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List of works by Davide Marenduzzo

A Coarse Grained Model for DNA and Polymer Packaging: Statics and Dynamics

A growing bacterial colony in two dimensions as an active nematic

scientific article published in Nature Communications

A minimal physical model captures the shapes of crawling cells ⬇️

scientific article published on 21 January 2015

A new interpolation formula for semiflexible polymers

scientific article published on 07 January 2005

A one-dimensional statistical mechanics model for nucleosome positioning on genomic DNA ⬇️

scientific article published on 12 February 2016

A self-quenched defect glass in a colloid-nematic liquid crystal composite

scientific article published on 01 October 2011

A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction

scientific article published on 07 January 2015

A single nucleotide resolution model for large-scale simulations of double stranded DNA.

scientific article published on 15 November 2016

Active Growth and Pattern Formation in Membrane-Protein Systems

scientific article published on 01 June 2018

Active Model H: Scalar Active Matter in a Momentum-Conserving Fluid ⬇️

scientific article published on 28 October 2015

Active polar fluid flow in finite droplets

scientific article published on 18 February 2014

Activity-induced clustering in model dumbbell swimmers: the role of hydrodynamic interactions ⬇️

scientific article published on 25 August 2014

Activity-induced phase separation and self-assembly in mixtures of active and passive particles ⬇️

scientific article published on 06 January 2015

Anchoring-driven spontaneous rotations in active gel droplets

scientific article published on 01 September 2017

Biopolymer organization upon confinement.

scientific article published on 28 June 2010

Bistable defect structures in blue phase devices.

scientific article

Bulk rheology and microrheology of active fluids

scientific article published on 04 October 2012

Chemotactic clusters in confined run-and-tumble bacteria: a numerical investigation.

scientific article

Chemotactic sensing towards ambient and secreted attractant drives collective behaviour of E. coli.

scientific article

Clustering and Pattern Formation in Chemorepulsive Active Colloids. ⬇️

scientific article published on 16 December 2015

Colloidal Spherocylinders at an Interface: Flipper Dynamics and Bilayer Formation

scientific article published on 06 July 2017

Colloidal templating at a cholesteric-oil interface: assembly guided by an array of disclination lines

scientific article published on 30 April 2013

Colloids in a bacterial bath: simulations and experiments

scientific article published in 2011

Colloids in active fluids: anomalous microrheology and negative drag.

scientific article published on 11 July 2012

Colloids in cholesterics: size-dependent defects and non-stokesian microrheology

scientific article published on 22 October 2010

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

scientific article published on 01 October 2021

Confined cubic blue phases under shear.

scientific article published on 27 June 2012

Continuum Theory of Phase Separation Kinetics for Active Brownian Particles

scientific article published in Physical Review Letters

Contractile and chiral activities codetermine the helicity of swimming droplet trajectories.

scientific article published on 17 April 2017

Correction: Curvature-driven positioning of Turing patterns in phase-separating curved membranes

scientific article published on 01 April 2016

Curvature-driven positioning of Turing patterns in phase-separating curved membranes

scientific article published on 24 March 2016

Cytoplasmic streaming in plant cells: the role of wall slip.

scientific article published on 15 February 2012

DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting

scientific article

Depletion effects and loop formation in self-avoiding polymers

scientific article published on 26 October 2006

Different pulling modes in DNA overstretching: A theoretical analysis

article

Dry active turbulence in a model for microtubule-motor mixtures

scientific article published on 12 July 2019

Dynamic Monte Carlo versus Brownian dynamics: A comparison for self-diffusion and crystallization in colloidal fluids

scientific article published on 01 May 2010

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

scientific article published on 19 August 2019

Dynamical Scaling and Phase Coexistence in Topologically Constrained DNA Melting.

scientific article published on 12 September 2017

Dynamical scaling of the DNA unzipping transition

scientific article published on 28 December 2001

Dynamics of an anchored polymer molecule under an oscillating force

scientific article published on 20 February 2007

Dynamics of polymer packaging.

scientific article published in November 2004

Dynamics of self-threading ring polymers in a gel. ⬇️

scientific article published in August 2014

Effect of DNA conformation on facilitated diffusion.

scientific article published on April 2013

Ejection dynamics of polymeric chains from viral capsids: effect of solvent quality

scientific article

Electric field controlled columnar and planar patterning of cholesteric colloids ⬇️

scientific article published on 30 April 2015

Enhanced diffusion of tracer particles in dilute bacterial suspensions.

