Using ion-trapping techniques, selected laboratory experiments on ion-molecule reactions of astrophysical interest have been performed. For the first time a carbon beam source has been integrated into an ion trapping machine for studying collisions between ions and neutral carbon atoms and molecules. Results are presented for the interaction of D3+ ions stored in a ring-electrode trap (RET), with a beam of hot neutral carbon molecules, Cn (n = 1, 2, 3). The measured reaction rate coefficients are up to a factor two smaller than values presently used in astrophysical models. In order to complete our knowledge about the ion chemistry involving three carbon atoms, detailed investigations of reactions of C3+, C3H+ and C3H3+ with H2 and HD have been performed between 15 K and room temperature. These studies have been performed in a second apparatus, a variable-temperature 22-pole trap machine (VT-22PT). Results include reactive collisions, deuteration and radiative association. It is discussed in connection with the increase in lifetime of the C3+ + H2 collision complexes with falling temperature, what could be responsible for producing more C3H+ at 15 K. Tunneling is excluded. In C3+ + HD collisions an isotope effect has been detected, the C3D+ product ions being slightly more abundant than C3H+. Comparison of the reaction of C3H+ primary ions with HD and H2 gas revealed that the deuterated molecules are significantly more reactive. The process of radiative association of C3H+ and for the first time of C3+ with hydrogen molecules has been observed. An analysis of the data shows that radiative association becomes slower, if the neutral reactant is deuterated. Finally, the theoretical prediction from ab initio calculations that C3H3+ does not exchange an H for a D in collisions with HD, has been proven in an ion trap experiment. Careful analysis of all competing processes allows the conclusion that the rate coefficient is smaller than 4x10-16 cm3s-1 at 15 K. / Unter Verwendung von zwei Speicherapparaturen wurden ausgewählte, astrophysikalische wichtige Ionen-Molekülreaktionen untersucht. Durch die Kombination einer Kohlenstoffquelle mit einem Ionenspeicher, in dem so Reaktionen zwischen Ionen und Kohlenstoffmolekülen oder -atomen untersucht werden können, wurde Neuland betreten. Es werden Ergebnisse vorgestellt für die Reaktion von D3+ Ionen, die in einem Ringelektrodenspeicher gefangen sind, mit einem Strahl von heißen Cn (n = 1, 2, 3). Die gemessenen Ratenkoeffizienten sind nur halb so groß wie die Werte, die in astrophysikalischen Modellen verwendet werden. Um die Kenntnis über alle möglichen Reaktionen, bei denen drei C-Atome beteiligt sind, abzurunden, wurden zwischen 15 K und Zimmertemperatur die Reaktionen zwischen C3+, C3H+ und C3H3+ Ionen mit H2 und HD in vielen Details untersucht. Diese Experimente wurden in einer zweiten Apparatur durchgeführt, in der ein temperaturvariabler 22-Polspeicher das zentrale Element ist (VT-22PT). Berichtet werden Ergebnisse zu reaktiven Stößen, zur Deuterierung von Kohlenwasserstoffen und zur Strahlungsassoziation. In der Diskussion bleibt offen, was - in Verbindung mit der von 300 K zu 15 K zunehmenden Lebensdauer - der Grund dafür sein kann, daß die Bildung des exothermen Produkts C3H+ anwächst. Der Tunneleffekt scheidet aus. Bei der Reaktion C3+ + HD wurde ein Isotopeneffekt beobachtet, das C3D+ Produkt wird etwas häufiger gebildet als C3H+. Ein Vergleich der Reaktion zwischen C3H+ Ionen mit HD bzw. H2 zeigt, daß das deuterierte Molekül wesentlich reaktiver ist. Es wurden Ratenkoeffizienten für die Strahlungsassoziation von H2 Molekülen mit C3H+ und erstmals mit C3+ Ionen gemessen. Die Auswertung der Daten zeigt, dass der Prozeß langsamer abläuft, wenn der neutrale Stoßpartner deuteriert ist. Schließlich wurde experimentell die theoretische Vorhersage überprüft, dass C3H3+ keinen H-D Austausch mit HD eingeht. Eine sorgfältige Analyse aller konkurrierenden Prozesse ergab, dass bei 15 K der Raten koeffizient kleiner als 4x10-16 cm3s-1 ist.

