Tsinghua-A::Modeling::GILLESPIE Algorithm

Gillespie algorithm

the reverse process of the gene between the two Loxp sites could not be well described by the DDE or ODE equations since after the reverse process, the gene will have chance to flip again. This process is a discrete, stochastic process instead of a continuous, deterministic process. To make the model more convincing, we use Gillespie algorithm, which is a kind of stochastic simulation algorithm to generate a statistically correct trajectory (possible solution) of a stochastic equation.readmore

Our model

In our model , we use Gillespie algorithm to simulate the process of inversion. Here we use Markov chain to describe the process of inversion. We assume that the state ‘A’ , ‘B’ , ‘C’ , ‘D’ , is the original state , the state after inversion , the Intermediate state when A forms holiday junction, the Intermediate state when B forms holiday junction respectively. readmore

A better model

1000 genes which are in state ‘A’ are seen as a whole in the above model. To make the simulation more convincing, we then simulate the trajectory of every single molecule. After that we synthesize all trajectories to get the final result.readmore