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In this thesis, a systematic study of the structural characterization of the capsular polysaccharides of Streptococcus pneumoniae is conducted using Molecular Modelling methods. S.pneumoniae causes invasive pneumococcal disease (IPD), a leading cause of death in children under five. The serotypes in group 6 are amongst the most common of IPD causing serotypes. We performed structural characterization of serogroup 6 to understand the structural relationships between serotypes 6A, 6B, 6C and 6D in an attempt to understand the cross protection seen within the group. The 6B saccharide has been included in the early conjugate vaccine (PCV-7), and has shown to elicit protection against the 6B as well as offer some cross-protection against 6A. 6A has since been included in the latter conjugate vaccines in the hopes of eliciting stronger protection against 6A and 6C. Molecular Dynamics simulations were used to investigate the conformations of oligosaccharides with the aim of elucidating a conformational rationale for why small changes in the carbohydrate primary structure result in variable efficacy. We began by examining the Potential of Mean Force (PMF) plots of the disaccharide subunits which make up the Serogroup 6 oligosaccharides. The PMFs showed the free energy proles along the torsional angles space of the disaccharides. This conformational information was then used to build the four oligosaccharides on which simulations were conducted. These simulations showed that serotype pairs 6A/6C and 6B/6D have similar structures.

A method was developed for finding charge and current distribution in nanoscale electronic devices such as MOS capacitors and resonant tunneling diodes. A system of differential equations, comprised of the Poisson and Schrödinger equations, was solved iteratively to find the electric field and charge distribution inside devices under simulation. The proposed solution method was based on the non-equilibrium Green’s function approach, but expands on that approach by using spatially varying quasi-Fermi levels to construct density operators. The proposed method was applied to several example device models. The simulation results are presented. Calculated charge distributions in FET transistors were found to have necessary features: for example, the results showed inversion layer formation. However, the calculated current-voltage curves differed significantly from published experimental results and other simulators. Other published methods for charge transport simulation are compared to the proposed method.

This thesis includes the modification and optimization to an electric field mill based on micromachining technology. The sensor was originally designed to overcome the disadvantages of the conventional macroscopic field mill. Although it achieved all these listed above with a minimum detectable field strength at 42 V/m, some drawbacks are yet to be settled. In order to overcome these drawbacks, modifications are studied and put forward. Metal coating of the sensor surface could lead to a good electrical grounding that addresses the charging problem. Non-resonant working design was established with a shutter displacement around 5μm. Finite element simulations were set up to look into the optimizations of the structure parameters of the sensor, focusing on the shutter and electrodes. Moreover, the fabrication process was also studied with attempts of each step carried out in the NSFL of University of Manitoba.

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