Nous étudions la dynamique non linéaire en champ moyen de la formation de molécules diatomiques par photo-association ou magnéto-association d’atomes ultra froids pour un système entièrement atomique dans l’état initial. Nous montrons que dans la limite d’une forte interaction non linéaire entre un système atome-molécule ultra froid et un champ électromagnétique quasi résonnant, le processus de formation du condensat moléculaire peut évoluer suivant deux scénarios en fonction des caractéristiques du champ : régime faiblement oscillatoire ou régime fortement oscillatoire. Dans le cas du régime faiblement oscillatoire, le nombre de molécules augmente sans oscillations prononcées des populations atomiques et moléculaires alors que de fortes oscillations de Rabi apparaissent dans le second cas. Nous présentons des solutions analytiques décrivant la dynamique temporelle du système dans ces deux cas. Nous étudions ensuite l’influence de la diffusion élastique entre particules sur la dynamique de formation cohérente de molécules sous l’action d’un champ extérieur représenté par le modèle de Landau-Zener. Nous déterminons une solution approchée qui décrit bien toute la dynamique temporelle de formation moléculaire dans ce cas général. / We study the nonlinear mean-field dynamics of diatomic molecule formation at coherent photo- and magneto-association of ultracold atoms focusing on the case when the system is initially in the all-atomic state. We show that in the limit of strongly nonlinear interaction between an ultra-cold atomic-molecular system and a quasi-resonant electromagnetic field, the molecule formation process, depending on the characteristics of the associating field, may evolve according two different scenarios, namely, weak- and strong-oscillatory regimes. In the first case the number of molecules increases without pronounced oscillations of atom-molecule populations, while in the second case high-amplitude Rabi-type oscillations arise. Assuming an arbitrary external field configuration, we construct analytical solutions to describe the system’s temporal dynamics in the both interaction regimes. Further, we investigate the influence of inter-particle elastic scattering on the dynamics of coherent molecule formation subject to an external field configuration of the resonance-crossing Landau-Zener model. We derive an approximate solution which for the first time describes the whole temporal dynamics of the molecule formation in this general case.

L’objectif consistant à élaborer des «aimants par conception» peut être atteint en adaptant les structures moléculaires des complexes de coordination. Les molécules conçues devraient présenter les caractéristiques requises pour des applications spécifiques, qui résultent de leur riche diversité structurale. Des complexes mononucléaires à base de Ni avec une grande anisotropie magnétique et des molécules polynucléaires à base de Ni et de Co sont préparés et étudiés dans cette thèse. Les synthèses, les études magnétiques et les propriétés électrochimiques des complexes contenant un ligand pontant non innocent sont étudiées. Les complexes mononucléaires Ni(II) à géométrie bipyramide trigonale sont préparés avec des ligands axiaux et les contre-anions différents. L'effet de la nature des ligands axiaux et du changement structural induit par les contre-anions sur l'anisotropie magnétique est étudié expérimentalement et analysé à l'aide de calculs théoriques. Des molécules organiques sont utilisées pour concevoir des complexes trinucléaires à grande anisotropie magnétique et à couplage d'échange faible. Plusieurs complexes polynucléaires à base de Ni et de Co où le TTC³⁻ agit comme un ligand pontant innocent et le HHTP³⁻ comme un ligand non innocent typique sont cristallisés avec diverses structures (TTC = Trithiocyanurate; HHTP = Hexahydroxytriphénylène). Pour les complexes contenant le ligand non innocent (HHTP), les anions radicalaires sont produits par électrochimie. La combinaison de la spectro-électrochimie et de la spectroscopie à résonance paramagnétique électronique couplée à des études d'électrochimie permet d'étudier la délocalisation des électrons sur les radicaux organiques générés et le couplage d'échange entre les ions métalliques. / The objective of elaborating “magnets by design” can be achieved by tailoring the molecular structures of coordination complexes. The designed molecules are expected to exhibit the characteristics required for specific applications, virtually resulting from their rich structural diversity. Mononuclear Ni-based complexes with large magnetic anisotropy and polynuclear Ni- and Co-based molecules are designed in this dissertation. The syntheses, magnetic studies, and electrochemical properties of the complexes containing non-innocent bridge ligand are investigated. The Ni(II) mononuclear complexes with trigonal bipyramid geometry are prepared by tuning the axial ligands and the counter anions. The effect of the nature of the axial ligands and the structural change induces by the counter anions on magnetic anisotropy is studied experimentally and analyzed with the help of theoretical calculations. Large organic molecules are used to design trinuclear complexes with large magnetic anisotropy and weak exchange coupling. Several polynuclear Ni- and Co-based complexes with TTC³⁻ acting as an innocent bridging ligand and HHTP as a typical non-innocent ligand, are crystallized with various structures (TTC = Trithiocyanurate; HHTP = Hexahydroxytriphenylene). For the complexes containing the non-innocent ligand (HHTP), radical anions are produced by electrochemistry. The combination of spectroelectrochemical and Electron Paramagnetic Spectroscopy coupled to electrochemistry studies allow investigating the delocalization of the electrons on the generated organic radicals and the exchange coupling among the metal ions.

