Doctor of Philosophy / Department of Physics / Vinod Kumarappan / In general, molecules in the gas phase are free to rotate, and measurements made on such samples are averaged over a randomly oriented distribution of molecules. Any orientation dependent information is lost in such measurements. The goal of the work presented here is to a) mitigate or completely do away with orientational averaging, and b) make fully resolved orientation dependent measurements. In pursuance of similar goals, over the past 50 years chemists and physicists have developed techniques to align molecules, or to measure their orientation and tag other quantities of interest with the orientation. We focus on laser induced alignment of asymmetric top molecules. The first major contribution of our work is the development of an effective method to align all molecular axes under field-free conditions. The method employs a sequence of nonresonant, impulsive laser pulses with varied ellipticities. The efficacy of the method is first demonstrated by solution of the time dependent Schr\"{o}dinger equation for iodobenzene, and then experimentally implemented to three dimensionally align 3,5 difluoroiodobenzene. Measurement from molecules aligned in this manner greatly reduces orientational averaging. The technique was developed via a thorough understanding and extensive computations of the dynamics of rotationally excited asymmetric top molecules. The second, and perhaps more important, contribution of our work is the development of a new measurement technique to extract the complete orientation dependence of a variety of molecular processes initiated by ultrashort laser pulses. The technique involves pump-probe measurements of the process of interest from a rotational wavepacket generated by impulsive excitation of asymmetric top molecules. We apply it to make the first measurement of the single ionization probability of an asymmetric top molecule in a strong field as a function of all relevant alignment angles. The measurement and associated calculations help identify the orbital from which the electron is ionized. We expect that this technique will be widely applicable to ultrafast-laser driven processes in molecules and provide unique insight into molecular physics and chemistry.

Deep level mining is widely practised throughout South Africa, particularly in the gold sector, where the extraordinary depths of vertical hoisting present an array of challenges. The accurate and secure positioning of a conveyance next to a station has been and continues to be one of the unresolved challenges that have led to many serious injuries and equipment damage. The literature study presented in this dissertation highlights some of the complexities associated with properly docking a conveyance and investigates some current, proposed and similar systems to address the issue. From the study it was found that no satisfactory device existed prompting a systematic design of a conveyance arresting device capable of securing a conveyance in a vertical shaft at any level. Proper definition of the system requirements was obtained and summarised into 16 groups. The system requirements play an important role in the design process by setting the direction but also featuring in concept screening and evaluation. In order to generate concepts a variety of creativity inspiring techniques were employed facilitating a systematic search for a solution. Application of the techniques, Brainstorming, Synectics, TRIZ, 2500 Engineering Principles, Sourcebooks and a Morphological chart resulted in the synthesis of 9 concepts. Screening and evaluation was performed on these concepts and the most suitable concept identified. The proposed concept is a simple system where two sets of beams are extended into the shaft in order to have the conveyance settle onto the supporting shaft steelwork. Once the conveyance came to a rest on the steelwork a second set of beams are extended beneath the steelwork to positively lock the conveyance in position. This required the geometric design of the system to ensure adequate strength to satisfy a factor of safety of ten. Design decisions were made on the section properties of the clamp beam by comparing a solid section and a box section. A supporting frame is used to guide the beams, with consideration given to the most appropriate method of attaching this support frame to the conveyance. The first choice was to have the beams extend from the rear of the conveyance but due to the moments and forces involved the conveyance roof structure could not support this configuration. The support frame was instead affixed directly to the conveyance Transom. In order to support the findings of the conventional calculations performed on the system components the system was subjected to finite element analysis. The results obtained from the simulation corresponded well for the simple components and varied somewhat in the more complex shapes attributed to the assumptions made to ease the conventional calculations. Weight and reliability in a harsh shaft environment was identified as critical design parameters and motivated the use of exotic high strength materials. The high strength of the materials made is possible to design a system with practical dimensions of adequate strength supported by the conventional and modelled calculations. Even though high strength materials were used in the design the overall system weigh is dissatisfying. A potentially successful and practical device was designed but certain factors such as weight, cost, conveyance structure and infrastructure modifications threaten the implementation of the design. This dissertation sets a sound foundation for future development and the continued search for a practical simple solution to this age old challenge. / MIng (Mechanical Engineering), North-West University, Potchefstroom Campus, 2015

