Protein Structure and Folding

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Table of contents

1 Introduction 
1.1 AlgebraicModelling of RNA and Proteins
1.2 Agent-basedModelling and Simulation
1.3 Organisation of theManuscript
1.4 Modélisation algébrique de l’ARN et des protéines
1.5 Modélisation et simulation basées sur des agents
1.6 Organisation du manuscrit
I AlgebraicModels 
2 Background andMethods for the Part I 
2.1 Basic Introduction toMolecular Biology and Gene Expression
2.1.1 RNA Translation
2.1.2 Protein Structure and Folding
2.1.3 Functional RNA
2.1.4 RNAWorld
2.1.5 Haemoglobin and Anaemias
2.2 AlgebraicModelling of Biological Systems
2.2.1 Calculus of Communicating Systems
2.2.2 Labelled Transition Systems
2.2.3 Hennessy-Milner Logic
2.2.4 From Algebraic to Agent-basedModels
3 RNAs and Proteins equivalence 
3.1 Introduction
3.2 Results
3.2.1 Bisimilarity equivalence
3.2.2 Higher abstraction level model
3.3 Discussion
3.4 Conclusions
4 Algebraic Study of ProteinMisfolding 
4.1 Introduction
4.1.1 DNA replication and gene expressionmodels
4.1.2 Formal description of HBB gene replication and expression
4.2 Results
4.3 Discussion
4.4 Conclusions
5 Algebraic Characterisation of Non-coding RNA 
5.1 Introduction
5.2 Results
5.2.1 Ligand Binding Function
5.2.2 Enzymatic Function
5.2.3 Model checking
5.3 Conclusions
II Agent-based Simulation ofMetabolic pathways 
6 Background andMethods for the Part II 
6.1 Introduction to Yeasts’ Glycolysis
6.2 Agent-based approach
6.2.1 Agent-based Simulator forMetabolic Pathways
6.2.2 From a KineticModel to aMultiagent Simulation
6.2.3 Choosing a Reference KineticModel
6.2.4 Defining the Input for the Simulation
6.2.5 Simulation Output and Visualisation
7 Testing in Silico the Bimolecular Interactions 
7.1 Introduction
7.2 IntegrativeMethods for this Chapter
7.2.1 Long-distance Electrodynamic Interactions
7.2.2 Modelling the Whole Glycolytic Pathway
7.2.3 Simulating a Large Number ofMolecules
7.3 Results
7.4 Discussion
7.5 Conclusions
8 Interaction-as-perception inMetabolic Reactions 
8.1 Introduction
8.2 IntegrativeMethods for this Chapter
8.2.1 Multi-agentModelling and Simulation
8.2.2 Simplicial Data Analysis
8.2.3 Interaction-as-perception Paradigm
8.3 Results
8.4 Discussion
8.5 Conclusions
9 Conclusions