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Fig. 2 | BMC Systems Biology

Fig. 2

From: Distinguishing the rates of gene activation from phenotypic variations

Fig. 2

Illustrations of the energy landscapes and transition paths with slow switching rates. a A global view of the quasi-potential energy landscape of the genetic switching system. Switching paths from off to on state (purple solid curve) and from on to off state (red solid curve) are deterministic paths between two stable fixed points. We call the steady state with relatively large number of proteins as on state, whereas the steady state with relatively small number of proteins is off state. b The two-layer decomposition of subfigure A. Jumps between two layers are rare events compared with reactions on each individual landscape. c, d Averaged switching trajectories from simulations. We take the two stable fixed points in the deterministic dynamics as the starting and ending points. Darkness of the shading points represents the average duration time on reactive trajectories. We keep track of the trajectories from the time that gene states change to the time that the system reaches new stable state. We use principal curve to characterize the averaged switching trajectories (green dashed curves). The results suggest that the average switching paths are along deterministic paths. The parameters are K R =100, K R0=0.1, k P =51.5, d R =0.7, d P =1.4, d G =0.0014, k G =0.028, k G0=0.00028, and K=3000

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