Using ion-trapping techniques, selected laboratory experiments on ion-molecule reactions of astrophysical interest have been performed. For the first time a carbon beam source has been integrated into an ion trapping machine for studying collisions between ions and neutral carbon atoms and molecules. Results are presented for the interaction of D3+ ions stored in a ring-electrode trap (RET), with a beam of hot neutral carbon molecules, Cn (n = 1, 2, 3). The measured reaction rate coefficients are up to a factor two smaller than values presently used in astrophysical models. In order to complete our knowledge about the ion chemistry involving three carbon atoms, detailed investigations of reactions of C3+, C3H+ and C3H3+ with H2 and HD have been performed between 15 K and room temperature. These studies have been performed in a second apparatus, a variable-temperature 22-pole trap machine (VT-22PT). Results include reactive collisions, deuteration and radiative association. It is discussed in connection with the increase in lifetime of the C3+ + H2 collision complexes with falling temperature, what could be responsible for producing more C3H+ at 15 K. Tunneling is excluded. In C3+ + HD collisions an isotope effect has been detected, the C3D+ product ions being slightly more abundant than C3H+. Comparison of the reaction of C3H+ primary ions with HD and H2 gas revealed that the deuterated molecules are significantly more reactive. The process of radiative association of C3H+ and for the first time of C3+ with hydrogen molecules has been observed. An analysis of the data shows that radiative association becomes slower, if the neutral reactant is deuterated. Finally, the theoretical prediction from ab initio calculations that C3H3+ does not exchange an H for a D in collisions with HD, has been proven in an ion trap experiment. Careful analysis of all competing processes allows the conclusion that the rate coefficient is smaller than 4x10-16 cm3s-1 at 15 K. / Unter Verwendung von zwei Speicherapparaturen wurden ausgewählte, astrophysikalische wichtige Ionen-Molekülreaktionen untersucht. Durch die Kombination einer Kohlenstoffquelle mit einem Ionenspeicher, in dem so Reaktionen zwischen Ionen und Kohlenstoffmolekülen oder -atomen untersucht werden können, wurde Neuland betreten. Es werden Ergebnisse vorgestellt für die Reaktion von D3+ Ionen, die in einem Ringelektrodenspeicher gefangen sind, mit einem Strahl von heißen Cn (n = 1, 2, 3). Die gemessenen Ratenkoeffizienten sind nur halb so groß wie die Werte, die in astrophysikalischen Modellen verwendet werden. Um die Kenntnis über alle möglichen Reaktionen, bei denen drei C-Atome beteiligt sind, abzurunden, wurden zwischen 15 K und Zimmertemperatur die Reaktionen zwischen C3+, C3H+ und C3H3+ Ionen mit H2 und HD in vielen Details untersucht. Diese Experimente wurden in einer zweiten Apparatur durchgeführt, in der ein temperaturvariabler 22-Polspeicher das zentrale Element ist (VT-22PT). Berichtet werden Ergebnisse zu reaktiven Stößen, zur Deuterierung von Kohlenwasserstoffen und zur Strahlungsassoziation. In der Diskussion bleibt offen, was - in Verbindung mit der von 300 K zu 15 K zunehmenden Lebensdauer - der Grund dafür sein kann, daß die Bildung des exothermen Produkts C3H+ anwächst. Der Tunneleffekt scheidet aus. Bei der Reaktion C3+ + HD wurde ein Isotopeneffekt beobachtet, das C3D+ Produkt wird etwas häufiger gebildet als C3H+. Ein Vergleich der Reaktion zwischen C3H+ Ionen mit HD bzw. H2 zeigt, daß das deuterierte Molekül wesentlich reaktiver ist. Es wurden Ratenkoeffizienten für die Strahlungsassoziation von H2 Molekülen mit C3H+ und erstmals mit C3+ Ionen gemessen. Die Auswertung der Daten zeigt, dass der Prozeß langsamer abläuft, wenn der neutrale Stoßpartner deuteriert ist. Schließlich wurde experimentell die theoretische Vorhersage überprüft, dass C3H3+ keinen H-D Austausch mit HD eingeht. Eine sorgfältige Analyse aller konkurrierenden Prozesse ergab, dass bei 15 K der Raten koeffizient kleiner als 4x10-16 cm3s-1 ist.

