## Continuous Time Markov Chains

Most of our models will be formulated as continuous time Markov chains. On this page we describe the workings of these processes and how we simulate them.

Definition. We say that an event happens at rate r(t) if an occurence between times t and t + dt has probability about r(t)dt when dt is small.

Fact. When r(t) is a constant r, the times t[i] between occurrences are independent exponentials with mean 1/r, and we have a Poisson process with rate r.

Markov chains in continuous time are defined by giving the rates q(x,y) at which jumps occur from state x to state y. In many cases (including all our examples) q(x,y) can be written as p(x,y)Q where Q is a constant that represents the total jump rate. In this case we can construct the chain by taking one step according to the transition probability p(x,y) at each point of a Poisson process with rate Q.

If we throw away the information about the exponential holding times in each state, the resulting sequence of states visited is a discrete time Markov chain, which is called the embedded discrete time chain. In our simulations, the total flip rate Q at any one time is a multiple of the number of sites, CQ. Since the number of sites is typically tens of thousands, we lose very little accuracy by simulating TCQ steps and calling the result the state at time T.

To build the discrete time chain we must pick from the various transitions with probabilities proportional to their rates. In our particle systems we can do this by picking a site at random, applying a stochastic updating rule, and then repeating the procedure. Because of this, continuous time is occasionally referred to as asynchronous updating. This is to distinguish that porcedure from the synchronous updating of a discrete time process which updates all of the sites simultaneously.