34 citations · 52 across the 8 of their papers we have counts for
8 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…
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…
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…
On the validity of some equilibrium models for thermodiffusion
Mario Araujo-Rocha, Alejandro Diaz-Marquez, Guillaume Stirnemann
When applied to binary solutions, thermal gradients lead to the generation of concentration-gradients and thus to inhomogeneous systems. While being known for more than 150 years,…
Explicit models of motions to understand protein side-chain dynamics
Nicolas Bolik-Coulon, Olivier Languin-Cattoën, Diego Carnevale +5
Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forg…
When does TMAO fold a polymer chain and urea unfold it?
Jagannath Mondal, Guillaume Stirnemann, B. J. Berne
Longstanding mechanistic questions about the role of protecting osmolyte trimethylamine N- oxide (TMAO) which favors protein folding and the denaturing osmolyte urea are addressed…