The synapse, the minimal element required for interneuronal communication in the nervous sytems, is a structure with a great deal of plasticity, capable of undergoing changes that alter transmission strength, and even forming new connections. This property has great implications for a number of processes, including circuit formation and learning and memory. However, the proteins behind this synaptic plasticity are still not fully understood. To uncover and characterize the proteins that regulate the plastic nature of the synapse, I turned to the Drosophilalarval neuromuscular junction (NMJ), a powerful and accessible model system. I began by examining synaptic cell adhesion, as Cell Adhesion Molecules (CAMs) have long been implicated in synaptic outgrowth as well as learning and memory. CAMs have traditionally been thought of as molecules that mediate cell adhesion between the pre- and postsynaptic membrane. However, through the course of the studies presented here I demonstrate a CAM function that goes beyond simple cell adhesion, acting as a receptor that transduces adhesive signals to the intracellular space. In particular, I have demonstrated a role for the Drosophila CAM, Fasciclin II(FasII), in a signaling complex involving the Amyloid Precursor Protein-Like (APPL) and the Drosophila homolog of X11/MINT/Lin-10 (dX11). Further results show that deletion of either APPL or dX11 inhibits the FasII mediated outgrowth. These studies show that during NMJ expansion the transinteraction between FasII molecules in the pre- and postsynaptic membrane results in the recruitment of APPL and dX11 to the presynaptic cell surface, and the initiation of a signaling cascade that leads to bouton outgrowth. The next question addressed here was regarding the cytoskeletal changes that must occur during synapse remodeling. In particular I centered on the evolutionarily conserved cell polarity complex aPKC-Par3-Par6, which is know to regulate axon growth, the cell cytoskeleton during polarized cell division, and learning and memory. To understand the role of the cytoskeleton during NMJ expansion, I examined the organization of microtubules and actin during this process. Further, I identified atypical protein kinase C (aPKC) as a regulator of microtubule dynamics. I found that aPKC is required for regulating the degree of stabilization of synaptic microtubules. This stabilization requires the Microtubule Associated Protein-1B (MAP1B) homolog Futsch, which I demonstrated was required for aPKC to associate with and stabilize the microtubule cytoskeleton. The process of synaptic expansion not only requires modifications to the presynapse, but to the postsynapse as well. Previous work demonstrates that levels of the scaffolding proteins DrosophilaMembrane Associated Guanlyate Kinase (MAGUK) protein Discs-large (DLG), as well as the vertebrate homolog Postsynaptic Density-95 (PSD-95), which are concentrated at synapses, determine the size of postsynaptic membranes. To identify the underlying mechanisms of the regulation of postsynaptic size, we performed a yeast two hybrid screen, searching for DLG interacting proteins. We found a novel interaction between DLG, and a t-SNARE, GUK-interacting Syntaxin (Gtaxin; GTX), and went on to demonstrate that this interaction is required for proper postsynaptic membrane addition. Strong hypomorphic mutations in either dlg or gtx show a dramatic reduction in postsynaptic expansion. Overexpression of DLG produces an increase of synaptic GTX, as well as an increase in postsynaptic size, and an increased formation of GTX positive SNARE complexes. Taken together, these observations suggest that the MAGUK DLG regulates postsynaptic membrane addition by modulating the formation of a SNARE complex of the t-SNARE Gtaxin, and by targeting GTX to sites of postsynaptic membrane addition. In summary, the studies performed in this thesis probe a trans-synaptic adhesion based signaling complex required for presynaptic expansion, a specific pathway for dynamic microtubule stabilization required for pre- and postsynaptic expansion, and how a scaffolding protein regulates postsynaptic membrane expansion. These processes are all interconnected to maintain the efficacy of the synapse. The studies conducted revealed important information about how these processes are accomplished, and constitute an important step to elucidate the mechanisms by which synapse plasticity occurs at the level of single synaptic terminals.

Master of Science / Department of Physics / Brett D. Esry / In the last 20 years, advancements in laser technology have allowed for the production of intense laser pulses with durations in the femtosecond (10⁻¹⁵ second) regime, giving scientists the ability to probe nuclear dynamics on their natural time scale. Study of the dissociated fragments created by these intense fields can be used to learn about the molecular structure and dynamics. The work presented in this thesis focuses on controlling this light–molecule interaction in such a way that we can preferentially dissociate the molecule to a desired final product. The hydrogen molecular ion, HD⁺, as well as LiF serve as simple systems that can be studied theoretically for a broad range of laser parameters. Our goal in using these relatively simple systems is to capture the essential physics of the light–molecule interaction and develop general methods to describe these interactions in more complex systems.

