The Living Cell as a Multi-agent Organisation: A Compositional Organisation Model of Intracellular Dynamics

Abstract

Within the areas of Computational Organisation Theory and Artificial Intelligence, techniques have been developed to simulate and analyse dynamics within organisations in society. Usually these modelling techniques are applied to factories and to the internal organisation of their process flows, thus obtaining models of complex organisations at various levels of aggregation. The dynamics in living cells are often interpreted in terms of well-organised processes, a bacterium being considered a (micro)factory. This suggests that organisation modelling techniques may also benefit their analysis. Using the example of Escherichia coli it is shown how indeed agent-based organisational modelling techniques can be used to simulate and analyse E.coli's intracellular dynamics. Exploiting the abstraction levels entailed by this perspective, a concise model is obtained that is readily simulated and analysed at the various levels of aggregation, yet shows the cell's essential dynamic patterns.

Illustrating the Contrasting Roles of Self-Organization in Biological Systems with Two Case Histories of Collective Decision Making in the Honey Bee

“…The results showed that given the external circumstances, it was effective, given overall properties put forward by biological experts. Next to the domain of honeybee colonies the formal approaches put forward in this paper have also been used for modeling other biological processes, for instance in [11] a model of the living cell is presented.…”

Simulation and Analysis of Complex Biological Processes: an Organisation Modelling Perspective

“…The example model for E. coli's dynamics was inspired by [4]. Global properties of the organisation as a whole can be expressed in terms of interaction with an Environment (which is not shown in Figure 1 and 2, since we consider it not being part of the organisation).…”

“…For this example, these were all intergroup role interaction properties, role behaviour properties and transfer properties. The specific timing parameters used for the simulation were inspired by [4].…”