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Workshops

Mesoscopic Modeling in Physics of Molecular and Cell Biology

October 10, 2016 to October 13, 2016
Location : Toulouse, France (CECAM-FR-GSO) - CEMES campus

Organisers

  • Nicolas DESTAINVILLE (Université Toulouse III-Paul Sabatier, France)
  • Manoel MANGHI (Université Toulouse III-Paul Sabatier, France)
  • John PALMERI (CNRS & Université de Montpellier, France)
  • Roland R. NETZ (Free University of Berlin, Germany)
  • Aloïs WÜRGER (Université de Bordeaux, France)

Supports

   CECAM

Laboratoire d'excellence NEXT

IRSAMC federation

L2C laboratory

Description

 

Program & Practical information

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With the involvement of an increasing number of physicists in the field of mesocsopic modeling of molecular and cellular biological processes, huge progress has been accomplished in the two past decades.

However many questions remain unsolved and the spectacular development of experimental techniques (e.g. as microscopy at super-resolution and single molecule experiments) promises that the number of open questions will keep growing in the future.

This workshop intends to gather theoretical physicists specialized in statistical physics and soft matter, and working on different subjects related to molecular and cell biology, but using very similar paradigms and tools. They belong to:

  • coarse-grained models (where a small group of atoms is modeled as one particle)
  • effective mesoscopic models (where elementary particles are as large as molecules or subparts of macromolecules)
  • analytical approaches using mesoscopic models from the statistical physics, eventually coupled to hydrodynamics, elasticity, or electrostatics.

The adequate numerical techniques are Monte Carlo simulations, Brownian dynamics with or without hydrodynamic interactions, metadynamics, lattice-Boltzmann methods or dissipative particle dynamics.

Standard analytical tools are commonly used in this field, such as Markov chains, Langevin & Smoluchowski equations, elasticity theory, field-theoretic approaches, hydrodynamics, charged fluids, etc. 

One important goal of this workshop is to focus on the application of these various techniques to the physical mechanisms, depending on the time or the length scales under study and the biological issue.

The molecular or supra-moecular consituents of a cell, which are modeled using these physical techniques can be categorized as follows (without exhaustivity):

  • cell membranes and their organizaition (micro-patterning, rafts collective signal transduction, translocation) [1-11]
  • micro-flagella, responsible for propulsion of certain cells [12-14]
  • the cell nucleus and the spatial organization of genes [15-18]
  • nucleic acids, nucleosomes and chromatin in bacteria eukaryotes or virus [19-27]
  • the cytoskeleton and its consitutants as actin, micro-tubules, molecular motors [28-31]

By promoting debates on the recent progress in these related topics, we expect to favor cross-fertilization between european and world-wide actors in this field. Young researchers (and Ph.D. students) making up the next generation are also strongly welcome and some of them invited.

References

[1] B. Alberts, et al., Molecular biology of the cell (Garland Publishing, New York, 2002).
[2] N. Destainville, F. Dumas, L. Salomé, Journal of Chemical Biology 1, 37 (2008).
[3] P. F. Lenne, A. Nicolas, Soft Matter 5, 2841 (2009).
[4] S.W. Hell, J. Wichmann, Optics Letters 19, 780 (1994).
[5] D. Lingwood, K. Simons, Science 327, 46 (2010).
[6] R. Phillips, T. Ursell, P. Wiggins, P. Sens, Nature 459, 379 (2009).
[7] N. Destainville, Europhysics Letters 91, 58001 (2010).
[8] T. Gurry, O. Kahramanogullari, R.G. Endres, PLoS ONE 4, e6148 (2009).
[9] P.J. Photos, H. Bermudez, H. Aranda-Espinoza, J. Shillcock, D.E. Discher, Soft Matter 3, 364 (2007)
[10] S. Buyukdagli, M. Manghi, J. Palmeri, Physical Review Letters 105, 158103 (2010).
[11] M. Muthukumar, Polymer Translocation, (Taylor and Francis, Boca Raton, 2011).
[12] M. Manghi, X. Schlagberger, R.R. Netz, Physical Review Letters 96, 068101 (2006).
[13] S.J. Ebbens, J.R. Howse, Soft Matter 6, 726 (2010).
[14] J. Elgeti, R.G. Winkler, G. Gompper, Reports on Progress in Physics 78, 056601 (2015).
[15] P. Fraser, W. Bickmore, Nature 447, 413 (2007).
[16] E. Lieberman-Aiden et al., Science 326, 289 (2009).
[17] A. Rosa A, R. Everaers, PLoS Computational Biology 4, e1000153 (2008).
[18] J. Mateos-Langerak, et al., Proceedings of the National Academy of Sciences USA 106, 3812 (2009).
[19] G.N. Hayrapetyan, et al., Physical Review Letters 113, 068101 (2014).
[20] J. Yan, J. F. Marko. Physical Review Letters 93, 108108 (2004).
[21] M. Manghi, J. Palmeri, N. Destainville, Journal of Physics: Condensed Matter 21, 034104 (2009).
[22] H. Schiessel, Journal of Physics: Condened. Matter 15, R699 (2003). 7
[23] A. Bancaud, at al., Molecular Cell 27, 135 (2007).
[24] O. BĂ©nichou, C. Chevalier, B. Meyer, R. Voituriez, Physical Review Letters 106, 038102 (2011).
[25] P. Grayson, L. Han, T. Winther, R. Phillips., Proceedings of the National Academy of Sciences USA, 104,14652 (2007).
[26] A. Siber, A.L. Bozicc, R. Podgornik, Physical Chemistry Chemical Physics 14, 37466 (2012).
[27] A.A. Lawati, I. Ali, M. Al Barwani, PLoS ONE 8, e52958 (2013).
[28] I. Neri, N. Kern, A. Parmeggiani, New Journal of Physics 15, 085005 (2013).
[29] N. Destainville, Soft Matter 4, 1288 (2008).
[30] D Pantaloni, C. Le Clainche, M.F. Carlier, Science 292, 1502 (2001).
[31] S. Etienne-Manneville, Traffic 5, 470 (2004).