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In Gram-negative bacteria, the Outer membrane (OM) acts as a first barrier to screen unwanted compounds whilst enabling ions and very small solutes to diffuse into the cell. Most of nutrients and essential ions are effectively transported across a membrane via the outer membrane proteins (OMPs). The water-filled β- barrel OMPs are called porins. These pores are classified into two groups, non- specific and substrate-specific porins. Each of them has different mechanisms to facilitate its substrate translocation. To reveal the process of substrate permeation and selectivity in microscopic detail, molecular dynamics (MD) simulations and applications were performed in this thesis. The studies in this thesis focus on a series of classical porins. These proteins share similar feature where extracellular loop(s) (generally loop 3 (L3)) is folded into the middle of the pore and act as a constriction site which is important for substrate specificity and selectivity. The studies firstly concentrate on the structural properties and dynamics of the general trimeric porins, OmpC and OmpF whose sequences share 60% identity. OmpC and OmpF are found to have similar mechanism of latching loop (L2) to maintain trimeric stability. The smaller pore size allows OmpC to be more cation-selective than OmpF. Additionally, the major driving force for cation permeation in both porins is not from electrostatic properties. This differs from the phosphate-selective porin, trimeric OprP, where a phosphate diffusion depends on electrostatic interactions with positively charged pore-lining residues. The charge brush-like behavior of interior Arg and Lys residues plays a major role in phosphate selectivity. Also, the free energy profiles (PMF) reveal two key regions that are important for differentiating phosphate from other anions. The brush-like mechanism of OprP were also implanted to the simplified model pores in order to determine the possibility of transferring phosphate-selective properties of OprP to a model which may be useful for future design of nanopores. It is found that the duplication of functional residues and pore cavity can turn a model into the highly phosphate-selective pore. Importantly, the phosphate-binding affinity is dependent on the ability of the pore to interfere and occupy the hydration shell of a translocating phosphate where such ability can be maximized by an increase in sidechain flexibility. In case of uptake of more complex substrates, OpdK also employs a constriction site to select its substrate, aromatic vanillate (VNL) with total charge of -1. Unlike ion-specific porins, the free VNL is attracted by polar and aromatic interactions and sequentially directed through the periplasmic vestibule by charged residues insides the pore. The correct orientation of VNL on arrival is crucial for OpdK to recognize and enable the permeation process.

Computer simulations allow researchers to study the dynamics and interactions of biological molecules in ways that cannot be currently achieved in experiments. In this work, I have used computer simulations to study the following systems: (1) carbohydrate-carbohydrate and carbohydrate-amino acid interactions using all-atom molecular dynamics simulations, and (2) protein-protein interactions using coarse-grained implicit solvent models. My first studies involved simulating carbohydrate and amino acid systems using atomistic force fields. During my initial simulations, I observed that carbohydrates were interacting too favorably leading them to aggregate in conditions under which they experimentally remain soluble. To alleviate this issue, I surgically modified the carbohydrate-carbohydrate interaction parameters in order to match osmotic pressure data from experiment. This approach was successful while preserving many of the correct features of the original force field. Next, I observed similar issues in carbohydrate-amino acid simulations and used the same methodology to correct carbohydrate-amino acid parameters. I showed that the modified parameters also worked well in simulations of much larger systems, allowing realistic simulations to be performed on polymeric sugars such as dextran and the peptidoglycan layer of the cell wall. In a more recent and separate study, I have attempted to parameterize very coarse-grained models of proteins (for eventual use in cellular scale simulations) using experimental osmotic second virial coefficients. I found that a 10 residue-per-bead model including electrostatic interactions could approximately match most of the second virial coefficient data obtained from experiment. In contrast, a more simplified, spherical model of proteins could not adequately reproduce experiment. Although more work will be required to establish a better quantitative agreement with experiment, my results indicate that even very coarse models of proteins can produce reasonably accurate simulations of protein-protein interactions.

The term Virtual Patient (VP) refers to the use of virtual characters which embody patients in a virtual environment. They are implemented in computer simulations to create realistic clinical encounters. VPs have been used successfully in health education to promote and foster clinical communication skills. Additionally, computer simulations offer the advantage of being standardized, safe, repeatable, and do not require as much resources as role-play simulations which rely on actors. This thesis addresses the design and evaluation of a VP-based system aimed for clinical trainees, and uses the field of audiology as a case study. The system is designed to simulate real client encounters and allows students to practice using a standard set of procedures that they have to master in their profession. A wide range of VPs have been implemented for this purpose. The system was evaluated with audiology students, reinforcing the ecological validity of the research. The design of the system was guided by an iterative process of implementation, usability testing, and experiments focusing on students' learning outcomes. The Clinical Audiology Simulator (CAS) was evaluated during five experiments, assessing students learning gains following exposure to the CAS. Learning gains have been assessed through the use of role-play simulations and paper assessments. The procedures evaluated are clinical history taking, pure tone audiometry, and speech audiometry. A further experiment assessed the impact of additional formative feedback on students learning gains, using the pure tone audiometry procedure as an example. The results of these experiments suggest that the system has a great potential to foster students learning, with measurable gains in some of these procedures. They also indicate that feedback and its delivery take an important role in this process. This thesis elaborates how VP-based simulations can reinforce young clinicians' ability to learn procedural skills. I highlight some of the challenges a researcher faces in designing and evaluating such systems, focusing on the implementation of interaction scripts for the VPs, the assessment of learning gains and transfer of skills, and the evaluation of computer simulations as part of a curriculum. VPs have the potential to promote clinical trainees' learning of skills, and to provide students with more opportunities for safe practice in a field where beginning trainees often have few opportunities for actual hands on experience.

