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Center for Nonlinear Studies |
Large protein-DNA complexes play central roles in regulating transcription, DNA replication, and other biological processes. However, there are currently no mathematical methods for efficiently describing such multi-particle complexes in terms of components, interaction energies, and assembly rules. Here we describe mathematical structures that address this need, as well as a diagrammatic formalism that facilitates analytic computations. Our methods can dramatically simplify the analysis of both equilibrium and non-equilibrium stochastic biochemical systems. In particular, the diagrammatic techniques we present greatly facilitate the calculation of partition functions for thermodynamic models of transcriptional regulation.
Host: William Hlavacek