Contact Info
Department of Applied Mathematics
University of Waterloo
Waterloo, Ontario
Canada N2L 3G1
Phone: 519-888-4567, ext. 32700
Fax: 519-746-4319
PDF files require Adobe Acrobat Reader
MC 6496
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.
Contact Info
Department of Applied Mathematics
University of Waterloo
Waterloo, Ontario
Canada N2L 3G1
Phone: 519-888-4567, ext. 32700
Fax: 519-746-4319
PDF files require Adobe Acrobat Reader
The University of Waterloo acknowledges that much of our work takes place on the traditional territory of the Neutral, Anishinaabeg and Haudenosaunee peoples. Our main campus is situated on the Haldimand Tract, the land granted to the Six Nations that includes six miles on each side of the Grand River. Our active work toward reconciliation takes place across our campuses through research, learning, teaching, and community building, and is co-ordinated within the Office of Indigenous Relations.