Publications by Davide Marenduzzo

Passive polymers in active turbulence undergo a collapse-stretch transition DOI
Zahra K. Valei, Davide Marenduzzo and Tyler N. Shendruk, Newton, 2, p. 1-16 (2026)
Geometry and relaxation dynamics of nematic loops DOI
F. Aprile, A.J.H. Houston, G. Gonnella, D. Marenduzzo, T. N. Shendruk and G. Negro, European Physical Society Letters (EPL), 156, 2, p. 1-7 (2026)
Spontaneous phase separation and pattern formation in a lyotropic nematic mixture DOI
Ana Bensabat, Orlaith Skelton, Jochen Arlt, M. Bjelogrlic, Davide Marenduzzo, Giuseppe Negro, Tyler N. Shendruk and Tiffany A. Wood, Proceedings of the National Academy of Sciences of the United States of America, 123, 28, p. 1-9 (2026)
Clifford algebras and liquid crystalline fermions DOI
N. Johnson, L. C. Head, O. D. Lavrentovich, A. N. Morozov, G. Negro, E. Orlandini, C. A. Smith, G. M. Vasil and D. Marenduzzo, Physical Review X, 15, 4, p. 1-19 (2025)
Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription DOI
Michael Chiang, Cleis Battaglia, Giada Forte, Chris A Brackley, Nick Gilbert and Davide Marenduzzo, Physical Review Letters, 135, 15, p. 158401 (2025)
Oscillation in the SIRS model DOI
Davide Marenduzzo, Aidan T. Brown, Craig W. Miller and Graeme J. Ackland, Journal of Theoretical Biology, 611, p. 1-12 (2025)
Modelling transcriptional silencing and its coupling to 3D genome organisation DOI
M. Semeraro, G. Negro, D. Marenduzzo and G. Forte, Soft Matter, 21, 35, p. 6975-6983 (2025)
Equilibrium phases and phase transitions in multicritical magnetic polymers DOI
Alberto Raiola, Emanuele Locatelli, Davide Marenduzzo and Enzo Orlandini, Soft Matter, 20, 26, p. 5296-5311 (2025)
Bridging-mediated compaction of mitotic chromosomes DOI
Giada Forte, Lora Boteva, Nick Gilbert, Peter R. Cook and Davide Marenduzzo, Nucleus, 16, 1, p. 1-10 (2025)
Formation of Topological Bigels in Mixtures of Colloidal Rings and Polymers DOI
Andrea Bonato, Davide Marenduzzo and Enzo Orlandini, Physical Review Letters, 134, 18, p. 1-6 (2025)
To promote network connectivity in colloidal rod suspensions, end with a tip DOI
Gavin Melaugh, Samuel G.V. Charlton, Bonnie Mccallion, Davide Marenduzzo and Cait E. Macphee, Physical Review E, 111, 4, p. 1-11 (2025)
Role of cellular filamentation in bacterial aggregation and cluster-cluster assembly DOI
Samuel Charlton, G. Melaugh, Davide Marenduzzo, Cait MacPhee and Eleonora Secchi, Physical Review E, 111, 2, p. 1-12 (2025)
Topology controls flow patterns in active double emulsions DOI
Giuseppe Negro, Louise C. Head, Livio N. Carenza, Tyler N. Shendruk, Davide Marenduzzo, Giuseppe Gonnella and Adriano Tiribocchi, Nature Communications, 16, 1, p. 1-11 (2025)
Diffusive evaporation dynamics in polymer solutions is ubiquitous DOI
Max Huisman, Wilson C. K. Poon, Patrick B. Warren, Simon Titmuss and Davide Marenduzzo, Soft Matter, 21, 8, p. 1508-1515 (2025)
A unified-field theory of genome organization and gene regulation DOI
Giuseppe Negro, Massimiliano Semeraro, Peter R. Cook and Davide Marenduzzo, iScience, 27, 12, p. 1-16 (2024)
Majorana quasiparticles and topological phases in 3D active nematics DOI
Louise C. Head, Giuseppe Negro, Livio N. Carenza, Nathan Johnson, Ryan R. Keogh, Giuseppe Gonnella, Alexander Morozov, Enzo Orlandini, Tyler N. Shendruk, Adriano Tiribocchi and Davide Marenduzzo, Proceedings of the National Academy of Sciences of the United States of America, 121, 52 (2024)
Genome-wide chromosome architecture prediction reveals biophysical principles underlying gene structure DOI
Michael Chiang, Chris A Brackley, Catherine Naughton, Ryu-Suke Nozawa, Cleis Battaglia, Davide Marenduzzo and Nick Gilbert, Cell Genomics, 4, 12 (2024)
Multiphase field model of cells on a substrate: From three dimensional to two dimensional DOI
Michael Chiang, Austin Hopkins, Benjamin Loewe, Davide Marenduzzo and M. Cristina Marchetti, Physical Review E, 110, 4, p. 1-15 (2024)
Intercellular Friction and Motility Drive Orientational Order in Cell Monolayers DOI
Michael Chiang, Austin Hopkins, Benjamin Loewe, M. Cristina Marchetti and Davide Marenduzzo, Proceedings of the National Academy of Sciences (PNAS), 121, 40, p. 1-7 (2024)
Modeling the 3D Spatiotemporal Organization of Chromatin Replication DOI
G. Forte, S. Buonomo, P. R. Cook, N. Gilbert, D. Marenduzzo and Enzo Orlandini, PRX Life, 2, 3 (2024)
Entangled nematic disclinations using multi-particle collision dynamics DOI
Louise C. Head, Yair A. G. Fosado, Davide Marenduzzo and Tyler N. Shendruk, Soft Matter, 20, 36, p. 7157-7173 (2024)