The development of several organ systems through modeling and shaping of the tissue structure occurs from signaling through axon guidance molecules. The Slit family of ligands has been shown to regulate branching morphogenesis in mammary gland duct development and loss of Slit gene expression during this time leads to the formation of hyperplastic, disorganized lesions suggesting a potential role for Slits in cancer formation. Characterization of human pancreatic ductal adenocarcinoma cell lines showed a loss of SLIT2 expression in cells that contain activated Kras. Loss of SLIT2 expression was associated with DNA methylation of CpG sites within the SLIT2 core promoter and chromatin enrichment of repressive histone modifications at the SLIT2 transcriptional start site. Additionally, treatment of pancreatic ductal adenocarcinoma cell lines with demethylating agent 5-aza-2'-deoxycytidine led to SLIT2 re-expression while treatment with histone deacetylase inhibitor Trichostatin A did not. Mir-218-1 is an intronic microRNA encoded within intron 15 of the SLIT2 gene. Expression of mir-218-1 does not correlate with SLIT2 mRNA expression suggesting that it is transcribed from a promoter independent of the SLIT2 gene promoter. Pancreatic ductal adenocarcinoma cell lines showed a peak of H3K4me3 chromatin enrichment localized to a 1kb region within intron 4 of the SLIT2 gene denoting a candidate alternative promoter for mir-218-1. A concordant peak of H4ac chromatin enrichment overlapped the peak of H3K4me3 enrichment and transcriptional activity was measured from the 1kb region in all pancreatic ductal adenocarcinoma cell lines. A NF-κB binding site was also predicted to exist within the 1kb region. Transfection with two independent siRNAs to NF-κB led to an increase in both pre-mir-218-1 and mature mir-218-1 while treatment with an inhibitor to IκB kinase led to an increase in pre-mir-218-1 expression. Additionally, the p65 subunit of NF-κB was found to bind to the candidate mir-218-1 alternative promoter in pancreatic ductal adenocarcinoma cell lines that do not contain DNA CpG methylation at the predicted NF-κB binding site. It was discovered that miR-218 is a modulator of ARF6 expression suggesting a role in the inhibition of pancreatic ductal adenocarcinoma cell invasion through modulation of the actin cytoskeleton. Overexpression with a miR-218 precursor showed that miR-218 is an inhibitor of pancreatic ductal adenocarcinoma cell invasion in two dimensions. Additionally, it was found that while miR-218 does not have an affect on the ability of pancreatic ductal adenocarcinoma cells to form functional invadopodia, miR-218 is an inhibitor of the extracellular matrix degradation properties of mature invadopodia. Interestingly, the effect of miR-218 on pancreatic ductal adenocarcinoma cell invasion or extracellular matrix degradation is not reliant on the cell's dependency on Kras signaling for growth and survival. Collectively, these observations indicate that understanding the transcriptional regulation of SLIT2 and mir-218-1 expression as well as their signaling properties may provide a step toward the development of diagnostic tests and therapeutic treatments for patients with invasive or metastatic pancreatic ductal adenocarcinoma.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Bacterial chemotaxis, as observed for Escherichia coli, in a field of chemoattractant molecules is characterised by a run-and-tumble motion. The motion is effected by the clockwise (CW) or counter-clockwise (CCW) rotation of flagella; filamentous appendages attached to molecular motors on the cell body. Runs appear when all flagella turn in the CCW-direction and are used to maintain a favourable direction. Tumbles emerge as soon as one flagellum starts to turn CW and are used for reorientation. Because of the variation observed between individual bacteria displaying run-and-tumble motion, we choose to model this behaviour within a probabilistic framework. An important feature of the chemotactic ability of E.coli is that the cell increases run while moving in the right direction and shortens it in the opposite case. This underlines that tumbles are used for reorientation. It has been found from experiments that there can be significant variation in the tumble fashion depending on the fraction of CW-rotating motors (Turner et al., 2000). The change in angle produced when fewer flagella are rotating CW was found to be smaller when compared to the case for many CW-rotating flagella. In addition, the change of direction contributed by a small portion of CW-rotating flagella is rarely significant for bacteria with many flagella. Based on these observations, we have distinguished between models for the one-flagellated and the multi-flagellated cases. Furthermore, since the tumbling angle change increases with the fraction of CW-rotating motors, it would not be impossible to have some cases where the amount of turn produced by the CW-rotating motors induces the bacterium to have a change of direction greater than 2π. But, this feature could not have been observed because when the bacterium tumbles it can effectuate several revolutions before resuming to a new direction. Therefore, we do not restrict our change of direction to (0,2π) to allow the bacteria to have the possibility to effectuate change of directions of magnitude greater than 2π. To this end, we differentiate between the probability of having directional change of magnitude α and α +2π . Thus we do not use angle change distributions that are defined modulo 2π such as