4 papers
Collaborate to decorrelate in path space: Hamiltonian replica exchange transition interface sampling (HRETIS)
Sina Safaei, Parham Rezaee, An Ghysels
We present Hamiltonian Replica Exchange Transition Interface Sampling (HRETIS), a path sampling framework designed to efficiently sample rare events in systems with complex potenti…
Generalized Path Reweighting and History-Dependent Free Energies
Titus S. van Erp, Daniel T. Zhang, Elias Wils +2
Transition interface sampling (TIS) and replica exchange TIS (RETIS) are powerful methods for computing rates of rare events inaccessible to straightforward molecular dynamics (MD)…
Estimating Full Path Lengths and Kinetics from Partial Path Transition Interface Sampling Simulations
Wouter Vervust, Elias Wils, Sina Safaei +2
Assessing the time scale of biological processes using molecular dynamics (MD) simulations with sufficient statistical accuracy is a challenging task, as processes are often rare a…
Path sampling challenges in large biomolecular systems: RETIS and REPPTIS for ABL-imatinib kinetics
Wouter Vervust, Daniel T. Zhang, Enrico Riccardi +2
Predicting the kinetics of drug-protein interactions is crucial for understanding drug efficacy, particularly in personalized medicine, where protein mutations can significantly al…