Potestio Lab
@r_potestio
Followers
634
Following
3K
Media
154
Statuses
518
Research team led by Raffaello Potestio at the University of Trento, Italy. Multi-scale modelling, computational biophysics, statistical mechanics, and pizza.
Trento, Trentino-Alto Adige
Joined November 2016
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": Co-organized with @ai_ngrosso.
0
2
4
1
1
10
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.
0
0
0
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.
1
0
0
In this work, we apply advanced sampling techniques from statistical physics—specifically, the Wang-Landau algorithm—to map the entire loss landscape of neural networks.
1
0
0
🥳 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. @MeleMargherita_ @ai_ngrosso @UniTrento @INFN_ @DondersInst.
openreview.net
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...
1
1
2
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.
0
0
0
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
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. The development of...
1
0
0
Turn old photos into videos and see friends and family come to life. Try Grok Imagine, free for a limited time.
709
1K
5K
Our approach highlights subtle differences in the behaviour of the molecule between the apo and the zinc-bound state; these features do not manifest on major, large-amplitude rearrangements of the protein structure, hence they are rather difficult to highlight.
1
0
0
In this paper we make use of the recently developed mapping entropy optimisation workflow, or MEOW, to investigate the allosteric behaviour of the metal-operated CzrA transcription repressor.
1
0
0
📢🥳 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.
1
0
0
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! 🥳.
0
2
4
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.
0
1
1
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.
1
1
1
We investigated the behaviour of RNA2 both as a freely-folding molecule and within a mean-field, multi-scale depiction of the capsid. We found out that the encapsidated RNA2 differs significantly from the freely-folding counterpart, as shown by the emergence of long-range motifs.
1
0
0
Despite its biophysical significance, little structural data on the RNA content of CCMV is available. In this paper, we assess the conformational dynamics of the RNA2 fragment of CCMV making use of coarse-grained molecular dynamics simulations, employing the oxRNA2 model.
1
0
0
Here we study the che cowpea chlorotic mottle virus (CCMV), a very popular system to investigate the balance between electrostatic and topological features of single-stranded RNA viruses.
1
0
1
📢📢📢 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.
1
4
2
👇.
For a PhD student, choosing a good lab is 10 times more important than choosing a particular topic to study.
0
1
3