User profiles for D. Marenduzzo
Davide MarenduzzoUniversity 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 …
… 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
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 …
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 …
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…
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 …
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 …
… 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 …
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
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 …
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 …
particles via the “depletion” mechanism. High enough polymer concentrations lead to phase …
Continuum theory of phase separation kinetics for active Brownian particles
… 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 …
transferable to the Pe シ 100 case where our kinetic studies will be conducted. Mapping …