Jonathan Weare
Associate Professor of Mathematics
Courant Institute of Mathematical Sciences
New York University
251 Mercer Street
New York, NY 10012-1185
weare [AT] cims [DOT] nyu [DOT] edu

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Trajectory stratification of stochastic dynamics
with A.R. Dinner, J.C. Mattingly, J. Tempkin, and B. Van Koten, SIAM Reviews: Research Spotlight, 60(4), 909–938
Umbrella sampling: a powerful method to sample tails of distributions
with C. Matthews, A. Kravstov, and E. Jennings, Monthly Notices of the Royal Astronomical Society, 480(3), 4069-4079


Simulating the stochastic dynamics and cascade failure of power networks
with C. Matthews, B. Stadie, M. Anitescu, and C. Demarco
Ensemble preconditioning for Markov chain Monte Carlo simulation
with B. Leimkuhler and C. Matthews, Statistics and Computing, 28(2) 277-290

Fast randomized iteration: diffusion Monte Carlo through the lens of numerical linear algebra

with L.H. Lim, SIAM Reviews: Research Spotlight, 59(3) 547-587


Eigenvector method for umbrella sampling enables error analysis
with E. Thiede, B. Van Koten, and A. Dinner, Journal of Chemical Physics, 145(8) 084115

Multiple time-step dual-Hamiltonian hybrid molecular dynamics Monte Carlo canonical propagation algorithm
with Y. Chen, S. Kale, A. Dinner, and B. Roux, Journal of Chemical Theory and Computation, 12(4) 1449-1458


Sharp entrywise perturbation bounds for Markov chains
with E. Thiede and B. Van Koten, SIAM Journal on Matrix Analysis and Applications, 36(3), 917-941

The Brownian fan
with M. Hairer, Communications in Pure and Applied Mathematics, 68(1) 1-60


Finding chemical reaction paths with a multilevel preconditioning protocol
with S. Kale, S. Olaseni, and A. Dinner, Journal of Chemical Theory and Simulation, 10(12), 5467-5475

Distinguishing meanders of the Kuroshio using machine learning
with D. Plotkin and D. Abbot, Journal of Geophysical Research - Oceans, 119(10) 6593-6604

Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations
with J. Tempkin, B. Qui, M. Saunders, B. Roux, and A. Dinner, Journal of Chemical Physics, 140(18) 184114

Improved diffusion Monte Carlo
with M. Hairer, Communications in Pure and Applied Mathematics, 67(12) 1995-2021

Nucleotide regulation of the structure and dynamics of G-actin
with M. Saunders, J. Tempkin, A. Dinner, B. Roux, and G. Voth, Biophysical Journal, 106(8) 1710-1720


The relaxation of a family of broken bond crystal surface models
with J. Marzuola, Physical Review E, 88 032403

The theory of ultra coarse graining I, general principles
with J. Dama, A. Sinitskiy, M. McCullagh, B. Roux, A. Dinner, and G. Voth, Journal of Chemical Theory and Computation, 9(5) 2466-2480

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method
with B. Roux, Journal of Chemical Physics, 138(8) 084107

Minimizing memory as an objective for coarse-graining
with N. Guttenberg, J. Dama, M. Saunders, A. Dinner, and G. Voth, Journal of Chemical Physics, 138(9) 094111

Extending molecular simulation time scales: Parallel-in-time integrations for high-lelel quantum chemistry and complex force representations
with E. Bylaska and J.H. Weare, Journal of Chemical Physics, 139 074114

Data assimilation in the low noise regime with applications to the Kuroshio with E. Vanden-Eijnden, Monthly Weather Review, 141 1822-1841


Steered transition path sampling
with N. Guttenberg and A. Dinner, Journal of Chemical Physics, 136 234103

Rare event simulation for small noise diffusions
with E. Vanden-Eijnden, Communications in Pure and Applied Mathematics, 65(12) 1770-1803

An affine-invariant sampler for exoplanet fitting and discovery in radial velocity data
with F. Hou, J. Goodman, D. Hogg, and C. Schwab, The Astrophysical Journal, 75 198


The evolution of a crystal surface: analysis of a 1D step train connecting two facets in the ADL regime
with H. Al Hajj Shehadeh and R.V. Kohn, Physica D, 240 1771-1784


Ensemble samplers with affine invariance
with J. Goodman, Communications in Applied Mathematics and Computational Science, 5 65-80


Particle filtering with path sampling and an application to a bimodal ocean current model
Journal of Computational Physics, 228 4312-4331

Variance reduction for particle filters of systems with time-scale separation
with D. Givon and P. Stinis, IEEE Transactions on Signal Processing, 57(2) 424-435


Efficient Monte Carlo sampling by parallel marginalization
Proceedings of the National Academy of Science, 104(31) 12657-12662