This diploma thesis deals with the real use of operation research method in conjunction with logistics Cross-Docking technology. It is possible to solve this conjunction with either routing problems along with its modifications or simulations methods. The theoretical part describes routing problems, routing problems with time windows, simulations methods with their possibilities of real use and logistics technologies. A model of a Cross-Docking terminal that was created in the program Simul8 can be found in the practical part of this thesis. The goal of the simulation was to ensure smooth flow of products through the terminal without any long queues in the terminal. Routing problems designed to minimize the length of its routes can be found in the second half of the practical part. Other possible real application is routing problems on the real problem. The solution for this task was found using the modelling system MPL for Windows.

This diploma focuses on the real use of operations research methods in conjunction with logistics technologies. The aim is to show the way of optimization and simulation methods application and to evaluate if these methods are suitable tools for logistics technology application. Following logistic technologies were analysed: Just in Time, Kanban, Cross-Docking and Hub and Spoke. Used mathematical tools include: mixed linear programming models, distribution models, methods of multi-criteria evaluation and simulation models. On the basis of mathematical models 4 examples of new technologies introduction or analysis of already functioning systems have been solved.

This thesis implements solution for automatic docking for a mobile robot using visual markers. After initial survey of already implemented works, new docking solution is proposed. Feasibility of the solution is verified with tests of marker detection precision. The implementation is tested in a simulation and with a real robot. The functionality of the proposed solution is verified by long-term tests. The result of this work is robot’s ability to navigate known environment to find and dock a charging station. After charging the robot is able to safely disconnect from the station.

Nitric oxide (NO) is an important signaling molecule in plants. In the pollen of Arabidopsis thaliana, NO causes re-orientation of the growing tube and this response is mediated by 3′,5′-cyclic guanosine monophosphate (cGMP). However, in plants, NO-sensors have remained somewhat elusive. Here, the findings of an NO-binding candidate, Arabidopsis thaliana DIACYLGLYCEROL KINASE 4 (ATDGK4; AT5G57690) is presented. In addition to the annotated diacylglycerol kinase domain, this molecule also harbors a predicted heme-NO/oxygen (H-NOX) binding site and a guanylyl cyclase (GC) catalytic domain which have been identified based on the alignment of functionally conserved amino acid residues across species. A 3D model of the molecule was constructed, and from which the locations of the kinase catalytic center, the ATP-binding site, the GC and H-NOX domains were estimated. Docking of ATP to the kinase catalytic center was also modeled. The recombinant ATDGK4 demonstrated kinase activity in vitro, catalyzing the ATP-dependent conversion of sn-1,2-diacylglycerol (DAG) to phosphatidic acid (PA). This activity was inhibited by the mammalian DAG kinase inhibitor R59949 and importantly also by the NO donors diethylamine NONOate (DEA NONOate) and sodium nitroprusside (SNP). Recombinant ATDGK4 also has GC activity in vitro, catalyzing the conversion of guanosine-5'-triphosphate (GTP) to cGMP. The catalytic domains of ATDGK4 kinase and GC may be independently regulated since the kinase but not the GC, was inhibited by NO while Ca2+ only stimulates the GC. It is likely that the DAG kinase product, PA, causes the release of Ca2+ from the intracellular stores and Ca2+ in turn activates the GC domain of ATDGK4 through a feedback mechanism. Analysis of publicly available microarray data has revealed that ATDGK4 is highly expressed in the pollen. Here, the pollen tubes of mis-expressing atdgk4 recorded slower growth rates than the wild-type (Col-0) and importantly, they showed altered NO responses. Specifically, the mis-expressing atdgk4 pollen tubes have growth rates that were less affected by NO and showed reduced bending angles when challenged by an NO source. Further works on atdgk4 knockout/knockdown mutants will reveal the biological functions of ATDGK4 in NO and/or cGMP signaling in the pollen, and in the broader fertilization process.

