Publications by Davide Michieletto

School of Physics and Astronomy

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Rheology and programmable gelation of DNA tadpoles DOI
Jennifer Harnett, Saminathan Ramakrishnan, Elizabeth P. Holmes, Alice L.B. Pyne and Davide Michieletto, Soft Matter, 22, 41, p. 7057-7066 (2026)
Designing DNA nanostar hydrogels for sequence-specific degradation and antibody release DOI
Giorgia Palombo, Christine A. Merrick, Jennifer Harnett, Susan Rosser, Davide Michieletto and Yair Augusto Gutiérrez Fosado, Soft Matter, 22, 32, p. 5401–5410 (2026)
NANOG Assembles into Self-Limiting Aging Micelles That Drive a Sol-Gel Transition and Modulate DNA Dynamics DOI
Amandine Hong-Minh, Yair Augusto Gutierrez Fosado, Abbie Guild, Nicholas Mullin, Laura Spagnolo, Ian Chambers and Davide Michieletto, Physical Review Letters, 137, 1, p. 1-7 (2026)
Shortcut learning in geometric knot classification DOI
Djordje Mihajlovic and Davide Michieletto, Machine Learning: Science and Technology, 7, 3, p. 1-18 (2026)
Yeast condensin acts as a transient intermolecular crosslinker in entangled DNA DOI
Filippo Conforto, Antonio Valdes, Willem Vanderlinden and Davide Michieletto, Nucleic Acids Research, 54, 3, p. 1-9 (2026)
Organisation and dynamics of individual DNA segments in topologically complex genomes DOI
Saminathan Ramakrishnan, Guglielmo Grillo, Auro Varat Patnaik, Luca Tubiana and Davide Michieletto, Nucleic Acids Research, 53, 20, p. 1-9 (2025)
Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search DOI
Andrea Bonato, Jae Won Jang, Do Gyun Kim, Kyoung Wook Moon, Davide Michieletto and Je Kyung Ryu, Nucleic Acids Research, 53, 14, p. 1-12 (2025)
Topology-Controlled Microphase Separation and Interconversion of Twist and Writhe Domains in Supercoiled Annealed Polyelectrolytes DOI
Roman Staňo, Christos N. Likos, Davide Michieletto and Jan Smrek, Physical Review Letters, 135, 4, p. 1-8 (2025)
Topologically-crosslinked hydrogels based on γ-cyclodextrins DOI
Ella Sapsford and Davide Michieletto, Communications Chemistry, 8, 1, p. 1-11 (2025)
Topological linking determines elasticity in limited valence networks DOI
Giorgia Palombo, Simon Weir, Davide Michieletto and Yair Augusto Gutierrez Fosado, Nature Materials, 24, 3, p. 454-461 (2025)
Kinetoplast DNA: a polymer physicist’s topological Olympic dream DOI
Davide Michieletto, Nucleic Acids Research, 53, 2, p. 1-9 (2025)
Link to Densify: Topological Transitions and Origin of Hysteresis During the Compression and Decompression of Amorphous Ices DOI
Yair Augusto GutiErrez Fosado, Davide Michieletto and Fausto Martelli, Physical Review Letters, 133, 26, p. 1-6 (2024)
Fluidification of entangled polymers by loop extrusion DOI
Filippo Conforto, Yair Gutierrez Fosado and Davide Michieletto, Physical Review Research, 6, 3, p. 1-10 (2024)
Loops are Geometric Catalysts for DNA Integration DOI
Cleis Battaglia and Davide Michieletto, Nucleic Acids Research, 52, 14, p. 8184-8192 (2024)
Topology in soft and biological matter DOI
L Tubiana, GP Alexander, A Barbensi, D Buck, JHE Cartwright, M Chwastyk, M Cieplak, I Coluzza, S Copar, D Michieletto et al., Physics Reports, 1075, p. 1-137 (2024)
Runaway Transition in Irreversible Polymer Condensation with Cyclisation DOI
Maria Panoukidou, Simon Weir, Valerio Sorichetti, Yair Gutierrez Fosado, Martin Lenz and Davide Michieletto, Physical Review Research, 6, 2, p. 1-13 (2024)
Effects of Monovalent and Divalent Cations on the Rheology of Entangled DNA DOI
Jennifer Harnett, Simon Weir and Davide Michieletto, Soft Matter, 20, 19, p. 3980-3986 (2024)
