Publications

• O. Henrich, D. Marenduzzo, K. Stratford, M. E. Cates, 'Ordering dynamics of blue phases: kinetic stabilization of an amorphous network', Proc. Natl. Acad. Sci. USA, accepted for publication (2010).
• D. Marenduzzo, C. Micheletti, E. Orlandini, 'Biopolymer organisation upon compaction', J. Phys. Condens. Matt., in press (2010).
• M. E. Cates, D. Marenduzzo, I. Pagonabarraga, J. Tailleur, 'Arrested phase separation in reproducing bacteria creates a generic route to pattern formation', Proc. Natl. Acad. Sci. USA, in press (2010).
• D. Marenduzzo, E. Orlandini, F. Seno, A. Trovato, 'Different pulling modes in DNA overstretching: a theoretical analysis', Phys. Rev. E. 81, 051926 (2010).
• C. Valeriani, R. J. Allen, D. Marenduzzo, 'Non-equilibrium dynamics of an active colloidal chucker', J. Chem. Phys. 132, 204904 (2010).
• E. Sanz, D. Marenduzzo, 'Dynamic Monte-Carlo versus Brownian dynamics: a comparison for self-diffusion and crystallization in colloidal fluids', J. Chem. Phys. 132, 194102 (2010).
• O. Henrich, D. Marenduzzo, K. Stratford, M. E. Cates, 'Domain growth in cholesteric blue phases: hybrid lattice Boltzmann simulations', Comp. Math. with Appl. 59, 2360 (2010).
• C. Barrett-Freeman, M. R. Evans, D. Marenduzzo, J. Tailleur, 'The role of noise and advection in absorbing state phase transitions', EPL 90, 16003 (2010).
• O. Henrich, D. Marenduzzo, K. Stratford, M. E. Cates, 'Thermodynamics of blue phases in electric fields', Phys. Rev. E 81, 031706 (2010).
• D. Marenduzzo, E. Orlandini, 'Hydrodynamics of non-homogeneous active gels', Soft Matter 6, 774 (2010).
• D. Marenduzzo, E. Orlandini, A. Stasiak, D. W. Sumners, L. Tubiana, C. Micheletti, 'DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting', Proc. Natl. Acad. Sci. USA 106, 22269 (2009).
• M. E. Cates, O. Henrich, D. Marenduzzo, K. Stratford, 'Lattice Boltzmann simulations of liquid crystalline fluids: active gels and blue phases', Soft Matter 5, 3791 (2009).
• P. R. Cook, D. Marenduzzo, 'Entropic organization of interphase chromosomes', J. Cell. Biol. (2009).
• D. Marenduzzo, E. Orlandini, 'Topological and entropic repulsion in biopolymers', JSTAT, L09002 (2009).
• R. Lenarcic, S. Halbedel, L. Visser, M. Shaw, L. Wu, J. Errington, D. Marenduzzo, L. W. Hamoen, 'Localization of DivIVA by targeting to negatively curved membranes', EMBO J. 28, 2272 (2009).
• D. Marenduzzo, A. Maritan, E. Orlandini, F. Seno, A. Trovato, 'Phase diagrams for DNA denaturation under stretching forces', JSTAT, L04001 (2009).
• D. Marenduzzo, 'Statistics of confined polymers and the melting of a DNA spool', Europhys. Lett. 85, 38005 (2009).
• E. Orlandini, M. E. Cates, D. Marenduzzo, L. Tubiana, J. M. Yeomans, 'Hydrodynamics of active liquid crystals: a hybrid lattice Boltzmann approach', Mol. Cryst. Liq. Cryst. 494, 293 (2008).
• C. Barrett-Freeman, M. R. Evans, D. Marenduzzo, W. C. K. Poon, 'Nonequilibrium phase transition in the sedimentation of reproducing particles', Phys. Rev. Lett. 101, 100602 (2008).
• M. E. Cates, S. M. Fielding, D. Marenduzzo, E. Orlandini, J. M. Yeomans, 'Shearing active gels close to the isotropic-nematic transition', Phys. Rev. Lett. 101, 068102 (2008).
