Energy as Syntax - an attempt at a thermodynamical framework for combinatorial molecular networks

Add to your list(s) Download to your calendar using vCal

• Vincent Danos, University of Edinburgh School of Informatics
• Thursday 17 June 2010, 15:30-16:30
• Small Lecture Room, Microsoft Research, Roger Needham Building, 7 J J Thomson Avenue, Cambridge CB3 0FB.

If you have a question about this talk, please contact Microsoft Research Cambridge Talks Admins.

Rule-based approaches (as in our own Kappa, or BNGL , or many other propositions allowing the consideration of `reaction classes`) offer some means to capture combinatorial molecular interactions. This is trying to fill a need that seems ever more pressing – as molecular biology uncovers more amazing combinational structures. Here, we propose to pair these approaches with the use of a class of local energy functionals to guarantee their thermodynamical correctness. In so doing we get a more physically realistic, less parameter-hungry, and more structured approach to the modeling/programming of combinatorial molecular networks. The formalism we 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 inspired by Julien Ollivier’s ANC - a general allosteric language for protein networks. Joint work with: E. Lai (Cambridge), N. Oury (Edinburgh, CSBE ) and J. Ollivier (Edinburgh, CSBE and McGill)

This talk is part of the Microsoft Research Cambridge, public talks series.

This talk is included in these lists:

• All Talks (aka the CURE list)
• Cambridge Centre for Data-Driven Discovery (C2D3)
• Cambridge talks
• Chris Davis' list
• Guy Emerson's list
• Interested Talks
• Microsoft Research Cambridge, public talks
• Optics for the Cloud
• PMRFPS's
• School of Technology
• Small Lecture Room, Microsoft Research, Roger Needham Building, 7 J J Thomson Avenue, Cambridge CB3 0FB
• Trust & Technology Initiative - interesting events
• bld31
• ndk22's list
• personal list
• rp587

Note that ex-directory lists are not shown.