We present a model for describing a portion of cytoplasm with components involved in metabolic pathways. Each enzyme, metabolite and complex is represented by an autonomous software agent. The molecules have 3D shapes, i.e. spheres with a radius proportional to their weight and move with Brownian motion in a virtual cell space. When an enzyme or a complex encounters an affine substrate for a metabolic reaction, then such reaction can take place, according to Michaelis-Menten kinetics. We have developed a prototype simulator with which we have tested our model using the glycolysis as a sample pathway. The validation of the model has been performed on a small portion of cytoplasm with a limited number of components.

A spatial model and simulator for metabolic pathways

CANNATA, Nicola;CORRADINI, Flavio;MERELLI, Emanuela;TESEI, Luca
2008

Abstract

We present a model for describing a portion of cytoplasm with components involved in metabolic pathways. Each enzyme, metabolite and complex is represented by an autonomous software agent. The molecules have 3D shapes, i.e. spheres with a radius proportional to their weight and move with Brownian motion in a virtual cell space. When an enzyme or a complex encounters an affine substrate for a metabolic reaction, then such reaction can take place, according to Michaelis-Menten kinetics. We have developed a prototype simulator with which we have tested our model using the glycolysis as a sample pathway. The validation of the model has been performed on a small portion of cytoplasm with a limited number of components.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11581/337196
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