230 citations · 256 across the 4 of their papers we have counts for
4 papers
RNA Dynamics from Experimental and Computational Approaches
Giovanni Bussi, Massimiliano Bonomi, Paraskevi Gkeka +16
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining…
Autoencoders for dimensionality reduction in molecular dynamics: collective variable dimension, biasing and transition states
Zineb Belkacemi, Marc Bianciotto, Herve Minoux +3
The heat shock protein 90 (Hsp90) is a molecular chaperone that controls the folding and activation of client proteins using the free energy of ATP hydrolysis. The Hsp90 active sit…
Chasing Collective Variables using Autoencoders and biased trajectories
Zineb Belkacemi, Paraskevi Gkeka, Tony Lelièvre +1
Free energy biasing methods have proven to be powerful tools to accelerate the simulation of important conformational changes of molecules by modifying the sampling measure. Howeve…
Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems
Paraskevi Gkeka, Gabriel Stoltz, Amir Barati Farimani +14
Machine learning encompasses a set of tools and algorithms which are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as…