Davide Marenduzzo

Affiliations

SUPA School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.

Publications (57)

Complex small-world regulatory networks emerge from the 3D organisation of the human genome.

Nature communications

Avec: C A Brackley , N Gilbert , D Michieletto , A Papantonis , M C F Pereira , P R Cook , D Marenduzzo

Mechanisms for destabilisation of RNA viruses at air-water and liquid-liquid interfaces.

Nature communications

Avec: C A Brackley , A Lips , A Morozov , W C K Poon , D Marenduzzo

Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin.

Cell

Avec: Carlos Sacristan , Kumiko Samejima , Lorena Andrade Ruiz , Moonmoon Deb , Maaike L A Lambers , Adam Buckle , Chris A Brackley , Daniel Robertson , Tetsuya Hori , Shaun Webb , Robert Kiewisz , Tristan Bepler , Eloïse van Kwawegen , Patrik Risteski , Kruno Vukušić , Iva M Tolić , Thomas Müller-Reichert , Tatsuo Fukagawa , Nick Gilbert , Davide Marenduzzo , William C Earnshaw , Geert J P L Kops

Can the AMOEBA forcefield be used for high pressure simulations? The extreme case of methane and water.

The Journal of chemical physics

Avec: Matthew Kerr , Graeme J Ackland , Davide Marenduzzo , Giovanni B Brandani , Ciprian G Pruteanu

Entangled nematic disclinations using multi-particle collision dynamics.

Soft matter

Avec: Louise C Head , Yair A G Fosado , Davide Marenduzzo , Tyler N Shendruk

Yield-stress transition in suspensions of deformable droplets.

Science advances

Avec: Giuseppe Negro , Livio Nicola Carenza , Giuseppe Gonnella , Fraser Mackay , Alexander Morozov , Davide Marenduzzo

Chromosome compaction and chromatin stiffness enhance diffusive loop extrusion by slip-link proteins.

Soft matter

Avec: A Bonato , C A Brackley , J Johnson , D Michieletto , D Marenduzzo

Statistical mechanics of a single active slider on a fluctuating interface.

Physical review. E

Avec: F Cagnetta , M R Evans , D Marenduzzo

Plectoneme dynamics and statistics in braided polymers.

Physical review. E

Avec: Giada Forte , Michele Caraglio , Davide Marenduzzo , Enzo Orlandini

Polymer Modeling Predicts Chromosome Reorganization in Senescence.

Cell reports

Avec: Michael Chiang , Davide Michieletto , Chris A Brackley , Nattaphong Rattanavirotkul , Hisham Mohammed , Davide Marenduzzo , Tamir Chandra

Nucleosome positions alone can be used to predict domains in yeast chromosomes.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Oliver Wiese , Davide Marenduzzo , Chris A Brackley

Electrostatic potential between charged particles at an oil-water interface.

Physical review. E

Avec: Alexander Morozov , Iain Muntz , Job H J Thijssen , Davide Marenduzzo

Renormalization group study of the dynamics of active membranes: Universality classes and scaling laws.

Physical review. E

Avec: Francesco Cagnetta , Viktor Škultéty , Martin R Evans , Davide Marenduzzo

Bridging condensins mediate compaction of mitotic chromosomes.

The Journal of cell biology

Avec: Giada Forte , Lora Boteva , Filippo Conforto , Nick Gilbert , Peter R Cook , Davide Marenduzzo

Topological phases and curvature-driven pattern formation in cholesteric shells.

Soft matter

Avec: G Negro , L N Carenza , G Gonnella , D Marenduzzo , E Orlandini

Active turbulence and spontaneous phase separation in inhomogeneous extensile active gels.

Soft matter

Avec: Renato Assante , Dom Corbett , Davide Marenduzzo , Alexander Morozov

Combinatorics and topological weights of chromatin loop networks.

Physical review. E

Avec: Andrea Bonato , Michael Chiang , Dom Corbett , Sergey Kitaev , Davide Marenduzzo , Alexander Morozov , Enzo Orlandini

Competition between local erasure and long-range spreading of a single biochemical mark leads to epigenetic bistability.

Physical review. E

Avec: Marco Ancona , Davide Michieletto , Davide Marenduzzo

Magnetic polymer models for epigenetics-driven chromosome folding.

