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Projects

Please contact the webadmin from 'contact' page (top right of this page) if you would like your project be listed. You can use this site as your project homepage and make your model downloadable here.

Folder Bacterial Chemotaxis
A modeling project for bacterial chemotaxis. 4 models have been implemented on E-Cell3, with reference to previously published models.
Folder Circadian rhythm
Cyanobacteria and Drosophila circadian clock models have been implemented to estimate its network and reproduce experimental oscillations. Analysis tools for these mathematical models have been developed at the same time.
Folder Erythrocyte
A steady state computer model of the human erythrocyte has been constructed with three major metabolic pathways, glycolysis, the pentose phosphate pathway, nucleotide metabolism, and also ion transport systems. Simulation experiments of Glucose-6-phosphate dehydrogenase (G6PD) deficiency have been carried out using the model. We are currently expanding the model to include not only metabolic pathways, but also the following functions for model robustness and tolerance: pH dependence of enzymes, osmotic balance, electroneutrality, and oxygen and carbon dioxide transportation by hemoglobin. Hybrid stoichiometric and kinetic modeling mothods are being applied (Yugi. K. and Nakayama. Y. et al.). Automated tools for transforming kinetic equations into S-system and GMA forms have been developed for calculating steady-state concentration of intermediates.
Folder Mitochondrion
Our goal is to understand and control dynamics of mitochondrial metabolism through computer simulation in a whole organelle scale. For this purpose, we constructed a mitochondrial model which includes the respiratory chain, the TCA cycle, the fatty acid beta-oxidation, and the metabolite transport system at the inner-membrane. Currently, dynamic behaviors of the model is examined with emphasis on pathological application.
Folder Myocardium
Electrophysiological behavior of the myocardial cell is a budle of more than ten ion channels activities. While biological character of each ion channel is elucidated by latest experimental techniques, it is still difficult to illustrate the whole. We are trying to analyse the complicated behavior of the myocardial cell by in silico approach.
Document E-Cell IDE
 
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