J. Weare

Most-cited papers

Ensemble samplers with affine invariance
Jonathan R Goodman, J. Weare
20102,540 citations Open access
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On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method.
B. Roux, J. Weare
2013Journal of Chemical Physics195 citations Open access
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The Theory of Ultra-Coarse-Graining. 1. General Principles.
James F. Dama, Anton V. Sinitskiy, Martin McCullagh, J. Weare +3 more
2013Journal of Chemical Theory and Computation158 citations
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Rare Event Simulation of Small Noise Diffusions
E. Vanden-Eijnden, J. Weare
2012119 citations
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Can AI weather models predict out-of-distribution gray swan tropical cyclones?
Qiang Y. Sun, P. Hassanzadeh, Mohsen Zand, A. Chattopadhyay +2 more
2024Proceedings of the National Academy of Sciences of the United States of America96 citations Open access
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Galerkin approximation of dynamical quantities using trajectory data.
E. Thiede, D. Giannakis, A. Dinner, J. Weare
2018Journal of Chemical Physics86 citations Open access
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Ensemble preconditioning for Markov chain Monte Carlo simulation
B. Leimkuhler, Charles Matthews, J. Weare
2016Statistics and computing66 citations Open access
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Practical rare event sampling for extreme mesoscale weather.
R. Webber, D. Plotkin, M. O'Neill, D. Abbot +1 more
2019Chaos61 citations Open access
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Data Assimilation in the Low Noise Regime with Application to the Kuroshio
E. Vanden-Eijnden, J. Weare
201260 citations Open access
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Particle filtering with path sampling and an application to a bimodal ocean current model
J. Weare
2009Journal of Computational Physics48 citations
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Long-timescale predictions from short-trajectory data: A benchmark analysis of the trp-cage miniprotein
J. Strahan, Adam Antoszewski, Chatipat Lorpaiboon, B. P. Vani +2 more
2020Journal of Chemical Theory and Computation46 citations Open access
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AN AFFINE-INVARIANT SAMPLER FOR EXOPLANET FITTING AND DISCOVERY IN RADIAL VELOCITY DATA
Fengji Hou, J. Goodman, D. Hogg, J. Weare +1 more
201146 citations Open access
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Eigenvector method for umbrella sampling enables error analysis.
E. Thiede, Brian Van Koten, J. Weare, A. Dinner
2016Journal of Chemical Physics41 citations Open access
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Insulin dissociates by diverse mechanisms of coupled unfolding and unbinding
Adam Antoszewski, Chi-Jui Feng, B. P. Vani, E. Thiede +4 more
2020bioRxiv38 citations Open access
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Fast Randomized Iteration: Diffusion Monte Carlo through the Lens of Numerical Linear Algebra
Lek-Heng Lim, J. Weare
2015SIAM Review37 citations Open access
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Learning forecasts of rare stratospheric transitions from short simulations
J. Finkel, R. Webber, E. Gerber, D. Abbot +1 more
2021Monthly Weather Review35 citations Open access
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Predicting rare events using neural networks and short-trajectory data
J. Strahan, J. Finkel, A. Dinner, J. Weare
2022Journal of Computational Physics33 citations Open access
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Relaxation of a family of broken-bond crystal-surface models.
J. Marzuola, J. Weare
2013Physical review. E, Statistical, nonlinear, and soft matter physics33 citations Open access
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Steered transition path sampling.
N. Guttenberg, A. Dinner, J. Weare
2012Journal of Chemical Physics33 citations Open access
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Umbrella sampling: a powerful method to sample tails of distributions
Charles Matthews, J. Weare, Andrey V. Kravtsov, E. Jennings
2017Monthly notices of the Royal Astronomical Society32 citations Open access
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Revealing the Statistics of Extreme Events Hidden in Short Weather Forecast Data
J. Finkel, E. Gerber, D. Abbot, J. Weare
2022AGU Advances29 citations Open access
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Integrated Variational Approach to Conformational Dynamics: A Robust Strategy for Identifying Eigenfunctions of Dynamical Operators
Chatipat Lorpaiboon, E. Thiede, R. Webber, J. Weare +1 more
2020Journal of Physical Chemistry B27 citations Open access
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Beyond Walkers in Stochastic Quantum Chemistry: Reducing Error using Fast Randomized Iteration.
Samuel M. Greene, R. Webber, J. Weare, Timothy C. Berkelbach
2019Journal of Chemical Theory and Computation27 citations Open access
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The evolution of a crystal surface: Analysis of a one-dimensional step train connecting two facets in the ADL regime
Hala Al Hajj Shehadeh, R. Kohn, J. Weare
201126 citations
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Maximizing Simulated Tropical Cyclone Intensity With Action Minimization
D. Plotkin, R. Webber, M. O'Neill, J. Weare +1 more
2019Journal of Advances in Modeling Earth Systems25 citations Open access
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Trajectory stratification of stochastic dynamics
A. Dinner, Jonathan C. Mattingly, Jeremy O. B. Tempkin, B. V. Koten +1 more
2016SIAM Review24 citations Open access
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Minimizing memory as an objective for coarse-graining.
