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Koichi Takahashi, Japan

What Invited talk
When 2010-10-18
from 09:00 to 10:00
Where Fraunhofer IGD Rostock, Joachim-Jungius-Str., Room 114
Contact Name Koichi Takahashi
Contact Email ktakahashi@riken.jp
Contact Phone +81-45-503-9270
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last modified 2010-11-16 18:23

Particle reaction-diffusion simulations of cellular signaling pathways


The advent of advanced laser microscopy produced the pressing computational need to precisely model cellular biochemistry with molecular details.  We have been developing high-performance particle reaction-diffusion simulation methods including the enhanced Greens Function Reaction Dynamics (eGFRD) and a microscopic lattice reaction-diffusion method called Spatiocyte. Together with some visualization, data analysis and rule-based modeling software components, these simulation methods are being implemented on our cellular simulation platform called E-Cell System Version 4. In addition to such computational aspects of our projects, I will also talk about an application of the eGFRD simulation method on a dual phosphorylation cycle of mitogen-activated protein kinase (MAPK) and the use of the Spatiocyte method to reveal self-organization mechanisms underlying cellular signaling systems.


Koichi Takahashi

Laboratory for Biochemical Simulation
Planning Office for the Center for Computational and Quantitative Life Science
RIKEN


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