Past exam of the mathematics course of the University of Cambridge / 2024 / iii / Paper 356 / 1 / a / Solution

Write the molecular copy numbers as $\mathbf{x}=(x_1,x_2,x_3,x_4)$ and use the power-law reaction propensity convention of the paper. The seven propensities and stoichiometric vectors areA channel is assigned zero propensity whenever its update would leave the nonnegative integer lattice.

The Gillespie algorithm starts from $\mathbf{x}=(5,0,0,0)$ and $t=0$. At the current state compute $a_0={\sum }_{r=1}^7{a}_r$. If $a_0=0$, terminate the path. Otherwise draw independent random variables $U_1,U_2$ from the uniform distribution on $(0,1)$, set the next waiting time toand choose the least index $r$ satisfyingThen update $t\leftarrow t+\tau$ and $\mathbf{x}\leftarrow \mathbf{x}+{\nu }_r$, and repeat. The minimum of the seven competing reaction clocks has an exponential distribution of rate $a_0$, while reaction $r$ wins with probability $a_r/a_0$.