Parallel Stochastic simulation of cell-cell communication with spatially resolved reaction-diffusion kinetics

Dnr:

SNIC 2017/7-31

Type:

SNAC Small

Principal Investigator:

Adrien Coulier

Affiliation:

Uppsala universitet

Start Date:

2017-02-27

End Date:

2018-02-01

Primary Classification:

10203: Bioinformatik (beräkningsbiologi) (tillämpningar under 10610)

Webpage:

Allocation

Abstract

Our goal is to develop a new algorithm to parallelize the stochastic simulation of Reaction-Diffusion models involving many biological cells. By separating the internal mechanics and the communication mechanics into two different update steps, we can get scalable parallelism. The goal of this SNIC project is to monitor the error induced by our algorithm as the timestep length is reduced.