A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg. in fulfilment of the requirements tor the degree of Master of Science / This thesis develops the theoretical basis of the qualitative frame based modelling technique, a paradigm recently proposed by Starfield for the modelling of ecosystems with a multiplicity of stable states. This technique is a refinement of the State-and- Transition conceptual model of Westoby et al which involves the division of the ecosystem dynamics into a catelog of stable 'states' and a suite of transitions between these states. The frame models of Starfield associate with each stable configuration of the ecosystem a qualitative rule based model for the key processes in that stable configuration. The aims of this thesis are the following, 1. A rigorous definition of frame modelling of dynamic ecosystems is proposed, and this theoretical foundation is used to demonstrate that qualitative frame models may be used to mode! dynamic ecosystems to an arbitrary accuracy. 2. The development of implementation software. A qualitative rule based frame modelling environment is presented. and a specification for an improved environment is proposed based on the theoretical work. / Andrew Chakane 2019

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Canegro is a leading sugarcane crop simulation model and has been used extensively in agronomic research and management. The model has been under development since the late 1980s at the South African Sugarcane Research Institute (SASRI). The Decision Support System for Agrotechnology Transfer (DSSAT) is a software package containing models for a wide range of field crops, and utilities for processing, storing and analysing model inputs and outputs. Canegro was included as part of version 3.1 of DSSAT in the mid-1990s. The SASRI Canegro model was subsequently developed further, but these changes were never integrated, nor incorporated, into DSSAT. DSSAT has also developed substantially, and as of version 4 adopted a modular Cropping System Model (CSM) structure, providing numerous scientific and practical advantages over previous non-modular versions. The DSSAT-Canegro v.3 model was not modified to use this modular structure. Following recognition of the advantages offered by DSSAT and its modular CSM, a project was initiated to incorporate the Canegro model into the DSSAT CSM. The project entailed: (i) restructuring and integrating the current Canegro plant growth and development code into the DSSAT v4 CSM modular framework, making use of its generic modules for management, soil, weather and the energy balance; (ii) verification of DSSAT CSM Canegro model results against the current SASRI version of Canegro to ensure that the new model produced similar results to the original model, for a set of simulated situations; and (iii) evaluation of the new DSSAT CSM Canegro model against experimental datasets. The new DSSAT v4 CSM Canegro model has been verified to behave identically to the SASRI Canegro model when the water balance is not modelled and growth can occur at climatic potential rates. When the water balance is simulated but where the crop is not stressed, near identical output is produced by both models. Under water-stressed conditions, some discrepancies appear between the two models, due to differences in the calculation of reference evaporation, soil surface evaporation and runoff. Validation of the new model against data from 16 experimental crops produced root mean squared errors of 6.62 t ha-1 for stalk dry mass and 3.59 t ha-1 for sucrose mass – very similar to published values for Canegro. This project has yielded a functional, well-documented, maintainable and user-friendly version of the Canegro model, which is available for universal use via the official release of the DSSAT v4.5. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.

The purpose of the thesis was to investigate the influence communication architecture decisions have on the performance of a simulation system with distributed components. In particular, the objective was to assess the relative importance of factors affecting reliability and variability of an external data interface to the performance of the simulation, as compared to factor within the simulation itself.

Thesis (M.Sc.(Engineering)--University of the Witwatersrand, 1990.

