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Biological and Chemical Physics

University of Richmond

Biocircuits

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Splitting Nodes And Linking Channels: A Method For Assembling Biocircuits From Stochastic Elementary Units, Cameron Ferwerda, Ovidiu Lipan Nov 2016

Splitting Nodes And Linking Channels: A Method For Assembling Biocircuits From Stochastic Elementary Units, Cameron Ferwerda, Ovidiu Lipan

Physics Faculty Publications

Akin to electric circuits, we construct biocircuits that are manipulated by cutting and assembling channels through which stochastic information flows. This diagrammatic manipulation allows us to create a method which constructs networks by joining building blocks selected so that (a) they cover only basic processes; (b) it is scalable to large networks; (c) the mean and variance-covariance from the Pauli master equation form a closed system; and (d) given the initial probability distribution, no special boundary conditions are necessary to solve the master equation. The method aims to help with both designing new synthetic signaling pathways and quantifying naturally existing ...