402 citations · 8.7k across the 191 of their papers we have counts for
12 papers · 1 filter
Debye-Hückel potential at an interface between two media
Alexander Morozov, Iain Muntz, Job H. J. Thijssen +1
Electrostatic interactions between point charges embedded into interfaces separating dielectric media are omnipresent in soft matter systems and often control their stability. Such…
Kinetic roughening in active interfaces
Francesco Cagnetta, Martin R. Evans, Davide Marenduzzo
The essential features of many interfaces driven out of equilibrium are described by the same equation---the Kardar-Parisi-Zhang (KPZ) equation. How do living interfaces, such as t…
Solid-Liquid Transition of Deformable and Overlapping Active Particles
Benjamin Loewe, Michael Chiang, Davide Marenduzzo +1
Experiments and theory have shown that cell monolayers and epithelial tissues exhibit solid-liquid and glass-liquid transitions. These transitions are biologically relevant to our…
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…
Dynamic clustering and re-dispersion in concentrated colloid-active gel composites
G. Foffano, J. S. Lintuvuori, K. Stratford +2
We study the dynamics of quasi-two-dimensional concentrated suspensions of colloidal particles in active gels by computer simulations. Remarkably, we find that activity induces a d…
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…
A nonequilibrium strategy for fast target search on the genome
F. Cagnetta, D. Michieletto, D. Marenduzzo
Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search me…
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…
Transcriptional bursts in a non-equilibrium model for gene regulation by supercoiling
Marco Ancona, Alessandro Bentivoglio, Chris A. Brackley +2
We analyse transcriptional bursting within a stochastic non-equilibrium model which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. We fi…
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…