This thesis has been focused around the Diels Alder reaction with the goal to design an enzyme catalyzed reaction pathway. To achieve this goal computer aided enzyme design was utilized. Common traditional methods of computational chemistry (B3LYP, MP2) do not do well when calculating reaction barriers or even reaction energies for the Diels Alder reaction. New calcu- lation methods were developed and tested. This was the focus of the first part of the thesis, by choosing a small system, extensive and heavy calculations could be done with CBS-QB3. Then by benchmarking faster methods of calculation (SCS-MP2, M06-2X) against the results, they could be graded by efficiency and cost. This was done anticipating that the same accuracy could be applied to larger systems where CBS-QB3 cannot be used. In the second part activating groups were investigated for both the diene and the dienophile, along with their effects on reaction rates. A qualitative analysis was done. This is important not only for the uncatalyzed reaction, but also interesting when searching for possible substrates for the enzyme reaction. In the last part the thesis presents a designed enzyme that catalyzes Diels Alder in silico using ∆5−3−Keto steroid isomerase. Using empirical calculations, the enzyme was scanned for catalytic activity. The catalytic effect was then showed with ab initio Quantum chemical calculations.

In an era where automation has been transforming the industrial arena, it is important not to lose focus on the health of employees who are still engaged in manual work. Employee health both physical and mental plays a vital role in the overall performance of a company, so it must be taken care of. In the case of cross-docking warehouses where there is a need for manual laborers due to the intricacies in handling products of various sizes and weights, the importance of taking care of the health of its employees becomes more vital. In the modern world of the supply chain, a cross-docking warehouse plays a vital role in providing more efficiency to the system. The type of goods handled by these cross-docking warehouses is vast and this, in turn, brings about the need to implement manual labor onto the production. This study focuses on the main physical and psychosocial problems faced by the workers in a cross-docking warehouse and how it can be improved. Here questionnaires and interviews are used to study and develop better practices and methods to improve everyday work. This thesis focuses on one of the largest cross-docking warehouses situated in Jönköping, Sweden. Here COPSOQ version III is used to find the various main psychosocial problem areas faced by the employees and unstructured interviews are used to pinpoint the main physical problems and their causes. Preventive measures to combat the problems are suggested and are supported by literature reviews.

