Author's posts
Apr 14
Controlling knot interactions through confinement
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
The SBP group participates in the NET4EXA project
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
Density of states in neural networks: an in-depth exploration of learning in parameter space
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
A Multiscale Analysis of the CzrA Transcription Repressor Highlights the Allosteric Changes Induced by Metal Ion Binding
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
Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model
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 …
Jul 26
Topology in soft and biological matter
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
EXCOGITO, an Extensible Coarse-Graining Toolbox for the Investigation of Biomolecules by Means of Low-Resolution Representations
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
8th Workshop “Physics of Biomolecules: Structure, Dynamics and Function”
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 …
Dec 15
SBP Winter Solstice dinner
On December 13, 2023 our group gathered for a social dinner before the winter break. It was a great opportunity to further tighten personal interactions and human connections in our team, and enjoy an easy-going the incipient holiday atmosphere!
Nov 29
Postdoctoral position available
The postdoctoral position (1.5 Years) is aimed at developing a computational model of selective polymeric sponges for metal ions capture (more details – call – application page). This research is Funded by the European Union under NextGenerationEU. PRIN 2022RYP9YT_004 “SCOPE: Selective capture of metals by polymeric sponges”. The successful applicant will be part of a vibrant collaboration including both experimental and computational physicists and chemists from the …
