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Title: Computational spin dynamics and visualisation of large spin systems
Author: Charnock, Gareth Trevor Patrick
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2012
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The thesis commences with a detailed review of the background theory of spin dynamics simulations. State space rest riction is introduced via a "top-down" approach. Common terms that make up the spin Hamiltonian are reviewed, and it is noted that the mathemat ical forms of these terms can be categorised in one of three ways. The review of the background theory complete, w::counts are given of the following four areas of research: 1. Formal conditions are established for the validity of state space restriction via spin order pruning, based on tracking the density matrix norm through spin order subspaces. The primary predictor for success is seen t o be the ratio of the largest eigenvalue to the relaxation rate. The lower this ratio; the fewer spin orders are required. 2. Software based around the Spin XML format , suitable for constructing and visualising large spin systems, is presented. Both a functional specification and a discussion of the internals are given. 3. A potential applicat ion of state space restriction, called "direct structure fitting" , (DSF) is explored. In DSF, a candidate chemical structure is optimised directly by minimising the difference between its predicted spectrum and an experimental spectrum. The following examples of successful fits are provided: cyanomethyl, propargyl, and tyrosyl radicals, in the liquid state, and, tyrosyl embedded in two ribonuclease reductase proteins in the powder state. 4. A new model of the pseudocontact shift, which assumes a delocalised electron, is presented. Mathematical subtleties are resolved that would otherwise lead to the failure of numerical evaluation if left untreated. Techniques to improve efficiency are discussed , and the resulting program runs comfortably on workstation-grade hardware on protein sized datasets. E. Coli DNA Polymerase III is investigated as an example, and evidence is presented that suggests that the new model would predict significant differences in structures if used in conjunction with molecular dynamics based structural refinement
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available