dynamics.

Aaron R. Dinner, Jonathan C. Mattingly, Jeremy O. B. Tempkin, Brian Van Koten, Jonathan Weare

SIAM Rev., 2018

2015

Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data.

Alan L. Hutchison, Mark Maienschein-Cline, Andrew H. Chiang, S. M. Ali Tabei, Herman Gudjonson, Neil Bahroos, Ravi Allada, Aaron R. Dinner

PLoS Comput. Biol., 2015

2012

Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle.

Yihan Lin, Ying Li, Sean Crosson, Aaron R. Dinner, Norbert F. Scherer

PLoS Comput. Biol., 2012

Discovering transcription factor regulatory targets using gene expression and binding data.

Mark Maienschein-Cline, Jie Zhou, Kevin P. White, Roger Sciammas, Aaron R. Dinner

Bioinform., 2012

2009

CHARMM: The biomolecular simulation program.

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

J. Comput. Chem., 2009

2006

Monte Carlo simulations of biomolecules: The MC module in CHARMM.

Jie Hu, Ao Ma, Aaron R. Dinner

J. Comput. Chem., 2006

2000

Local deformations of polymers with nonplanar rigid main-chain internal coordinates.

Aaron R. Dinner

J. Comput. Chem., 2000