3 papers
physics.comp-ph2025
The dawn of alchemical free-energy methods in biomolecular simulations
Daniele Macuglia, Giovanni Ciccotti, Benoît Roux
From the onset of fundamental statistical mechanical constructs formulated in the late 19th century, alchemical free-energy methods slowly emerged and transitioned to become operat…
physics.comp-ph2025
Mass-Zero constrained molecular dynamics for electrostatic interactions
Federica Troni, Davide Grassano, Jayashree Narayan +2
Optimal exploitation of supercomputing resources for the evaluation of electrostatic forces remains a challenge in molecular dynamics simulations of very large systems. The most ef…
physics.comp-ph2024
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…