N. Guttenberg, James F. Dama, Marissa G. Saunders, G. Voth +2 more
2013Journal of Chemical Physics23 citations
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Ensemble Markov chain Monte Carlo with teleporting walkers
Michael A. Lindsey, J. Weare, Anna Zhang
2021SIAM/ASA J. Uncertain. Quantification22 citations Open access
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Stratification as a general variance reduction method for Markov chain Monte Carlo
A. Dinner, E. Thiede, Brian Van Koten, J. Weare
2017SIAM/ASA J. Uncertain. Quantification22 citations Open access
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Improved Diffusion Monte Carlo
Martin Hairer, J. Weare
201222 citations Open access
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Rare Event Sampling Improves Mercury Instability Statistics
D. Abbot, R. Webber, S. Hadden, D. Seligman +1 more
2021Astrophysical Journal21 citations Open access
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Nucleotide regulation of the structure and dynamics of G-actin.
Marissa G. Saunders, Jeremy O. B. Tempkin, J. Weare, A. Dinner +2 more
2014Biophysical Journal21 citations Open access
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SHARP ENTRYWISE PERTURBATION BOUNDS FOR MARKOV CHAINS
E. Thiede, Brian Van Koten, J. Weare
2014SIAM Journal on Matrix Analysis and Applications20 citations Open access
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Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction.
J. Strahan, Spencer C. Guo, Chatipat Lorpaiboon, A. Dinner +1 more
2023Journal of Chemical Physics19 citations Open access
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Path Properties of Atmospheric Transitions: Illustration with a Low-Order Sudden Stratospheric Warming Model
J. Finkel, D. Abbot, J. Weare
2020Journal of the Atmospheric Sciences19 citations Open access
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Efficient Monte Carlo sampling by parallel marginalization
J. Weare
2007Proceedings of the National Academy of Sciences of the United States of America19 citations Open access
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AI-Boosted Rare Event Sampling to Characterize Extreme Weather.
Amaury Lancelin, Alexander Wikner, L. Dubus, C. Le Priol +4 more
2025Physical Review Letters18 citations Open access
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Using pretrained graph neural networks with token mixers as geometric featurizers for conformational dynamics
Zihan Pengmei, Chatipat Lorpaiboon, Spencer C. Guo, J. Weare +1 more
2024Journal of Chemical Physics18 citations Open access
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Improved Fast Randomized Iteration Approach to Full Configuration Interaction.
Samuel M. Greene, R. Webber, J. Weare, Timothy C. Berkelbach
2020Journal of Chemical Theory and Computation17 citations Open access
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Variance Reduction for Particle Filters of Systems With Time Scale Separation
D. Givon, P. Stinis, J. Weare
2007IEEE Transactions on Signal Processing17 citations Open access
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Computing transition path theory quantities with trajectory stratification.
B. P. Vani, J. Weare, A. Dinner
2022Journal of Chemical Physics16 citations Open access
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Augmented transition path theory for sequences of events.
Chatipat Lorpaiboon, J. Weare, A. Dinner
2022Journal of Chemical Physics14 citations Open access
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Accurate estimates of dynamical statistics using memory.
Chatipat Lorpaiboon, Spencer C. Guo, J. Strahan, J. Weare +1 more
2023Journal of Chemical Physics13 citations Open access
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Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.
E. Bylaska, J. Weare, J. Weare
2013Journal of Chemical Physics13 citations Open access
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Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics — Monte Carlo Canonical Propagation Algorithm
Yunjie Chen, Seyit Kale, J. Weare, A. Dinner +1 more
2016Journal of Chemical Theory and Computation12 citations Open access
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Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations.
Jeremy O. B. Tempkin, Bo Qi, Marissa G. Saunders, B. Roux +2 more
2014Journal of Chemical Physics12 citations Open access
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Simple Physics and Integrators Accurately Reproduce Mercury Instability Statistics
D. Abbot, David M. Hernandez, S. Hadden, R. Webber +2 more
2022Astrophysical Journal10 citations Open access
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BAD-NEUS: Rapidly converging trajectory stratification.
J. Strahan, Chatipat Lorpaiboon, J. Weare, Aaron R. Dinner
2024Journal of Chemical Physics9 citations Open access
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Data-driven transition path analysis yields a statistical understanding of sudden stratospheric warming events in an idealized model
J. Finkel, R. Webber, E. Gerber, D. Abbot +1 more
2021Journal of the Atmospheric Sciences9 citations Open access
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A metric on directed graphs and Markov chains based on hitting probabilities
Z. Boyd, Nicolas Fraiman, J. Marzuola, P. Mucha +2 more
2020SIAM Journal on Mathematics of Data Science9 citations Open access
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