Browsing by Author "Wessels, FJ"

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    Feasibility analysis of a bacterial isolation technology.
    (Stellenbosch : Stellenbosch University, 2024-02) Wessels, FJ; Nieuwoudt, MJ; Hoffmann, JE; Grobbelaar, M; Stellenbosch University. Faculty of Engineering. Dept. of Mechanical and Mechatronic Engineering.
    ENGLISH ABSTRACT: Currently it is highly challenging to use whole genome sequencing on expectorated sputum samples for the detection and analysis of Mycobacterium tuberculosis. This is due, in large part, to the lack of a suitable sample preparation process that can take expectorated sputum as input and output highly purified Mycobacterium tuberculosis genomic material. This thesis proposes a new strategy for combining existing methods in the literature into such a sputum sample preparation process. To initiate this new strategy, the project selects and tests the feasibility of a cell isolation technology for the final stage in the sample preparation process. Through a comparison of candidate cell isolation technologies in terms of the stakeholder requirements for the sample preparation process, the deterministic lateral displacement method was identified as the most promising technology for the application. More specifically, the approach involved employing two sequential deterministic lateral displacement arrays that use cylindrical and I-shaped obstacles to evaluate the Mycobacterium tuberculosis rod-shaped cells based on their diameter and length, respectively. This would, in theory, allow the Mycobacterium tuberculosis rods to be separated from a first group of cells that are larger than the diameter of the rods and a second group of cells that are smaller than the length of the rods. Then, if the lower limit of the first group of cells overlapped with the upper limit of the second group of cells, only purified Mycobacterium tuberculosis cells would remain at the end of the two arrays. To investigate the feasibility of using this method for the final stage in the sample preparation process, Computational Fluid Dynamics flow simulations were used to design a 2000:1 scale model of the proposed geometry. The experiments on this upscaled model provided an enhanced perspective of the problem on two fronts, which should be of value to future work on this topic. Firstly, the upscaled experiments generated high resolution footage of the particle behaviour, which is difficult to do at the microscale. This footage allowed for the identification and analysis of behavioural patterns in the model Mycobacterium tuberculosis cells. Most notably, this showed that motion occurs predominantly in the xy-plane, that rotating rocking motion punctuated by periodic flipping dominates the contactless flow, and that various particle-to-obstacle interactions occur in a rigid hierarchy. Secondly, the upscaled device allowed for a detailed quantification of the flow field, which is next to impossible at the microscale. These flow measurements show that the I-shaped obstacles pose a 38.6% higher fluidic resistance than the cylindrical obstacles at a column slant angle of 1.59°. These upscaled results provide an ideal foundation for future numerical investigations, as they provide both high-quality qualitative data of the particle behaviour and high-quality quantitative data of the flow field. This data may be used as validation benchmarks for future simulations that continue the investigation started here.