Physical review. E

Avec: Davide Colì , Enzo Orlandini , Davide Michieletto , Davide Marenduzzo

Darcy's Law without Friction in Active Nematic Rheology.

Physical review letters

Avec: Fraser Mackay , John Toner , Alexander Morozov , Davide Marenduzzo

Dynamic clustering and re-dispersion in concentrated colloid-active gel composites.

Soft matter

Avec: G Foffano , J S Lintuvuori , K Stratford , M E Cates , D Marenduzzo

Pressure-Induced Miscibility Increase of CH

The journal of physical chemistry. B

Avec: Ciprian G Pruteanu , Davide Marenduzzo , John S Loveday

Rotation and propulsion in 3D active chiral droplets.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Livio Nicola Carenza , Giuseppe Gonnella , Davide Marenduzzo , Giuseppe Negro

A simulation study of aggregation mediated by production of cohesive molecules.

Soft matter

Avec: Gavin Melaugh , Davide Marenduzzo , Alexander Morozov , Rosalind J Allen

Physical principles of retroviral integration in the human genome.

Nature communications

Avec: D Michieletto , M Lusic , D Marenduzzo , E Orlandini

Lamellar ordering, droplet formation and phase inversion in exotic active emulsions.

Scientific reports

Avec: F Bonelli , L N Carenza , G Gonnella , D Marenduzzo , E Orlandini , A Tiribocchi

capC-MAP: software for analysis of Capture-C data.

Bioinformatics (Oxford, England)

Avec: Adam Buckle , Nick Gilbert , Davide Marenduzzo , Chris A Brackley

Soft channel formation and symmetry breaking in exotic active emulsions.

Scientific reports

Avec: L N Carenza , G Gonnella , A Lamura , D Marenduzzo , G Negro , A Tiribocchi

Local Yield and Compliance in Active Cell Monolayers.

Physical review letters

Avec: Austin Hopkins , Michael Chiang , Benjamin Loewe , Davide Marenduzzo , M Cristina Marchetti

Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Enzo Orlandini , Davide Marenduzzo , Davide Michieletto

Solid-Liquid Transition of Deformable and Overlapping Active Particles.

Physical review letters

Avec: Benjamin Loewe , Michael Chiang , Davide Marenduzzo , M Cristina Marchetti

Pattern formation in active model C with anchoring: bands, aster networks, and foams.

Soft matter

Avec: Ivan Maryshev , Alexander Morozov , Andrew B Goryachev , Davide Marenduzzo

Nonequilibrium Strategy for Fast Target Search on the Genome.

Physical review letters

Avec: F Cagnetta , D Michieletto , D Marenduzzo

Mechanistic modeling of chromatin folding to understand function.

Nature methods

Avec: Chris A Brackey , Davide Marenduzzo , Nick Gilbert

Bridging-induced phase separation induced by cohesin SMC protein complexes.

Science advances

Avec: Je-Kyung Ryu , Céline Bouchoux , Hon Wing Liu , Eugene Kim , Masashi Minamino , Ralph de Groot , Allard J Katan , Andrea Bonato , Davide Marenduzzo , Davide Michieletto , Frank Uhlmann , Cees Dekker

Predictive Polymer Models for 3D Chromosome Organization.

Methods in molecular biology (Clifton, N.J.)

Avec: Michael Chiang , Giada Forte , Nick Gilbert , Davide Marenduzzo , Chris A Brackley

Universal properties of active membranes.

Physical review. E

Avec: Francesco Cagnetta , Viktor Škultéty , Martin R Evans , Davide Marenduzzo

Simulations of DNA denaturation dynamics under constrained conditions.

Journal of physics. Condensed matter : an Institute of Physics journal

Avec: A Al Qanobi , D Marenduzzo , I Ali

Topological gelation of reconnecting polymers.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Andrea Bonato , Davide Marenduzzo , Davide Michieletto , Enzo Orlandini

Ultra-long-range interactions between active regulatory elements.

Genome research

Avec: Elias T Friman , Ilya M Flyamer , Davide Marenduzzo , Shelagh Boyle , Wendy A Bickmore

Topological Spectra and Entropy of Chromatin Loop Networks.

Physical review letters

Avec: Andrea Bonato , Michael Chiang , Dom Corbett , Sergey Kitaev , Davide Marenduzzo , Alexander Morozov , Enzo Orlandini

Intercellular friction and motility drive orientational order in cell monolayers.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Michael Chiang , Austin Hopkins , Benjamin Loewe , M Cristina Marchetti , Davide Marenduzzo

Soft matter science and the COVID-19 pandemic.

