Kruger, T.P.J. (Tjaart)2016-10-142016-10-142016-09-012016Nöthling, JA 2016, Exciton dynamics in photosynthetic molecular aggregates, MSc Dissertation, University of Pretoria, Pretoria, viewed yymmdd <http://hdl.handle.net/2263/57276>S2016http://hdl.handle.net/2263/57276Dissertation (MSc)--University of Pretoria, 2016.Almost all of the energy that sustains life on Earth was captured from sunlight during the process of photosynthesis. In the first step of this process, photons are absorbed by aggregates of pigment molecules called light-harvesting complexes. In these complexes, pigment molecules are carefully arranged by protein backbones and are consequently able to absorb excitation at much higher pigment concentration than for the same pigments in solution. The close proximity of pigment molecules in light-harvesting complexes may cause significant interaction between them and consequent delocalisation of excitation over more than one pigment molecule. These delocalised states are called exciton states. The electronic degrees of freedom of pigment molecules are modulated by the large number of vibrational modes in the protein backbone and pigments themselves. In many light-harvesting complexes, the interaction between pigment molecules are much stronger than interaction with the vibrational modes. In such systems, a formalism called Redfield theory, which treats interaction with vibrations perturbatively, can be used to calculate exciton dynamics. In this dissertation, we give an overview of the process of photosynthesis and the physical mechanisms underlying light-harvesting. We then derive the Redfield equation and explain its use in systems containing a single or multiple excitations. We illustrate calculation of Redfield-dynamics by computing the exciton dynamics in three systems: a six-member ring demonstrating essential features of exciton dynamics; FMO, a conduit for excitation in green sulphur bacteria and LHCII, the main light-harvesting complex in green plants.en© 2016 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria.UCTDDissertation10571460