User profiles for D. Marenduzzo

Davide Marenduzzo

University of Edinburgh
Verified email at ph.ed.ac.uk
Cited by 15329

[HTML][HTML] The depletion attraction: an underappreciated force driving cellular organization

D Marenduzzo, K Finan, PR Cook - The Journal of cell biology, 2006 - ncbi.nlm.nih.gov
… 1 come into contact, D and d are the diameters of the large and small spheres, n the volume
D thus determines the scale of the attraction (as d, n, and T are usually constant). Results …

Polymers with spatial or topological constraints: Theoretical and computational results

C Micheletti, D Marenduzzo, E Orlandini - Physics Reports, 2011 - Elsevier
In this review, we provide an organized summary of the theoretical and computational results
that are available for polymers subject to spatial or topological constraints. Because of the …

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

PR Cook, D Marenduzzo - Nucleic acids research, 2018 - academic.oup.com
… In Figure 4Ai, e acts on both d and p, and it is easy to imagine that d and p initiate coordinately
because the two polymerases involved sit side-by-side in the same factory. (iii) Promoters …

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

…, PR Cook, D Marenduzzo - Proceedings of the …, 2013 - National Acad Sciences
… (D) Both the fraction of beads in clusters and average cluster size increase with time (two
polymerases or two NFκB complexes form one cluster if center-to-center distance is <36 nm). (E…

[HTML][HTML] Entropy-driven genome organization

D Marenduzzo, C Micheletti, PR Cook - Biophysical journal, 2006 - cell.com
… The attractive energy at contact is ∼3/2(D/d)nk B T, where D and d are the diameters of the
large and small spheres, n is the volume fraction of the small spheres, k B is the Boltzmann …

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

…, S Kelly, PR Cook, D Marenduzzo - Nucleic acids …, 2016 - academic.oup.com
… gives further details) with a lower f d value, presumably because gaps between successive
… S2A), the contact map, rosettogram and f d all point to a more disorganized structure, which …

Arrested phase separation in reproducing bacteria creates a generic route to pattern formation

ME Cates, D Marenduzzo… - Proceedings of the …, 2010 - National Acad Sciences
We present a generic mechanism by which reproducing microorganisms, with a diffusivity
that depends on the local population density, can form stable patterns. For instance, it is …

Pattern formation in self-propelled particles with density-dependent motility

FDC Farrell, MC Marchetti, D Marenduzzo, J Tailleur - Physical review letters, 2012 - APS
We study the behavior of interacting self-propelled particles, whose self-propulsion speed
decreases with their local density. By combining direct simulations of the microscopic model …

Phase separation and rotor self-assembly in active particle suspensions

…, ME Cates, D Marenduzzo… - Proceedings of the …, 2012 - National Acad Sciences
Adding a nonadsorbing polymer to passive colloids induces an attraction between the
particles via the “depletion” mechanism. High enough polymer concentrations lead to phase …

Continuum theory of phase separation kinetics for active Brownian particles

J Stenhammar, A Tiribocchi, RJ Allen, D Marenduzzo… - Physical review …, 2013 - APS
… We thus assume that v ゙ and D ゙ obtained from the (homogeneous) Pe シ 40 system are
transferable to the Pe シ 100 case where our kinetic studies will be conducted. Mapping …