Magister Pharmaceuticae - MPharm / Malaria disease poses substantial health risks to many nations, especially in Africa, where it primarily affects pregnant women, children, and immunocompromised patients. However, current antimalarial drugs have limitations such as low safety profile and particularly widespread treatment failure due to the increasing resistance of Plasmodium falciparum, the major causative organism to artemisinin-based therapy (ACT) and other chemotherapeutics. In the light of this, there is a pressing need for new antimalarial drugs with novel mechanisms of action and satisfactory pharmacokinetic properties, which has led to the current study. Furthermore, current antimalarial drugs target specific stages of the Plasmodium life cycle. For instance, chloroquine targets the erythrocytic stage while primaquine targets the liver stage. However, these therapies cannot achieve complete elimination of the parasite once the life cycle has been established in the body. Hence, the goal of this study is to combat resistance by finding novel compounds that can bind to a multiple-staged protein in Plasmodium falciparum. Based on this consideration, falstatin was chosen as the protein target for this study because it was observed to play a crucial role in the degradation of haemoglobin, rupture of erythrocytes by mature schizonts, and subsequent invasion of erythrocytes by free merozoites. Hence, the protein, falstatin can be targeted to inhibit cell growth and cause plasmodial cell death in merozoites as well as schizonts of Plasmodium falciparum. Therefore, it is intended that compounds that bind to falstatin could serve as novel antimalarials that target multiple stages of the Plasmodium life cycle. Consequently, this study explored the structure-based virtual screening approach to identify compounds that could bind to the protein target, falstatin in Plasmodium falciparum. An extensive literature review identified falstatin as the multi-staged drug target for this study, while homology modelling was used to generate the three-dimensional structure of falstatin. Molecular docking was conducted to predict the binding energy of compiled antiplasmodial compounds to falstatin while druglikeness analysis was used to prioritize compounds according to their ADMET (absorption, distribution, metabolism, excretion and toxicity) properties. The top-ranked compound, based on a novel ligand scoring function, was then subjected to molecular dynamics (MD). Following this step, rescoring analysis was performed on the top 5 compounds using the Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) scoring function to gain insight into their component binding energies. Thereafter, a pharmacophore hypothesis was developed based on the 5 top-ranking compounds in order to screen other compound libraries in the future. From the results, TCMDC 131646, TCMDC-124274, TCMDC-138266, TCMDC 123844 and TCMDC 131234 possessed good binding energies and satisfactory ADMET properties showing high ligand scores of 77.1, 75.4, 75.4, 75.4 and 73.1 respectively (on a total scale of 100). Also, the study revealed that the top-ranked compound, TCMDC 131646 had a binding energy of -6.15 KJ/mol, contained no toxicophore and conformed to Lipinski, Egan and Muegge rules of druglikeness. Findings from the MD simulation demonstrated that TCMDC 131646 strongly interacted with the protein, falstatin. Morealso, the study revealed that TCMDC 131646 is structurally diverse from chloroquine, artemisinin, artemether and lumefantrine, indicating that it may possess a distinct mechanism of action. The rescoring analysis of TCMDC-131646, TCMDC 124274, TCMDC-138266, TCMDC 123844 and TCMDC 131234 predicted negative binding energies ≤ -4.662 KJ/mol for the top compounds, further indicating that these compounds are likely to bind strongly with falstatin. Additionally, the developed pharmacophore hypothesis contained -H-N-C=O and N-H moieties which strongly suggested that the presence of electron-withdrawing groups could be vital for the inhibition of falstatin at the active site. Overall, TCMDC 131646 was predicted to be a drug-like and safe compound that could inhibit falstatin in Plasmodium falciparum. Chemical-disease co-occurrence analysis in literature revealed that this compound showed in-vitro antiplasmodial activity at an IC50 of 0.226μM and has also shown in vitro activity for neuralgia, hyperalgesia and arthritis. The research recommends TCMDC 131646 as a potential antimalarial hit compound that could yield novel analogues by hit expansion. However, confirmatory in-vitro and in-vivo studies are required to substantiate these predictions

