Potestio Lab

So, ACS it is! #ACSSpring2025 #SanDiego #chemistry #physics

@nanophononics Tetragonal with (remote) defects!

@r_potestio hcp or fcc?

Closely-packed group meeting! 😊 #physics #biophysics #teamwork

Biophysics, Stat Mech and Machine Learning will meet in Trento from July 7th to 11th, 2025 in our StatPhys29 Satellite Workshop "Molecular biophysics at the transition state: from statistical mechanics to AI": indico.ectstar.eu/event/252/. Co-organized with @ai_ngrosso.

This research is the result of a collaborative effort among the teams at the University of Trento, INFN-TIFPA, and the Donders Institute, and we are grateful for the support of our colleagues and institutions. #MachineLearning #DeepLearning #NeuralNetworks #StatPhysics

Our findings provide a detailed characterization of the density of states across network configurations, shedding light on the interplay between data structure, network architecture, and class imbalance.

🥳 We are pleased to announce the publication of our paper “Density of States in Neural Networks: An In-Depth Exploration of Learning in Parameter Space” in Trans. on Machine Learning Research. openreview.net/forum?id=BLDtW… @MeleMargherita_ @ai_ngrosso @UniTrento @INFN_ @DondersInst

The method, which is based on concepts from coarse-graining theory, allowed us to make better sense of the allosteric mechanism of CzrA through a novel, intrinsically multi-body analysis of plain MD simulations.

The MEOW approach, implemented in the EXCOGITO software suite, attributes to atoms and residues a relevance score based on their dynamical and energetic properties, and allows one to rationalise their functional behaviour. pubs.acs.org/doi/full/10.10…

📢🥳 PAPER ALERT! 🥳📢 We are happy to advertise the publication on JPCB of the paper “A Multiscale Analysis of the CzrA Transcription Repressor Highlights the Allosteric Changes Induced by Metal Ion Binding”, by M. Rigoli, R. Potestio and R. Menichetti. pubs.acs.org/doi/full/10.10…

Our PhD student Camilla Spreti @Camilla_Spreti just gave a talk at the yearly PhD Workshop of the Physics Dept. of the University of Trento @UniTrento, illustrating her research on enhanced sampling of small stat mech systems. Excellent job! 🥳 ppw2024.physics.unitn.it/home

This work proposes a novel protocol for the in silico study of complex, relevant, and fascinating systems such as RNA viruses, and discusses the potential and the challenges inherent in multi-scale modelling of RNA molecules.

The role of the N-terminal tails of the CCMV subunits is also highlighted as a critical feature in the construction of a proper electrostatic model of the CCMV capsid.

📢📢📢 Paper alert! 📢📢📢 Our latest effort is out! "Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model", by G. Mattiotti, M. Micheloni, L. Petrolli, L. Rovigatti, L. Tubiana, S. Pasquali, R. Potestio onlinelibrary.wiley.com/doi/10.1002/ma…