project.overview

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Kirchhoff/connectivity matrix is analogous to the
Transition Rate Matrix of Master Equation
Formalism

• Applications to macromolecular dynamics
• Rotational dynamics of polymers (DRIS)
• (Bahar, Erman Monnerie, Adv Polym Sci. 1994)
• Folding dynamics of model proteins
• (Ozkan, Bahar Dill, Nature Struct Biol. 2001)

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FOR MORE INFO
Ozkan, Bahar Dill, Nature Struct Biol, 2001.
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Negative F-values come from redirected flow in
parallel processes
Destabilization can lead to higher folding rates
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Computational models methods for

• Large assemblies, complexes of proteins
• Membranes and cytosolic fibrous systems
• Cellular pathways. Signaling regulation of cell
  cycle

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ATM signalling pathways
http//www.biocarta.com/pathfiles/atmPathway.asp
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Bridging the Gap between Molecular and Cellular
Scales
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Computational challenges

• multiscale representations of dynamics
• extracting rules from microscopic simulations,
  for macroscopic approaches
• bridging continuous and discrete models