Efficient abstraction and execution of stochastic simulation models

Stochasticity is found throughout cell-biological models when describing phenomena such as diffusion and the resulting random interactions of entities. This thesis is concerned with the efficient execution of these models. We cover the fundamentals of modeling from the bottom up. Reaction systems are a main topic, particularly those that use Stochastic Simulation Algorithms. We discuss efficient variations of these algorithms, including their parallel execution. Furthermore, the limitations of static reaction systems will be overcome by introducing dynamic compartmentalization.