Can the AMOEBA forcefield be used for high pressure simulations? The extreme case of methane and water DOI
Matthew Kerr, Graeme J. Ackland, Davide Marenduzzo, Giovanni B. Brandani and Ciprian G. Pruteanu, The Journal of Chemical Physics, 161, 5, p. 1-9 (2024)
An integrated electromagnetic, molecular and lasing model for liquid crystal laser optimization
Ieva Pakamoryte, D. Marenduzzo, Nick Polydorides and Philip J. W. Hands (2024)
Combinatorics and topological weights of chromatin loop networks DOI
Andrea Bonato, Michael Chiang, Dom Corbett, Sergey Kitaev, Davide Marenduzzo, Alexander Morozov and Enzo Orlandini, Physical Review E, 109, 6, p. 1-13 (2024)
Topological Spectra and Entropy of Chromatin Loop Networks DOI
Andrea Bonato, Michael Chiang, Dom Corbett, Sergey Kitaev, Davide Marenduzzo, Alexander Morozov and Enzo Orlandini, Physical Review Letters, 132, 24, p. 1-6 (2024)
Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin DOI
Carlos Sacristan, Kumiko Samejima, Lorena Andrade Ruiz, Moonmoon Deb, Maaike L. A. Lambers, Adam Buckle, Chris A. Brackley, Daniel Robertson, Tetsuya Hori, Shaun Webb, Davide Marenduzzo et al., Cell, 187, 12, p. 3006-3023.e26 (2024)
Bridging condensins mediate compaction of mitotic chromosomes DOI
Giada Forte, Lora Boteva, Filippo Conforto, Nick Gilbert, Peter R. Cook and Davide Marenduzzo, Journal of Cell Biology, 223, 1, p. 1-14 (2023)
Transcription modulates chromatin dynamics and locus configuration sampling DOI
Giada Forte, Adam Buckle, Shelagh Boyle, Davide Marenduzzo, Nick Gilbert and Chris A. Brackley, Nature Structural & Molecular Biology, 30, 9, p. 1275-1285 (2023)
Ultra-long-range interactions between active regulatory elements DOI
Elias T. Friman, Ilya M. Flyamer, Davide Marenduzzo, Shelagh Boyle and Wendy A. Bickmore, Genome Research, 33, 8, p. 1269-1284 (2023)
Liquid crystal lasers: Improving the stability of liquid crystal lasers using a combined molecular-electromagnetic model
Ieva Pakamoryte, D. Marenduzzo, Nick Polydorides and Philip J. W. Hands (2023)
Shapes and dynamic regimes of a polar active fluid droplet under confinement DOI
A. Tiribocchi, M. Durve, M. Lauricella, A. Montessori, D. Marenduzzo and S. Succi, Physics of Fluids, 35, 6, p. 1-35 (2023)
Yield-stress transition in suspensions of deformable droplets DOI
Giuseppe Negro, Livio Nicola Carenza, Giuseppe Gonnella, Fraser Mackay, Alexander Morozov and Davide Marenduzzo, Science Advances, 9, 22, p. 1-7 (2023)
Improving the stability of liquid crystal lasers using a combined molecular-electromagnetic model
Ieva Pakamoryte, D. Marenduzzo, Nick Polydorides and Philip J. W. Hands (2023)
Active turbulence and spontaneous phase separation in inhomogeneous extensile active gels DOI
Renato Assante, Dom Corbett, Davide Marenduzzo and Alexander Morozov, Soft Matter, 19, 2, p. 189-198 (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)
Local Yield and Compliance in Active Cell Monolayers DOI
Austin Hopkins, Michael Chiang, Benjamin Loewe, Davide Marenduzzo and M. Cristina Marchetti, Physical Review Letters, 129, 14, p. 1-7 (2022)
Predicting genome organisation and function with mechanistic modelling DOI
Michael Chiang, Chris A Brackley, Davide Marenduzzo and Nick Gilbert, Trends in Genetics, 38, 4, p. 364-378 (2022)
Cholesteric Shells: Two-Dimensional Blue Fog and Finite Quasicrystals DOI
L. N. Carenza, G. Gonnella, D. Marenduzzo, G. Negro and E. Orlandini, Physical Review Letters, 128, 2, p. 1-7 (2022)
Mechanisms for destabilisation of RNA viruses at air-water and liquid-liquid interfaces DOI
C. A. Brackley, A. Lips, A. Morozov, W. C.K. Poon and D. Marenduzzo, Nature Communications, 12, 1, p. 1-6 (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)
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)
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)
Swimming suppresses correlations in dilute suspensions of pusher microorganisms DOI
Viktor Škultéty, Cesare Nardini, Joakim Stenhammar, Davide Marenduzzo and Alexander Morozov, Physical Review X, 10, 3 (2020)
Soft matter science and the COVID-19 pandemic DOI
Wilson C K Poon, Aidan T Brown, Susana O. L. Direito, Daniel J M Hodgson, Lucas Le Nagard, Alex Lips, Cait E MacPhee, Davide Marenduzzo, John R Royer, Andreia F Silva, Job H J Thijssen and Simon Titmuss, Soft Matter (2020)
Electrostatic potential between charged particles at an oil-water interface DOI
Alexander Morozov, Iain Muntz, J. H. J. Thijssen and D. Marenduzzo, Physical Review E, 102, 2 (2020)
Pattern formation in active model C with anchoring: bands, aster networks, and foams DOI