scientific article

Entropic elasticity and dynamics of the bacterial chromosome: A simulation study.

scientific article published in July 2017

Entropic organization of interphase chromosomes.

scientific article published on 14 September 2009

Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains. ⬇️

scientific article published in March 2017

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin.

scientific article published on 7 November 2017

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

scientific article (publication date: 9 December 2016)

Extrusion without a motor: a new take on the loop extrusion model of genome organization. ⬇️

scientific article published on 4 January 2018

Facilitated diffusion on confined DNA

scientific article published on 22 February 2012

Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity

scientific article published on 17 October 2012

Filling an Emulsion Drop with Motile Bacteria ⬇️

scientific article published on 22 December 2014

Flow of Deformable Droplets: Discontinuous Shear Thinning and Velocity Oscillations

scientific article published on 15 November 2017

Genome organization: experiments and modeling

scientific article published on 2 February 2017

HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types.

scientific article published on 20 April 2018

Hydrodynamic instabilities in active cholesteric liquid crystals ⬇️

scientific article published on 24 April 2017

Hydrodynamic oscillations and variable swimming speed in squirmers close to repulsive walls

scientific article published on 01 September 2016

Influence of ions on genome packaging and ejection: a molecular dynamics study

article published in 2011

Interfacial self-assembly of a bacterial hydrophobin

scientific article published on 13 April 2015

Interplay between shear flow and elastic deformations in liquid crystals.

scientific article published in July 2004

Intracellular facilitated diffusion: searchers, crowders, and blockers.

scientific article

Is the kinetoplast DNA a percolating network of linked rings at its critical point? ⬇️

scientific article published on 13 May 2015

Kinetic theory of pattern formation in mixtures of microtubules and molecular motors.

scientific article published in February 2018

Knotting of random ring polymers in confined spaces.

scientific article

Lateral dynamics of proteins with polybasic domain on anionic membranes: a dynamic Monte-Carlo study.

scientific article published on March 2011

Lattice Boltzmann algorithm for three-dimensional liquid-crystal hydrodynamics

scientific article published on 01 August 2004

Lattice Boltzmann algorithm to simulate isotropic-nematic emulsions.

scientific article published on 27 October 2006

Light-induced self-assembly of active rectification devices ⬇️

scientific article

Localisation of DivIVA by targeting to negatively curved membranes

scientific article published on 28 May 2009

Mechanical unfolding of directed polymers in a poor solvent: critical exponents

scientific article published on 29 April 2003

Mechanically Driven Growth of Quasi-Two-Dimensional Microbial Colonies

scientific article published on 14 October 2013

Microfluidic flow of cholesteric liquid crystals ⬇️

scientific article published on 27 October 2016

Mixtures of Blue Phase Liquid Crystal with Simple Liquids: Elastic Emulsions and Cubic Fluid Cylinders

scientific article published on 01 July 2018

Modelling the effect of myosin X motors on filopodia growth.

scientific article published on 27 January 2014

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS ⬇️

scientific article published on 01 April 2014

Monte Carlo and event-driven dynamics of Brownian particles with orientational degrees of freedom.

scientific article published in September 2011

Motility of active nematic films driven by "active anchoring"

scientific article published on 01 September 2017

Non-equilibrium dynamics of an active colloidal "chucker".

scientific article published in May 2010

Non-equilibrium effects of molecular motors on polymers

scientific article published on 01 July 2019

Non-equilibrium phase transition in a model for supercoiling-dependent DNA transcription

scientific article published on 01 May 2018

Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes.

scientific article published on January 2011

Nonequilibrium Chromosome Looping via Molecular Slip Links

scientific article published on 26 September 2017

Nonequilibrium phase transition in the sedimentation of reproducing particles

scientific article published on 05 September 2008

Nonequilibrium-driven motion in actin networks: comet tails and moving beads.

scientific article published on 5 June 2007

Nonlinear dynamics and rheology of active fluids: simulations in two dimensions

scientific article published on 13 April 2011

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization.

scientific article

Numerical calculations of the phase diagram of cubic blue phases in cholesteric liquid crystals.

scientific article published on 20 January 2005

Pattern Formation in Polymerizing Actin Flocks: Spirals, Spots, and Waves without Nonlinear Chemistry ⬇️

scientific article published on 30 November 2016

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

scientific article published on 28 August 2020

Pattern formation in chemically interacting active rotors with self-propulsion ⬇️

scientific article published on 15 August 2016

Permeative flows in cholesteric liquid crystals.

