Abstract

To address the pressing computational need to precisely model cellular biochemistry with microscopic details, we have been developing a high-performance Brownian Dynamics method called eGFRD (enhanced Greens Function Reaction Dynamics), developed in collaboration with ten Wolde at AMOLF, Amsterdam and Tanase-Nicola in University of Michigan. eGFRD even further accelerates a previously proposed high-performance method called GFRD by making the computation from synchronous- to asynchronous-discrete-event through introduction of the concept called first-passage processes.  This new method is exact (based directly on analytical solutions of the diffusion-reaction equation), high-performance (orders of magnitude faster than conventional BD methods), extendable (different types of diffusion and boundary conditions can be efficiently implemented) and thus opens a possibility to applications of exact particle methods to cellular-level problems which has previously been unrealistic due to high computational costs.

CV

Koichi Takahashi, Ph.D. is a Human Frontier Science Program (HFSP) Cross-Disciplinary Fellow at the Molecular Sciences Institute, Berkeley, California.   His research interests span every technological and scientific areas relevant to cell modeling and simulation, and include effects of non-idealistic nature of intracellular media on signaling pathways, single cell measurement techniques such as correlation spectroscopy, asynchronous discrete event simulation algorithms, and high-performance computing.  He is a founding steering committee member of the E-Cell Project, and is the creator of the cellular simulation platform E-Cell System.  He earned his Ph.D. from Keio University in 2004.