Ivan Maryshev, Alexander Morozov, Andrew B. Goryachev and Davide Marenduzzo, Soft Matter (2020)
Interaction between Nearly Hard Colloidal Spheres at an Oil-Water Interface DOI
Iain Muntz, Franceska Waggett, Michael Hunter, Andrew B. Schofield, Paul Bartlett, Davide Marenduzzo and Job H. J. Thijssen, Physical Review Research, 2, 2 (2020)
Mechanistic modeling of chromatin folding to understand function DOI
Chris A Brackey, Davide Marenduzzo and Nick Gilbert, Nature Methods (2020)
A nonequilibrium strategy for fast target search on the genome DOI
F. Cagnetta, D. Michieletto and D. Marenduzzo, Physical Review Letters, 124 (2020)
Darcy's law without friction in active nematic rheology DOI
Fraser MacKay, John Toner, Alexander Morozov and D. Marenduzzo, Physical Review Letters, 124, 18 (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)
Kinetic roughening in active interfaces DOI
Francesco Cagnetta, Martin R. Evans and Davide Marenduzzo, EPJ Web of Conferences, EDP Sciences, 230 (2020)
Bridging-induced microphase separation: photobleaching experiments, chromatin domains, and the need for active reactions. DOI
Chris Brackley and Davide Marenduzzo, Briefings in functional genomics (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)
Pressure-induced Miscibility Increase of CH4 in H2O: A Computational Study Using Classical Potentials DOI
Ciprian G. Pruteanu, Davide Marenduzzo and John S. Loveday, Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry), 123, 38, p. 8091-8095 (2019)
A simulation study of aggregation mediated by production of cohesive molecules DOI
Gavin Melaugh, Davide Marenduzzo, Alexander Morozov and Rosalind Allen, Soft Matter (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)
Nucleosome positions alone can be used to predict domains in yeast chromosomes DOI
Oliver Wiese, Davide Marenduzzo and Chris Brackley, Proceedings of the National Academy of Sciences (PNAS) (2019)
Dynamic clustering and re-dispersion in concentrated colloid-active gel composites DOI
Giulia Foffano, Juho Sakari Lintuvuori, Kevin Stratford, Mike Cates and Davide Marenduzzo, 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)
Dry active turbulence in a model for microtubule-motor mixtures DOI
Ivan Maryshev, Andrew Goryachev, Davide Marenduzzo and Alexander Morozov, Soft Matter (2019)
capC-MAP: software for analysis of Capture-C data DOI
Adam Buckle, Davide Marenduzzo and Chris Brackley, Bioinformatics (2019)
Transcriptional bursts in a non-equilibrium model for gene regulation by supercoiling DOI
Marco Ancona, Alessandro Bentivoglio, Chris A. Brackley, Giuseppe Gonnella and Davide Marenduzzo, Biophysical Journal (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)
Statistical mechanics of a single active slider on a fluctuating interface DOI
Francesco Cagnetta, Martin R. Evans and Davide Marenduzzo, Physical Review E (2019)
Microfluidic chiral liquid crystal droplet generation towards chemical sensing applications
Jason Norman, Margaret Normand, Anne Pawsey, Davide Marenduzzo and Philip Hands (2019)
Physical Principles of Retroviral Integration in the Human Genome DOI
D. Michieletto, M. Lusic, D. Marenduzzo and E. Orlandini, Nature Communications, 10 (2019)
Rheology and microrheology of deformable droplet suspensions DOI
M. Foglino, A. N. Morozov and D. Marenduzzo, Soft Matter, 14, 46, p. 9361-9367 (2018)
Transcription-driven genome organization: DOI
Peter R. Cook and Davide Marenduzzo, Nucleic Acids Research, 46, 19, p. 9895-9906 (2018)
Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci DOI
Adam Buckle, Chris A. Brackley, Shelagh Boyle, Davide Marenduzzo and Nick Gilbert, Molecular Cell, 72, 4, p. 786-797.e11 (2018)
A growing bacterial colony in two dimensions as an active nematic DOI
D. Dell'Arciprete, M. L. Blow, A. T. Brown, F. D. C. Farrell, J. S. Lintuvuori, A. F. McVey, D. Marenduzzo and W. C. K. Poon, Nature Communications, 9 (2018)
Mixtures of blue phase liquid crystal with simple liquids DOI
J. S. Lintuvuori, K. Stratford, M. E. Cates and D. Marenduzzo, Physical Review Letters, 121, 3 (2018)
Active Growth and Pattern Formation in Membrane-Protein Systems DOI
F. Cagnetta, M. R. Evans and D. Marenduzzo, Physical Review Letters, 120, 25, p. 1-5 (2018)
Hydrodynamic bifurcation in electro-osmotically driven periodic flows DOI
Alexander Morozov, Davide Marenduzzo and Ronald G. Larson, Physical Review Fluids, 3, 6 (2018)
HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types DOI
