Abstract

This thesis is primarily concerned with studying the phenomenon of self-assembly, particularly among proteins, at the nanoscale level. It analyses the problem of how to simulate nanoscale structures, and describes in detail a suite of computer programs that support generic nanoscale simulation. Using this program, the assembly of actin and tubulin is examined in detail, as well as the generation of abstract geometric structures and a simplified model of viral capsid proteins.

The simulation program is then used to extend a number of other computational analysis methods, and applied to the problem of determining the structure of plant cell plasmodesmata. This is done using a combination of 3-D modelling, image analysis, and using the nanoscale simulator to model the deposition of stain particles. The resultant model is then analysed using a new technique, dubbed 'virtual electron microscopy', which attempts to simulate the action of an electron microscope.