25 citations · 42 across the 10 of their papers we have counts for
12 papers
Functional understanding of structural components in polypseudorotaxane gels
Ella Sapsford, Andrea Bonato, Simon Weir +4
Biomedical devices, wearable interfaces, and soft robots require compliant soft materials with reliable mechanical performance, yet the molecular principles needed to design such m…
Design Principles for Programmable Topological Soft Networks
Andrea Bonato, Davide Marenduzzo, Enzo Orlandini
Physical crosslinks in conventional gels are static and spatially localised, fundamentally limiting their capacity to adapt, self-heal, or perform mechanical work. Topological gels…
Topological localisation and motility of active knots
Andrea Bonato, Davide Marenduzzo, Enzo Orlandini +1
Nonequilibrium active polymers provide a minimal framework to investigate biopolymers such as DNA and chromatin under the action of molecular motors. Here we study active ring poly…
Counting unlabelled multigraphs with three nodes
Andrea Bonato
Unlabeled multigraphs have diverse applications across scientific fields, from transportation and social networks to polymer physics. In particular, multigraphs are essential for s…
Topological weight and structural diversity of polydisperse chromatin loop networks
Andrea Bonato, Enrico Carlon, Sergey Kitaev +2
Current biophysical models for transcriptionally active chromatin view this as a polymer with sticky sites, mimicking transcription units such as promoters and enhancers which inte…
Topological spectra and entropy of chromatin loop networks
Andrea Bonato, Dom Corbett, Sergey Kitaev +3
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins,…
Combinatorics and topological weights of chromatin loop networks
Andrea Bonato, Dom Corbett, Sergey Kitaev +3
Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combin…
Spontaneous Unidirectional Loop Extrusion Emerges from Symmetry Breaking of SMC Extension
Andrea Bonato, Jae-Won Jang, Kyoung-Wook Moon +2
DNA loop extrusion is arguably one of the most important players in genome organization. The precise mechanism by which loop extruding factors (LEFs) work is still unresolved and m…
Three-Dimensional Loop Extrusion
Andrea Bonato, Davide Michieletto
Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computatio…
Simplifying Topological Entanglements by Entropic Competition of Slip-Links
Andrea Bonato, Davide Marenduzzo, Davide Michieletto
Topological entanglements are abundant, and often detrimental, in polymeric systems in biology and materials science. Here we theoretically investigate the topological simplificati…
Chromosome Compaction and Chromatin Stiffness Enhance Diffusive Loop Extrusion by Slip-Link Proteins
Andrea Bonato, Chris A. Brackley, James Johnson +2
We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. W…
Diffusive Limits of the Master Equation in Inhomogeneous Media
F. Sattin, A. Bonato, L. Salasnich
Diffusion is the macroscopic manifestation of disordered molecular motion. Mathematically, diffusion equations are partial differential equations describing the fluid-like large-sc…