• C. Micheletti, D. Marenduzzo, E. Orlandini, D. W. Sumners, 'Simulations of knotting in confined DNA rings', Biophys. J. 95, 3591 (2008).
• D. Marenduzzo, 'Computer simulations of DNA packing inside bacteriophages: elasticity, electrostatics and entropy', Computational and Mathematical Methods in Medicine 9, 317 (2008).
• I. Ali, D. Marenduzzo, J. M. Yeomans, 'Ejection dynamics from viral capsids: effect of solvent quality', Biophys. J. 94, 4159 (2008).
• G. P. Alexander, D. Marenduzzo, 'Cubic blue phases in electric fields', Europhys. Lett. 81, 66004 (2008).
• D. Marenduzzo, E. Orlandini, M. E. Cates, J. M. Yeomans, 'Lattice Boltzmann simulations of spontaneous flow in active liquid crystals: the role of boundary conditions', J. Non-Newtonian Fluid Mech. 149, 56 (2008).
• D. Marenduzzo, E. Orlandini, 'Dynamics of fibers growing inside soft vesicles', Europhys. Lett. 80, 488004 (2007).
• D. Marenduzzo, E. Orlandini, M. E. Cates, J. M. Yeomans, 'Steady-state hydrodynamic instabilities of active liquid crystals: Hybrid Lattice Boltzmann simulations', Phys. Rev. E 76, 031921 (2007).
• N. J. Burroughs, D. Marenduzzo, 'Non-equilibrium driven motion in actin networks: comet tails and moving beads', Phys. Rev. Lett. 98, 238302 (2007).
• D. Marenduzzo, E. Orlandini, J. M. Yeomans, 'Hydrodynamics and rheology of active liquid crystals: a numerical investigation', Phys. Rev. Lett. 98, 118102 (2007).
• A. K. Chattopadhyay, D. Marenduzzo, 'Dynamics of anchored polymers under an oscillating force', Phys. Rev. Lett. 98, 088101 (2007).
• D. Marenduzzo, I. Faro-Trindade, P. R. Cook, 'What are the molecular ties maintaining genomic loops ?', Trends in Genetics 23, 126 (2007).
• E. Orlandini, D. Marenduzzo, J. M. Yeomans, 'Viscoelastic flows of cholesteric liquid crystals', Mol. Cryst. Liq. Cryst. 465, 1 (2007).
• P. Bertoncello, I. Ciani, D. Marenduzzo, P. R. Unwin, 'Partitioning of redox species into ultra-thin nafion films: theory and experimental measurement', J. Phys. Chem. C 111, 294 (2007).
• D. Marenduzzo, K. Finan, P. R. Cook, 'The depletion attraction: an under-appreciated force driving cellular organization', J. Cell. Biol. 175, 681 (2006).
• N. M. Toan, D. Marenduzzo, P. R. Cook, C. Micheletti, 'Depletion effects and loop formation in self-avoiding polymers', Phys. Rev. Lett. 97, 178302 (2006).
• D. Marenduzzo, E. Orlandini, 'Entropic approach curves of a polymer of fixed topology', Europhys. Lett. 76, 519 (2006).
• N. Sulaiman, D. Marenduzzo, J. M. Yeomans, 'Electric field effects on an isotropic droplet dispersed in a nematic liquid crystal cell', Phys. Rev. E 74, 041708 (2006).
• D. R. Daniels, D. Marenduzzo, M. S. Turner, 'Stall, spiculate or runaway - the fate of fibers growing towards fluctuating membranes', Phys. Rev. Lett. 97, 098101 (2006).
• A. Rosa, D. Marenduzzo, S. Kumar,'Stretching of a self-interacting semiflexible polymer', Europhys. Lett. 75, 818 (2006).
• I. Ali, D. Marenduzzo, J. M. Yeomans, 'Polymer packaging and ejection in viral capsids: shape matters', Phys. Rev. Lett. 96, 208102 (2006).
• D. Marenduzzo, E. Orlandini, J. M. Yeomans, 'Permeative flows in cholesterics: shear and Poiseuille flows', J. Chem. Phys. 124, 204906 (2006).
