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 regulatory networks.
Copyright © 2016 American Physical Society. This article first appeared in Physical Review E: 94, 052404 (2016), 1-15.
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Ferwerda, Cameron, and Ovidiu Lipan. "Splitting nodes and linking channels: A method for assembling biocircuits from stochastic elementary units." Physical Review E 94 (November 10, 2016): 1-15. doi:10.1103/physreve.94.052404.