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Classical and quantum simulations of DNA/spermine systems

Shepherd, Jack William (2015) Classical and quantum simulations of DNA/spermine systems. MSc by research thesis, University of York.

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Abstract

A study of the effects of the presence of multiple spermine molecules in the major groove of poly-d(A)_{20}.poly-d(T)_{20} on the A-B transition has been carried out, alongside a survey of the long-term effect of a single spermine molecule diffusing into various DNA sequences. The transition from A- to B-form was found to be slowed by spermine, and further slowed as more spermine was added. In some cases, the presence of spermine induced an unstable backbone shift away from both the canonical A- and B-forms, which eventually decayed rapidly into previously seen behaviour. The interactions between various sequences of DNA and spermine indicated that the strength of the interaction can be affected by the DNA sequence. The efficacy of the molecular dynamics force field was assessed using ab initio quantum mechanics as a reference. The classical approximation was found to give results which were consistently lower in magnitude than those from the quantum calculations, and in thymine a regular site of considerable inaccuracy was observed. This represents a novel finding and a target for future development of molecular dynamics techniques.

Item Type: Thesis (MSc by research)
Keywords: DFT, Density Functional Theory, ONETEP, AMBER, DNA, Spermine, Molecular Dynamics, Thymine, DNA conformation, Polyamines, Multiscale modelling
Academic Units: The University of York > Physics (York)
Depositing User: Mr Jack William Shepherd
Date Deposited: 08 Apr 2015 14:46
Last Modified: 01 Jan 2016 01:18
URI: http://etheses.whiterose.ac.uk/id/eprint/8465

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