Publications in Refereed Journals


2016
Trajectory stratification of stochastic dynamics
with
A. Dinner, J. Mattingly, J. Tempkin, and B. Van Koten, submitted pdf

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

with L.-H. Lim, SIAM Reviews: Research Spotlight, accepted pdf

Eigenvector method for umbrella sampling enables error analysis

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

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 pdf

2015
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 pdf

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

2014
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 pdf

Distinguishing meanders of the Kuroshio using machine learning

with D. Plotkin and D. Abbot, Journal of Geophysical Research - Oceans, 119(10), 6593-6604
pdf

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 pdf

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

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

2013
The relaxation of a family of broken bond crystal surface models
with J. Marzuola, Physical Review E, 88, 032403 pdf

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 pdf

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

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 pdf

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 pdf

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

2012
Steered transition path sampling
with N. Guttenberg and A. Dinner, Journal of Chemical Physics, 136 234103 pdf

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

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, 745:198 pdf

2011
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 pdf

2010 Ensemble samplers with affine invariance
with J. Goodman, Communications in Applied Mathematics and Computational Science, 5, 65-80 pdf

2009 Particle filtering with path sampling and an application to a bimodal ocean current model
Journal of Computational Physics, 228 4312-4331 pdf

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 pdf

2007 Efficient Monte Carlo sampling by parallel marginalization
Proceedings of the National Academy of Science, 104(31) 12657-12662 pdf