Plasmas involving strong electron drift in crossed electric and magnetic fields are of great interest for a number of applications such as space propulsion and material processing plasma sources. Specific applications include Hall thrusters, which are high efficiency, low thrust propulsion systems used on many missions for satellite orbit corrections and for future planned interplanetary missions, as well as magnetrons of various configurations used in plasma deposition devices. Similar conditions also exist in the E-layer of the ionosphere and on the Sun. Despite many successful applications of Hall thrusters and other Hall plasma sources, some aspects of their operation are still poorly understood. A particularly important problem is the anomalous electron transport, which greatly exceeds classical collisional values. Hall plasma devices exhibit numerous turbulent fluctuations in a wide frequency range and it is believed that fluctuations resulting from plasma instabilities are likely one of the main causes of the observed anomalous transport. Plasma turbulence also affects many other important processes such as electron injection, location of the ionization region and wall erosion among others that influence the operation and efficiency of Hall thrusters. In Hall thrusters, the E0xB0 flow is made unstable due to gradients in the plasma density, temperature and magnetic field. The gradient drift instabilities are long wavelength instabilities that propagate in the azimuthal direction. A fluid theory of these unstable modes is proposed. It is shown that a full account of the compressibility of the electron flow in inhomogeneous magnetic field leads to quantitative modifications of the previously obtained instability criteria and characteristics of the unstable modes. The ExB drift also drives ion sound type instabilities in Hall thrusters. The reactive/dissipative response of the closure current to the thruster walls drives these negative energy modes. A model for this type of instabilities is proposed and analyzed for typical Hall thruster conditions. It is shown how wall parameters modify the characteristic growth rate and frequency of the unstable modes and the related anomalous transport. Nonlinear phenomena are important to understand different aspects of the Hall thruster plasma dynamics. A nonlinear fluid model for the typical Hall thruster plasma is proposed. The model takes into account electron inertia, electron collisions with neutrals, density gradients as well as various nonlinear terms that arise from the electron drift and nonlinear polarization that were included via the gyroviscous cancellation. The proposed model includes the long wavelength and the low hybrid modes destabilized by density gradients and collisions. This system of fluid equations was implemented using the computational framework BOUT++ from which a set of nonlinear simulations of plasma turbulence was performed. It is shown from these first principles nonlinear simulations that small scale low hybrid oscillations result in an anomalous electron current significantly exceeding the classical collisional current.

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The topic of this thesis arose out of a desire to meet the need for a practical means of supplementing the preparation of Higher Diploma of Education (H.D.E.) students for their future role as first-year teachers. It was established that this need was not adequately filled by conventional university teacher-training methods. The literature about computerised simulation of role-playing and teaching activities was investigated and the investigation indicated that such simulations had been relatively successful. A published American computer simulation, TENURE, in which the student plays the role of a first-year teacher, was selected for modification to meet the needs of South African students. This program is implemented in the TUTOR computer language and runs on the Control Data South Africa PLATO system. In order to determine the needs of South African students, two groups of Rhodes University students worked through the simulation as it was being modified. The modifications were adapted according to the students' responses to a questionnaire. The simulation has been tested by 72 H.D.E. students and several educationists and the response has been positive

