206 citations · 559 across the 15 of their papers we have counts for
15 papers
Multi-Resolution Wire-Fencing for Efficient Path Sampling
Simen Z. Stenersen Michler, Lukas Baldauf, Titus S. van Erp
Path sampling methods enable the computation of thermodynamic and kinetic properties through Monte Carlo (MC) moves that generate trajectories from short forward and backward molec…
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)…
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…
Enhanced path sampling using subtrajectory Monte Carlo moves
Daniel T. Zhang, Enrico Riccardi, Titus S. van Erp
Path sampling allows the study of rare events like chemical reactions, nucleation and protein folding via a Monte Carlo (MC) exploration in path space. Instead of configuration poi…
Exchanging replicas with unequal cost, infinitely and permanently
Sander Roet, Daniel T. Zhang, Titus S. van Erp
We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably differen…
The dynamics of the DNA denaturation transition
Titus S. van Erp, Michel Peyrard
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of len…