Solution

ID: past-exam-of-the-biological-physics-course-of-the-university-of-oxford/2019/3/d/solution

Write , , , and . The repressilator in the stated logic approximation is
Assume . Initially low Z allows X production; high Y blocks Z; and Y is initially at its unrepressed steady level. X first rises through at , turning Y production off. Y then decays through at , where , allowing Z to rise. Z reaches at and switches X production off. At this point , so X falls through at and releases Y production.
Y's rise then switches Z off, Z's fall releases X again, and the sequence repeats. Every segment is exponential relaxation towards one if its production gate is on, or towards zero if off. For a rising segment starting at , the next threshold time is ; for a falling segment starting at , it is . These rules determine the whole trace without pretending the concentrations are square waves. X, Z and Y peak in sequence after the stated initial condition; the last panel of the figure in solution gives an illustrative trajectory.
The delayed sequence of three inhibitory links supplies negative feedback with finite response times. Equal rates make the cycling symmetric after the initial transient, not simultaneous. If , repression is never reliably engaged and the proteins approach their unrepressed levels instead; oscillation is not implied for arbitrary thresholds or for every smooth regulatory law replacing the ideal relay.

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