Soft matter

Avec: 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 , Simon Titmuss

Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus.

Physical review letters

Avec: Davide Michieletto , Davide Colì , Davide Marenduzzo , Enzo Orlandini

Bridging-induced microphase separation: photobleaching experiments, chromatin domains and the need for active reactions.

Briefings in functional genomics

Avec: C A Brackley , D Marenduzzo

Non-equilibrium effects of molecular motors on polymers.

Soft matter

Avec: M Foglino , E Locatelli , C A Brackley , D Michieletto , C N Likos , D Marenduzzo

Dry active turbulence in a model for microtubule-motor mixtures.

Soft matter

Avec: Ivan Maryshev , Andrew B Goryachev , Davide Marenduzzo , Alexander Morozov

Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling.

Biophysical journal

Avec: Marco Ancona , Alessandro Bentivoglio , Chris A Brackley , Giuseppe Gonnella , Davide Marenduzzo

Actomyosin Contraction Induces In-Bulk Motility of Cells and Droplets.

Biophysical journal

Avec: Thomas Le Goff , Benno Liebchen , Davide Marenduzzo

RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis.

Science advances

Avec: Shu Zhang , Nadine Übelmesser , Natasa Josipovic , Giada Forte , Johan A Slotman , Michael Chiang , Henrike Johanna Gothe , Eduardo Gade Gusmao , Christian Becker , Janine Altmüller , Adriaan B Houtsmuller , Vassilis Roukos , Kerstin S Wendt , Davide Marenduzzo , Argyris Papantonis

Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids.

Journal of the Royal Society, Interface

Avec: G Forte , D Michieletto , D Marenduzzo , E Orlandini

Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling.

Proceedings of the National Academy of Sciences of the United States of America

Avec: Yair A G Fosado , Davide Michieletto , Chris A Brackley , Davide Marenduzzo

Predicting genome organisation and function with mechanistic modelling.

Trends in genetics : TIG

Avec: Michael Chiang , Chris A Brackley , Davide Marenduzzo , Nick Gilbert

Cholesteric Shells: Two-Dimensional Blue Fog and Finite Quasicrystals.

Physical review letters

Avec: L N Carenza , G Gonnella , D Marenduzzo , G Negro , E Orlandini

The crucial role of adhesion in the transmigration of active droplets through interstitial orifices.

Nature communications

Avec: A Tiribocchi , M Durve , M Lauricella , A Montessori , D Marenduzzo , S Succi

Transcription modulates chromatin dynamics and locus configuration sampling.

Nature structural & molecular biology

Avec: Giada Forte , Adam Buckle , Shelagh Boyle , Davide Marenduzzo , Nick Gilbert , Chris A Brackley

Motility induced phase separation of deformable cells.

Soft matter

Avec: Austin Hopkins , Benjamin Loewe , Michael Chiang , Davide Marenduzzo , M Cristina Marchetti

