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SUMMARY:Energy as Syntax - an attempt at a thermodynamical framework for c
 ombinatorial molecular networks - Vincent Danos\, University of Edinburgh 
 School of Informatics
DTSTART:20100617T143000Z
DTEND:20100617T153000Z
UID:TALK25281@talks.cam.ac.uk
CONTACT:Microsoft Research Cambridge Talks Admins
DESCRIPTION:Rule-based approaches (as in our own Kappa\, or BNGL\, or many
  other propositions allowing the consideration of `reaction classes`) offe
 r some means to capture combinatorial molecular interactions. This is tryi
 ng to fill a need that seems ever more pressing - as molecular biology unc
 overs more amazing combinational structures. Here\, we propose to pair the
 se approaches with the use of a class of local energy functionals to guara
 ntee their thermodynamical correctness. In so doing we get a more physical
 ly realistic\, less parameter-hungry\, and more structured approach to the
  modeling/programming of combinatorial molecular networks. The formalism w
 e present is related to Saiz and Vilar`s energy-based description of macro
 -molecular assemblies (‘Stochastic dynamics of macromolecular - assembly
  networks’\, Mol Syst Biol - 2006)\; it is also related and eminently in
 spired by Julien Ollivier’s ANC - a general allosteric language for prot
 ein networks.\nJoint work with: E. Lai (Cambridge)\, N. Oury (Edinburgh\, 
 CSBE) and J. Ollivier (Edinburgh\, CSBE and McGill) \n
LOCATION:Small Lecture Room\, Microsoft Research\, Roger Needham Building\
 , 7 J J Thomson Avenue\, Cambridge CB3 0FB
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