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Fig. 4 | BMC Bioinformatics

Fig. 4

From: Periodic synchronization of isolated network elements facilitates simulating and inferring gene regulatory networks including stochastic molecular kinetics

Fig. 4

Implementation of biochemical reactions in CaiNet. a Sketch of an exemplary biochemical reaction comprised of two basic enzyme turnover reactions (upper panel). The two enzymes mutually take each others product and catalyze it to each others substrate. During each time step, molecule numbers and molecule fluxes need to be synchronized to ensure mass conservation (lower panel). b Comparison of time trajectories of product levels of the biochemical reaction sketched in a simulated with CaiNet using two different synchronization time steps \(\Delta t\) (yellow/purple and green/blue lines) with the numerical solution of an ODE solver (dashed blue/dashed red lines). If the time-step \(\Delta t\) is too large, the transient behavior of CaiNet deviates from an ODE-solver. If the time-step \(\Delta t\) is sufficiently small, the transient behavior of CaiNet approximates the ODE-solver well

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BMC Bioinformatics

ISSN: 1471-2105

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