226 citations · 695 across the 31 of their papers we have counts for
5 papers · 1 filter
Density of states in neural networks: an in-depth exploration of learning in parameter space
Margherita Mele, Roberto Menichetti, Alessandro Ingrosso +1
Learning in neural networks critically hinges on the intricate geometry of the loss landscape associated with a given task. Traditionally, most research has focused on finding spec…
A multi-scale analysis of the CzrA transcription repressor highlights the allosteric changes induced by metal ion binding
Marta Rigoli, Raffaello Potestio, Roberto Menichetti
Allosteric regulation is a widespread strategy employed by several proteins to transduce chemical signals and perform biological functions. Metal sensor proteins are exemplary in t…
Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model
Giovanni Mattiotti, Manuel Micheloni, Lorenzo Petrolli +3
The cowpea chlorotic mottle virus (CCMV) has emerged as an exemplary model system to assess the balance between electrostatic and topological features of ssRNA viruses, specificall…
Low-resolution descriptions of model neural activity reveal hidden features and underlying system properties
Riccardo Aldrigo, Roberto Menichetti, Raffaello Potestio
The analysis of complex systems such as neural networks is made particularly difficult by the overwhelming number of their interacting components. In the absence of prior knowledge…
EXCOGITO, an extensible coarse-graining toolbox for the investigation of biomolecules by means of low-resolution representation
Marco Giulini, Raffaele Fiorentini, Luca Tubiana +2
Bottom-up coarse-grained (CG) models proved to be essential to complement and sometimes even replace all-atom representations of soft matter systems and biological macromolecules.…