Many biomolecular processes involve mechanical force-induced reactions in the cell, such as translocation, and mechanical stretching of biopolymers. Recent advances in single molecule manipulation techniques make it possible to apply mechanical force to individual biomolecules and study their dynamics. To gain molecular level understanding of these processes and to interpret the single-molecule experiments, we used Langevin dynamics simulations of coarse-grained biopolymer models. Our result show that the mechanism of translocation of proteins through pores depends on the pore diameter, on the magnitude of the pulling force and on whether the force is applied at the N- or the C-terminus of the chain. In addition, the translocation kinetics of peptides varies with their stability. The mechanism of protein translocation is found to be different from that of a structureless polypeptide of the same length. We further showed that unfolding mechanism of translocation process is different from when the same protein is stretched between its C- and N-termini. We also studied the mechanical and chemical/thermal denaturation of proteins. We observed that the free energy profile along the mechanical reaction coordinate and the chemical reaction coordinate are different. In our protein model, the mechanical and chemical/thermal denaturation cannot be simply explained in terms of a simple onedimensional free energy landscape. We further analyzed the spontaneous folding and refolding under a constant force and found that refolding generally occurs via different mechanisms. Similarly, we investigated the protein unfolding/refolding under the applied force that varies with a constant loading rate. This study shows that unfolding/refolding pathways are generally similar for low loading/unloading rates while they become different for high loading/unloading rates. Finally, we studied the dynamics of molecular friction knots formed by a pair of polymer strands. We examined different knot types, and different polymer sequences. Depending on the knot type and the nature of the polymer, we observed two different behaviors when the force F is exerted to separate the polymer strands. The knot between polymer strands can be strong (the time [tau] the knot stays tied increases with the force F applied to separate the strands) or weak ([tau]decreases with increasing F).

A significant percentage of computational time in compositional simulations is spent performing flash calculations to determine the equilibrium compositions of hydrocarbon phases in situ. Flash calculations must be done at each time step for each grid block; thus billions of such calculations are possible. It would be very important to reduce the computational time of flash calculations significantly so that more grid blocks or components may be used. In this dissertation, three different methods are developed that yield fast, robust and accurate phase behavior calculations useful for compositional simulation and other applications. The first approach is to express the mixing rule in equations-of-state (EOS) so that a flash calculation is at most a function of six variables, often referred to as reduced parameters, regardless of the number of pseudocomponents. This is done without sacrificing accuracy and with improved robustness compared with the conventional method. This approach is extended for flash calculations with three or more phases. The reduced method is also derived for use in stability analysis, yielding significant speedup. The second approach improves flash calculations when K-values are assumed constant. We developed a new continuous objective function with improved linearity and specified a small window in which the equilibrium compositions must lie. The calculation speed and robustness of the constant K-value flash are significantly improved. This new approach replaces the Rachford-Rice procedure that is embedded in the conventional flash calculations. In the last approach, a limited compositional model for ternary systems is developed using a novel transformation method. In this method, all tie lines in ternary systems are first transformed to a new compositional space where all tie lines are made parallel. The binodal curves in the transformed space are regressed with any accurate function. Equilibrium phase behavior calculations are then done in this transformed space non-iteratively. The compositions in the transformed space are translated back to the actual compositional space. The new method is very fast and robust because no iteration is required and thus always converges even at the critical point because it is a direct method. The implementation of some of these approaches into compositional simulators, for example UTCOMP or GPAS, shows that they are faster than conventional flash calculations, without sacrificing simulation accuracy. For example, the implementation of the transformation method into UTCOMP shows that the new method is more than ten times faster than conventional flash calculations.

published_or_final_version / abstract / toc / Civil Engineering / Master / Master of Philosophy

Although increased genome sequencing e orts have increased our understanding of genomic variability within many bacterial species, there has been limited application of this knowledge towards assessing current molecular typing methods and developing novel molecular typing methods. This thesis reports a novel in silico comparative genomic framework where the performance of typing methods is assessed on the basis of the discriminatory power of the method as well as the concordance of the method with a whole-genome phylogeny. Using this framework, we designed a comparative genomic ngerprinting (CGF) assay for Listeria monocytogenes through optimized molecular marker selection. In silico validation and assessment of the CGF assay against two other molecular typing methods for L. monocytogenes (multilocus sequence typing (MLST) and multiple virulence locus sequence typing (MVLST)) revealed that the CGF assay had better performance than these typing methods. Hence, optimized molecular marker selection can be used to produce highly discriminatory assays with high concordance to whole-genome phylogenies. The framework described in this thesis can be used to assess current molecular typing methods against whole-genome phylogenies and design the next generation of high-performance molecular typing methods from whole-genome sequence data. / xiii, 100 leaves : ill. ; 29 cm