Dans la cellule, les protéines évoluent dans un environnement très dense et interagissent ainsi avec un grand nombre de partenaires spécifiques et non-spécifiques qui entrent en compétition. L’objectif de ma thèse est de caractériser les propriétés physiques et évolutives des surfaces protéiques pour comprendre comment la pression de sélection s’exerce sur les protéines, façonnant leurs interactions et régulant ainsi cette sévère compétition.Pour cela, j’ai développé une méthodologie permettant de caractériser la propension des protéines à interagir avec les protéines de leur environnement, par des approches de docking. La cartographie moléculaire permettant la visualisation et la comparaison des propriétés de la surface des protéines, j’ai donc mis en place un nouveau cadre théorique basé sur une représentation des paysages énergétiques d'interaction par des cartes d'énergies. Ces cartes (en deux dimensions) reflètent de manière synthétique la propension des surfaces protéiques à engager des interactions avec d’autres protéines. Elles sont donc d’un grand intérêt pratique pour déterminer les régions des surfaces protéiques les plus enclines à engager des interactions avec d’autres molécules.Ce nouveau cadre théorique a permis de montrer que les surfaces des protéines comprennent des régions de différents niveaux d'énergies de liaison (régions chaudes, intermédiaires et froides pour les régions d'interaction favorables, intermédiaires et défavorables respectivement).Une partie importante de la thèse a consisté à caractériser les propriétés physico-chimiques et évolutives de ces différentes régions. L'autre partie a consisté à appliquer cette méthode sur plusieurs systèmes : complexes homomériques, protéines du cytosol de S. cerevisiae, familles d'interologues. Ce travail ouvre la voie à un grand nombre d'applications en bioinformatique structurale, telles que la prédiction de sites de liaison, l’annotation fonctionnelle ou encore le design de nouvelles interactions.En conclusion, la stratégie mise en place lors de ma thèse permet d’explorer la propension d’une protéine à interagir avec des centaines de partenaires d'intérêts, et donc d'investiguer le comportement d’une protéine dans un environnement cellulaire spécifique. Cela va donc au-delà de l'utilisation classique du docking "binaire" puisque notre stratégie fournit une vision systémique des interactions protéiques à l’échelle des "résidus". / In the crowded cell, proteins interact with their functional partners, but also with a large number of non-functional partners that compete with the functional ones. The goal of this thesis is to characterize the physical properties and the evolution of protein surfaces in order to understand how selection pressure exerts on proteins, shaping their interactions and regulating this severe competition.To do this I developed a framework based on docking calculations to characterize the propensity of protein surfaces to interact with other proteins. Molecular cartography enables the visualization and the comparison of surface properties of proteins. I implemented a new theoretical framework based on the representation of interaction energy landscapes by 2-D energy maps. These maps reflect in a synthetic manner the propensity of the surface of proteins to interact with other proteins. These maps are useful from a practical point view for determining the regions of protein’s surface that are more prone to interact with other proteins. Our new theoretical framework enabled to show that the surface of proteins harbor regions with different levels of propensity to interact with other proteins (hot regions, intermediate and cold regions to favorable, intermediate and unfavorable regions respectively).A large part of this thesis work consisted in characterizing the physico-chemical properties and the evolution of these regions. The other part of this thesis work consisted in applying this methodology on several study systems: homomeric complexes, cytosolic proteins from S. cerevisiae, families of interologs. This work opens the way to numerous practical applications in structural bioinformatics, such as binding site prediction, functional annotation and the design of new interactions.To conclude, the strategy implemented in this work enable the exploration of the propensity of a protein to interact with hundred of protein partners. It thus enables the investigation of the behavior of a protein in a crowded environment. This application goes beyond the classical use of protein docking as a, because our strategy provides a systemic point of view of protein interactions at an atomic resolution.

Les interactions ARN-protéine interviennent dans de nombreux processus cellulaires fondamentaux. L'obtention de détails à l'échelle atomique de ces interactions nous éclaire sur leurs fonctions, mais permet également d'envisager la conception rationnelle de ligands pouvant les moduler. Lorsque les deux techniques majeures que sont la RMN et la cristallographie aux rayons X ne permettent pas d'obtenir une structure 3D entre les deux partenaires, des approches de docking peuvent être utilisées pour apporter des modèles. L'application de ces approches aux complexes ARN-protéine se heurtent cependant à une difficulté. Ces complexes résultent en effet souvent de la liaison spécifique d'une courte séquence d'ARN simple-brin (ARNsb) à sa protéine cible. Hors, la flexibilité inhérente aux segments simples-brins impose dans une approche classique de docking d'explorer un large ensemble de leur espace conformationnel. L'objectif du projet est de contourner cette difficulté par le développement d'une approche de docking dite "par fragments". Ce dernier s'est fait à partir de domaines de liaison à l'ARN très représentés dans le monde du vivant. Les résultats ont montré une excellente capacité prédictive de l'approche à partir de la séquence de l'ARN. Ils ont de plus montré un potentiel intéressant dans la prédiction de séquences d'ARN simple-brin préférentiellement reconnues par des domaines de liaisons à l'ARN. / RNA-protein interactions mediate numerous fundamental cellular processes. Atomic scale details of these interactions shed light on their functions but can also allow the rational design of ligands that could modulate them. NMR and X-ray crystallography are the 2 main techniques used to resolve 3D highresolution structures between two interacting molecules. Docking approaches can also be utilized to give models as an alternative. However, the application of these approaches to RNA-protein complexes is hampered by an issue. RNA-protein interactions often relies on the specific recognition of a short singlestranded RNA (ssRNA) sequence by the protein. The inherent flexibility of the ssRNA segment would impose, in a classical docking approach, to explore their resulting large conformation space which is not computationally reliable. The goal of this project is to overcome this barrier by using a fragment-based docking approach. This approach developed from some of the most represented RNA-binding domains showed excellent results in the prediction of the ssRNA-protein binding mode from the RNA sequence and also a great potential to predict preferential RNA binding sequences.

