148 citations · 1k across the 43 of their papers we have counts for
47 papers
The Polymer Physics of Kinetoplast DNA as a Polymerised Membrane
Takahiro Sakaue, Davide Michieletto
We analyze the conformational and dynamical properties of the kinetoplast DNA (kDNA), a massive sheet-like structure made from thousands of circular DNA molecules, found in the mit…
Organisation and dynamics of individual DNA segments in topologically complex genomes
Saminathan Ramakrishnan, Auro Varat Patnaik, Guglielmo Grillo +2
Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, ma…
Single-Molecule Morphology of Topologically Digested Olympic Networks
Saminathan Ramakrishnan, Zihao Chen, Yair Augusto Gutierrez Fosado +5
The kinetoplast DNA (kDNA) is the archetype of a two-dimensional Olympic network, composed of thousands of DNA minicircles and found in the mitochondrion of certain parasites. The…
Spontaneous Unidirectional Loop Extrusion Emerges from Symmetry Breaking of SMC Extension
Andrea Bonato, Jae-Won Jang, Kyoung-Wook Moon +2
DNA loop extrusion is arguably one of the most important players in genome organization. The precise mechanism by which loop extruding factors (LEFs) work is still unresolved and m…
Loops are Geometric Catalysts for DNA Integration
Cleis Battaglia, Davide Michieletto
The insertion of HIV and other DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of these insertions are not random and occupy specifi…
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…
Single-Molecule Structure and Topology of Kinetoplast DNA Networks
Pinyao He, Allard J. Katan, Luca Tubiana +2
The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understandi…
Geometric Predictors of Knotted and Linked Arcs
Joseph L Sleiman, Robin H Burton, Michele Caraglio +2
Inspired by how certain proteins "sense" knots and entanglements in DNA molecules, here we ask if there exist local geometric features that may be used as a read-out of the underly…
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…
Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation
Davide Michieletto, Yair Fosado, Elias Melas +3
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in biophysics. Most of the existing models…
DNA topology dictates strength and flocculation in DNA-microtubule composites
Karthik R. Peddireddy, Davide Michieletto, Gina Aguirre +3
Polymer composites are ubiquitous in biology and industry alike, owing to their emergent desirable mechanical properties not attainable in single-species systems. At the same time,…
Dynamical Entanglement and Cooperative Dynamics in Entangled Solutions of Ring and Linear Polymers
Davide Michieletto, Takahiro Sakaue
Understanding how entanglements affect the behaviour of polymeric complex fluids is an open challenge in many fields. To elucidate the nature and consequence of entanglements in de…
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…
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…
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…
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…
Supercoiling Enhances DNA Mobility by Reducing Threadings and Entanglements
Jan Smrek, Davide Michieletto
DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA…
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…
Separation of Geometrical and Topological Entanglement in Confined Polymers Driven Out-Of-Equilibrium
Davide Michieletto, Enzo Orlandini, Matthew S Turner +1
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined in…
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…