Simulation of mitochondrial metabolism using multi-agents system

TL;DR

This paper explores using multi-agent systems to model mitochondrial metabolism, offering an alternative to complex differential equation models by capturing spatial and structural details of mitochondrial pathways.

Contribution

It introduces a multi-agent modeling approach tailored to mitochondrial metabolism, addressing limitations of traditional differential equation models in representing spatial and structural complexities.

Findings

Multi-agent systems can effectively model mitochondrial pathways.

The approach captures enzyme localization and membrane architecture.

Potential for simplifying complex metabolic models.

Abstract

Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or enzymatic complex build of several subunits). In our Mitochondria in Silico Project, MitoScop, we study the metabolism of the mitochondria, an intra-cellular organelle. Many ordinary differential equation models are available in the literature. They well fit experimental results on flux values inside the metabolic pathways, but many parameters are di$\pm$cult to transcribe with such models: localization of enzymes, rules about the reactions scheduler, etc Moreover, a model of a significant part of mitochondrial metabolism could become very complex and contain more than 50 equations. In this context, the multi-agents systems appear as an alternative to model the metabolic pathways. Firstly, we have looked after membrane design. The mitochondria is a particular case because the inner mitochondrial space, ie matricial space, is delimited by two membranes: the inner and the outer one. In addition to matricial enzymes, other enzymes are located inside the membranes or in the inter-membrane space. Analysis of mitochondrial metabolism must take into account this kind of architecture.