455 citations · 2.7k across the 72 of their papers we have counts for
15 papers · 1 filter
Machine learning understands knotted polymers
Anna Braghetto, Sumanta Kundu, Marco Baiesi +1
Simulated configurations of flexible knotted rings confined inside a spherical cavity are fed into long-short term memory neural networks (LSTM NNs) designed to distinguish knot ty…
The rise and fall of branching: a slowing down mechanism in relaxing wormlike micellar networks
Marco Baiesi, Stefano Iubini, Enzo Orlandini
A mean-field kinetic model suggests that the relaxation dynamics of wormlike micellar networks is a long and complex process due to the problem of reducing the number of free end-c…
Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation
Davide Michieletto, Yair Fosado, Elias Melas +3
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in biophysics. Most of the existing models…
Aging of living polymer networks: a model with patchy particles
Stefano Iubini, Marco Baiesi, Enzo Orlandini
Microrheology experiments show that viscoelastic media composed by wormlike micellar networks display complex relaxations lasting seconds even at the scale of micrometers. By mappi…
Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures
Federico Norbiato, Flavio Seno, Antonio Trovato +1
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the prese…
Topological Sieving of Rings According to their Rigidity
Stefano Iubini, Enzo Orlandini, Davide Michieletto +1
We present a novel mechanism for resolving the mechanical rigidity of nanoscopic circular polymers that flow in a complex environment. The emergence of a regime of negative differe…
Exploring the correlation between the folding rates of proteins and the entanglement of their native states
Marco Baiesi, Enzo Orlandini, Flavio Seno +1
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a…
Linking in domain-swapped protein dimers
Marco Baiesi, Enzo Orlandini, Antonio Trovato +1
The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structu…
Torque-Induced Rotational Dynamics in Polymers: Torsional Blobs and Thinning
Michiel Laleman, Marco Baiesi, Boris P. Belotserkovskii +3
By using the blob theory and computer simulations, we investigate the properties of a linear polymer performing a stationary rotational motion around a long impenetrable rod. In pa…
Rings in Random Environments: Sensing Disorder Through Topology
Davide Michieletto, Marco Baiesi, Enzo Orlandini +1
In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which hal…
Unwinding Dynamics of a Helically Wrapped Polymer
Jean-Charles Walter, Marco Baiesi, Enrico Carlon +1
We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and unwinding from it. This dynamics is of interest in several problems in biology and c…
Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for growth polarity
Marco Baiesi, Flavio Seno, Antonio Trovato
The prion-forming C-terminal domain of the fungal prion HET-s forms infectious amyloid fibrils at physiological pH. The conformational switch from the non-prion soluble form to the…
A lattice polymer study of DNA renaturation dynamics
A. Ferrantini, M. Baiesi, E. Carlon
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a d…
A graph theoretical analysis of the energy landscape of model polymers
Marco Baiesi, Lorenzo Bongini, Lapo Casetti +1
In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dyna…
RNA denaturation: excluded volume, pseudoknots and transition scenarios
M. Baiesi, E. Orlandini, A. L. Stella
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknot…