Title: Multicale Simulation of Reaction-Diffusion Systems
Speaker: Adithya Vijaykumar, University of Amsterdam & AMOLF, Netherlands
Abstract:
In signalling pathways (for eg. MAPK), the microscopic dynamics of the proteins is crucial for the macroscopic response of the system. This means that non-trivial dynamics at the microscopic scale like rebinding, qualitatively changes the macroscopic behaviour. Algorithms that capture
the microscopic dynamics is computationally inefficient to simulate a network wide simulation. On the other hand, algorithms that perform network wide simulations integrate out microscopic dynamics and hence does not accurately predict the response. I, for the first time have developed a multi-scale scheme, MD-GFRD, that defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. I then applied this scheme to simulate a portion of the MAPK signalling pathway and predicted the response of the system for two different scenarios.