2 papers
physics.chem-ph2026
Auto-WHATMD : Automated Wasserstein-based High-dimensional feature extraction Analysis of Trajectories from Molecular Dynamics
Sosuke Asano, Ikki Yasuda, Katsuhiro Endo +2
Comparing multiple protein systems with variation such as different binding ligands or mutations, and understanding their effects is one of the objectives in molecular dynamics sim…
cond-mat.stat-mech2025
Navigating Phase Transitions with Path-Finding Algorithms: A Strategic Approach to Replica Exchange Monte Carlo
Akie Kowaguchi, Katsuhiro Endo, Kentaro Nomura +3
The replica exchange method is a powerful tool for overcoming slow relaxation in molecular simulations, but its efficiency depends strongly on the choice of the number and interval…