Pathways and Energy Landscapes

PhD Thesis by Semen Trygubenko

Html versions

• Pathways and Energy Landscapes, html version, Latex2Html (*)
• Pathways and Energy Landscapes, html version, TeX4ht (**)

Pdf files by section

• Title page, Declaration, Acknowledgements, Dedication, Abstract, Contents, List of Abbreviations, and Glossary of Symbols
• Chapter 1: Introduction
• Chapter 2: Finding Rearrangement Pathways
• Chapter 3: Properties of Rearrangement Pathways
• Chapter 4: Ensembles of Rearrangement Pathways
• Chapter 5: Conclusions
• Appendix A: Rotamers in the CHARMM19 force field
• Appendix B: Algorithms
• Appendix C: Pathway Sums for Chain Graphs
• Appendix D: Total Escape Probability for Chain Graphs
• Appendix E: Finding the Shortest and the Fastest Paths
• References
• Publications

As a single file

• Pathways and Energy Landscapes, pdf [8.6Mb]
• Pathways and Energy Landscapes, bzipped ps [5.3Mb]
• Pathways and Energy Landscapes, gzipped ps [6.6Mb]

Bzipped postscript files by section

• Title page, Declaration, Acknowledgements, Dedication, Abstract, Contents, List of Abbreviations, and Glossary of Symbols [257Kb]
• Chapter 1: Introduction [187Kb]
• Chapter 2: Finding Rearrangement Pathways [2.4Mb]
• Chapter 3: Properties of Rearrangement Pathways [584Kb]
• Chapter 4: Ensembles of Rearrangement Pathways [1.3Mb]
• Chapter 5: Conclusions [184Kb]
• Appendix A: Rotamers in the CHARMM19 force field [1.5Mb]
• Appendix B: Algorithms [183Kb]
• Appendix C: Pathway Sums for Chain Graphs [182Kb]
• Appendix D: Total Escape Probability for Chain Graphs [181Kb]
• Appendix E: Finding the Shortest and the Fastest Paths [2.4Mb]
• References [203Kb]
• Publications [179Kb]

(*) Latex2html utility, which was used to translate Latex version into html, could not cope with this document. Conversion problems that I've spotted include reordering of equations and artwork, spurious vertical and horizontal black lines in graphics files, some images are erroneously shaded grey. Also, certain mathematical symbols, e.g. $\mathcal{T}$, were not converted at all, and appear as gibberish alfanumeric references, etc., so it is better to use ps or pdf files above.

(**) TeX4ht utility, 15 years later, couldn't cope either :)