402 citations · 8.7k across the 191 of their papers we have counts for
15 papers · 1 filter
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…
Soft channel formation and symmetry breaking in exotic active emulsions
L. N. Carenza, G. Gonnella, A. Lamura +3
We use computer simulations to study the morphology and rheological properties of a bidimensional emulsion resulting from a mixture of a passive isotropic fluid and an active contr…
Polymer Modelling Predicts Chromosome Reorganisation in Senescence
Michael Chiang, Davide Michieletto, Chris A. Brackley +4
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polyme…
Genome organization: experiments and modelling
N. Gilbert, D. Marenduzzo
This is an introduction to the special issue Genome organization: experiments and simulations, published in Chromosome Research, volume 25, issue 1 (2017).
Simulating topological domains in human chromosomes with a fitting-free model
C. A. Brackley, D. Michieletto, F. Mouvet +4
We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinforma…
Non-Equilibrium Effects of Molecular Motors on Polymers
M. Foglino, E. Locatelli, C. A. Brackley +3
We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The p…
Mechanistic Modelling of Chromatin Folding to Understand Function
Chris A. Brackley, Davide Marenduzzo, Nick Gilbert
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity,…
Bridging-induced microphase separation: photobleaching experiments, chromatin domains, and the need for active reactions
Chris A. Brackley, Davide Marenduzzo
We review the mechanism and consequences of the "bridging-induced attraction", a generic biophysical principle which underpins some existing models for chromosome organisation in 3…
Extrusion without a motor: a new take on the loop extrusion model of genome organization
C. A. Brackley, J. Johnson, D. Michieletto +4
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangeme…
Electrostatic inactivation of RNA viruses at air-water and liquid-liquid interfaces
C. A. Brackley, A. Lips, A. Morozov +2
Understanding the interactions between viruses and surfaces or interfaces is important, as they provide the principles underpinning the cleaning and disinfection of contaminated su…
Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations
Peter R. Cook, Davide Marenduzzo
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains…
Soft matter science and the COVID-19 pandemic
Wilson C K Poon, Aidan T Brown, Susana O. L. Direito +9
Much of the science underpinning the global response to the COVID-19 pandemic lies in the soft matter domain. Coronaviruses are composite particles with a core of nucleic acids com…
Pattern formation in active model C with anchoring: bands, aster networks, and foams
Ivan Maryshev, Alexander Morozov, Andrew B. Goryachev +1
We study the dynamics of pattern formation in a minimal model for active mixtures made of microtubules and molecular motors. We monitor the evolution of the (conserved) microtubule…
Rotation and propulsion in 3d active chiral droplets
Livio Nicola Carenza, Giuseppe Gonnella, Davide Marenduzzo +1
Chirality is a recurrent theme in the study of biological systems, in which active processes are driven by the internal conversion of chemical energy into work. Bacterial flagella,…
Swimming suppresses correlations in dilute suspensions of pusher microorganisms
Viktor Škultéty, Cesare Nardini, Joakim Stenhammar +2
Active matter exhibits various forms of non-equilibrium states in the absence of external forcing, including macroscopic steady-state currents. Such states are often too complex to…