the von Mises distribution or the wrapped normal distribution. The chemotactic ability of the bacterium is modelled by representing the CCW-bias of a single flagellum as a function of the chemoattractant concentration. The model includes the temporal memory of chemoattractant concentration that the bacterium has, which usually spans about 4s. The information about the quality of the current direction of the bacterium is transmitted to the flagellar motor by assuming that this one varies with the chemoattractant concentration level. In addition, the saturation of the bias is incorporated by assuming that the bacterium performs a temporal comparison of the receptor occupancy. The present CCW-bias-Model accounts for the chemotactic ability of the bacterium as well as its adaptation to uniform chemoattractant environment. The models of one-flagellated and multi-flagellated bacterial motion, are used to investigate two main problems. The first one consists of determining the optimal tumbling angle strategy of the bacteria. The second one consists of looking at the effects of the tumble variation on the chemotactic efficiency of the bacteria. In order to address these questions, the chemotactic efficiency measure is defined in such a way that it reflects the ability of the bacteria to converge and to stay in a near neighbourhood of the source so that they gain more nutrients. Since its movement is entirely governed by its single flagellum, the one flagellated bacterium is more able to effectuate a run motion. Tumbling events are modelled to be all equivalent because there is not any fraction of flagella to consider. On the other hand, the tumble variation of the multi-flagellated bacteria is modelled by assuming that the directional change during a tumble is a function of the fraction of CW-rotating motors. By assuming that the number of CW-rotating flagella follows a binomial distribution, we suppose that the multi-flagellated bacteria are less able to effectuate a run motion. This also implies that the change of direction produced by fewer CW-rotating flagella are more likely to happen, and this compensates the lack of run. The models show that the optimal tumbling angle change for the bacteria is less than 2π and that higher flagellated bacteria have higher chemotacitc efficiency. As the number of flagella of the bacteria increases, there can be more tumble variation, in this case the bacteria are more capable of adjusting their direction. There could be some situation were the bacteria are not moving to the right direction, but do not require a large change of direction. This ability to adjust their direction accordingly allows them to converge nearer to the source and to gain more nutrients. In addition, the dependence of the tumbling angle on the fraction of CW-rotating flagella of the mutli-flagellated bacteria, implies that there is a correlation between the tumbling angle deviation and the external environment, because the rotational states CCW-CW of the flagella depends on the external cue. Consequently, it would not be impossible that the average magnitude of tumbling angle change depends on the external environment. To investigate this possibility we analyse the distribution of the tumbling tendency of a single bacterium over time, which is the distribution over time of the average positive tumbling change of the bacterium, within zerogradient environment and within non-zero-gradient environment. We defined the average of these tumbling tendency over time as the directional persistence. We observe that the directional persistence within these different nonzero- gradient environment remains the same. However, the difference between the directional persistence within zero-gradient and non-zeros gradient environment gets larger as the number of flagella of the cell increases. There is more correlation between the external environment and the tumbling tendency of the bacterium. Which is the reason why the higher flagellated bacteria responds the best to the external environment by having the higher chemotactic performance. Finally, the total directional persistence generated by the optimal tumbling angle change of the bacteria is the average directional persistence of the bacteria regardless of their number of flagella. Its value, predicted by the model is 1.54 rad within a non-zero-gradient environment and 1.63 rad within a zero-gradient environment. / AFRIKAANSE OPSOMMING: Bakteriese chemotakse, soos waargeneem word vir Escherichia coli, in ’n veld van chemiese lokmiddel molekules word gekenmerk deur ’n hardloopen- tuimel beweging. Die beweging word bewerkstellig deur die regsom of linksom rotasie van flagella; filamentagtige aanhangsels geheg aan molekulêre motors op die selliggaam. ’n Hardloop aksie kom voor as al die flagella linksom roteer en word gebruik om ’m voordelige koers te handhaaf. Tuimels kom voor sodra een van die flagella regsom draai en word gebruik vir heroriënteering. Van wee die variasie wat waargeneem word tussen individuele bakterieë wat hardloop-en-tuimel bewegiging vertoon, verkies ons ’n probabilistiese raamwerk om in te werk. ’n Belangrike eienskap van die chemotakse vermoë van E. coli is dat die sel meer gereeld hardloop terwyl dit in die regte rigting beweeg en minder gereeld in die teenoorgestelde geval. Dit beklemtoon dat tuimels gebruik word vir heroriënteering. Dit is al eksperimenteel vasgestel dat daar betekenisvolle variasie kan wees in die tuimel wyse, wat afhang van die breukdeel regsom roterende