Single-molecule morphology of topologically digested olympic networks DOI
Saminathan Ramakrishnan, Zihao Chen, Yair Augusto Gutierrez Fosado, Luca Tubiana, Willem Vanderlinden, Nicholas Jon Savill, Achim Schnaufer and D. Michieletto, PRX Life, 2 (2024)
Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription DOI
Marta Russo, Viviana Piccolo, Danilo Polizzese, Elena Prosperini, Carolina Borriero, Sara Polletti, Fabio Bedin, Mattia Marenda, Davide Michieletto, Gaurav Madappa Mandana et al., Genes & Development, 37, 21-24, p. 1017-1040 (2023)
Dynamic ParB-DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation DOI
Miloš Tišma, Richard Janissen, Hammam Antar, Alejandro Martin-Gonzalez, Roman Barth, Twan Beekman, Jaco Van Der Torre, Davide Michieletto, Stephan Gruber and Cees Dekker, Nucleic Acids Research, 51, 21, p. 11856-11875 (2023)
Geometric Learning of Knot Topology DOI
Joseph Lahoud Sleiman, Filippo Conforto, Yair Augusto Gutierrez Fosado and Davide Michieletto, Soft Matter, 20, 1, p. 71-78 (2023)
Single-Molecule Structure and Topology of Kinetoplast DNA Networks DOI
Pinyao He, Allard J. Katan, Luca Tubiana, Cees Dekker and Davide Michieletto, Physical Review X, 13, 2, p. 1-13 (2023)
Fluidification of entanglements by a DNA bending protein DOI
Yair A. G. Fosado, Jamieson Howard, Simon Weir, Agnes Noy, Mark C Leake and Davide Michieletto, Physical Review Letters, 130, 5, p. 1-6 (2023)
Topological gelation of reconnecting polymers DOI
Andrea Bonato, Davide Marenduzzo, D. Michieletto and Enzo Orlandini, Proceedings of the National Academy of Sciences (PNAS), 119, 44, p. 1-8 (2022)
Geometric Predictors of Knotted and Linked Arcs DOI
Joseph L. Sleiman, Robin H. Burton, Michele Caraglio, Yair Augusto Gutiérrez Fosado and D. Michieletto, ACS Polymers Au, 2, 5, p. 341-350 (2022)
Rheology and Viscoelasticity of Proteins and Nucleic Acids Condensates DOI
Davide Michieletto and Mattia Marenda, JACS Au, 2, 7, p. 1506-1521 (2022)
Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation DOI
Davide Michieletto, Yair Fosado, Elias Melas, Marco Baiesi, Luca Tubiana and Enzo Orlandini, Nucleic Acids Research, 50, 8, p. 4659-4668 (2022)
Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events DOI
Je-Kyung Ryu, Sang-Hyun Rah, Richard Janissen, Jacob W. J. Kerssemakers, Andrea Bonato, Davide Michieletto and Cees Dekker, Nucleic Acids Research, 50, 2, p. 820-832 (2022)
Three-Dimensional Loop Extrusion DOI
Andrea Bonato and Davide Michieletto, Biophysical Journal, 120, 24, p. 5544-5552 (2021)
Simplifying Topological Entanglements by Entropic Competition of Slip-Links DOI
Andrea Bonato, Davide Marenduzzo and Davide Michieletto, Physical Review Research, 3, 4, p. 1-9 (2021)
Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction DOI
Jorine M. Eeftens, Manya Kapoor, Davide Michieletto and Clifford P. Brangwynne, Nature, 12, 1, p. 1-12 (2021)
Complex small-world regulatory networks emerge from the 3D organisation of the human genome DOI
C. A. Brackley, N Gilbert, D. Michieletto, A Papantonis, M.C.F. Pereira, P. R. Cook and D. Marenduzzo, Nature Communications, 12, 1, p. 1-14 (2021)
Topological Tuning of DNA Mobility in Entangled Solutions of Supercoiled Plasmids DOI
Jan Smrek, Jonathan Garamella, Rae Robertson-Anderson and D. Michieletto, Science Advances, 7, 20, p. 1-9 (2021)
Parameter-free Molecular Super-Structures Quantification in Single-Molecule Localisation Microscopy DOI
Mattia Marenda, Elena Lazarova, Sebastian van de Linde, Nick Gilbert and Davide Michieletto, Journal of Cell Biology, 220, 5, p. 1-15 (2021)