• D. Marenduzzo, C. Micheletti, P. R. Cook, 'Entropy-driven genome organisation', Biophys. J. 90, 3712 (2006).
• J. R. Banavar, M. Cieplak, A. Flammini, T. X. Hoang, R. D. Kamien, T. Lezon, D. Marenduzzo, A. Maritan, F. Seno, Y. Snir, A. Trovato, 'Geometry of proteins: hydrogen bonding, sterics and marginally compact tubes', Phys. Rev. E 73, 031921 (2006).
• J. F. Stromer, D. Marenduzzo, C. V. Brown, J. M. Yeomans, E. P. Raynes, 'Electric-field induced disclination migration in a Grandjean-Cano wedge', J. Appl. Phys. 99, 064911 (2006).
• N. J. Burroughs, D. Marenduzzo, 'Growth of a semiflexible polymer close to a fluctuating obstacle: application to cytoskeletal actin fibres and test of ratchet models', J. Phys.: Condens. Matt. 18, S357 (2006).
• C. Micheletti, D. Marenduzzo, E. Orlandini, D. W. Sumners, 'Knotting of random ring polymers in confined spaces', J. Chem. Phys. 124, 064903 (2006).
• M. Bon, D. Marenduzzo, P. R. Cook, 'Modelling a self-avoiding chromatin loop: relation to the packing problem, action-at-a-distance, and nuclear context', Structure 14, 197 (2006).
• N. J. Burroughs, D. Marenduzzo, 'Three-dimensional dynamic Monte-Carlo simulations of elastic actin-like ratchets', J. Chem. Phys. 123, 174908 (2005).
• D. Marenduzzo, T. X. Hoang, F. Seno, M. Vedruscolo, A. Maritan, 'On the form of growing strings', Phys. Rev. Lett. 95, 098103 (2005).
• A. Dupuis, D. Marenduzzo, E. Orlandini, J. M. Yeomans, 'Rheology of cholesteric blue phases', Phys. Rev. Lett. 95, 097801 (2005).
• D. Marenduzzo, E. Orlandini, J. M. Yeomans, 'Switching hydrodynamics of multi-domain, twisted nematic, liquid crystal devices', Europhys. Lett. 71, 604 (2005).
• D. Marenduzzo, A. Dupuis, E. Orlandini, J. M. Yeomans, 'Lattice Boltzmann simulations of cholesteric liquid crystals: permeative flows, doubly twisted textures and cubic blue phases', Mol. Cryst. Liq. Cryst. 435, 835 (2005).
• E. Orlandini, D. Marenduzzo, J. M. Yeomans, 'Shear dynamics in cholesterics', Comp. Phys. Comm. 169, 122 (2005).
• I. Ali, D. Marenduzzo, C. Micheletti, J. M. Yeomans, 'A coarse grained model for DNA and polymer packaging: statics and dynamics', J. Theor. Med. 6, 115 (2005).
• N. M. Toan, D. Marenduzzo, C. Micheletti, 'Inferring a polymer's effective diameter from its stretching response', Biophys. J. 89, 80 (2005).
• D. Marenduzzo, C. Micheletti, H. Seyed-allaei, A. Trovato, A. Maritan, 'Continuum model for polymers with finite thickness', J. Phys. A 38, L277 (2005), online version.
• A. Rosa, T. X. Hoang, D. Marenduzzo, A. Maritan, 'A new interpolation formula for semiflexible polymers', Biophys. Chem. 115, 251 (2005).
• A. Dupuis, D. Marenduzzo, J. M. Yeomans, 'Numerical calculations of the phase diagram of cubic blue phases in cholesteric liquid crystals', Phys. Rev. E 71, 011703 (2005).
• D. Marenduzzo, A. Flammini, A. Trovato, J. R. Banavar, A. Maritan, 'Physics of thick polymers', J. Pol. Sci. B 43, 650 (2005).
