Laplacian Dynamics with Synthesis and Degradation.

Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady state solutions of biochemical reaction networks with synthesis and degradation. Our approach is based on a labeled directed graph G and the associated system of linear non-homogeneous differential equations with first-order degradation and zeroth-order synthesis. We also present a theorem which provides necessary and sufficient conditions for the dynamics to engender a unique stable steady state. Although the dynamics are linear, one can apply this framework to nonlinear systems by encoding nonlinearity into the edge labels. We answer an open question from our previous work concerning the non-positiveness of the elements in the inverse of a perturbed Laplacian matrix. Moreover, we provide a graph theoretical framework for the computation of the inverse of such a matrix. This also completes our previous framework and makes it purely graph theoretical. Lastly, we demonstrate the utility of this framework by applying it to a mathematical model of insulin secretion through ion channels in pancreatic β-cells.