187 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- University of EdinburghGB29 papers
- MRC Human Genetics Unit12 papers
- University of BathGB7 papers
- Edinburgh Cancer ResearchGB6 papers
- University of PaduaIT3 papers
- Aoyama Gakuin UniversityJP2 papers
- Istituto Nazionale di Fisica Nucleare, Sezione di PadovaIT2 papers
- Western General HospitalGB2 papers
- Centre National de la Recherche ScientifiqueFR1 paper
- Delft University of TechnologyNL1 paper
- Hausdorff Center for MathematicsDE1 paper
- Hiroshima International UniversityJP1 paper
30 papers
Yeast condensin acts as a transient intermolecular crosslinker in entangled DNA
Filippo Conforto, Antonio Valdes, Willem Vanderlinden +1
Structural-Maintenance-of-Chromosome (SMC) complexes such as condensins organise the folding of chromosomes. However, their role in modulating the entanglement of DNA and chromatin…
Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription
Michael Chiang, Cleis Battaglia, Giada Forte +3
Transcriptional noise, or heterogeneity, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we…
Topological Linking Determines Elasticity in Limited Valence Networks
Giorgia Palombo, Simon Weir, Davide Michieletto +1
Understanding the relationship between the microscopic structure and topology of a material and its macroscopic properties is a fundamental challenge across a wide range of systems…
Effects of Monovalent and Divalent Cations on the Rheology of Entangled DNA
Jennifer Harnett, Simon Weir, Davide Michieletto
In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled lambda DNA solutions. We show that monovalent cations moderately i…
Geometric Learning of Knot Topology
Joseph Lahoud Sleiman, Filippo Conforto, Yair Augusto Gutierrez Fosado +1
Knots are deeply entangled with every branch of science. One of the biggest open challenges in knot theory is to formalise a knot invariant that can unambiguously and efficiently d…
Discrete fragmentation equations with time-dependent coefficients
Lyndsay Kerr, Wilson Lamb, Matthias Langer
We examine an infinite, linear system of ordinary differential equations that models the evolution of fragmenting clusters, where each cluster is assumed to be composed of identica…
Runaway Transition in Irreversible Polymer Condensation with Cyclisation
Maria Panoukidou, Simon Weir, Valerio Sorichetti +3
The process of polymer condensation, i.e. the formation of bonds between reactive end-groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing p…
Higher-Order Interactions and Their Duals Reveal Synergy and Logical Dependence beyond Shannon-Information
Abel Jansma
Information-theoretic quantities reveal dependencies among variables in the structure of joint, marginal, and conditional entropies, but leave some fundamentally different systems…
Fluidification of entanglements by a DNA bending protein
Yair A. G. Fosado, Jamieson Howard, Simon Weir +3
In spite of the nanoscale and single-molecule insights into how nucleoid associated proteins (NAPs) interact with DNA, their role in modulating the mesoscale viscoelasticity of the…
Rheology and Viscoelasticity of Proteins and Nucleic Acids Condensates
Davide Michieletto, Mattia Marenda
Phase separation is as familiar as watching vinegar separating from oil in vinegrette. The observation that phase separation of proteins and nucleic acids is widespread in living c…
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…
Topological digestion drives time-varying rheology of entangled DNA fluids
Davide Michieletto, Philip Neill, Simon Weir +4
Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to pac…
Non-Equilibrium Living Polymers
Davide Michieletto
Systems of "living" polymers are ubiquitous in industry and are traditionally realised using surfactants. Here I review the state-of-the-art of living polymers and discuss non-equi…
Persistence Homology Of Entangled Rings
Fabio Landuzzi, Takenobu Nakamura, Davide Michieletto +1
Topological constraints (TCs) between polymers determine the behaviour of complex fluids such as creams, oils and plastics. Most of the polymer solutions used every day life employ…
Higher-order interactions in statistical physics and machine learning: A model-independent solution to the inverse problem at equilibrium
Sjoerd Viktor Beentjes, Ava Khamseh
The problem of inferring pair-wise and higher-order interactions in complex systems involving large numbers of interacting variables, from observational data, is fundamental to man…
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…
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…
Higher order corrections to spin correlations in top quark pair production at the LHC
Arnd Behring, Michal Czakon, Alexander Mitov +2
We calculate, for the first time, the next-to-next-to leading order (NNLO) QCD corrections to spin correlations in top quark pair production at the LHC. The NNLO corrections play a…
An annotated list of bivalent chromatin regions in human ES cells: a new tool for cancer epigenetic research
Franck Court, Philippe Arnaud
CpG islands (CGI) marked by bivalent chromatin in stem cells are believed to be more prone to aberrant DNA methylation in tumor cells. The robustness and genome-wide extent of this…
Machine learning determination of dynamical parameters: The Ising model case
Guido Cossu, Luigi Del Debbio, Tommaso Giani +2
We train a set of Restricted Boltzmann Machines (RBMs) on one- and two-dimensional Ising spin configurations at various values of temperature, generated using Monte Carlo simulatio…
Magnetic Polymer Models for Epigenomic Organisation and Phase Separation
Davide Coli, Davide Michieletto, Davide Marenduzzo +1
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay be…