Réseau de co-auteurs

D Marenduzzo 16 collaborations

Michael Chiang 10 collaborations

Chris A Brackley 9 collaborations

Alexander Morozov 9 collaborations

Davide Michieletto 8 collaborations

Nick Gilbert 7 collaborations

Enzo Orlandini 7 collaborations

D Michieletto 6 collaborations

C A Brackley 5 collaborations

Giada Forte 5 collaborations

E Orlandini 5 collaborations

L N Carenza 4 collaborations

G Gonnella 4 collaborations

Andrea Bonato 4 collaborations

Benjamin Loewe 4 collaborations

M Cristina Marchetti 4 collaborations

Adam Buckle 3 collaborations

Giuseppe Gonnella 3 collaborations

G Negro 3 collaborations

Dom Corbett 3 collaborations

A Tiribocchi 3 collaborations

Austin Hopkins 3 collaborations

Ciprian G Pruteanu 2 collaborations

Yair A G Fosado 2 collaborations

Giuseppe Negro 2 collaborations

Livio Nicola Carenza 2 collaborations

Fraser Mackay 2 collaborations

F Cagnetta 2 collaborations

Job H J Thijssen 2 collaborations

Francesco Cagnetta 2 collaborations

Viktor Škultéty 2 collaborations

Martin R Evans 2 collaborations

Sergey Kitaev 2 collaborations

Marco Ancona 2 collaborations

Davide Colì 2 collaborations

Ivan Maryshev 2 collaborations

Andrew B Goryachev 2 collaborations

Shelagh Boyle 2 collaborations

N Gilbert 1 collaboration

A Papantonis 1 collaboration

M C F Pereira 1 collaboration

P R Cook 1 collaboration

A Lips 1 collaboration

A Morozov 1 collaboration

W C K Poon 1 collaboration

Carlos Sacristan 1 collaboration

Kumiko Samejima 1 collaboration

Lorena Andrade Ruiz 1 collaboration

Moonmoon Deb 1 collaboration

Maaike L A Lambers 1 collaboration

Daniel Robertson 1 collaboration

Tetsuya Hori 1 collaboration

Shaun Webb 1 collaboration

Robert Kiewisz 1 collaboration

Tristan Bepler 1 collaboration

Eloïse van Kwawegen 1 collaboration

Patrik Risteski 1 collaboration

Kruno Vukušić 1 collaboration

Iva M Tolić 1 collaboration

Thomas Müller-Reichert 1 collaboration

Tatsuo Fukagawa 1 collaboration

William C Earnshaw 1 collaboration

Geert J P L Kops 1 collaboration

Matthew Kerr 1 collaboration

Graeme J Ackland 1 collaboration

Giovanni B Brandani 1 collaboration

Louise C Head 1 collaboration

Tyler N Shendruk 1 collaboration

A Bonato 1 collaboration

J Johnson 1 collaboration

M R Evans 1 collaboration

Michele Caraglio 1 collaboration

Nattaphong Rattanavirotkul 1 collaboration

Hisham Mohammed 1 collaboration

Tamir Chandra 1 collaboration

Oliver Wiese 1 collaboration

Iain Muntz 1 collaboration

Lora Boteva 1 collaboration

Filippo Conforto 1 collaboration

Peter R Cook 1 collaboration

Renato Assante 1 collaboration

John Toner 1 collaboration

G Foffano 1 collaboration

J S Lintuvuori 1 collaboration

K Stratford 1 collaboration

M E Cates 1 collaboration

John S Loveday 1 collaboration

Gavin Melaugh 1 collaboration

Rosalind J Allen 1 collaboration

M Lusic 1 collaboration

F Bonelli 1 collaboration

A Lamura 1 collaboration

Chris A Brackey 1 collaboration

Je-Kyung Ryu 1 collaboration

Céline Bouchoux 1 collaboration

Hon Wing Liu 1 collaboration

Eugene Kim 1 collaboration

Masashi Minamino 1 collaboration

Ralph de Groot 1 collaboration

Allard J Katan 1 collaboration

Frank Uhlmann 1 collaboration

Cees Dekker 1 collaboration

A Al Qanobi 1 collaboration

I Ali 1 collaboration

Elias T Friman 1 collaboration

Ilya M Flyamer 1 collaboration

Wendy A Bickmore 1 collaboration

Wilson C K Poon 1 collaboration

Aidan T Brown 1 collaboration

Susana O L Direito 1 collaboration

Daniel J M Hodgson 1 collaboration

Lucas Le Nagard 1 collaboration

Alex Lips 1 collaboration

Cait E MacPhee 1 collaboration

John R Royer 1 collaboration

Andreia F Silva 1 collaboration

Simon Titmuss 1 collaboration

M Foglino 1 collaboration

E Locatelli 1 collaboration

C N Likos 1 collaboration

Alessandro Bentivoglio 1 collaboration

Thomas Le Goff 1 collaboration

Benno Liebchen 1 collaboration

Shu Zhang 1 collaboration

Nadine Übelmesser 1 collaboration

Natasa Josipovic 1 collaboration

Johan A Slotman 1 collaboration

Henrike Johanna Gothe 1 collaboration

Eduardo Gade Gusmao 1 collaboration

Christian Becker 1 collaboration

Janine Altmüller 1 collaboration

Adriaan B Houtsmuller 1 collaboration

Vassilis Roukos 1 collaboration

Kerstin S Wendt 1 collaboration

Argyris Papantonis 1 collaboration

G Forte 1 collaboration

M Durve 1 collaboration

M Lauricella 1 collaboration

A Montessori 1 collaboration

S Succi 1 collaboration