8 papers
Controlled Langevin Dynamics for Sampling of Feedforward Neural Networks Trained with Minibatches
Alessandro Zambon, Francesca Caruso, Riccardo Zecchina +1
Sampling the parameter space of artificial neural networks according to a Boltzmann distribution provides insight into the geometry of low-loss solutions and offers an alternative…
The standard coil or globule phases cannot describe the denatured state of structured proteins and intrinsically disordered proteins
F. Righini, G. Potel, R. Capelli +1
The concepts of globule and random coil were developed to describe the phases of homopolymers and then used to characterize the denatured state of structured cytosolic proteins and…
Sampling the space of solutions of an artificial neural network
Alessandro Zambon, Enrico M. Malatesta, Guido Tiana +1
The weight space of an artificial neural network can be systematically explored using tools from statistical mechanics. We employ a combination of a hybrid Monte Carlo algorithm wh…
Length-dependent residence time of contacts in simple polymeric models
E. Marchi, G. Tiana
Starting from the reported experimental evidence that the residence time of contacts between the ends of biopolymers is length dependent, we investigate the kinetics of contact bre…
Predicting the binding of small molecules to proteins through invariant representation of the molecular structure
R. Beccaria, A. Lazzeri, G. Tiana
We present a computational scheme for predicting the ligands that bind to a pocket of known structure. It is based on the generation of a general abstract representation of the mol…
Effective model of protein--mediated interactions in chromatin
Francesco Borando, Guido Tiana
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show thro…
Structure of the space of folding protein sequences defined by large language models
A. Zambon, R. Zecchina, G. Tiana
Proteins populate a manifold in the high-dimensional sequence space whose geometrical structure guides their natural evolution. Leveraging recently-developed structure prediction t…
Native state of natural proteins optimises local entropy
Matteo Negri, Guido Tiana, Riccardo Zecchina
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic st…