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Table of Contents
Supervisor's Foreword; Abstract; Acknowledgments; Contents; List of Publications; 1 Introduction; 1.1 The Cell Cycle; 1.2 General Principles of the DNA Replication Process; 1.3 Aims of This Thesis; 1.4 Origin Licensing; 1.5 Origin Firing During DNA Synthesis; 1.6 Replication Timing, Origin Positioning, and the Random Completion Problem; 1.7 Mathematical Modelling of DNA Replication; 1.8 The Spatio-Temporal Organisation of Replication Forks; References; 2 Optimal Origin Placement for Minimal Replication Time; [DELETE]; 2.1 Properties of Origins of Replication in Saccharomyces cerevisiae
2.2 A Mathematical Model for Optimal Origin Positions2.2.1 A Simplified Two Origin Model; 2.2.2 Many Origin Loci; 2.2.3 Evolutionary Pressure Drives Yeast Origin Loci to Optimal Positions; 2.2.4 Loci Competence and Circular Chromosomes; 2.3 Optimal Origin Loci and Stochasticity in Origin Activation Time; 2.4 Summary; References; 3 Actively Replicating Domains Randomly Associate into Replication Factories; [DELETE]; 3.1 Summary of Experimental Procedure; 3.2 The Diffusion Time Scale of Two Replicating Dots; 3.3 Binding Energy; 3.4 Test of the Analytical Result Versus Computer Simulations
3.5 Fit to Experimental Data of Replisome Association3.6 Genome-Wide Replication Data and the Number of Forks Per Factory; 3.7 Summary; References; 4 Summary and Conclusions; [DELETE]
2.2 A Mathematical Model for Optimal Origin Positions2.2.1 A Simplified Two Origin Model; 2.2.2 Many Origin Loci; 2.2.3 Evolutionary Pressure Drives Yeast Origin Loci to Optimal Positions; 2.2.4 Loci Competence and Circular Chromosomes; 2.3 Optimal Origin Loci and Stochasticity in Origin Activation Time; 2.4 Summary; References; 3 Actively Replicating Domains Randomly Associate into Replication Factories; [DELETE]; 3.1 Summary of Experimental Procedure; 3.2 The Diffusion Time Scale of Two Replicating Dots; 3.3 Binding Energy; 3.4 Test of the Analytical Result Versus Computer Simulations
3.5 Fit to Experimental Data of Replisome Association3.6 Genome-Wide Replication Data and the Number of Forks Per Factory; 3.7 Summary; References; 4 Summary and Conclusions; [DELETE]