A Rule-based Approach to the Modelling of Bacterial Ecosystems.
From: BioComputing and Computational Biology Research Group, Department of Computer Science, The University of Liverpool, Liverpool L69 3BX, UK. cvlachos@btinternet.com
Bio Systems
- Publish Date: Apr 2006
- ISSN: 0303-2647
- Volume: 84
- Issue: 1
- Pages: 49-72
- Medium: Print
- Language: English
- Citation (JAMA): Vlachos C, Paton R C, Saunders J R, et al. A Rule-based Approach to the Modelling of Bacterial Ecosystems.. BioSystems Apr 2006;84:49-72
Abstract
This paper presents an approach to ecological/evolutionary modelling that is inspired by natural bacterial ecosystems and bacterial evolution. An individual-based artificial ecosystem model is proposed, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by rule-based learning classifier systems. The proposed ecosystem model consists of a n-dimensional environmental grid, which can contain different types of artificial resources in arbitrary arrangements. The resources provide the energy that is necessary for the organisms to sustain life, and can trigger different types of behaviour in the organisms, such as movement towards nutrients and away from toxic substances, growth, and the controlled release of signalling resources. The balance between energy and material is modelled carefully to ensure that the ecosystem is dissipative. Those organisms that are able to efficiently exploit the available resources gradually accumulate enough energy to reproduce (by binary fission) and generate copies of themselves in the environment. Organisms are also able to produce their own resources, which can potentially be used as markers to send signals to other organisms (a behaviour known as quorum sensing). The complex relationships between stimuli and actions in the organisms are stochastically altered by means of mutations, thus enabling the organisms to adapt to their environment and maximise their lifespan and reproductive success. In this paper, the proposed bacterial ecosystem model is defined formally and its structure is discussed in detail. This is followed by results from simulation experiments that illustrate the model’s operation and how it can be used in evolutionary modelling/computing scenarios.
Mesh Headings (Keywords): Bacteria, Bacterial Physiology, Computer Simulation, Ecosystem, Energy Metabolism, Evolution, Models, Biological, Mutation, User-Computer Interface
Check for Full Text / PubMed Unique Identifier (PMID): 16386355
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