76 citations · 143 across the 9 of their papers we have counts for
10 papers
RNA folding landscapes from explicit solvent all-atom simulations
Gianmarco Lazzeri, Cristian Micheletti, Samuela Pasquali +1
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complex…
10 simple rules to create a serious game, illustrated with examples from structural biology
Marc Baaden, Olivier Delalande, Nicolas Ferey +3
Serious scientific games are games whose purpose is not only fun. In the field of science, the serious goals include crucial activities for scientists: outreach, teaching and resea…
Ab initio RNA folding
Tristan Cragnolini, Philippe Derreumaux, Samuela Pasquali
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, expe…
The coarse-grained HiRE-RNA model for de novo calculations of RNA free energy surfaces, folding pathways and complex structure prediction
Tristan Cragnolini, Yoann Laurin, Philippe Derreumaux +1
HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed inte…
Coarse-grained simulations of RNA and DNA duplexes
Tristan Cragnolini, Philippe Derreumaux, Samuela Pasquali
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can inves…
Mean Field and the Single Homopolymer
S. Pasquali, J. K. Percus
We develop a statistical model for a confined chain molecule based on a monomer grand canonical ensemble. The molecule is subject to an external chemical potential, a backbone inte…