84 citations · 85 across the 5 of their papers we have counts for
5 papers
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…
Exact Topology of Dynamic Probability Surface of an Activated Process by Persistent Homology
Farid Manuchehrfar, Huiyu Li, Wei Tian +2
To gain insight into reaction mechanism of activated processes, we introduce an exact approach for quantifying the topology of high-dimensional probability surfaces of the underlyi…
A novel mechanism for energy activation in biomolecules
Shanshan Wu, Ao Ma
An activated process consists of energy activation and barrier crossing; the former is a prerequisite for the latter. Barrier crossing has been studied extensively, but energy acti…
Kinetic energy flows in activated dynamics of biomolecules
Huiyu Li, Ao Ma
Protein conformational changes are activated processes essential for protein functions. Activation in a protein differs from activation in a small molecule in that it involves dire…
Recent Developments in Methods for Identifying Reaction Coordinates
Wenjin Li, Ao Ma
In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number o…