scientific article published on 4 May 2004

Permeative flows in cholesterics: shear and Poiseuille flows.

scientific article published in May 2006

Phase behaviour of active Brownian particles: the role of dimensionality

scientific article published on 01 March 2014

Phase diagram of force-induced DNA unzipping in exactly solvable models

scientific article published on 14 August 2001

Phase separation and rotor self-assembly in active particle suspensions

scientific article published on 5 March 2012

Phoretic Interactions Generically Induce Dynamic Clusters and Wave Patterns in Active Colloids

scientific article published on 28 June 2017

Polymer Packaging and Ejection in Viral Capsids: Shape Matters

scientific article published in Physical Review Letters

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci

scientific article published on 18 October 2018

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

scientific article

Quantifying disorder through conditional entropy: an application to fluid mixing

scientific article

Rheology and microrheology of deformable droplet suspensions

scientific article published on 01 November 2018

Rheology of cholesteric blue phases.

scientific article published on 23 August 2005

Rheology of distorted nematic liquid crystals

Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses

scientific article published on 08 August 2017

Role of Correlations in the Collective Behavior of Microswimmer Suspensions

scientific article published in Physical Review Letters

Scalar φ4 field theory for active-particle phase separation

scientific article published in Nature Communications

Self-assembling knots of controlled topology by designing the geometry of patchy templates.

scientific article

Self-assembly and nonlinear dynamics of dimeric colloidal rotors in cholesterics

scientific article published on 23 December 2011

Self-assembly of colloid-cholesteric composites provides a possible route to switchable optical materials ⬇️

scientific article published on 18 June 2014

Shaping epigenetic memory via genomic bookmarking

scientific article published on 28 November 2017

Shear dynamics in cholesterics

article

Shear dynamics of an inverted nematic emulsion ⬇️

scientific article published in October 2016

Shearing self-propelled suspensions: arrest of coarsening and suppression of giant density fluctuations

scientific article published on 29 September 2011

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

scientific article

Simulating topological domains in human chromosomes with a fitting-free model

scientific article published on September 2016

Soft matter science and the COVID-19 pandemic

scientific article published on 10 September 2020

Space exploration by the promoter of a long human gene during one transcription cycle

scientific article published on 8 January 2013

Spiral and never-settling patterns in active systems

scientific article published on 17 January 2014

Spontaneous flow in polar active fluids: the effect of a phenomenological self propulsion-like term

scientific article published on 14 January 2016

Spontaneous motility of passive emulsion droplets in polar active gels

scientific article published on 26 August 2014

Spontaneous symmetry breaking in active droplets provides a generic route to motility.

scientific article

Stall, spiculate, or run away: The fate of fibers growing towards fluctuating membranes.

scientific article published on 29 August 2006

Steady-state hydrodynamic instabilities of active liquid crystals: Hybrid lattice Boltzmann simulations

scientific article published on 24 September 2007

Stepwise unfolding of collapsed polymers.

scientific article

Stochastic Model of Supercoiling-Dependent Transcription ⬇️

scientific article published on 27 June 2016

Stretching of a polymer below the theta point

scientific article published on 25 February 2003

Switching dynamics in cholesteric liquid crystal emulsions

scientific article published in August 2017

Switching hydrodynamics in liquid crystal devices: a simulation perspective

scientific article published on July 2014

Switching hydrodynamics in multi-domain, twisted nematic, liquid-crystal devices

The Bacterial Hydrophobin BslA is a Switchable Ellipsoidal Janus Nanocolloid

scientific article published on 17 September 2015

The depletion attraction: an underappreciated force driving cellular organization.

scientific article published on December 2006

Thermodynamics of DNA packaging inside a viral capsid: the role of DNA intrinsic thickness

scientific article published on 01 July 2003

Thermodynamics of blue phases in electric fields.

scientific article published on 22 March 2010

Three-dimensional dynamic Monte Carlo simulations of elastic actin-like ratchets.

scientific article published in November 2005

Topological constraints strongly affect chromatin reconstitution in silico.

scientific article published on 28 November 2014

Topological friction strongly affects viral DNA ejection

scientific article

Topological patterns in two-dimensional gel electrophoresis of DNA knots ⬇️

scientific article

Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations

article

Viscoelastic Flows of Cholesteric Liquid Crystals

What are the molecular ties that maintain genomic loops?

scientific article published on 5 February 2007

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