Since the beginning of human civilization, medicinal plants have been used to treat a variety of infectious and non-infectious diseases. The therapeutic properties of phytochemicals have been recognized since ancient human history. The genus Helichrysum Mill. with its attractive flowers consist of an estimated 500‒600 species in the Asteraceae family. In South Africa and Namibia there are about 244‒250 species with tremendous morphological diversity. Several Helichrysum species are widely used by the indigenous population to treat various disorders such as wounds, infections, respiratory conditions, headaches, coughs, colds and fevers. Several of the Helichrysum species exhibit antiviral activity with the most relevant to this study being the discovery of anti-human immunodeficiency virus (anti-HIV) and anti-reverse transcriptase (anti-RT) activity of some species. Drug discovery and development, from the early stages of a promising compound to the final medication, is an intensive, expensive and incremental process. The ultimate goal is to identify a molecule with the desired effect in the human body and to establish its quality, safety and efficacy for treating patients. The ability to combine high-throughput analytical techniques like metabolomic and other experimental approaches with drug discovery will speed up the development of safer, more effective and better-targeted therapeutic agents. The rapidly emerging field of metabolomics and molecular docking analysis provides valuable information on drug activity, toxicity, customized drug treatments and can predict therapeutic outcomes. Extraction of the aerial parts of 32 Helichrysum species was done using polar [methanol (MeOH) 50%: distilled water (dH2O) 50%] and non-polar [hexane (Hex), dichloromethane (DCM) and acetone (Ace)] solvent systems. Anti-human immunodeficiency virus bioassays on the live HI virus revealed that polar extracts of H. mimetes and H. chrysargyrum at 2.5 μg/mL and 25 μg/mL, polar and non-polar extracts of H. infuscum at 25 μg/mL and polar and non-polar extracts of H. zeyheri, H. setosum, H. platypterum and H. kraussii at 2.5 and 25 μg/mL, had higher than 90% inhibitory activity. The polar extract of H. mimetes also exhibited reverse transcriptase (RT) inhibition as a possible indication of the mechanism of action. Proton nuclear magnetic resonance (1H NMR) spectra of the polar extracts exhibited the presence of aromatic compounds and carbohydrate moieties. Principal component analysis (PCA) of the polar extracts showed clustering related to the activity of the extracts with good predictability scores (Q2 > 0.5). However, orthogonal projections to latent structures discriminant analysis (OPLS-DA) predictability of the model was low based on the Q2 at approximately 0.25. Quinic acid (QA), isolated from H. mimetes showed promising anti-RT activity [50% inhibition concentration (IC50) = 53.82 μg/mL] which was comparable to the positive drug control, doxorubicin (IC50 = 40.31 μg/mL). The molecular docking study revealed the probable binding site and conformation of QA within cavity 4, with a docking score of -8.03. The docking score of doxorubicin within cavity 4 was -7.87. With this study, it was shown that metabolomic analysis as a tool to predict anti-HIV activity in Helichrysum species can be valuable to shorten the process. Moreover, the study of molecular docking revealed the mechanism action of quinic acid and doxorubicin against RT. / Thesis (PhD)--University of Pretoria, 2019. / Plant Production and Soil Science / PhD / Unrestricted