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Table of Contents
Intro; Supervisor's Foreword; Abstract; Acknowledgements; Contents; Abbreviations; 1 Introduction; 1.1 Modelling DNA; 1.1.1 Single-Nucleotide Level Coarse-Grained DNA Models; 1.1.2 Modelling of DNA Nanotechnological Systems; 1.1.3 The oxDNA Model; 1.2 Thesis Structure; References; 2 Simulation Methods; 2.1 Simulation Methods; 2.1.1 Molecular Dynamics Simulations; 2.1.2 Monte Carlo Simulations; 2.1.3 Umbrella Sampling; 2.1.4 Weighted Histogram Analysis Method; References; 3 Non-equilibrium Bio-Molecular Unfolding Under Tension; 3.1 Introduction; 3.2 Theory
3.3 Application of Non-equilibrium Landscape Analysis to Two DNA Hairpins3.3.1 Benchmarking with Experimental Results; 3.3.2 Non-equilibrium Landscape Reconstructions; 3.4 Application of Non-equilibrium Landscape Analysis to a Novel System: DNA Origami Handles; 3.4.1 System Description and Methods; 3.4.2 Results; 3.5 Conclusions and Outlook; References; 4 Force-Induced Unravelling of DNA Origami; 4.1 Introduction; 4.2 Methods; 4.3 Rothemund Tile; 4.4 10-Helix Bundle; 4.5 7-Tile Biosensor; 4.6 Conclusions; References; 5 Measuring Internal Forces in Single-Stranded DNA; 5.1 Introduction
5.1.1 Models of ssDNA Elasticity5.2 Force Propagation in the oxDNA Model; 5.2.1 Theory; 5.2.2 Secondary Structure; 5.2.3 Method for Calculating Internal Forces in ssDNA Simulations; 5.3 Application of Internal Force Calculation to a Single-Molecule Force Clamp; 5.3.1 Introduction and System Description; 5.3.2 Simulations; 5.3.3 Results; 5.4 Conclusion and Outlook; References; 6 Conclusions; References; Appendix A Experimental Methods and Additional Details Supplementary to Chap. 4; References; Appendix Curriculum Vitae; Education; Major awards; Selected other scholarships & awards
Research experiencePublications; In peer-reviewed journals; Science book reviews; Other; Presentations; Invited Talks; Poster Presentations; Teaching experience; Supervision experience; Other employment experience; Selected Volunteering experience; Extra-curricular experience; Computer skills
3.3 Application of Non-equilibrium Landscape Analysis to Two DNA Hairpins3.3.1 Benchmarking with Experimental Results; 3.3.2 Non-equilibrium Landscape Reconstructions; 3.4 Application of Non-equilibrium Landscape Analysis to a Novel System: DNA Origami Handles; 3.4.1 System Description and Methods; 3.4.2 Results; 3.5 Conclusions and Outlook; References; 4 Force-Induced Unravelling of DNA Origami; 4.1 Introduction; 4.2 Methods; 4.3 Rothemund Tile; 4.4 10-Helix Bundle; 4.5 7-Tile Biosensor; 4.6 Conclusions; References; 5 Measuring Internal Forces in Single-Stranded DNA; 5.1 Introduction
5.1.1 Models of ssDNA Elasticity5.2 Force Propagation in the oxDNA Model; 5.2.1 Theory; 5.2.2 Secondary Structure; 5.2.3 Method for Calculating Internal Forces in ssDNA Simulations; 5.3 Application of Internal Force Calculation to a Single-Molecule Force Clamp; 5.3.1 Introduction and System Description; 5.3.2 Simulations; 5.3.3 Results; 5.4 Conclusion and Outlook; References; 6 Conclusions; References; Appendix A Experimental Methods and Additional Details Supplementary to Chap. 4; References; Appendix Curriculum Vitae; Education; Major awards; Selected other scholarships & awards
Research experiencePublications; In peer-reviewed journals; Science book reviews; Other; Presentations; Invited Talks; Poster Presentations; Teaching experience; Supervision experience; Other employment experience; Selected Volunteering experience; Extra-curricular experience; Computer skills