• C. Micheletti, D. Marenduzzo, 'Modelling DNA as a flexible thick polymer: application to DNA elasticity and packaging thermodynamics', in 'Physical and Numerical Models in Knot Theory', Calvo, Rawdon and Stasiak Editors, World Scientific Press, Singapore (2005).
• I. Ali, D. Marenduzzo, J. M. Yeomans, 'Dynamics of polymer packaging', J. Chem. Phys. 121, 8635 (2004).
• D. Marenduzzo, A. Maritan, A. Rosa, F. Seno, 'Step-wise unfolding of collapsed polymers', Eur. Phys. J. E 15, 83 (2004).
• D. Marenduzzo, E. Orlandini, J. M. Yeomans, 'Interplay between shear flow and elastic deformations in liquid crystals', J. Chem. Phys. 121, 582 (2004).
• D. Marenduzzo, E. Orlandini, J. M. Yeomans, 'Permeative flows in cholesteric liquid crystals', Phys. Rev. Lett. 92, 188301 (2004).
• C. Denniston, D. Marenduzzo, E. Orlandini, J. M. Yeomans, 'Lattice Boltzmann simulations of three-dimensional liquid crystal hydrodynamics', Phil. Trans. R. Soc. Lond. A 362, 1745 (2004).
• A. Rosa, T. X. Hoang, D. Marenduzzo, A. Maritan, 'Elasticity of semiflexible polymers with and without self-interactions', Macromolecules 36, 10095 (2003).
• D. Marenduzzo, E. Orlandini, J. M. Yeomans, 'Rheology of distorted nematic liquid crystals', Europhys. Lett. 64, 406 (2003)
• D. Marenduzzo, C. Micheletti, 'Thermodynamics of DNA packaging inside a viral capsid: The role of DNA intrinsic thickness', J. Mol. Biol. 330, 485 (2003).
• J. R. Banavar, A. Flammini, D. Marenduzzo, A. Maritan, A. Trovato, 'Tubes near the edge of compactedness and folded protein structures', J. Phys.: Cond. Matt. 15, S1787 (2003).
• A. Rosa, D. Marenduzzo, A. Maritan, F. Seno, 'Mechanical unfolding of directed polymers in a poor solvent: critical exponents', Phys. Rev. E 67, 041802 (2003).
• D. Marenduzzo, A. Maritan, A. Rosa, F. Seno, 'Stretching of a polymer below the theta point'. Phys. Rev. Lett. 90, 088301 (2003).
• J. R. Banavar, A. Flammini, D. Marenduzzo, A. Maritan, A. Trovato, 'Geometry of compact tubes and folded protein structures', ComPlexUs 1, 4 (2003).
• S. M. Bhattacharjee, D. Marenduzzo, 'DNA sequence from the unzipping force ? One mutation problem', J. Phys. A 35, L349 (2002).
• D. Marenduzzo, A. Maritan, F. Seno, 'Force-induced unfolding of a homopolymer on a fractal lattice: exact results versus mean-field predictions', J. Phys. A 35, L233 (2002).
• D. Marenduzzo, S. M. Bhattacharjee, A. Maritan, E. Orlandini, F. Seno, 'Dynamical scaling of the DNA unzipping transition', Phys. Rev. Lett. 88, 028102 (2002).
• E. Orlandini, S. M. Bhattacharjee, D. Marenduzzo, A. Maritan, F. Seno, 'Mechanical denaturation of DNA: existence of a low-temperature denaturation', J. Phys. A 34, L751 (2001).
• D. Marenduzzo, A. Trovato, A. Maritan, 'Phase diagram of force-induced DNA unzipping in exactly solvable models', Phys. Rev. E 64, 031901 (2001).

Theses

• 'Phases of polymers and biopolymers', PhD thesis (October 2002, SISSA/ISAS, Trieste, Italy), supervisor: Prof. A. Maritan.
• 'Thermal and mechanical denaturation of DNA', MD thesis (October 2000, SISSA/ISAS, Trieste, Italy), supervisor: Prof. A. Maritan.
• 'Quantum field theories of monopoles and charges', BS thesis (in italian, March 1998, Padova, Italy), supervisor: Prof. P. A. Marchetti.