[HTML][HTML] Variational deep learning of equilibrium transition path ensembles

AN Singh, DT Limmer - The Journal of Chemical Physics, 2023 - pubs.aip.org
We present a time-dependent variational method to learn the mechanisms of equilibrium
reactive processes and efficiently evaluate their rates within a transition path ensemble. This …

Master equations for finite state mean field games with nonlinear activations

Y Gao, W Li, JG Liu - arXiv preprint arXiv:2212.05675, 2022 - arxiv.org
We formulate a class of mean field games on a finite state space with variational principles
resembling those in continuous-state mean field games. We construct a controlled continuity …

An optimal control method to compute the most likely transition path for stochastic dynamical systems with jumps

W Wei, T Gao, X Chen, J Duan - Chaos: An Interdisciplinary Journal of …, 2022 - pubs.aip.org
Many complex real world phenomena exhibit abrupt, intermittent, or jumping behaviors,
which are more suitable to be described by stochastic differential equations under non …

Revisit of macroscopic dynamics for some non-equilibrium chemical reactions from a Hamiltonian viewpoint

Y Gao, JG Liu - Journal of Statistical Physics, 2022 - Springer
Most biochemical reactions in living cells are open systems interacting with environment
through chemostats to exchange both energy and materials. At a mesoscopic scale, the …

Controlling conservation laws I: Entropy–entropy flux

W Li, S Liu, S Osher - Journal of Computational Physics, 2023 - Elsevier
We study a class of variational problems for regularized conservation laws with Lax's
entropy-entropy flux pairs. We first introduce a modified optimal transport space based on …

Structure preserving schemes for Fokker–Planck equations of irreversible processes

C Liu, Y Gao, X Zhang - Journal of Scientific Computing, 2024 - Springer
In this paper, we construct structure preserving schemes for solving Fokker–Planck
equations associated with irreversible processes. The proposed method is first order in time …

A selection principle for weak KAM solutions via Freidlin–Wentzell large deviation principle of invariant measures

Y Gao, JG Liu - SIAM Journal on Mathematical Analysis, 2023 - SIAM
This paper reinterprets the Freidlin–Wentzell variational construction of the rate function in
the large deviation principle for invariant measures from the weak KAM perspective …

Optimal control for sampling the transition path process and estimating rates

J Yuan, A Shah, C Bentz, M Cameron - Communications in Nonlinear …, 2024 - Elsevier
Many processes in nature such as conformal changes in biomolecules and clusters of
interacting particles, genetic switches, mechanical or electromechanical oscillators with …

A finite expression method for solving high-dimensional committor problems

Z Song, MK Cameron, H Yang - SIAM Journal on Scientific Computing, 2025 - SIAM
Transition path theory (TPT) is a mathematical framework for quantifying rare transition
events between a pair of selected metastable states and. Central to TPT is the committor …

Radiomics on spatial‐temporal manifolds via Fokker–Planck dynamics

JB Stevens, BA Riley, J Je, Y Gao, C Wang… - Medical …, 2024 - Wiley Online Library
Background Delta radiomics is a high‐throughput computational technique used to describe
quantitative changes in serial, time‐series imaging by considering the relative change in …