The study of phenomena such as protein folding and conformational changes in molecules
is a central theme in chemical physics. Molecular dynamics (MD) simulation is the primary …

A polymer network fractures by breaking covalent bonds, but the experimentally measured
strength of the polymer network is orders of magnitude lower than the strength of covalent …

The study of rare events in molecular and atomic systems such as conformal changes and
cluster rearrangements has been one of the most important research themes in chemical …

Nongradient SDEs with small white noise often arise when modeling biological and ecological
time-irreversible processes. If the governing SDE were gradient, the maximum likelihood …

Transition path theory (TPT) is a mathematical framework for quantifying rare transition events
between a pair of selected metastable states $A$ and $B$. Central to TPT is the committor …

We present algorithms for solving high-frequency acoustic scattering problems in complex
domains. The eikonal and transport partial differential equations from the WKB/geometric …

QPot is an R package for analyzing two-dimensional systems of stochastic differential
equations. It provides users with a wide range of tools to simulate, analyze, and visualize the …

We develop a family of compact high-order semi-Lagrangian label-setting methods for solving
the eikonal equation. These solvers march the total 1-jet of the eikonal, and use Hermite …

The concept of metastability has caused a lot of interest in recent years. The spectral
decomposition of the generator matrix of a stochastic network exposes all of the transition …

We develop computational tools for spectral analysis of stochastic networks representing
energy landscapes of atomic and molecular clusters. Physical meaning and some properties of …