2 papers
physics.bio-ph2025
ProTDyn: a foundation Protein language model for Thermodynamics and Dynamics generation
Yikai Liu, Haoyang Zheng, Lining Mao +3
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by hi…
physics.chem-ph2025
Constructing Generalized Sample Transition Probabilities with Biased Simulations
Yanbin Wang, Jakub Rydzewski, Ming Chen
In molecular dynamics (MD) simulations, accessing transition probabilities between states is crucial for understanding kinetic information, such as reaction paths and rates. Howeve…