309 citations · 3.4k across the 84 of their papers we have counts for
49 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…
Topological Phases and Curvature-Driven Pattern Formation in Cholesteric Shells
Giuseppe Negro, Livio Nicola Carenza, Giuseppe Gonnella +2
We study the phase behaviour of cholesteric liquid crystal shells with different geometries. We compare the cases of tangential and no anchoring at the surface, focussing on the fo…
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…
Phase diagrams of confined square lattice links
EJ Janse van Rensburg, E Orlandini
We study by Monte Carlo simulations and scaling analysis two models of pairs of confined and dense ring polymers in two dimensions. The pair of ring polymers are modelled by square…
Cholesteric shells: two-dimensional blue fog and finite quasicrystals
Livio Nicola Carenza, Giuseppe Gonnella, Davide Marenduzzo +2
We study the phase behaviour of a quasi-two dimensional cholesteric liquid crystal shell. We characterise the topological phases arising close to the isotropic-cholesteric transiti…
Separation of Geometrical and Topological Entanglement in Confined Polymers Driven Out-Of-Equilibrium
Davide Michieletto, Enzo Orlandini, Matthew S Turner +1
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined in…
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…
Magnetic Polymer Models for Epigenetics-Driven Chromosome Folding
Davide Colì, Davide Michieletto, Davide Marenduzzo +1
Epigenetics is a driving force of important and ubiquitous phenomena in nature such as cell differentiation or even metamorphosis. Oppositely to its widespread role, understanding…
Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus
Davide Michieletto, Davide Colí, Davide Marenduzzo +1
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that ar…
Plectoneme dynamics and statistics in braided polymers
Giada Forte, Michele Caraglio, Davide Marenduzzo +1
Braids composed of two interwoven polymer chains exhibit a buckling transition whose origin has been explained through the onset of plectonemic structures. Here we study, by a comb…
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…
Synergy of Topoisomerase and Structural-Maintenance-of-Chromosomes Proteins Creates a Universal Pathway to Simplify Genome Topology
Enzo Orlandini, Davide Marenduzzo, Davide Michieletto
Topological entanglements severely interfere with important biological processes. For this reason, genomes must be kept unknotted and unlinked during most of a cell cycle. Type II…
Magnetic Polymer Models for Epigenomic Organisation and Phase Separation
Davide Coli, Davide Michieletto, Davide Marenduzzo +1
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay be…
Rheology of an inverted cholesteric droplet under shear flow
Federico Fadda, Giuseppe Gonnella, Antonio Lamura +2
The dynamics of a quasi two-dimensional isotropic droplet in a cholesteric liquid crystal medium under symmetric shear flow is studied by lattice Boltzmann simulations. We consider…
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…
Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses
Davide Michieletto, Enzo Orlandini, Davide Marenduzzo +1
Elucidating the physics of a concentrated suspension of ring polymers, or of an ensemble of ring polymers in a complex environment, is an important outstanding question in polymer…
Switching dynamics in cholesteric liquid crystal emulsions
Federico Fadda, Giuseppe Gonnella, Davide Marenduzzo +2
In this work we numerically study the switching dynamics of a 2D cholesteric emulsion droplet immersed in an isotropic fluid under an electric field, which is either uniform or rot…
Epigenetic Transitions and Knotted Solitons in Stretched Chromatin
Davide Michieletto, Enzo Orlandini, Davide Marenduzzo
The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establis…
Entropic elasticity and dynamics of the bacterial chromosome: a simulation study
M. C. F. Pereira, C. A. Brackley, J. S. Lintuvuori +2
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we c…
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…
Single-file escape of colloidal particles from microfluidic channels
Emanuele Locatelli, Matteo Pierno, Fulvio Baldovin +3
Single-file diffusion is a ubiquitous physical process exploited by living and synthetic systems to exchange molecules with their environment. It is paramount quantifying the escap…
A Polymer Model with Epigenetic Recolouring Reveals a Pathway for the de novo Establishment and 3D Organisation of Chromatin Domains
Davide Michieletto, Enzo Orlandini, Davide Marenduzzo
One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a fram…
Topological Patterns in Two-dimensional Gel Electrophoresis of DNA Knots
Davide Michieletto, Davide Marenduzzo, Enzo Orlandini
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accura…
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…