Anne Zirkel, Milos Nikolic, Konstantinos Sofiadis, Jan-Philipp Mallm, Chris A. Brackley, Henrike Gothe, Oliver Drechsel, Christian Becker, Janine Altmueller, Natasa Josipovic, Davide Marenduzzo et al., Molecular Cell, 70, 4, p. 730-744.e6 (2018)
Kinetic theory of pattern formation in mixtures of microtubules and molecular motors DOI
Ivan Maryshev, Davide Marenduzzo, Andrew B. Goryachev and Alexander Morozov, Physical Review E, 97, 2 (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)
Flow of Deformable Droplets DOI
M. Foglino, A. N. Morozov, O. Henrich and D. Marenduzzo, Physical Review Letters, 119, 20 (2017)
Epigenetic Transitions and Knotted Solitons in Stretched Chromatin DOI
Davide Michieletto, Enzo Orlandini and Davide Marenduzzo, Scientific Reports (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)
Anchoring-driven spontaneous rotations in active gel droplets DOI
Ana Azevedo da luz fialho, M. L. Blow and D. Marenduzzo, Soft Matter, 13, 35, p. 5933-5941 (2017)
Role of Correlations in the Collective Behavior of Microswimmer Suspensions DOI
Joakim Stenhammar, Cesare Nardini, Rupert W. Nash, Davide Marenduzzo and Alexander Morozov, Physical Review Letters, 119, 2, p. 1-6 (2017)
Colloidal spherocylinders at an interface: Flipper dynamics and bilayer formation DOI
T. Li, G. Brandani, D. Marenduzzo and P.S. Clegg, Physical Review Letters, 119, 1 (2017)
Phoretic Interactions Generically Induce Dynamic Clusters and Wave Patterns in Active Colloids DOI
Benno Liebchen, Davide Marenduzzo and Michael E. Cates, Physical Review Letters, 118, 26 (2017)
Contractile and chiral activities codetermine the helicity of swimming droplet trajectories DOI
Elsen Tjhung, Michael E. Cates and Davide Marenduzzo, Proceedings of the National Academy of Sciences (PNAS), 114, 18, p. 4631-4636 (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)
Genome organization: experiments and modeling DOI
Nick Gilbert and Davide Marenduzzo, Chromosome Research, 25, 1, p. 1-4 (2017)
Exploiting native forces to capture chromosome conformation in mammalian cell nuclei DOI
Lilija Brant, Theodore Georgomanolis, Milos Nikolic, Chris A Brackley, Petros Kolovos, Wilfred van Ijcken, Frank G Grosveld, Davide Marenduzzo and Argyris Papantonis, Molecular Systems Biology, 12, 12, p. 891 (2016)
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)
Hydrodynamic oscillations and variable swimming speed in squirmers close to repulsive walls DOI
Juho Lintuvuori, Aidan Brown, Kevin Stratford and Davide Marenduzzo, Soft Matter, Advance Article (2016)
Pattern formation in chemically interacting active rotors with self-propulsion DOI
Benno Liebchen, Michael E. Cates and Davide Marenduzzo, Soft Matter, 12, 35, p. 7259-7264 (2016)
Stochastic Model of Supercoiling-Dependent Transcription DOI
C. A. Brackley, J. Johnson, A. Bentivoglio, S. Corless, N. Gilbert, G. Gonnella and D. Marenduzzo, Physical Review Letters, 117, 1 (2016)
Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains DOI
Chris A. Brackley, James Johnson, Steven Kelly, Peter R. Cook and Davide Marenduzzo, Nucleic Acids Research, 44, 8, p. 3503–3512 (2016)
Light-induced self-assembly of active rectification devices DOI
Joakim Stenhammar, Raphael Wittkowski, Davide Marenduzzo and Michael E. Cates, Science Advances, 2, 4 (2016)
Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models DOI
Chris A Brackley, Jill M Brown, Dominic Waithe, Christian Babbs, James Davies, Jim R Hughes, Veronica J Buckle and Davide Marenduzzo, Genome Biology, 17, 1 (2016)
Curvature-driven positioning of Turing patterns in phase-separating curved membranes DOI
Andrew Goryachev, Giulio Vandin, Davide Marenduzzo and Enzo Orlandini, Soft Matter (2016)
A one-dimensional statistical mechanics model for nucleosome positioning on genomic DNA DOI
S Tesoro, I Ali, A N Morozov, N Sulaiman and D Marenduzzo, Physical Biology, 13, 1 (2016)
Spontaneous flow in polar active fluids: the effect of a phenomenological self propulsion-like term DOI
Francesco Bonelli, Giuseppe Gonnella, Adriano Tiribocchi and Davide Marenduzzo, The European Physical Journal E (EPJ E), 39, 1, p. 1-10 (2016)
Clustering and Pattern Formation in Chemorepulsive Active Colloids DOI
Benno Liebchen, Davide Marenduzzo, Ignacio Pagonabarraga and Michael E. Cates, Physical Review Letters, 115, 25 (2015)
Active Model H DOI
Adriano Tiribocchi, Raphael Wittkowski, Davide Marenduzzo and Michael E. Cates, Physical Review Letters, 115, 18 (2015)
The Bacterial Hydrophobin BslA is a Switchable Ellipsoidal Janus Nanocolloid DOI
Giovanni B Brandani, Marieke Schor, Ryan Morris, Nicola Stanley-Wall, Cait E MacPhee, Davide Marenduzzo and Ulrich Zachariae, Langmuir, 31, 42, p. 11558–11563 (2015)