Deep level mining is widely practised throughout South Africa, particularly in the gold sector, where the extraordinary depths of vertical hoisting present an array of challenges. The accurate and secure positioning of a conveyance next to a station has been and continues to be one of the unresolved challenges that have led to many serious injuries and equipment damage. The literature study presented in this dissertation highlights some of the complexities associated with properly docking a conveyance and investigates some current, proposed and similar systems to address the issue. From the study it was found that no satisfactory device existed prompting a systematic design of a conveyance arresting device capable of securing a conveyance in a vertical shaft at any level. Proper definition of the system requirements was obtained and summarised into 16 groups. The system requirements play an important role in the design process by setting the direction but also featuring in concept screening and evaluation. In order to generate concepts a variety of creativity inspiring techniques were employed facilitating a systematic search for a solution. Application of the techniques, Brainstorming, Synectics, TRIZ, 2500 Engineering Principles, Sourcebooks and a Morphological chart resulted in the synthesis of 9 concepts. Screening and evaluation was performed on these concepts and the most suitable concept identified. The proposed concept is a simple system where two sets of beams are extended into the shaft in order to have the conveyance settle onto the supporting shaft steelwork. Once the conveyance came to a rest on the steelwork a second set of beams are extended beneath the steelwork to positively lock the conveyance in position. This required the geometric design of the system to ensure adequate strength to satisfy a factor of safety of ten. Design decisions were made on the section properties of the clamp beam by comparing a solid section and a box section. A supporting frame is used to guide the beams, with consideration given to the most appropriate method of attaching this support frame to the conveyance. The first choice was to have the beams extend from the rear of the conveyance but due to the moments and forces involved the conveyance roof structure could not support this configuration. The support frame was instead affixed directly to the conveyance Transom. In order to support the findings of the conventional calculations performed on the system components the system was subjected to finite element analysis. The results obtained from the simulation corresponded well for the simple components and varied somewhat in the more complex shapes attributed to the assumptions made to ease the conventional calculations. Weight and reliability in a harsh shaft environment was identified as critical design parameters and motivated the use of exotic high strength materials. The high strength of the materials made is possible to design a system with practical dimensions of adequate strength supported by the conventional and modelled calculations. Even though high strength materials were used in the design the overall system weigh is dissatisfying. A potentially successful and practical device was designed but certain factors such as weight, cost, conveyance structure and infrastructure modifications threaten the implementation of the design. This dissertation sets a sound foundation for future development and the continued search for a practical simple solution to this age old challenge. / MIng (Mechanical Engineering), North-West University, Potchefstroom Campus, 2015

BACKGROUND:Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree.RESULTS:We developed a new homology-based approach called Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods designed for estimating taxonomic composition at a relatively low taxonomic rank, TAEC demonstrates greater accuracy in quantification of genomes in a given microbial sample. We also applied TAEC on two real metagenomic datasets, oral cavity dataset and Crohn's disease dataset. Our results, while agreeing with previous findings at higher ranks of the taxonomy tree, provide accurate estimation of taxonomic compositions at the species/strain level, narrowing down which species/strains need more attention in the study of oral cavity and the Crohn's disease.CONCLUSIONS:By taking account of the similarity in the genomic sequence TAEC outperforms other available tools in estimating taxonomic composition at a very low rank, especially when closely related species/strains exist in a metagenomic sample.

Thesis (MAcc)--University of Stellenbosch, 2009.

