5 papers
Molecular signatures of pressure-induced phase transitions in a lipid bilayer
Yanna Gautier, Guillaume Stirnemann, Jérôme Hénin
Understanding how lipid bilayers respond to pressure is essential for interpreting the coupling between membrane proteins and their native environments. Here, we use all-atom molec…
Hamiltonian replica exchange augmented with diffusion-based generative models and importance sampling to assess biomolecular conformational basins and barriers
Zakarya Benayad, Guillaume Stirnemann
Enhanced sampling techniques are essential for exploring biomolecular conformational dynamics that occur on timescales inaccessible to conventional molecular dynamics (MD) simulati…
Clustering data by reordering them
Axel Descamps, Sélène Forget, Aliénor Lahlou +5
Grouping elements into families to analyse them separately is a standard analysis procedure in many areas of sciences. We propose herein a new algorithm based on the simple idea th…
ArcaNN: automated enhanced sampling generation of training sets for chemically reactive machine learning interatomic potentials
Rolf David, Miguel de la Puente, Axel Gomez +3
The emergence of artificial intelligence has profoundly impacted computational chemistry, particularly through machine-learned potentials (MLPs), which offer a balance of accuracy…
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…