3 papers
physics.chem-ph2024
Enhanced Sampling of Protein Conformational Changes via True Reaction Coordinates from Energy Relaxation
Huiyu Li, Ao Ma
The bottleneck in enhanced sampling lies in finding collective variables (CVs) that can effectively accelerate protein conformational changes. True reaction coordinates (tRCs) that…
physics.bio-ph2024
Reaction Coordinates are Optimal Channels of Energy Flow
Ao Ma, Huiyu Li
Reaction coordinates (RCs) are the few essential coordinates of a protein that control its functional processes, such as allostery, enzymatic reaction, and conformational change. T…
physics.chem-ph2022
Reactive Vortexes in a Naturally Activated Process: Non-Diffusive Rotational Fluxes at Transition State Uncovered by Persistent Homology
Farid Manuchehrfar, Huiyu Li, Ao Ma +1
Dynamics of reaction coordinates during barrier-crossing are key to understand activated processes in complex systems such as proteins. The default assumption from Kramers physical…