A Profile Hidden Markov Model (HMM) is a statistical model for representing a multiple sequence alignment (MSA). Profile HMMs are important tools for sequence homology detection and have been used in wide a range of bioinformatics applications including protein structure prediction, remote homology detection, and sequence alignment. Profile HMM methods result in accurate alignments on datasets with evolutionarily similar sequences; however, I will show that on datasets with evolutionarily divergent sequences, the accuracy of HMM-based methods degrade. My dissertation presents a new statistical model for representing an MSA by using a set of HMMs. The family of HMM (fHMM) approach uses multiple HMMs instead of a single HMM to represent an MSA. I present a new algorithm for sequence alignment using the fHMM technique. I show that using the fHMM technique for sequence alignment results in more accurate alignments than the single HMM approach. As sequence alignment is a fundamental step in many bioinformatics pipelines, improvements to sequence alignment result in improvements across many different fields. I show the applicability of fHMM to three specific problems: phylogenetic placement, taxonomic profiling and identification, and MSA estimation. In phylogenetic placement, the problem addressed is how to insert a query sequence into an existing tree. In taxonomic identification and profiling, the problems addressed are how to taxonomically classify a query sequence, and how to estimate a taxonomic profile on a set of sequences. Finally, both profile HMM and fHMM require a backbone MSA as input in order to align the query sequences. In MSA estimation, the problem addressed is how to estimate a ``de novo'' MSA without the use of an existing backbone alignment. For each problem, I present a software pipeline that implements the fHMM specifically for that domain: SEPP for phylogenetic placement, TIPP for taxonomic profiling and identification, and UPP for MSA estimation. I show that SEPP has improved accuracy compared to the single HMM approach. I also show that SEPP results in more accurate phylogenetic placements compared to existing placement methods, and SEPP is more computationally efficient, both in peak memory usage and running time. I show that TIPP more accurately classifies novel sequences compared to the single HMM approach, and TIPP estimates more accurate taxonomic profiles than leading methods on simulated metagenomic datasets. I show how UPP can estimate ``de novo'' alignments using fHMM. I present results that show UPP is more accurate and efficient than existing alignment methods, and estimates accurate alignments and trees on datasets containing both full-length and fragmentary sequences. Finally, I show that UPP can estimate a very accurate alignment on a dataset with 1,000,000 sequences in less than 2 days without the need of a supercomputer. / Computer Sciences / text

The necessity to align a multi component null corrector that is used to test the 8.4 [m] off axis parabola segments of the primary mirror of the Giant Magellan Telescope (GMT) initiated this work. Computer Generated Holograms (CGHs) are often a component of these null correctors and their capability to have multiplefunctionality allows them not only to contribute to the measurement wavefront but also support the alignment. The CGH can also be used as an external tool to support the alignment of complex optical systems, although, for the applications shown in this work, the CGH is always a component of the optical system. In general CGHs change the shape of the illuminating wavefront that then can produce optical references. The uncertainty of position of those references not only depends on the uncertainty of position of the CGH with respect to the illuminating wavefront but also on the uncertainty on the shape of the illuminating wavefront. A complete analysis of the uncertainty on the position of the projected references therefore includes the illuminating optical system, that is typically an interferometer. This work provides the relationships needed to calculate the combined propagation of uncertainties on the projected optical references. This includes a geometrical optical description how light carries information of position and how diffraction may alter it. Any optical reference must be transferred to a mechanically tangible quantity for the alignment. The process to obtain the position of spheres relative to the CGH pattern where, the spheres are attached to the CGH, is provided and applied to the GMT null corrector. Knowing the location of the spheres relative to the CGH pattern is equivalent to know the location of the spheres with respect to the wavefront the pattern generates. This work provides various tools for the design and analysis to use CGHs for optical alignment including the statistical foundation that goes with it.