Chapter 1 gives a brief introduction to statistical quality control (SQC) and provides background information regarding the research conducted in this thesis. We begin Chapter 2 with the design of Shewhart-type Phase I S2, S and R control charts for the situation when the mean and the variance are both unknown and are estimated on the basis of m independent rational subgroups each of size n available from a normally distributed process. The derivations recognize that in Phase I (with unknown parameters) the signaling events are dependent and that more than one comparison is made against the same estimated limits simultaneously; this leads to working with the joint distribution of a set of dependent random variables. Using intensive computer simulations, tables are provided with the charting constants for each chart for a given false alarm probability. Second an overview of the literature on Phase I parametric control charts for univariate variables data is given assuming that the form of the underlying continuous distribution is known. The overview presents the current state of the art and what challenges still remain. It is pointed out that, because the Phase I signaling events are dependent and multiple signaling events are to be dealt with simultaneously (in making an in-control or not-in-control decision), the joint distribution of the charting statistics needs to be used and the recommendation is to control the probability of at least one false alarm while setting up the charts. In Chapter 3 we derive and evaluate expressions for the run-length distributions of the Phase II Shewhart-type p-chart and the Phase II Shewhart-type c-chart when the parameters are estimated. We then examine the effect of estimating and on the performance of the p-chart and the c-chart via their run-length distributions and associated characteristics such as the average run-length, the false alarm rate and the probability of a “no-signal”. An exact approach based on the binomial and the Poisson distributions is used to derive expressions for the Phase II run-length distributions and the related Phase II characteristics using expectation by conditioning (see e.g. Chakraborti, (2000)). We first obtain the characteristics of the run-length distributions conditioned on point estimates from Phase I and then find the unconditional characteristics by averaging over the distributions of the point estimators. The in-control and the out-of-control properties of the charts are looked at. The results are used to discuss the appropriateness of the widely followed empirical rules for choosing the size of the Phase I sample used to estimate the unknown parameters; this includes the number of reference samples m and the sample size n. Chapter 4 focuses on distribution-free control charts and considers a new class of nonparametric charts with runs-type signaling rules (i.e. runs of the charting statistics above and below the control limits) for both the scenarios where the percentile of interest of the distribution is known and unknown. In the former situation (or Case K) the charts are based on the sign test statistic and enhance the sign chart proposed by Amin et al. (1995); in the latter scenario (or Case U) the charts are based on the two-sample median test statistic and improve the precedence charts by Chakraborti et al. (2004). A Markov chain approach (see e.g. Fu and Lou, (2003)) is used to derive the run-length distributions, the average run-lengths, the standard deviation of the run-lengths etc. for our runs rule enhanced charts. In some cases, we also draw on the results of the geometric distribution of order k (see e.g. Chapter 2 of Balakrishnan and Koutras, (2002)) to obtain closed form and explicit expressions for the run-length distributions and/or their associated performance characteristics. Tables are provided for implementation of the charts and examples are given to illustrate the application and usefulness of the charts. The in-control and the out-of-control performance of the charts are studied and compared to the existing nonparametric charts using criteria such as the average run-length, the standard deviation of the run-length, the false alarm rate and some percentiles of the run-length, including the median run-length. It is shown that the proposed “runs rules enhanced” sign charts offer more practically desirable in-control average run-lengths and false alarm rates and perform better for some distributions. Chapter 5 wraps up this thesis with a summary of the research carried out and offers concluding remarks concerning unanswered questions and/or future research opportunities. / Thesis (PhD)--University of Pretoria, 2009. / Mathematics and Applied Mathematics / unrestricted

DNA sequencing via nanopore translocation was a pipedream two decades ago. Today, biotech companies are releasing commercial devices. Yet many challenges still hover around the simple concept of threading a long DNA molecule through a small nanoscopic pore with the aim of extracting the DNA’s sequence along the process. In this thesis I use computer simulations to create what are in essence virtual pro- totypes for testing design ideas for the improvement of nanopore translocation devices. These ideas are based on the general concept of modifying the average shape of the initial DNA conformations. This is done, for example, by introducing new geometrical features to the nanopore’s surrounding or by the means of some external force. The goal of these simulations is not just to test design improvements, but also to systematically deconstruct the physical mechanisms involved in the translocation process. The roles of pore friction, initial polymer conformations, monomer crowding on the trans- side of the membrane, Brownian fluctuations, and polymer rigidity can, with careful consideration, be essentially muted at will. Computer simulations in this sense play the role of a sandbox in which the physics can be tinkered with, in order to assess and evaluate the magnitude of certain approximations found in theoretical modelling of translocation. This enables me to construct theoretical models that contain the necessary features pertaining to the different designs tested by simulations. The work presented here is thus constituted of both Langevin Dynamics simulations and adaptations of the Tension-Propagation theory of polymer translocation when the polymer is subject to the various test conditions.

It is impossible to determine the amount of money that is spent every replacing products damaged from wear, but it is safe to assume that it is in the millions of dollars. With metallic materials, liquid lubricants are often used to prevent wear from materials rubbing against one another. However, with polymeric materials, liquid lubricants cause swelling, creating an increase in friction and therefore increasing the wear. Therefore, a different method or methods to mitigate wear in polymers should be developed. For better understanding of the phenomenon of wear, scratch resistance testing can be used. For this project, classic molecular dynamics is used to study the mechanics of nanometer scale scratching on amorphous polymeric materials. As a first approach, a model was created for polyethylene, considering intramolecular and intermolecular interactions as well as mass and volume of the CH2 monomers in a polymer chain. The obtained results include analysis of penetration depth and recovery percentage related to indenter force and size.