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)
Electric Field Controlled Columnar and Planar Patterning of Cholesteric Colloids DOI
G. D'Adamo, D. Marenduzzo, C. Micheletti and E. Orlandini, Physical Review Letters, 114, 17 (2015)
Interfacial self-assembly of a bacterial hydrophobin DOI
Keith M. Bromley, Ryan J. Morris, Laura Hobley, Giovanni Brandani, Rachel M. C. Gillespie, Matthew McCluskey, Ulrich Zachariae, Davide Marenduzzo, Nicola R. Stanley-Wall and Cait. E. MacPhee, Proceedings of the National Academy of Sciences (PNAS), 112, 17, p. 5419-5424 (2015)
Motility-induced phase separation and coarsening in active matter DOI
Giuseppe Gonnella, Davide Marenduzzo, Antonio Suma and Adriano Tiribocchi, Comptes rendus physique, 16, 3, p. 316-331 (2015)
Self-assembling knots of controlled topology by designing the geometry of patchy templates DOI
Guido Polles, Davide Marenduzzo, Enzo Orlandini and Cristian Micheletti, Nature Communications, 6 (2015)
A simple model for DNA bridging proteins and bacterial or human genomes DOI
J. Johnson, Chris Brackley, P. R. Cook and D. Marenduzzo, Journal of Physics: Condensed Matter, 27, 6 (2015)
A minimal physical model captures the shapes of crawling cells DOI
E. Tjhung, A. Tiribocchi, D. Marenduzzo and M. E. Cates, Nature Communications, 6 (2015)
An introduction to the physics of active matter DOI
G. De Magistris and D. Marenduzzo, Physica a-Statistical mechanics and its applications, 418, p. 65-77 (2015)
Activity-Induced Phase Separation and Self-Assembly in Mixtures of Active and Passive Particles DOI
Joakim Stenhammar, Raphael Wittkowski, Davide Marenduzzo and Michael E. Cates, Physical Review Letters, 114, 1 (2015)
Filling an Emulsion Drop with Motile Bacteria DOI
I. D. Vladescu, E. J. Marsden, J. Schwarz-Linek, V. A. Martinez, J. Arlt, A. N. Morozov, D. Marenduzzo, M. E. Cates and W. C. K. Poon, Physical Review Letters, 113, 26, p. 1-5 (2014)
Motility-induced phase separation in an active dumbbell fluid DOI
A. Suma, G. Gonnella, D. Marenduzzo and E. Orlandini, European Physical Society Letters (EPL), 108, 5 (2014)
Topological constraints strongly affect chromatin reconstitution in silico DOI
C. A. Brackley, James Allan, David Keszenman Pereyra and D. Marenduzzo, Nucleic Acids Research, 43, 1, p. 63-73 (2014)
Activity-induced clustering in model dumbbell swimmers DOI
Akira Furukawa, Davide Marenduzzo and Michael E. Cates, Physical Review E, 90, 2 (2014)
Scalar φ4 field theory for active-particle phase separation DOI
Raphael Wittkowski, Adriano Tiribocchi, Joakim Stenhammar, Rosalind J. Allen, Davide Marenduzzo and Michael E. Cates, Nature Communications, 5 (2014)
Self-assembly of colloid-cholesteric composites provides a possible route to switchable optical materials DOI
Kevin Stratford, Oliver Henrich, Juho S. Lintuvuori, M. E. Cates and Davide Marenduzzo, Nature Communications, 5 (2014)
Switching hydrodynamics in liquid crystal devices: a simulation perspective DOI
Oliver Henrich, Davide Marenduzzo and Juho Lintuvuori, Soft Matter, 10, 26, p. 4580-4592 (2014)
Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS DOI
Chris Brackley, A. N. Morozov and D. Marenduzzo, The Journal of Chemical Physics, 140, 13 (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)
Active polar fluid flow in finite droplets DOI
Carl A. Whitfield, Davide Marenduzzo, Raphaël Voituriez and Rhoda J. Hawkins, The European Physical Journal E (EPJ E), 37, 2 (2014)
Modelling the effect of myosin X motors on filopodia growth DOI
M. R. Evans, A. B. Goryachev and D. Marenduzzo, Physical Biology, 11, 1 (2014)
Spiral and never-settling patterns in active systems DOI
X. Yang, D. Marenduzzo and M. C. Marchetti, Physical Review E, 89, 1 (2014)
Chemotactic clusters in confined run-and-tumble bacteria DOI
E. J. Marsden, C. Valeriani, I. Sullivan, M. E. Cates and D. Marenduzzo, Soft Matter, 10, 1, p. 157-165 (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)
Enhanced diffusion of tracer particles in dilute bacterial suspensions DOI
Alexander Morozov and Davide Marenduzzo, Soft Matter, 10, 16, p. 2748-2758 (2014)
Phase behaviour of active Brownian particles DOI
Joakim Stenhammar, Davide Marenduzzo, Rosalind J. Allen and Michael E. Cates, Soft Matter, 10, 10, p. 1489-1499 (2014)
Spontaneous motility of passive emulsion droplets in polar active gels DOI
G. De Magistris, A. Tiribocchi, C. A. Whitfield, R. J. Hawkins, M. E. Cates and D. Marenduzzo, Soft Matter, 10, 39, p. 7826-7837 (2014)
The dynamics of colloidal intrusions in liquid crystals DOI
