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Modern Molecular Dynamics force fields, such as the CHARMM36 and GLYCAM06 carbohydrate force fields, are parametrised to reproduce behaviours for specific molecules under specific conditions in order to be able to predict the behaviour of similar molecular systems, where there is often no experimental data. Coupled with the sheer number available, this makes choosing the appropriate force field a formidable task. For this reason it is important that modern force fields be regularly compared. Streptococcus pneumoniae is a cause of invasive pneumococcal disease (IPD) such as pneumonia and meningitis in children under five. While there are over 90 pneumococcal serotypes only a handful of these are responsible for disease. Immunisation with the conjugate vaccine PCV7, has markedly decreased invasive pneumoccocal disease. Following PCV7 immunisation, incidences of non-vaccine serotypes, especially serotype 19A, have increased. Serotype 19F's capsular polysaccharide differs from 19A's at a single linkage position. Where 19A possesses an a-D-Glcp-(1->3)-a-L-Rhap (G13R), 19F possesses an a-D-Glcp-(1->2)-a-L-Rhap (G12R) linkage. For this reason it was thought that a 19F conjugate would cross protect against 19A. Unfortunately PCV7 vaccination appears to have been largely ineffective against 19A disease. The lack of conformational information for the G12R and G13R disaccharides provided a good opportunity to compare the CHARMM and GLYCAM force fields. The dynamics of the G12R and G13R disaccharides were investigated under both CHARMM and GLYCAM.While we did identify some discrepancies, overall the force fields were in agreement in predicting a more flexible G12R than the more restricted G13R. While it is possible that these differences account for the lack of 19F to 19A cross protectionprotection, further research is required.

CTF3 is a test facility for a new CLIC high energy linear collider. For this beamsteering and beam focusing is vital. Because physically running a beamline and changingsetup is expensive and takes much effort it is beneficial to use a simulator for thebeamline. The transportation of the beam through the beamline can be representedwith matrix multiplications and for this reason MATLAB is a fitting environment tosimulate in. A Flight Path Simulator was written in MATLAB and was succefullyimplemented and tested for the CALIFES beamline of the two-beam test stand that ispart of the CTF3 facility. / <p>återuppladdning</p>

The application of high speed computers to simulate physical devices has pioneered many scientific advances in recent times. With a suitable model to simulate their activity, solar cells are excellent candidates for such applications. In this work, a computer program has been developed which models an N+-P-P+ solar cell in one dimension. This model is structured to allow solar cells of different materials to be used in the program, however, only silicon is used here in order to demonstrate the capabilities of the program.For purposes of simplicity, the following conditions are assumed. All solar radiation enters the cell at normal incidence. The cell's temperature is uniform throughout and is considered a constant in all calculations. Doping concentrations in individual cell regions are uniform. Generation and recombination rates are also uniform within each of the cell's three regions. Items common to the two-dimensional cell but superficial to the one-dimensional cell such as contacts, lateral current flow, edge effects and variations of any type in the lateral direction are assumed to be non-existent.Background information for those not familiar with the topic is given followed by a presentation of the equations used. The general method of numerical calculation is then explained. Examples of program output are discussed along with an example application of the program. An entire program listing is given in appendix B. / Department of Physics and Astronomy

Influenza has been one of the most infectious diseases for roughly 2400 years. The most effective way to prevent influenza outbreaks and eliminate their seasonal effects is vaccination. The distribution of influenza vaccine to various groups in the population becomes an important decision determining the effectiveness of vaccination for the entire population. We developed a simulation model using the Epifire C++ application program [2] to simulate influenza transmission under a given vaccination strategy. Our model can generate a network that can be configured with different degree distributions, transmission rates, number of nodes and edges, infection periods, and perform chain-binomial based simulation of SIR (Susceptible-Infectious-Recovered) disease transmission. Furthermore, we integrated NOMAD (Nonlinear Optimization by Mesh Adaptive Direct Search) for optimizing vaccine allocation to various age groups. We calibrate our model according to age specific attack rates from the 1918 pandemic. In our simulation model, we evaluate three different vaccine policies for 36 different scenarios and 1000 individuals: The policy of the Advisory Committee on Immunization Practices (ACIP), former recommendations of the Centers for Disease Control and Prevention (CDC), and new suggestions of the CDC. We derive the number of infected people at the end of each run and calculated the corresponding cost and years of life lost. As a result, we observe that optimized vaccine distribution ensures less infected people and years of life lost compared to the fore-mentioned policies in almost all cases. On the other hand, total costs for the policies are close to each other. Former CDC policy ensures slightly lower cost than other policies and our proposed in some cases.

Compounds which exhibit liquid crystal phases have been widely used in display technology. The majority of display applications utilize the nematic liquid crystal phase, which is a liquid-like phase which has partial orientational order at the molecular level. The nematic phase exhibits birifringence which can be manipulated through the application of an external field. Subsequently, all liquid crystal-based display technology utilizes the application of an external field to ???switch??? or tune the optical properties of a nematic domain into a desired optical state. In addition to an external field, the geometry and surface interactions of the liquid crystal domain must be precisely controlled in order for the display to operate properly. Liquid crystal displays (LCDs) utilize a rectangular domain, or pixel, within which the nematic domain is exposed to surface anchoring conditions that result in a twist of the nematic alignment through the thickness of the domain. In this work, a different type of liquid crystal domain that is elliptic is studied which is formed through ???bottom-up??? techniques, such as phase separation of a liquid crystal/polymer mixture to form a polymer-dispersed liquid crystal (PDLC) composite. Nematic domains within PDLCs are spheroidal, as opposed to rectangular for a pixel, and thus exhibit substantially different behaviour in the presence of an external field. The fundamental difference between spheroidal and rectangular nematic domains is that the former requires the presence of defects in nematic order while the latter does not. The overall objective of this work is to study, for a simplified elliptic cylinder domain, the formation of the nematic domain, the resulting domain texture in the presence of an external field, and the domain texture following release of the external field. These three states are directly related to applications of PDLC films as optical functional materials, where an external (electric) field is used to manipulate the optical properties of the film. The effects of geometry (aspect ratio), surface anchoring, and external field strength are studied through a simulation-based approach using the Landau-de Gennes theory of the nematic phase.

This thesis investigates the causes of the long wait-time for patients in Emergency department (ED) of Victoria General Hospital, and suggests changes for improvements. Two prominent simulation techniques have been used to replicate the ED in a simulation model. These are Discrete-event simulation (DES) and Agent-based modeling (ABM). While DES provides the basic modeling framework ABM has been used to incorporate human behaviour in the ED. The patient flow in the ED has been divided into 3 phases: input, throughput, and output. Model results show that there could be multiple interventions to reduce time taken to be seen by the doctor for the first time (also called WTBS) either in the output phase or in the input phase. The model is able to predict that a reduction in the output phase would cause reduction in the WTBS but it is not equipped to suggest how this reduction can be achieved. To reduce WTBS by making interventions in the input phase this research proposes a strategy called fast-track treatment (FTT). This strategy helps the model to dynamically re-allocate resources if needed to alleviate high WTBS. Results show that FTT can reduce WTBS times by up-to 40%.

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.