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Title: Methods, rules and limits of successful self-assembly
Author: Williamson, Alexander James
ISNI:       0000 0004 2709 2515
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2011
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The self-assembly of structured particles into monodisperse clusters is a challenge on the nano-, micro- and even macro-scale. While biological systems are able to self-assemble with comparative ease, many aspects of this self-assembly are not fully understood. In this thesis, we look at the strategies and rules that can be applied to encourage the formation of monodisperse clusters. Though much of the inspiration is biological in nature, the simulations use a simple minimal patchy particle model and are thus applicable to a wide range of systems. The topics that this thesis addresses include: Encapsulation: We show how clusters can be used to encapsulate objects and demonstrate that such `templates' can be used to control the assembly mechanisms and enhance the formation of more complex objects. Hierarchical self-assembly: We investigate the use of hierarchical mechanisms in enhancing the formation of clusters. We find that, while we are able to extend the ranges where we see successful assembly by using a hierarchical assembly pathway, it does not straightforwardly provide a route to enhance the complexity of structures that can be formed. Pore formation: We use our simple model to investigate a particular biological example, namely the self-assembly and formation of heptameric alpha-haemolysin pores, and show that pore insertion is key to rationalising experimental results on this system. Phase re-entrance: We look at the computation of equilibrium phase diagrams for self-assembling systems, particularly focusing on the possible presence of an unusual liquid-vapour phase re-entrance that has been suggested by dynamical simulations, using a variety of techniques.
Supervisor: Doye, J. P. K. Sponsor: Engineering and Physical Sciences Research Council
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Computational biochemistry ; Molecular biophysics (biochemistry) ; Classical thermodynamics,heat transfer (mathematics) ; Biology and other natural sciences (mathematics) ; Computer science (mathematics) ; Infectious diseases ; Viruses ; Chemistry & allied sciences ; Biophysical chemistry ; Computational chemistry ; Nanomaterials ; Physical & theoretical chemistry ; Theoretical chemistry ; Supramolecular chemistry ; Protein chemistry ; Condensed Matter Physics ; Theoretical physics ; Biophysics ; Technology and Applied Sciences ; Physics and CS ; Colloids ; proteins ; self-assembly ; Monte Carlo ; simulations