148 citations · 1k across the 43 of their papers we have counts for
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Competition between local erasure and long-range spreading of a single biochemical mark leads to epigenetic bistability
Marco Ancona, Davide Michieletto, Davide Marenduzzo
The mechanism through which cells determine their fate is intimately related to the spreading of certain biochemical (so-called epigenetic) marks along their genome. The mechanisms…
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…
Integrating Transposable Elements in the 3D Genome
Alexandros Bousios, Hans-Wilhelm Nuetzmann, Dorothy Buck +1
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) howeve…
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…
Maximally Stiffening Composites Require Maximally Coupled Rather Than Maximally Entangled Polymer Species
Davide Michieletto, Robert Fitzpatrick, Rae M Robertson-Anderson
Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes…
Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance
Y. A. G. Fosado, D. Michieletto, C. A. Brackley +1
We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for…