motors (Turner et al., 2000). Die hoekverskil afkomstig van minder regsom roterende flagella was vasgestel om kleiner te wees in vergelyking met die menig regsom roterende geval. Verder word die bydrae tot die hoekverskil van ’n klein breukdeel regsom roterende flagella selde beduidend vir bakterieë met baie flagella. As gevolg van hierdie waarnemings, tref ons onderskeid tussen modelle vir een-flagella en multiflagella gevalle. Aangesien die tuimel hoeksverskil vergroot saam met die breukdeel regsom roterende motore, is dit nie onmoontlik om gevalle te hê waar die hoeveelheid draaiaksie gegenereer deur die regsom roterende motore ’n rigtingsverskil groter as 2π kan bewerkstellig nie. Dit was nie moontlik om hierdie eienskap waar te neem nie aangesien die bakterieë ’n paar keer kan tuimel voordat ’n nuwe rigting vasgestel word. Vir hierdie rede beperk ons nie die hoeksverskil tot (0,2π) nie om die bakterieë toe te laat om rigtings veranderinge groter as 2π te ondergaan. Vir hierdie doel, onderskei ons tussen die waarskynlikheid van ’n rigtinsverskil met grootte α en α + 2π. Dus, gebruik ons nie hoekverskil verspreidings wat modulo 2 gedefinieer is nie, soos die von Mises verspreiding of omwinde normaalverdeling. Die chemotakse vermoë van die bakterium word gemodelleer deur die linksom sydigheid van ’n enkele flagellum as ’n funksie van die chemotakse lokmiddel konsentrasie voor te stel. Die model sluit in die tydelike geheue wat die bakterium besit oor chemotakse lokmiddel konsentrasie, wat gewoonlik oor 4s strek. Die informasie oor die kwaliteit van die huidige rigting van die bakterium word deur gegee na die flagella motor toe deur die aanname te maak dat dit wissel met die chemotakse lokmiddel konsentrasie vlak. Die versadiging van die sydigheid word geinkorporeer deur aan te neem dat die bakterium ’n temporale vergelyking maak tussen reseptor okkupasie. Die huidige linksom sydige model neem die bakterium chemotakse vermoë in ag, as ook aanpassing tot ’n uniforme chemotakse lokmiddel omgewing. Die modelle van een-flagella en multi-flagella bakteriële beweging word gebruik om twee hoof probleme te bestudeer. Die eerste, bestaan daaruit om vas te stel wat die optimale tuimel hoek strategie van die bakterieë is. Die tweede kyk na die uitwerking van tuimel variasie op chemotakse effektiwiteit. In orde om hierdie vra te adreseer word die chemotakse effektiwiteit op so mannier gedefinieer dat dit die bakteriese vermoë om die buurt om die oorsprong te nader en daar te bly. Aangesien die beweging heeltemal vasgestel word deur een flagella, in die een-flagella geval, is ’n bakterium meer in staat daartoe om ’n hardloop aksie te bewerkstellig. Tuimel voorvalle word as ekwivalent gemodeleer omdat daar geen breukdeel roterende flagella is om in ag te neem nie. In teenstelling, word die tuimel variasie van multi-flagella bakterieë gemodeleer deur die aanname te maak dat rigtingsverandering gedurende ’n tuimel ’n funksie is van die breukdeel regsom roterende motore. Deur die aanname te maak dat die getal regsom roterende flagella ’n binomiese verspreiding volg, veronderstel ons dat multi-flagella bakterieë minder in staat daartoe is om ’n hardloop aksie te onderneem. Hierdie impliseer ook dat rigtingverandering wat geproduseer word deur minder regsom roterende flagella meer geneig is om voor te kom en dan kompenseer vir ’n tekortkoming aan hardloop gebeure. Die modelle wys dat die optimale tuimelhoek verandering minder as 2 is en dat bakterieë met meer flagella meer chemotaksies effektief is. Soos die getal flagella vermeder, kan daar meer tuimel variasie wees, en in die geval is die bakterieë meer in staat om hul rigting te verander. Daar kan omstandighede wees waar die bakterieë nie in die regtige rigting beweeg nie, maar nie ’n groot rigtingsverskil nodig het nie. Hierdie vermoë om hul rigting byvolglik te verander stel hul in staat om nader aan die oorsprong te konvergeer en dus meer voedingstowwe op te neem. Die afhanklikheid van die tuimel hoek op die breukdeel regsom roterende flagella van multi-flagella bakterieë dui daarop dat daar ’n korrelasie is tussen die tuimel hoek afwyking en die eksterne omgewing, omdat die roterings toestand, regs- of linksom, van die flagella afhanklik is van die eksterne sein. As ’n gevolg, is dit nie onmoontlik dat die gemiddelde grootte van die tuimel hoek verandering van die eksterne omgewing afhang nie. Om hierdie moontlikheid te bestudeer, analiseer ons die verspreiding van die tuimel neiging van ’n enkele bakterium oor tyd, wat die verspreiding oor tyd van die gemiddelde positiewe tuimel verandering is, in ’n nulgradient en nie-nul-gradient omgewing. Ons het hierdie gemiddelde tuimel neigings oor tyd gedefinieer as die rigtings volharding. Ons het waargeneem dat die rigtings volharding binne verskillende nienul- gradient omgewings dieselfde bly. Nogtans is die verskil tussen die rigtings volharding binne nul-gradient en nie-nul-gradient omgewings groter soos die getal flagella vermeder. Daar is meer korrelasie tussen die eksterne omgewing en tuimel neiging van die bakterium. Dit is die rede hoekom bakterieë met meer flagella die beste reageer op die eksterne omgewing deur beter chemotakse effektiwiteit. Ten slotte, die totale rigtings volharding gegenereer deur die optimale tuimel hoek verandering is die gemiddelde rigtings volharding ongeag van die getal flagella. Die waarde wat deur die model voorspel word is 1.54 rad binne ’n nie-nul-gradient omgewing en 1.63 rad binne ’n nul-gradient omgewing.

