Badings, Matthijs (2021) The Implementation of a Coarse-Grained Model of Chondroitin Sulfates for Molecular Dynamics in GROMACS. Bachelor's Thesis, Applied Physics.
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Abstract
Chondroitin sulfates are long unbranched disaccharides, which play an important role in the extra cellular matrix of many types of tissue. An extra cellular matrix is a network of various types of molecules which provide structural support to cells. Working towards the eventual goal of developing a detailed computational model of the extra cellular matrix of the brain, a coarse-grained molecular dynamics model of two types of chondroitin sulfates, C4S and C6S, were implemented in GROMACS, a software used to perform molecular dynamics simulations. This molecular dynamics model is based on a model which was previously developed for Monte Carlo simulations by Bathe et al. Despite a number of differences between these two models, quantitatively similar results were obtained for the characteristic ratio. Although numerical values were not published for the Monte Carlo model, qualitative agreement was obtained for the persistence length as a function of ionic strength. When enabled, steric interactions were found to to have a very minor effect on the value of the characteristic ratio and ionic strength dependent persistence length, in accordance with observations from the Monte Carlo model.
| Item Type: | Thesis (Bachelor's Thesis) |
|---|---|
| Supervisor name: | Giessen, E. van der and Onck, P.R. and Shakibi, S. |
| Degree programme: | Applied Physics |
| Thesis type: | Bachelor's Thesis |
| Language: | English |
| Date Deposited: | 05 Jul 2021 12:30 |
| Last Modified: | 05 Jul 2021 12:30 |
| URI: | https://fse.studenttheses.ub.rug.nl/id/eprint/24921 |
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