A Guide to Modeling Reaction-Diffusion of Molecules with the E-Cell System

Chapter Details

Pub Date: 14 Jan 2013
Pages: 20
Chapter Category: Bioinformatics
Taken from the Book: E-Cell System: Basic Concepts and Applications
Book Series: Intelligence Unit
Edited by: Satya Nanda Vel Arjunan, Pawan K. Dhar and Masaru Tomita

Download PDF

All chapters PDFs are available for free under an Open Access license.

A Guide to Modeling Reaction-Diffusion of Molecules with the E-Cell System

Satya Nanda Vel Arjunan

About this Chapter

The E‑Cell System is an advanced platform intended for mathematical modeling and simulation of well‑stirred biochemical systems. We have recently implemented the Spatiocyte method as a set of plug in modules to the E‑Cell System, allowing simulations of complicated multicompartment dynamical processes with inhomogeneous molecular distributions. With Spatiocyte, the diffusion and reaction of each molecule can be handled individually at the microscopic scale. Here we describe the basic theory of the method and provide the installation and usage guides of the Spatiocyte modules. Where possible, model examples are also given to quickly familiarize the reader with spatiotemporal model building and simulation.

More chapters from the book

Analytical techniques in computational cell biology such as kinetic parameter estimation, Metabolic Control Analysis (MCA) and bifurcation analysis require l...

The thorough overview of the E‑Cell Simulation Environment in this chapter provides a foundation for understanding the systems biology research that uses t...

During cardiomyocyte development, early embryonic ventricular cells show spontaneous activity that disappears at a later stage. Dramatic changes in action po...

The Myeloid Differentiation Primary‑Response Protein 88 (MyD88)‑dependent and—independent pathways induce proinflammatory cytokines when toll‑like re...

Since a mature mammalian erythrocyte is enucleated and it is void of mitochondria, gene expression does not take place, while glycolysis is the only mechanis...

Bacterial organisms like Escherichia coli have developed mechanisms to detect and direct cell movement toward substrate when starved. Such behavior ...

In this work, we used E‑Cell, a software package aiming at large‑scale modeling with full object‑oriented modeling support, to analyze the 70kDa heat s...

An offshoot of classical bioinformatics, whole cell modeling integrates information from metabolic pathways, gene regulation and expression. This new area of...

While many inter‑organ and intra‑organ gene regulations have been found recently, raison d’être of such regulations are hardly explicated. We aimed li...

Computer simulations can be used to predict the dynamic behaviour of metabolic pathways and to provide evidence in support of clinical treatments for metabol...

The E‑Cell System is an advanced platform intended for mathematical modeling and simulation of well‑stirred biochemical systems. We have recently impleme...