G. Foffano, J. S. Lintuvuori, A. Tiribocchi and D. Marenduzzo, Liquid crystals reviews, 2, 1, p. 1-27 (2014)
Topological friction strongly affects viral DNA ejection DOI
D. Marenduzzo, C. Micheletti, E. Orlandini and D. W. Sumners, Proceedings of the National Academy of Sciences (PNAS), 110, 50, p. 20081-20086 (2013)
Rheology of cubic blue phases DOI
Oliver Henrich, Kevin Stratford, Peter V. Coveney, Michael Cates and Davide Marenduzzo, Soft Matter, 9, p. 10243 (2013)
Chemotactic Sensing towards Ambient and Secreted Attractant Drives Collective Behaviour of E. coli DOI
Tine Curk, Davide Marenduzzo and Jure Dobnikar, PLoS ONE, 8, 10 (2013)
Continuum Theory of Phase Separation Kinetics for Active Brownian Particles DOI
Joakim Stenhammar, Adriano Tiribocchi, Rosalind J. Allen, Davide Marenduzzo and Michael E. Cates, Physical Review Letters, 111, 14 (2013)
Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization DOI
Chris Brackley, Stephen Taylor, Argyris Papantonis, Peter R Cook and Davide Marenduzzo, Proceedings of the National Academy of Sciences (PNAS), 110, 38, p. E3605-11 (2013)
Intracellular Facilitated Diffusion DOI
Chris Brackley, M. E. Cates and D. Marenduzzo, Physical Review Letters, 111, 10 (2013)
Quantifying Disorder through Conditional Entropy DOI
Giovanni B. Brandani, Marieke Schor, Cait E. MacPhee, Helmut Grubmueller, Ulrich Zachariae and Davide Marenduzzo, PLoS ONE, 8, 6 (2013)
Colloidal Templating at a Cholesteric-Oil Interface: Assembly Guided by an Array of Disclination Lines DOI
J. S. Lintuvuori, Anne Pawsey, K. Stratford, M. E. Cates, P. S. Clegg and D. Marenduzzo, Physical Review Letters, 110, 18 (2013)
Effect of DNA conformation on facilitated diffusion DOI
Chris Brackley, Michael Cates and Davide Marenduzzo, Biochemical Society Transactions, 41, p. 582-588 (2013)
The knotted strands of life
Davide Marenduzzo, Cristian Micheletti and Enzo Orlandini, Physics world, 26, 4, p. 30-34 (2013)
Mechanically driven growth of quasi-two dimensional microbial colonies DOI
F. D. C. Farrell, O. Hallatschek, D. Marenduzzo and B. Waclaw, Physical Review Letters, 111 (2013)
Sedimentation of knotted polymers DOI
J. Piili, D. Marenduzzo, K. Kaski and R. P. Linna, Physical Review E, 87, 1 (2013)
Domain formation on curved membranes DOI
E. Orlandini, D. Marenduzzo and A. B. Goryachev, Soft Matter, 9, 39, p. 9311-9318 (2013)
Flexoelectric switching in cholesteric blue phases DOI
A. Tiribocchi, M. E. Cates, G. Gonnella, D. Marenduzzo and E. Orlandini, Soft Matter, 9, 19, p. 4831-4842 (2013)
Phase separation dynamics on curved surfaces DOI
Davide Marenduzzo and Enzo Orlandini, Soft Matter, 9, 4, p. 1178-1187 (2013)
Space exploration by the promoter of a long human gene during one transcription cycle DOI
Joshua D Larkin, Argyris Papantonis, Peter R Cook and Davide Marenduzzo, Nucleic Acids Research, 41, 4, p. 2216-2227 (2013)
Facilitated Diffusion on Mobile DNA DOI
Chris Brackley, M. E. Cates and D. Marenduzzo, Physical Review Letters, 109, 16 (2012)
Bulk rheology and microrheology of active fluids DOI
G. Foffano, J.S. Lintuvuori, A.N. Morozov, M.E. Cates, D. Marenduzzo and K. Stratford, The European Physical Journal E (EPJ E), 35, 10 (2012)
Equilibrium and dynamical behavior in the Vicsek model for self-propelled particles under shear DOI
Gustavo P. Saracco, Giuseppe Gonnella, Davide Marenduzzo and Enzo Orlandini, Central european journal of physics, 10, 5, p. 1109-1115 (2012)
Colloidal particles at the interface between an isotropic liquid and a chiral liquid crystal DOI
Anne Pawsey, Juho Lintuvuori, Tiffany Wood, Job Thijssen, Davide Marenduzzo and Paul Clegg, Soft Matter, 8, 32, p. 8422-8428 (2012)
Spontaneous symmetry breaking in active droplets provides a generic route to motility DOI
E. Tjhung, D. Marenduzzo and M.E. Cates, Proceedings of the National Academy of Sciences (PNAS), 109, 31, p. 12381-12386 (2012)
Confined cubic blue phases under shear DOI
Oliver Henrich, K. Stratford, D. Marenduzzo, P. V. Coveney and M. E. Cates, Journal of Physics: Condensed Matter, 24, 28, p. - (2012)
Colloids in Active Fluids DOI
G. Foffano, J. S. Lintuvuori, K. Stratford, M. E. Cates and D. Marenduzzo, Physical Review Letters, 109, 2 (2012)
Pattern Formation in Self-Propelled Particles with Density-Dependent Motility DOI
F. D. C. Farrell, M. C. Marchetti, D. Marenduzzo and J. Tailleur, Physical Review Letters, 108, 24, p. - (2012)
Cytoplasmic streaming in plant cells DOI
K. Wolff, D. Marenduzzo and M. E. Cates, Journal of the Royal Society. Interface, 9, 71, p. 1398-1408 (2012)
