5 papers
A self-adaptive tube restraint for free-energy calculations along path collective variables
Radu A. Talmazan, Cheng Giuseppe Chen, Chenyu Tang +1
Path collective variables (PCVs) reduce a high-dimensional transition to a progress coordinate, s, and an orthogonal distance, z. Computing the free energy along s often requires r…
From Static Pathways to Dynamic Mechanisms: A Committor-Based Data-Driven Approach to Chemical Reactions
Radu A. Talmazan, Christophe Chipot
As computational chemistry methods evolve, dynamic effects have been increasingly recognized to govern chemical reaction pathways in both organic and inorganic systems. Here, we in…
Breaking the Timescale Barrier: Generative Discovery of Conformational Free-Energy Landscapes and Transition Pathways
Chenyu Tang, Mayank Prakash Pandey, Cheng Giuseppe Chen +3
Molecular transitions -- such as protein folding, allostery, and membrane transport -- are central to biology yet remain notoriously difficult to simulate. Their intrinsic rarity p…
Following the Committor Flow: A Data-Driven Discovery of Transition Pathways
Cheng Giuseppe Chen, Chenyu Tang, Alberto MegÃas +4
The discovery of transition pathways to unravel distinct reaction mechanisms and, in general, rare events that occur in molecular systems is still a challenge. Recent advances have…
Iterative variational learning of committor-consistent transition pathways using artificial neural networks
Alberto MegÃas, Sergio Contreras Arredondo, Cheng Giuseppe Chen +3
This contribution introduces a neural-network-based approach to discover meaningful transition pathways underlying complex biomolecular transformations in coherence with the commit…