Disertacijoje nagrinėjami kelio trasos projektavimo dėsningumai, projektiniai sprendiniai žvyrkelių rekonstrukcijos projektuose ir jų sąsajos su automobilių kelių projektavimo normų nuostatomis. Disertacijos tikslas – pasiūlyti metodus kelio trasos projektinių sprendinių kokybei gerinti. Disertacijoje sprendžiami šie uždaviniai: nustatyti kelio trasos projektinių sprendinių sąsajas su automobilių kelių projektavimo normų nuostatomis, įvertinti esamos kelio trasos geometrinius parametrus numatomuose rekonstruoti žvyrkeliuose, atlikti lyginamuosius avaringumo tyrimus, įvertinti kelio trasos projektinių sprendinių kokybę žvyrkelių rekonstrukcijos projektuose, pateikti rekomendacijas Lietuvos Respublikos automobilių kelių projektavimo normų nuostatoms tobulinti. Disertaciją sudaro įvadas, 5 skyriai, bendrosios išvados ir rekomendacijos bei priedai. / The dissertation studies regularities for the design of road alignment, design solutions in the gravel road reconstruction projects and their links with the require-ments of road design standards. The aim of the dissertation – to suggest methods for improving the quality of design solutions. The following tasks are solved in the dissertation: to determine the links of design solutions of road alignment with the requirements of road design standards, to evaluate geometric parameters of the existing road alignment on the gravel roads to be reconstructed, to carry out comparative investigations of accident rate, to determine the quality of design solutions of road alignment in the gravel road reconstruction projects and to give recommendations for improving the requirements of the road design standards of the Republic of Lithuania. The dissertation consists of introduction, five chapters, general conclusions, recommendations and addenda.

The dissertation studies regularities for the design of road alignment, design solutions in the gravel road reconstruction projects and their links with the requirements of road design standards. The aim of the dissertation – to suggest methods for improving the quality of design solutions. The following tasks are solved in the dissertation: to determine the links of design solutions of road alignment with the requirements of road design standards, to evaluate geometric parameters of the existing road alignment on the gravel roads to be reconstructed, to carry out comparative investigations of accident rate, to determine the quality of design solutions of road alignment in the gravel road reconstruction projects and to give recommendations for improving the requirements of the road design standards of the Republic of Lithuania. The dissertation consists of introduction, five chapters, general conclusions, recommendations and addenda. / Disertacijoje nagrinėjami kelio trasos projektavimo dėsningumai, projektiniai sprendiniai žvyrkelių rekonstrukcijos projektuose ir jų sąsajos su automobilių kelių projektavimo normų nuostatomis. Disertacijos tikslas – pasiūlyti metodus kelio trasos projektinių sprendinių kokybei gerinti. Disertacijoje sprendžiami šie uždaviniai: nustatyti kelio trasos projektinių sprendinių sąsajas su automobilių kelių projektavimo normų nuostatomis, įvertinti esamos kelio trasos geometrinius parametrus numatomuose rekonstruoti žvyrkeliuose, atlikti lyginamuosius avaringumo tyrimus, įvertinti kelio trasos projektinių sprendinių kokybę žvyrkelių rekonstrukcijos projektuose, pateikti rekomendacijas Lietuvos Respublikos automobilių kelių projektavimo normų nuostatoms tobulinti. Disertaciją sudaro įvadas, 5 skyriai, bendrosios išvados ir rekomendacijos bei priedai.

This thesis introduces new techniques for finding genes in genomic sequences. Genes are regions of a genome encoding proteins of an organism. Identification of genes in a genome is an important step in the annotation process after a new genome is sequenced. The prediction accuracy of gene finding can be greatly improved by using experimental evidence. This evidence includes homologies between the genome and databases of known proteins, or evolutionary conservation of genomic sequence in different species. <br /><br /> We propose a flexible framework to incorporate several different sources of such evidence into a gene finder based on a hidden Markov model. Various sources of evidence are expressed as partial probabilistic statements about the annotation of positions in the sequence, and these are combined with the hidden Markov model to obtain the final gene prediction. The opportunity to use partial statements allows us to handle missing information transparently and to cope with the heterogeneous character of individual sources of evidence. On the other hand, this feature makes the combination step more difficult. We present a new method for combining partial probabilistic statements and prove that it is an extension of existing methods for combining complete probability statements. We evaluate the performance of our system and its individual components on data from the human and fruit fly genomes. <br /><br /> The use of sequence evolutionary conservation as a source of evidence in gene finding requires efficient and sensitive tools for finding similar regions in very long sequences. We present a method for improving the sensitivity of existing tools for this task by careful modeling of sequence properties. In particular, we build a hidden Markov model representing a typical homology between two protein coding regions and then use this model to optimize a component of a heuristic algorithm called a spaced seed. The seeds that we discover significantly improve the accuracy and running time of similarity search in protein coding regions, and are directly applicable to our gene finder.