96 citations · 441 across the 21 of their papers we have counts for
21 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 Probability Landscapes of Stochastic Phenotype Switching in Feed-Forward Loops: Phase Diagrams of Multimodality
Anna Terebus, Farid Manuchehrfar, Youfang Cao +1
Feed-forward loops (FFLs) are among the most ubiquitously found motifs of reaction networks in nature. However, little is known about their stochastic behavior and the variety of n…
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…
Modeling and simulation of nuclear architecture reorganization process using a phase field approach
Qing Cheng, Pourya Delafrouz, Jie Liang +2
We develop a special phase field/diffusive interface method to model the nuclear architecture reorganization process. In particular, we use a Lagrange multiplier approach in the ph…
Stochastic Evolution of Coagulation-Fragmentation processes using the Accurate Chemical Master Equation approach
Farid Manuchehrfar, Wei Tian, Tom Chou +1
Coagulation and fragmentation (CF) is a fundamental process by which particles attach to each other to form clusters while existing clusters break up into smaller ones. It is a ubi…
Discrete Flux and Velocity Fields of Probability and Their Global Maps in Reaction Systems
Anna Terebus, Chun Liu, Jie Liang
Stochasticity plays important roles in reaction systems. Vector fields of probability flux and velocity characterize time-varying and steady-state properties of these systems, incl…