Apr 23
R. Aldrigo, R. Menichetti, R. Potestio, Low-resolution descriptions of model neural activity reveal hidden features and underlying system properties, Phys. Rev. E (2025) 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, identifying a small but informative …
Apr 14
R. Rusková, L. Tubiana, R. Potestio, D. Račko, Controlling knot interactions through confinement, Macromolecules (2025) We investigate how confinement affects the mutual interactions between knots tied on a single polymer chain using extensive coarse-grained molecular dynamics simulations. We introduce a novel model of an infinite chain that prevents knots from escaping while allowing for the …
Feb 27
Members of the SBP group are actively involved in the NET4EXA project, a wide collaboration aimed at at implementing the next generation of European interconnect technology, comprising both hardware (switches and network interfaces) and matching software. Our group will test the infrastructure capabilities with applications of interest for the fields of applied statistical mechanics, soft …
Feb 27
M. Mele, R. Menichetti, A. Ingrosso, R. Potestio, Density of states in neural networks: an in-depth exploration of learning in parameter space, TMLR (2025) 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 specific weight configurations that minimize …
Jan 09
M. Rigoli, R. Potestio, R. Menichetti, A multi-scale analysis of the CzrA transcription repressor highlights the allosteric changes induced by metal ion binding, JPCB (2025) Allosteric regulation is a widespread strategy employed by several proteins to transduce chemical signals and perform biological functions. Metal sensor proteins are exemplary in this respect, e.g., in that they …
Nov 22
G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model, Macromol. Rapid Commun. (2024) The cowpea chlorotic mottle virus (CCMV) has emerged as a model system to assess the balance between electrostatic and topological features of single-stranded RNA …
Oct 16
On Friday October 25. at 14.00, Luca Tubiana will give an invited keynote webinar on Cassyni. The seminar will provide a showcase of the review “Topology in Soft and Biological Matter” recently published on Physics Reports, and will be held together with Angelo Rosa, Emanuele Locatelli, Davide Michieletto, Marco di Stefano, Simon Copar and Sophie …
Jul 26
L. Tubiana et al., Topology in soft and biological matter, Physics Reports (2024) Prof. Luca Tubiana is the lead author of a comprehensive review, involving more than 50 authors, that recapitulates the current state of the art on the topic of topological problems in the context of soft and biological matter. This review offers a …
Jul 26
M. Giulini, R. Fiorentini, L. Tubiana, R. Potestio, R. Menichetti, EXCOGITO, an Extensible Coarse-Graining Toolbox for the Investigation of Biomolecules by Means of Low-Resolution Representations, Journal of Chemical Information and Modeling (2024) 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. …
Feb 12
On February 5, 2024 our group participated to the 8th edition of the workshop Physics of Biomolecules: Structure, Dynamics and Function, which was held in Bressanone, Italy. We had a great time showcasing some of our work and enjoying the excellent presentations by a number of participants. As usual, a great occasion to share ideas …