Phase separation and rotor self-assembly in active particle suspensions DOI
J. Schwarz-Linek, C. Valeriani, A. Cacciuto, M. E. Cates, D. Marenduzzo, A. N. Morozov and W. C. K. Poon, Proceedings of the National Academy of Sciences (PNAS), 109, 11, p. 4052-4057 (2012)
Facilitated diffusion on confined DNA DOI
G. Foffano, D. Marenduzzo and E. Orlandini, Physical Review E, 85, 2 (2012)
Rheology of lamellar liquid crystals in two and three dimensions: a simulation study DOI
Oliver Henrich, K. Stratford, D. Marenduzzo, P. V. Coveney and M. E. Cates, Soft Matter, 8, 14, p. 3817-3831 (2012)
Self-Assembly and Nonlinear Dynamics of Dimeric Colloidal Rotors in Cholesterics DOI
J. S. Lintuvuori, K. Stratford, Michael Cates and D. Marenduzzo, Physical Review Letters, 107, 26, p. - (2011)
Bistable Defect Structures In Blue Phase Devices DOI
A. Tiribocchi, G. Gonnella, D. Marenduzzo, E. Orlandini and F. Salvadore, Physical Review Letters, 107, 23, p. - (2011)
Lateral dynamics of charged lipids and peripheral proteins in spatially heterogeneous membranes: Comparison of continuous and Monte Carlo approaches DOI
Vladimir Yu Kiselev, Marcin Leda, Alexey I. Lobanov, Davide Marenduzzo and Andrew B. Goryachev, The Journal of Chemical Physics, 135, 15, p. - (2011)
A Self-Quenched Defect Glass in a Colloid-Nematic Liquid Crystal Composite DOI
Tiffany Wood, Juho Lintuvuori, Andrew B Schofield, D. Marenduzzo and Wilson Poon, Science, 334, 6052, p. 79-83 (2011)
Shearing self-propelled suspensions: Arrest of coarsening and suppression of giant density fluctuations DOI
G. P. Saracco, G. Gonnella, D. Marenduzzo and E. Orlandini, Physical Review E, 84, 3, p. - (2011)
Monte Carlo and event-driven dynamics of Brownian particles with orientational degrees of freedom DOI
Flavio Romano, Cristiano De Michele, Davide Marenduzzo and Eduardo Sanz, The Journal of Chemical Physics, 135, 12, p. - (2011)
Influence of ions on genome packaging and ejection: A molecular dynamics study DOI
I. Ali and D. Marenduzzo, The Journal of Chemical Physics, 135, 9, p. - (2011)
Polymers with spatial or topological constraints: Theoretical and computational results DOI
Cristian Micheletti, Davide Marenduzzo and Enzo Orlandini, Physics Reports, 504, 1, p. 173 (2011)
Colloids in a bacterial bath: simulations and experiments DOI
Chantal Valeriani, Martin Li, John Novosel, Jochen Arlt and Davide Marenduzzo, Soft Matter, 7, 11, p. 5228-5238 (2011)
Nonlinear dynamics and rheology of active fluids: Simulations in two dimensions DOI
S. M. Fielding, D. Marenduzzo and M. E. Cates, Physical Review E, 83, 4, p. - (2011)
Structure of Blue Phase III of Cholesteric Liquid Crystals DOI
Oliver Henrich, K. Stratford, Michael Cates and D. Marenduzzo, Physical Review Letters, 106, 10, p. - (2011)
Lateral Dynamics of Proteins with Polybasic Domain on Anionic Membranes DOI
Vladimir Yu. Kiselev, Davide Marenduzzo and Andrew B. Goryachev, Biophysical Journal, 100, 5, p. 1261-1270 (2011)
Defect hydrodynamics in 2D polar active fluids DOI
J. Elgeti, M. E. Cates and D. Marenduzzo, Soft Matter, 7, 7, p. 3177-3185 (2011)
Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes DOI
Kieran Finan, Peter R. Cook and Davide Marenduzzo, Chromosome Research, 19, 1, p. 53-61 (2011)
Nonequilibrium steady states in polar active fluids DOI
Elsen Tjhung, Michael E. Cates and Davide Marenduzzo, Soft Matter, 7, 16, p. 7453-7464 (2011)
Switching dynamics in cholesteric blue phases DOI
A. Tiribocchi, G. Gonnella, D. Marenduzzo and E. Orlandini, Soft Matter, 7, 7, p. 3295-3306 (2011)
Colloids in Cholesterics: Size-Dependent Defects and Non-Stokesian Microrheology DOI
J. S. Lintuvuori, K. Stratford, M. E. Cates and D. Marenduzzo, Physical Review Letters, 105, 17, p. - (2010)
Switching and defect dynamics in multistable liquid crystal devices DOI
A. Tiribocchi, G. Gonnella, D. Marenduzzo and E. Orlandini, Applied Physics Letters, 97, 14, p. - (2010)
Ordering dynamics of blue phases entails kinetic stabilization of amorphous networks DOI
Oliver Henrich, Kevin Stratford, Davide Marenduzzo and Michael E. Cates, Proceedings of the National Academy of Sciences (PNAS), 107, 30, p. 13212-13215 (2010)
Biopolymer organization upon confinement DOI
D. Marenduzzo, C. Micheletti and E. Orlandini, Journal of Physics: Condensed Matter, 22, 28, p. - (2010)
Arrested phase separation in reproducing bacteria creates a generic route to pattern formation DOI
M. E. Cates, D. Marenduzzo, I. Pagonabarraga and J. Tailleur, Proceedings of the National Academy of Sciences (PNAS), 107, 26, p. 11715-11720 (2010)
Non-equilibrium dynamics of an active colloidal "chucker" DOI
