Coarse-grained computer simulation of fibre self-assembly.

PRYBYTAK, Pavel V. (2012). Coarse-grained computer simulation of fibre self-assembly. Doctoral, Sheffield Hallam University (United Kingdom)..

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Abstract

In this Thesis we present the results of a series of molecular computer simulation studies undertaken to investigate fibre self-assembly. The driving objective for this work has been to develop a generic coarse-grained model for peptide systems and examine its ability to exhibit free self-assembly of fibre structures at moderate computational cost. Firstly, the development of a model is addressed. The model is based on mixtures of disc-like Gay-Berne and spherical Lennard-Jones particles. The discs represent single-site models of peptide molecules, whereas the spheres represent solvent particles. An additional parameter in the disc-sphere potential is introduced to adjust solvent quality. Using this model, depending on variables such as the solvent quality, formation of either chromonic stacks or chiral fibres is observed. To explore the process of fibre self-assembly in more detail, larger systems are studied. Here, we find that, for a narrow temperature range, defect-free chiral fibres can freely self-assemble from an initially isotropic configuration. This occurs as a result of a complex multistage process, which can be controlled by adjusting the temperature. We study systems with different disc-disc interaction strengths and find that this parameter can be used to control the size and shape of a resultant fibre. We also investigate whether chiral fibres have a limiting radius. Further, we introduce a modified version of the model in which the discs rims have both solvophobic and solvophilic regions. Depending on the relative sizes of these regions, a range of different structures are formed ('Toblerone', bilayer-sheet, cord, triple-helix). These complex structures comprise solvent particles as well as discs, and their variety can be understood from the geometries of the contributing particle types. The formation kinetics of these assemblies are also investigated.

Item Type: Thesis (Doctoral)
Additional Information: Thesis (Ph.D.)--Sheffield Hallam University (United Kingdom), 2012.
Research Institute, Centre or Group: Sheffield Hallam Doctoral Theses
Depositing User: EPrints Services
Date Deposited: 10 Apr 2018 17:21
Last Modified: 30 May 2018 13:23
URI: http://shura.shu.ac.uk/id/eprint/20250

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