(A) Schematic of the gene regulatory networks encoded by the dynamic term (dotted line) and the static term (solid line). (B) Weights of the dynamic (dotted line) and static (solid line) enhancers. (C) Kymograph showing the dynamics of the concentration of morphogen caudal (cad) used in the simulated embryo. (D) Kymographs showing the dynamics of the concentration of proteins hunchback (hb) and Krüppel (Kr). (E) Final pattern of protein expression. The vertical lines identify the positions of the two cells whose trajectories are shown on the bottom subpanels of panel F. (F) Flow in the phase space defined by hb and Kr for different concentrations of morphogen cad. The green disk represents the stable fixed point corresponding to the fate with high concentration of hb. (Top subpanels) Projection of the trajectories of all cells in the hb-Kr phase space. The trajectories of cells that end up with high hb, Kr, and X concentrations are represented with transparent blue, red and black lines, respectively. (Bottom subpanels) Projection of the trajectories of the two cells identified on panel E. For a given cell, the part of the trajectory that is shown is from the initial time point until the time point when cad reaches the concentration used to compute the flow. (G) Speed in phase space of all cells as a function of the time since the formation of the fixed point. The top, middle, and bottom subpanels show the speed of the cells that end up with high hb, Kr, and X concentrations at the end of the simulation, respectively. The thick blue and red lines correspond to the speed of cells 1 and 2, respectively.