C. Valeriani, Rosalind Allen and D. Marenduzzo, The Journal of Chemical Physics, 132, 20, p. - (2010)
Dynamic Monte Carlo versus Brownian dynamics: A comparison for self-diffusion and crystallization in colloidal fluids DOI
E. Sanz and D. Marenduzzo, The Journal of Chemical Physics, 132, 19, p. - (2010)
Different pulling modes in DNA overstretching: A theoretical analysis DOI
D. Marenduzzo, E. Orlandini, F. Seno and A. Trovato, Physical Review E, 81, 5, p. - (2010)
Domain growth in cholesteric blue phases: Hybrid lattice Boltzmann simulations DOI
Oliver Henrich, D. Marenduzzo, K. Stratford and M. E. Cates, Computers & mathematics with applications, 59, 7, p. 2360-2369 (2010)
The role of noise and advection in absorbing state phase transitions DOI
C. Barrett-Freeman, M. R. Evans, D. Marenduzzo and J. Tailleur, European Physical Society Letters (EPL), 90, 1, p. - (2010)
Thermodynamics of blue phases in electric fields DOI
Oliver Henrich, D. Marenduzzo, K. Stratford and M. E. Cates, Physical Review E, 81, 3, p. - (2010)
Colloids in liquid crystals: a lattice Boltzmann study DOI
J .S. Lintuvuori, D. Marenduzzo, K. Stratford and M. E. Cates, Journal of Materials Chemistry, 20, 46, p. 10547-10552 (2010)
Hydrodynamics of non-homogeneous active gels DOI
D. Marenduzzo and E. Orlandini, Soft Matter, 6, 4, p. 774-778 (2010)
DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting DOI
Davide Marenduzzo, Enzo Orlandini, Andrzej Stasiak, De Witt Sumners, Luca Tubiana and Cristian Micheletti, Proceedings of the National Academy of Sciences (PNAS), 106, 52, p. 22269-22274 (2009)
Entropic organization of interphase chromosomes DOI
Peter R. Cook and Davide Marenduzzo, Journal of Cell Biology, 186, 6, p. 825-834 (2009)
Topological and entropic repulsion in biopolymers DOI
D. Marenduzzo and E. Orlandini, Journal of Statistical Mechanics: Theory and Experiment, p. - (2009)
Localisation of DivIVA by targeting to negatively curved membranes DOI
Rok Lenarcic, Sven Halbedel, Loek Visser, Michael Shaw, Ling Juan Wu, Jeff Errington, Davide Marenduzzo and Leendert W. Hamoen, EMBO Journal, 28, 15, p. 2272-2282 (2009)
Phase diagrams for DNA denaturation under stretching forces DOI
D. Marenduzzo, A. Maritan, E. Orlandini, F. Seno and A. Trovato, Journal of Statistical Mechanics: Theory and Experiment, p. - (2009)
Statistics of confined polymers and the melting of a DNA spool DOI
D. Marenduzzo, European Physical Society Letters (EPL), 85, 3, p. - (2009)
Lattice Boltzmann simulations of liquid crystalline fluids: active gels and blue phases DOI
M. E. Cates, Oliver Henrich, D. Marenduzzo and K. Stratford, Soft Matter, 5, 20, p. 3791-3800 (2009)
Simulations of knotting in confined circular DNA DOI
C. Micheletti, D. Marenduzzo, E. Orlandini and D. W. Sumners, Biophysical Journal, 95, 8, p. 3591-3599 (2008)
Nonequilibrium phase transition in the sedimentation of reproducing particles DOI
C. Barrett-Freeman, Martin R. Evans, D. Marenduzzo and Wilson Poon, Physical Review Letters, 101, 10, p. - (2008)
Shearing active gels close to the isotropic-nematic transition DOI
Michael Cates, S. M. Fielding, D. Marenduzzo, E. Orlandini and J. M. Yeomans, Physical Review Letters, 101, 6, p. - (2008)
Ejection dynamics of polymeric chains from viral capsids: Effect of solvent quality DOI
I. Ali, D. Marenduzzo and J. M. Yeomans, Biophysical Journal, 94, 11, p. 4159-4164 (2008)
Cubic blue phases in electric fields DOI
G. P. Alexander and D. Marenduzzo, European Physical Society Letters (EPL), 81, 6, p. - (2008)
Lattice Boltzmann simulations of spontaneous flow in active liquid crystals: The role of boundary conditions DOI
D. Marenduzzo, E. Orlandini, M. E. Cates and J. M. Yeomans, Journal of non-Newtonian fluid mechanics, 149, 1-3, p. 56-62 (2008)
Computer simulations of DNA packing inside bacteriophages: Elasticity, electrostatics and entropy DOI
D. Marenduzzo, Computational and mathematical methods in medicine, 9, 3-4, p. 317-325 (2008)
Hydrodynamic of Active Liquid Crystals: A Hybrid Lattice Boltzmann Approach DOI
E. Orlandini, M. E. Cates, D. Marenduzzo, L. Tubiana and J. M. Yeomans, Molecular Crystals and Liquid Crystals Science and Technology - Section A: Molecular Crystals and Liquid Crystals, 494, p. 293-308 (2008)
Steady-state hydrodynamic instabilities of active liquid crystals: Hybrid lattice Boltzmann simulations DOI
D. Marenduzzo, E. Orlandini, M. E. Cates and J. M. Yeomans, Physical Review E, 76, 3, p. - (2007)

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Publications by Davide Marenduzzo