402 citations · 8.7k across the 191 of their papers we have counts for
11 papers · 1 filter
Non-equilibrium chromosome looping via molecular slip-links
C. A. Brackley, J. Johnson, D. Michieletto +4
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic…
Microfluidic Flow of Cholesteric Liquid Crystals
Oliver Wiese, Davide Marenduzzo, Oliver Henrich
We explore the rheology and flow-induced morphological changes of cholesteric liquid crystal patterns subject to Poiseuille flow within a slab geometry, and under different anchori…
Shear dynamics of an inverted nematic emulsion
A. Tiribocchi, M. Da Re, D. Marenduzzo +1
Here we study theoretically the dynamics of a 2D and a 3D isotropic droplet in a nematic liquid crystal under a shear flow. We find a large repertoire of possible nonequilibrium st…
Pattern formation in polymerising actin flocks: spirals, spots and waves without nonlinear chemistry
Thomas Le Goff, Benno Liebchen, Davide Marenduzzo
We propose a model solely based on actin treadmilling and polymerisation which describes many characteristic states of actin wave formation: spots, spirals and travelling waves. In…
A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA
Y. A. G. Fosado, D. Michieletto, J. Allan +3
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a meso…
Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains
C. A. Brackley, B. Liebchen, D. Michieletto +3
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such obs…
A stochastic model of supercoiling-dependent transcription
C. A. Brackley, J. Johnson, A. Bentivoglio +4
We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unw…
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…
Pattern Formation in Chemically Interacting Active Rotors with Self-Propulsion
Benno Liebchen, Michael E. Cates, Davide Marenduzzo
We demonstrate that active rotations in chemically signalling particles, such as autochemotactic {\it E. coli} close to walls, create a route for pattern formation based on a nonli…
Chromosome-wide simulations uncover folding pathway and 3D organization of interphase chromosomes
Davide Michieletto, Davide Marenduzzo, Ajazul H. Wani
Three-dimensional interphase organization of metazoan genomes has been linked to cellular identity. However, the principles governing 3D interphase genome architecture and its fait…
Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
Chris A Brackley, Jill M Brown, Dominic Waithe +5
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation wi…