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Ordinary Differential Equations for Modelling Bacterial Interactions in the Gut

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Model Intestinal Microflora In Computer Simulation (MIMICS) Technical Report: Ordinary Differential Equations for Modelling Bacterial Interactions in the Gut. Michael H.F. Wilkinson Centre for High Performance Computing University of Groningen Landleven 1, 9747 AD Groningen, The Netherlands Phone: +31-50-363-3374 Fax: +31-50-363-3406 E-mail: [email protected] M.H.F. Wilkinson MIMICS technical Report Ordinary Differential Equations ii MIMICS Technical Reports The MIMICS project of the Centre for High Performance Computing of the University of Groningen is a project initiated by the International Study Group for New Antimicrobial Strategies (ISGNAS). Its aim is to explore computer simulation methods for the study of the intestinal microflora and its interactions with the host. MIMICS technical reports are intended to explain various technical issues involved in this modelling. As such, the main readership are persons involved in the MIMICS project, other ISGNAS projects, and those intending to implement similar models. Parts of the contents may be reproduced in articles at a later date. M.H.F. Wilkinson MIMICS technical Report Ordinary Differential Equations iii TABLE OF CONTENTS 1. INTRODUCTION 1 2. THE BASIC COMPONENTS OF INTERACTIONS 3 2.1 Enzyme activity, inhibition, and activation. 4 2.2 Substrate uptake 5 2.3 Secretion 8 2.4 Transport terms 9 3. THE INTERACTIONS PROPER 9 3.1 Pure food competition. 9 3.2 Parasitic food competition. 10 3.3 Toxin inactivation 13 3.4 Symbiotic food interactions. 15 3.5 Toxin production: 17 3.6 Predator-prey interactions 22 3.7 Decoys in predator-prey interactions 24 3.8 Direct binding site competition 25 3.9 Indirect binding site competition 26 3.10 Biofilm gel production 26 3.11 Biofilm gel destruction 27 3.12 "Meta-adherence" 28 3.13 "Quorum sensing" 28 3.14 Pathway clearing for strict oligotrophs by copiotrophs 28 4. DISCUSSION 30 5. REFERENCES AND FURTHER READING 31 M.H.F. Wilkinso

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