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The application and analysis of single-molecule spectroscopy data in photosynthesis
Thesis (PhD (Physics))--University of Pretoria, 2024.
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| Format: | Thesis |
| Language: | English |
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University of Pretoria
2025
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| _version_ | 1867613595990228992 |
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| access_status_str | Open Access |
| author2 | Kruger, T.P.J. (Tjaart) |
| author_browse | Kruger, T.P.J. (Tjaart) |
| author_facet | Kruger, T.P.J. (Tjaart) |
| collection | Thesis |
| dc_rights_str_mv | © 2023 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. |
| description | Thesis (PhD (Physics))--University of Pretoria, 2024. |
| format | Thesis |
| id | oai:repository.up.ac.za:2263/101678 |
| institution | University of Pretoria (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:38:39.160Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UPSpace — University of Pretoria Institutional Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | University of Pretoria |
| publisherStr | University of Pretoria |
| record_format | dspace |
| source_str | UPSpace — University of Pretoria Institutional Repository |
| spelling | oai:repository.up.ac.za:2263/101678 The application and analysis of single-molecule spectroscopy data in photosynthesis Kruger, T.P.J. (Tjaart) jbotha1951@gmail.com Botha, Joshua Leon UCTD Single-molecule spectroscopy Change-point analysis Light-harvesting complexes Unbiased statistical analysis Time-tagged single-photon detection Thesis (PhD (Physics))--University of Pretoria, 2024. Most of the energy that sustains life on earth can be traced back to photosynthesis, and so its importance is difficult to overstate. Our understanding of this crucial process is still growing as we develop ever-advanced techniques to investigate the world of proteins and their interactions with light. Single-molecule spectroscopy (SMS) has emerged as a transformative technique for studying molecular systems at the nanometre scale, offering unparalleled insights into dynamic processes and heterogeneity at the individual molecule level. However, effective utilisation of SMS data often requires sophisticated analytical tools and stable experimental setups, which can pose significant challenges to researchers. This thesis addresses these challenges through the development of Full SMS, a versatile analysis software suite and a custom-designed sample cell holder, which together provide an integrated framework to advance SMS-based studies. Full SMS is a comprehensive graphical user interface (GUI)-driven software package for processing and analysing multiparameter SMS datasets. These datasets typically include fluorescence intensity and lifetime, as well as spectral properties of single dye molecules, quantum dots, or fluorescent active biomolecules. The software enables detailed analysis through tools for statistical evaluation of fluorescence intensity, clustering, and level identification; lifetime decay fitting; and second-order correlation function calculations. Visualisation features include the display of fluorescence intensity and spectral traces, as well as raster-scan images, with robust filtering options to tailor data processing. A custom HDF5-based file structure ensures efficient storage, while flexible export capabilities facilitate integration into broader research work flows. Written in Python, Full SMS is open source and accessible to users without programming expertise, leveraging a multiprocess architecture for enhanced computational performance. Full SMS is used to analyse three sample types as case studies to showcase its utility and ease-of-use. Complementing the software, this thesis also presents a custom-designed sample cell holder, which extends the capabilities of the SMS experimental setup designed and assembled in-house at the University of Pretoria. This hardware innovation enhances stability and versatility, allowing for more robust and reproducible single molecule measurements under a wider range of experimental conditions. Together, these advancements provide a powerful platform for SMS, bridging the gap between complex experimental data and resulting insights, and significantly contributing to the field of single-molecule biophysics. National Research Foundation Physics PhD (Physics) Unrestricted Faculty of Natural and Agricultural Sciences None 2025-03-25T07:20:08Z 2025-03-25T07:20:08Z 2025-09 2024-12 Thesis * S2025 http://hdl.handle.net/2263/101678 https://doi.org/10.25403/UPresearchdata.28654784 https://doi.org/10.25403/UPresearchdata.28654784 en © 2023 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. application/pdf University of Pretoria |
| spellingShingle | UCTD Single-molecule spectroscopy Change-point analysis Light-harvesting complexes Unbiased statistical analysis Time-tagged single-photon detection The application and analysis of single-molecule spectroscopy data in photosynthesis |
| title | The application and analysis of single-molecule spectroscopy data in photosynthesis |
| title_full | The application and analysis of single-molecule spectroscopy data in photosynthesis |
| title_fullStr | The application and analysis of single-molecule spectroscopy data in photosynthesis |
| title_full_unstemmed | The application and analysis of single-molecule spectroscopy data in photosynthesis |
| title_short | The application and analysis of single-molecule spectroscopy data in photosynthesis |
| title_sort | application and analysis of single molecule spectroscopy data in photosynthesis |
| topic | UCTD Single-molecule spectroscopy Change-point analysis Light-harvesting complexes Unbiased statistical analysis Time-tagged single-photon detection |
| url | http://hdl.handle.net/2263/101678 https://doi.org/10.25403/UPresearchdata.28654784 https://doi.org/10.25403/UPresearchdata.28654784 |