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Simulation of confined tethered polymers
Thesis (MSc)--Stellenbosch University, 2025.
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Stellenbosch : Stellenbosch University
2025
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| _version_ | 1867614087098138624 |
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| access_status_str | Open Access |
| author | De Villiers, Cornelius Johannes |
| author2 | Muller-Nedebock, K. K. |
| author_browse | De Villiers, Cornelius Johannes Muller-Nedebock, K. K. |
| author_facet | Muller-Nedebock, K. K. De Villiers, Cornelius Johannes |
| author_sort | De Villiers, Cornelius Johannes |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2025. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/132133 |
| institution | Stellenbosch University (South Africa) |
| last_indexed | 2026-06-10T12:46:27.621Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/132133 Simulation of confined tethered polymers De Villiers, Cornelius Johannes Muller-Nedebock, K. K. Stellenbosch University. Faculty of Science. Dept. of Physics. Polymers -- Simulation methods Langevin equations Molecular dynamics -- Simulation methods Crosslinked polymers -- Mathematical models UCTD Thesis (MSc)--Stellenbosch University, 2025. de Villiers, C. J. 2025. Simulation of confined tethered polymers. Unpublished masters thesis. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/d69ca9a8-9eff-490c-900b-794ab3974230 ENGLISH ABSTRACT: We investigated the dynamics of polymers in the presence of a heat bath, with a special focus on semi-flexible p olymers u nder c onfinement an d tethering, which may mimic certain biological scenarios. We achieved this by Langevin dynamics simulation using the LAMMPS software package. We began with simulating a free Kremer-Grest polymer with a bending rigidity in a heat bath. For this setup, we were able to reproduce results consistent with the wormlike chain. Subsequently, we investigated how these standard results change when tethering the polymer to the tip of a cone. The tethering was done via fixing a tether to the tip of the cone, and bonding this tether to the middle of the polymer, splitting it into two halves. This tether was also modelled as a polymer. Further, the azimuthal angle of the cone was varied. We found results consistent with reducing the conformational freedom of the system. Finally, we further developed the system by introducing cross-links between the two halves of the polymer, examining how the degree of crosslinking affects the standard results. AFRIKAANSE OPSOMMING: Ons het die dinamika van polimere in die teenwoordigheid van ’n hittebad ondersoek, met ’n spesiale fokus op semi-buigsame polimere wat ingeperk en vasgemaak is, wat sekere biologiese omstandighede kan naboots. Ons het dit bereik deur Langevin-dinamika-simulasies met die LAMMPS-sagtewarepakket uit te voer. Ons het begin met die simulering van ’n vrye Kremer-Grest- polimeer met ’n buigstyfheid in ’n hittebad. Vir hierdie opstelling kon ons resultate produseer wat ooreenstem met die wurmagtige ketting. Daarna het ons ondersoek hoe hierdie standaardresultate verander wanneer die polimeer aan die punt van ’n keël vasgemaak word. Die vasmaak is gedoen deur ’n ket- ting aan die punt van die keël vas te maak, en hierdie ketting is aan die middel van die polimeer vasgemaak, wat dit in twee helftes verdeel. Hierdie ketting is ook gemodelleer as ’n polimeer, en verder is die asimutale hoek van die keël gevarieer. Ons het resultate gevind wat ooreenstem met die vermindering van die konformasievryheid van die sisteem. Laastens het ons die stelsel verder ontwikkel deur kruisbindings tussen die twee vertakkings van die polimeer in te stel, wat steeds in die helfte verdeel is deur die ketting, om te ondersoek hoe die aantal kruisbindings die standaardresultate beïnvloed. Masters 2025-05-27T09:39:46Z 2025-05-27T09:39:46Z 2025-03 Thesis https://scholar.sun.ac.za/handle/10019.1/132133 Stellenbosch University vi, 73 pages : illustrations application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Polymers -- Simulation methods Langevin equations Molecular dynamics -- Simulation methods Crosslinked polymers -- Mathematical models UCTD De Villiers, Cornelius Johannes Simulation of confined tethered polymers |
| title | Simulation of confined tethered polymers |
| title_full | Simulation of confined tethered polymers |
| title_fullStr | Simulation of confined tethered polymers |
| title_full_unstemmed | Simulation of confined tethered polymers |
| title_short | Simulation of confined tethered polymers |
| title_sort | simulation of confined tethered polymers |
| topic | Polymers -- Simulation methods Langevin equations Molecular dynamics -- Simulation methods Crosslinked polymers -- Mathematical models UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/132133 |
| work_keys_str_mv | AT devillierscorneliusjohannes simulationofconfinedtetheredpolymers |