Make or break: building soft materials with DNA
D. Michieletto, Physics world, March 2021, p. 48-52 (2021)
Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling DOI
Yair A. G. Fosado, Davide Michieletto, Chris A. Brackley and Davide Marenduzzo, Proceedings of the National Academy of Sciences (PNAS), 118, 10, p. 1-6 (2021)
Bridging-induced phase separation induced by cohesin SMC protein complexes DOI
Je-Kyung Ryu, Celine Bouchoux, Hon Wing Liu, Eugene Kim, Masashi Minamino, Ralph de Groot, Allard J Katan, Andrea Bonato, D. Marenduzzo, D. Michieletto, Frank Uhlmann et al., Science Advances, 7, 7, p. 1-10 (2021)
Dynamical Entanglement and Cooperative Dynamics in Entangled Solutions of Ring and Linear Polymers DOI
Davide Michieletto and Takahiro Sakaue, ACS MACRO LETTERS, 2021, 10, p. 129-134 (2020)
Non-Equilibrium Living Polymers DOI
Davide Michieletto, Entropy, 22, 10 (2020)
Persistence Homology Of Entangled Rings DOI
Fabio Landuzzi, Takenobu Nakamura, Davide Michieletto and Takahiro Sakaue, Physical Review Research, 2, 3 (2020)
Separation of Geometrical and Topological Entanglement in Confined Polymers Driven Out-Of-Equilibrium DOI
Davide Michieletto, Enzo Orlandini, Matthew S Turner and Cristian Micheletti, ACS MACRO LETTERS, 9, 8, p. 1081-1085 (2020)
Threading-Induced Dynamical Transition in Tadpole-Shaped Polymers DOI
Angelo Rosa, Jan Smrek, Matthew S Turner and Davide Michieletto, ACS MACRO LETTERS, 9, 5, p. 743-748 (2020)
A nonequilibrium strategy for fast target search on the genome DOI
F. Cagnetta, D. Michieletto and D. Marenduzzo, Physical Review Letters, 124 (2020)
Competition between local erasure and long-range spreading of a single biochemical mark leads to epigenetic bistability DOI
Marco Ancona, Davide Michieletto and Davide Marenduzzo, Physical Review E, 101, 4 (2020)
Integrating Transposable Elements in the 3D Genome DOI
Alexandros Bousios, Hans-Wilhelm Nuetzmann, Dorothy Buck and Davide Michieletto, Mobile DNA (2020)
Magnetic Polymer Models for Epigenetics-Driven Chromosome Folding DOI
Davide Colì, Enzo Orlandini, Davide Michieletto and Davide Marenduzzo, Physical Review E, 100, 5 (2019)
Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus DOI
Davide Michieletto, Davide Colí, Davide Marenduzzo and Enzo Orlandini, Physical Review Letters, 123, 22-29 (2019)
Polymer Modeling Predicts Chromosome Reorganization in Senescence DOI
Michael Chiang, Davide Michieletto, Chris A. Brackley, Nattaphong Rattanavirotkul, Hisham Mohammed, Davide Marenduzzo and Tamir Chandra, Cell Reports, 28, 12, p. P3212-3223.e6 (2019)
Maximally Stiffening Composites Require Maximally Coupled Rather Than Maximally Entangled Polymer Species DOI
Davide Michieletto, Robert Fitzpatrick and Rae M Robertson-Anderson, Soft Matter (2019)
Non-equilibrium effects of molecular motors on polymers DOI
Martina Foglino, E Locatelli, Chris Brackley, Davide Michieletto, C N Likos and Davide Marenduzzo, Soft Matter (2019)
Role of nuclear RNA in regulating chromatin structure and transcription DOI
Davide Michieletto and Nick Gilbert, Current opinion in cell biology, 58, p. 120-125 (2019)
Synergy of Topoisomerase and Structural-Maintenance-of-Chromosomes Proteins Creates a Universal Pathway to Simplify Genome Topology DOI
Enzo Orlandini, Davide Marenduzzo and Davide Michieletto, Proceedings of the National Academy of Sciences (PNAS), 116, 17, p. 8149-8154 (2019)
Physical Principles of Retroviral Integration in the Human Genome DOI
D. Michieletto, M. Lusic, D. Marenduzzo and E. Orlandini, Nature Communications, 10 (2019)