This thesis describes the design, construction, operation, and characterisation of an experimental apparatus that produces a source of internally cold, slow molecules that can be used for studying ion-molecule reactions at low temperatures. The apparatus combines buffer-gas cooling with a bent quadrupole velocity selector to cool both the translational and rotational degrees of freedom of the molecules. A cold cell (6 K) is filled with a buffer gas, such as helium, that exhibits sufficiently high vapour pressure for cryogenic applications. Hot molecules (150 to 300 K) enter the cell and thermalise with the buffer gas through collisions. Molecules are subsequently loaded into an electrostatic quadrupole guide, which acts as a velocity filter; only translationally cold polar molecules are guided around the bend. Using a buffer-gas-cooled source of molecules for electrostatic velocity selection, rather than a 300 K effusive source, yields a rotationally cold sample, with J ≤ 3. This rotational selectivity will enable the dependence of reaction cross sections on the reactant rotational state to be examined. Mass spectrometry is used to characterise cold molecular beams of ND3 and CH3F, while (2+1) REMPI spectra are recorded for the ammonia isotopologues. The peak velocity of guided ND3 is 75.86(0.70) ms-1 for standard conditions in a 6 K helium buffer gas cell (1.0 sccm ND3 flow rate, 0.6 mbar helium inlet pressure, ± 5 kV voltage). This corresponds to a peak kinetic energy of 6.92(0.13) K. (2+1) REMPI spectroscopy of the B1E''(v2'=5) ← X(1) transition enabled the rotational state distribution of guided ammonia molecules to be established. PGOPHER simulations of the experimental spectra suggest a rotational temperature of 10 K for ND3 molecules (from a 6 K helium buffer gas cell). The extent of translational and rotational cooling can be controlled by varying the molecular and buffer gas densities within the cell, by changing the temperature of the buffer gas cell (we can operate at 6 K or 17 K), or by changing the buffer gas. The translational temperature of guided ND3 is similar in a 6 K helium and 17 K neon buffer gas cell (peak kinetic energies of 6.92(0.13) K and 5.90(0.01) K, respectively) because the heavier neon gas has a slightly lower thermal velocity at 17 K than helium does at 6 K. Despite similar translational temperatures, the rotational temperature of guided ND3 is lower for molecules exiting the 6 K helium cell compared to the 17 K neon buffer gas cell (10 K and 15 K, respectively). The 6 K helium and 17 K neon buffer gas cells provide an excellent opportunity to investigate the effect of rotational cooling on branching ratios and reaction rates in low temperature ion-molecule reactions. The buffer gas cell and velocity guide described in this work will be combined with a linear Paul ion trap, to facilitate the study of cold ion-molecule reactions.

The influence of low molecular weight additives containing polar groups and modified polyolefin-based compatibilisers on polypropylene (PP)-clay nanocomposites (PPCN) has been studied, in terms of intercalation and degree of exfoliation achievable by melt state mixing processes. PPCN were prepared by melt mixing of two commercial pp homopolymers with organically modified clay (OMMT) in the presence of maleic anhydride grafted pp (PP-MA). X-ray diffraction (XRD) analysis shows that the interlayer spacing of clay increases dramatically, whilst transmission electron microscopy (TEM) results show a significant improvement of clay dispersion in the PP matrix, when nanocomposites are prepared with commercial PP containing short chain organic additives with polar groups (amide-type slip and antistatic additives). Subsequent studies based upon customised PP formulations, with short chain amide molecules (AM), confirm the intercalation of this additive into clay galleries. The maximum interiayer spacing is achieved with low concentrations of this additive (0.5 wt. %). Contact angle measurements and low shear melt flow properties (MF!) further confirm the diffusion of this additive (AM) into the clay galleries rather than migrating away from the bulk of the PPCN. The interaction between the polar group (CONH2) of this additive and polar sites of the clay surface appears to be the driving force for the intercalation. Although this additive intercalates and allows the formation of an intercalated nanocomposite structure with non homogeneous dispersion of clay, an exfoliated PPCN structure is yet to be formed with this additive alone. A new preparation method for PPCN has therefore been developed by co-intercalation of AM and PP-MA. PPCN were prepared by this method with a significant reduction of overall PP-MA concentration in the nanocomposite structure, relative to conventional PPCN prepared with compatibiliser (PP-MA) only. XRD and TEM analysis showed that nanocomposite structures are formed with significantly improved clay dispersion, compared to PPCN prepared using the conventional method. Quantification of clay exfoliation, using image analysis software, showed that higher degrees of exfoliation can be achieved in PPCN from this new cointercalation method. Normalised melt flow index (n-MFI) data showed the relationship between low shear flow properties and clay structure and is an appropriate parameter to examine clay exfoliation and its interaction with pp in PPCN. Enhanced thennal stability of PPCN, in comparison to pure PP, further demonstrates the improved clay dispersion in nanocomposite structures prepared by the co-intercalation method. A possible mechanism for the co-intercalation of AM and PP-MA into clay galleries has been proposed, based upon hydrogen bonding between these additives and the silicate layers. Rheological characterisation of PPCN, using capillary rheometry experiments at high shear rates, shows a shear thinning, pseudoplastic behaviour similar to pure PP. However, a comparatively higher concentration of AM appears to reduce the shear viscosity of PPCN. Die swelling behaviour revealed a reduction in melt elasticity in PPCN melts in comparison to unmodified PP. Reduced die swell occurs as a result, together with a delay in the onset of melt fracture. Sheet extrusion was used to produce PPCN products with increasing clay loading levels that were evaluated for a range of mechanical properties. Significant enhancement of modulus in PPCN is achieved in comparison to pure PP whilst maintaining similar strength characteristics. However, impact resistance of extruded PPCN sheets is not improved in comparison to unmodified PP. Results have been interpreted with reference to the degree of exfoliation, additive content and differences in PP crystallinity.