Dr. Robert Strehl | Ryerson University
Stochastic Micro- and Mesoscale Simulations of Biochemical Reaction-Diffusion Systems
In this talk, I will introduce two stochastic computational approaches for simulating biological signaling pathways at a micro-/mesoscale level:
The first approach is discrete in space and continuous in time and builds upon the widely used Gillespie's Stochastic Simulation Algorithm (SSA) by simulating a corresponding Reaction-Diffusion Master Equation. Gillespie's SSA is known to be exact but computationally expensive. The new (hybrid) approach decreases the computational runtime significantly while maintaining high accuracy. I will present some benchmark studies for biochemical reaction-diffusion models and discuss ideas for further applications to general transport problems at cell level.
The second approach is a particle-based method that monitors single constituents continuous in space. In the literature it is mostly referred to as Multi-Particle Collision (MPC) Model or Stochastic Rotation Dynamics. The collisions model diffusion transport and obey physical laws of conservation. MPC is known to be computational more efficient than many other particle-based collision models. I will demonstrate recent applications to intracellular pathways for chemotaxis and address some open challenges.