37 citations · 72 across the 9 of their papers we have counts for
10 papers
Markov State Models for Tracking Reaction Dynamics on Catalytic Nanoparticles
Caitlin A. McCandler, Chatipat Lorpaiboon, Timothy C. Berkelbach +1
Markov state models (MSMs) are a powerful tool to analyze and coarse-grain complex dynamical data into interpretable kinetic processes. This capability is particularly important in…
Hierarchical geometric deep learning enables scalable analysis of molecular dynamics
Zihan Pengmei, Spencer C. Guo, Chatipat Lorpaiboon +1
Molecular dynamics simulations can generate atomically detailed trajectories of complex systems, but analyzing these dynamics can be challenging when systems lack well-established…
An exact multiple-time-step variational formulation for the committor and the transition rate
Chatipat Lorpaiboon, Jonathan Weare, Aaron R. Dinner
For a transition between two stable states, the committor is the probability that the dynamics leads to one stable state before the other. It can be estimated from trajectory data…
Using pretrained graph neural networks with token mixers as geometric featurizers for conformational dynamics
Zihan Pengmei, Chatipat Lorpaiboon, Spencer C. Guo +2
Identifying informative low-dimensional features that characterize dynamics in molecular simulations remains a challenge, often requiring extensive manual tuning and system-specifi…
BAD-NEUS: Rapidly converging trajectory stratification
John Strahan, Chatipat Lorpaiboon, Jonathan Weare +1
An issue for molecular dynamics simulations is that events of interest often involve timescales that are much longer than the simulation time step, which is set by the fastest time…
Accurate estimates of dynamical statistics using memory
Chatipat Lorpaiboon, Spencer C. Guo, John Strahan +2
Many chemical reactions and molecular processes occur on timescales that are significantly longer than those accessible by direct simulation. One successful approach to estimating…
Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction
John Strahan, Spencer C. Guo, Chatipat Lorpaiboon +2
Understanding dynamics in complex systems is challenging because there are many degrees of freedom, and those that are most important for describing events of interest are often no…
Augmented Transition Path Theory for Sequences of Events
Chatipat Lorpaiboon, Jonathan Weare, Aaron R. Dinner
Transition path theory provides a statistical description of the dynamics of a reaction in terms of local spatial quantities. In its original formulation, it is limited to reaction…
Long-timescale predictions from short-trajectory data: A benchmark analysis of the trp-cage miniprotein
John Strahan, Adam Antoszewski, Chatipat Lorpaiboon +3
Elucidating physical mechanisms with statistical confidence from molecular dynamics simulations can be challenging owing to the many degrees of freedom that contribute to collectiv…
Integrated VAC: A robust strategy for identifying eigenfunctions of dynamical operators
Chatipat Lorpaiboon, Erik Henning Thiede, Robert J. Webber +2
One approach to analyzing the dynamics of a physical system is to search for long-lived patterns in its motions. This approach has been particularly successful for molecular dynami…