STATISTICAL MECHANICS AND MOLECULAR BIOLOGY

Chromatin 3D organization

xcoloc.jpg Chromosomes have a complex 3D spatial organization serving vital functional purposes, where distant DNA sites colocalize to form 'compartments'. The principles governing such a self-organization remain, though, elusive. We proposed a Statistical Mechanics model where chromosomes conformations are established by their interactions, in particular, with specific DNA-binding molecular factors. We showed that such interactions produce spontaneously definite conformational classes (with their 'scaling properties') and induce switch-like architectural transformations (via 'phase transitions') associated to, e.g., loci colocalization, chromosomal looping and territories. Our scenario can reconcile within a single framework current FISH and Hi-C experimental results.


colocpd.jpg Selected references:

  • M. Barbieri et al., "Complexity of chromatin folding is captured by the strings and binders switch model" ,PNAS 109, 16173 (2012)
  • M. Nicodemi et al., "Thermodynamic pathways to genome spatial organization in the cell nucleus" ,Biophys.Jou. 96, 2168 (2009)
  • M. Nicodemi, B. Panning, and A. Prisco, "A thermodynamic switch for chromosome colocalization", Genetics 179, 717 (2008)


    • Symmetry Breaking at X-Chromosome Inactivation

    symbreak.jpg
    In female mammal embryo, X-Chromosome Inactivation is the vital process whereby each cell inactivates one, randomly selected X to equalise X products w.r.t. males. Such a chromosome wide stochastic regulation has attracted substantial interests: it is unknown how the X's undergo random, yet opposite fates. We proposed a possible physical explanation: a Symmetry Breaking mechanism, with a related set of new 'particles' involved (see Figure) and a corresponding phase diagram. This scenario is supported by recent experiments.


    sbdiag.jpg Selected references:

  • M. Nicodemi and A. Prisco, "A Symmetry Breaking Model for X Chromosome Inactivation", Phys. Rev. Lett. 98, 108104 (2007)
  • A. Scialdone and M. Nicodemi, "Mechanics and Dynamics of X-Chromosome Pairing at X Inactivation", PLoS Comp.Bio. 4, e1000244 (2008)
  • A. Scialdone et al., "Conformation Regulation of the X Chromosome Inactivation Center: A Model" ,PLoS Comp. Bio. 7, e1002229 (2011)



    • STATISTICAL MECHANICS OF COMPLEX SYSTEMS
    IN PHYSICS

    Statistical Mechanics of Granular Media

    scaling.jpg Granular media are the second most dealt with material in human activities after water. As they are non-thermal systems (having zero kinetic energy), standard thermodynamics does not apply and a first principles theory for their description is still missing. We considered the idea that they could be described via a generalized Statistical Mechanics approach where time averages are replaced by suitable ensemble averages, at least in the limit of vanishing drive. We have been among the very first to test such a scenario in analytical and computer models and to derive the system phase diagram.


    gmpd.jpg Selected references:

  • M. Nicodemi, "Dynamical response functions in models of vibrated granular media", Phys. Rev. Lett. 82, 3734 (1999)
  • P. Richard, M. Nicodemi, R. Delannay, P. Ribiere, D. Bideau, "Slow relaxation and compaction of granular systems", Nature Materials 4, 121 (2005)
  • M. Pica Ciamarra, A. Coniglio, and M. Nicodemi,"Thermodynamics and Statistical Mechanics of Dense Granular Media", Phys. Rev. Lett. 97, 158001 (2006)

    • Rheology of Granular Media

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    The rheology of non-thermal systems such as granular suspensions is currently focus of intense research for both fundamental science and practical applications. We explored the nature of the system flow diagram and its flow regimes and found they are separated by sharp, yet stochastic transitions: (a) disordered grain flow, (b) ordered grain flow and (c) grain jamming. We discovered that disordered flow has an Ostwald-de Waele-type power-law shear-stress constitutive relation, while a nearly solid plug appears in ordered flow.


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    Selected references:

  • D.S. Grebenkov, M. Pica Ciamarra, M. Nicodemi, A. Coniglio, "Flow, ordering, and jamming of sheared granular suspensions" ,Phys. Rev. Lett. 100, 078001 (2008)
  • S. Brand, R.C. Ball, M. Nicodemi,"Stochastic transitions and jamming in granular pipe flow", Phys. Rev. E 83, 031309 (2011)




    • Last update 20/01/2010