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
2008-01-01
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.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
