Add new methods to Simulation class

[dileep-kishore]

1. Property for k_det (Currently if someone wants to estimate parameters they will have to create a new Simulation instance. This fixes that issue.)
2. clear method to clear the results (When reusing the same Simulation instance)
3. threshold - the upper limit for species numbers (Implement this through a custom propensity function ~ F(t, Xt, ...))