Synergistic interactions between DNA and actin trigger emergent viscoelastic behavior DOI
Robert Fitzpatrick, Davide Michieletto, Karthik R. Peddireddy, Cole Hauer, Carl Kyrillos, Bekele J. Gurmessa and Rae M. Robertson-Anderson, Physical Review Letters (2018)
Topological Sieving of Rings According to Their Rigidity DOI
Stefano Iubini, E. Orlandini, Davide Michieletto and Marco Baiesi, ACS MACRO LETTERS, 7 (2018)
Extrusion without a motor DOI
C A Brackley, J Johnson, D Michieletto, A N Morozov, M Nicodemi, P R Cook and D Marenduzzo, Nucleus, p. 1-10 (2018)
Shaping Epigenetic Memory via Genomic Bookmarking DOI
Davide Michieletto, Michael Chiang, Davide Coli, Argyris Papantonis, Enzo Orlandini, Peter R. Cook and Davide Marenduzzo, Nucleic Acids Research, 46, 1, p. 83-93 (2017)
Epigenetic Transitions and Knotted Solitons in Stretched Chromatin DOI
Davide Michieletto, Enzo Orlandini and Davide Marenduzzo, Scientific Reports (2017)
Glassiness and Heterogeneous Dynamics in Dense Solutions of Ring Polymers DOI
D. Michieletto, N. Nahali and A. Rosa, Physical Review Letters (2017)
Nonequilibrium Chromosome Looping via Molecular Slip Links DOI
C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook and D. Marenduzzo, Physical Review Letters, 119, 13, p. 1-5 (2017)
Dynamical Scaling and Phase Coexistence in Topologically-Constrained DNA Melting DOI
Y. A. G. Fosado, D. Michieletto and D. Marenduzzo, Physical Review Letters, 119 (2017)
Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses DOI
Davide Michieletto, Enzo Orlandini, Davide Marenduzzo and Matthew S. Turner, Polymers, 9, 8 (2017)
Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains
Chris Brackley, Benno Liebchen, Davide Michieletto, Francois Mouvet, Peter Cook and Davide Marenduzzo, Biophysical Journal, 112, 6 (2017)
Polymer model with Epigenetic Recoloring Reveals a Pathway for the de novo Establishment and 3D Organization of Chromatin Domains DOI
D. Michieletto, E. Orlandini and D. Marenduzzo, Physical Review X, 6, 4 (2016)
Simulating topological domains in human chromosomes with a fitting-free model DOI
C A Brackley, D Michieletto, F Mouvet, J Johnson, S Kelly, P. R. Cook and D Marenduzzo, Nucleus, 7, 5, p. 453-461 (2016)
A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA DOI
Y. A. G. Fosado, D. Michieletto, J. Allan, C. Brackley, O. Henrich and D. Marenduzzo, Soft Matter, 12, 47, p. 9458-9470 (2016)
On the Tree-Like Structure of Rings in Dense Solutions DOI
Davide Michieletto, Soft Matter, 12, 47 (2016)
A topologically driven glass in ring polymers DOI
Davide Michieletto and Matthew S Turner, Proceedings of the National Academy of Sciences (PNAS), 113, 19, p. 5195-5200 (2016)
Topological patterns in two-dimensional gel electrophoresis of DNA knots DOI
Davide Michieletto, Davide Marenduzzo and Enzo Orlandini, Proceedings of the National Academy of Sciences (PNAS), 112, 40, p. E5471-5477 (2015)
Is the kinetoplast DNA a percolating network of linked rings at its critical point? DOI
Davide Michieletto, Davide Marenduzzo and Enzo Orlandini, Physical Biology, 12, 3 (2015)
Rings in Random Environments DOI
Davide Michieletto, Marco Baiesi, Enzo Orlandini and Matthew S. Turner, Soft Matter (2014)
Threading Dynamics of Ring Polymers in a Gel DOI
Davide Michieletto, Davide Marenduzzo, Enzo Orlandini, Gareth P. Alexander and Matthew S. Turner, ACS MACRO LETTERS, 3, 3, p. 255-259 (2014)
Dynamics of self-threading ring polymers in a gel DOI
Davide Michieletto, Davide Marenduzzo, Enzo Orlandini, Gareth P. Alexander and Matthew S. Turner, Soft Matter, 10, 32, p. 5936-5944 (2014)