Dissertations / Theses on the topic 'Plasmodi'

We explore the effects of surface plasmon hybridization in graphene nanostructures and silver nanoparticles as applied to novel plasmonic phenomena. The analysis is based on the theory of surface plasmon hybridization under the boundary charges method. This method, which is based in the electrostatic approximation, has been largely used to predict the resonant frequencies in strongly coupled nanoparticle clusters. Here, we extend this formalism to analyze novel plasmonic phenomena such as the blueshift of modes in graphene plasmonics, near-field radiation, thermal transport and plasmon-induced hot carrier generation in silver nanoparticles. Furthermore, we develop analytical solutions for graphene nanodisks and metallic spheres that allow for fast and accurate modeling. The analytic models provide the basis to derive a large number of results, including prediction of hybrid eigenmodes and bandstructures, far-field response, and near-field response under thermally induced fluctuations. We predict that the strong near-filed coupling in graphene nanodisk stacks can induce a blueshift in the resonant frequencies up to the near-infrared part of the spectrum. We find that the strong near-filed coupling between disks can also lead to large values of radiative thermal conductance when thermally induced fluctuations are included. In this regard, an enhancement over the blackbody limit of up to two and four orders of magnitude was observed for co-planar and co-axial disk configurations. The strong coupling between coplanar disks was also explored for the development of plasmonic waveguides by considering long co-planar disk arrays. It was observed that the array posseses great potential for plasmonic waveguiding, with a strong degree of confinement for disks smaller than 200 nm. Thermal activation of the guided modes showed a thermal conductivity of up to 4.5 W/m K and thermal diffusivity of up to 1:4 x 10-3 m2/s. The large values of thermal diffusivity suggest the potential of graphene disk waveguides for thermotronic interconnects. The plasmon-induced hot carrier generation in silver nanosphere dimers was also studied. The modeling considered analytical solution for metallic nanospheres, from which the electrostatic potential of each sphere was obtained. Using these results, the hot carrier generation was explored under the basis of the Fermi golden rule. The results show a large number of hot carriers at the low frequency modes. This values exceed the number of generated hot carriers on a single sphere. The energy distribution of photogenerated electrons and holes showed a large energy gap that can be explored in photocatalysis and photovoltaic energy conversion.

A major challenge in modern photonics and nano-optics is the diffraction limit of light which does not allow field localisation into regions with dimensions smaller than half the wavelength. Localisation of light into nanoscale regions (beyond its diffraction limit) has applications ranging from the design of optical sensors and measurement techniques with resolutions as high as a few nanometres, to the effective delivery of optical energy into targeted nanoscale regions such as quantum dots, nano-electronic and nano-optical devices. This field has become a major research direction over the last decade. The use of strongly localised surface plasmons in metallic nanostructures is one of the most promising approaches to overcome this problem. Therefore, the aim of this thesis is to investigate the linear and non-linear propagation of surface plasmons in metallic nanostructures. This thesis will focus on two main areas of plasmonic research –– plasmon nanofocusing and plasmon nanoguiding. Plasmon nanofocusing – The main aim of plasmon nanofocusing research is to focus plasmon energy into nanoscale regions using metallic nanostructures and at the same time achieve strong local field enhancement. Various structures for nanofocusing purposes have been proposed and analysed such as sharp metal wedges, tapered metal films on dielectric substrates, tapered metal rods, and dielectric V-grooves in metals. However, a number of important practical issues related to nanofocusing in these structures still remain unclear. Therefore, one of the main aims of this thesis is to address two of the most important of issues which are the coupling efficiency and heating effects of surface plasmons in metallic nanostructures. The method of analysis developed throughout this thesis is a general treatment that can be applied to a diversity of nanofocusing structures, with results shown here for the specific case of sharp metal wedges. Based on the geometrical optics approximation, it is demonstrated that the coupling efficiency from plasmons generated with a metal grating into the nanofocused symmetric or quasi-symmetric modes may vary between ~50% to ~100% depending on the structural parameters. Optimal conditions for nanofocusing with the view to minimise coupling and dissipative losses are also determined and discussed. It is shown that the temperature near the tip of a metal wedge heated by nanosecond plasmonic pulses can increase by several hundred degrees Celsius. This temperature increase is expected to lead to nonlinear effects, self-influence of the focused plasmon, and ultimately self-destruction of the metal tip. This thesis also investigates a different type of nanofocusing structure which consists of a tapered high-index dielectric layer resting on a metal surface. It is shown that the nanofocusing mechanism that occurs in this structure is somewhat different from other structures that have been considered thus far. For example, the surface plasmon experiences significant backreflection and mode transformation at a cut-off thickness. In addition, the reflected plasmon shows negative refraction properties that have not been observed in other nanofocusing structures considered to date. Plasmon nanoguiding – Guiding surface plasmons using metallic nanostructures is important for the development of highly integrated optical components and circuits which are expected to have a superior performance compared to their electronicbased counterparts. A number of different plasmonic waveguides have been considered over the last decade including the recently considered gap and trench plasmon waveguides. The gap and trench plasmon waveguides have proven to be difficult to fabricate. Therefore, this thesis will propose and analyse four different modified gap and trench plasmon waveguides that are expected to be easier to fabricate, and at the same time acquire improved propagation characteristics of the guided mode. In particular, it is demonstrated that the guided modes are significantly screened by the extended metal at the bottom of the structure. This is important for the design of highly integrated optics as it provides the opportunity to place two waveguides close together without significant cross-talk. This thesis also investigates the use of plasmonic nanowires to construct a Fabry-Pérot resonator/interferometer. It is shown that the resonance effect can be achieved with the appropriate resonator length and gap width. Typical quality factors of the Fabry- Pérot cavity are determined and explained in terms of radiative and dissipative losses. The possibility of using a nanowire resonator for the design of plasmonic filters with close to ~100% transmission is also demonstrated. It is expected that the results obtained in this thesis will play a vital role in the development of high resolution near field microscopy and spectroscopy, new measurement techniques and devices for single molecule detection, highly integrated optical devices, and nanobiotechnology devices for diagnostics of living cells.

Attosecond pulses are ultrashort radiation bursts produced via high harmonic generation (HHG) during a highly nonlinear excitation process driven by a near infrared (NIR) laser pulse. Attosecond pulses can be used to probe the electron dynamics in ultrafast processes via the attosecond streaking technique, with a resolution on the attosecond time scale. In this thesis it is shown that both the generation of attosecond (AS) pulses and the probing of ultrafast processes by means of AS pulses, can be extended to cases in which the respective driving and streaking fields are produced by surface plasmons excited on nanostructures at NIR wavelengths. Surface plasmons are optical modes generated by collective oscillations of the surface electrons in resonance with an external source. In the first part of this thesis, the idea of high harmonic generation (HHG) in the enhanced field of a surface plasmon is analyzed in detail by means of numerical simulations. A NIR pulse is coupled into a surface plasmon propagating in a hollow core tapered waveguide filled with noble gas. The plasmon field intensity increases for decreasing waveguide radius, such that at the apex the field enhancement is sufficient for producing high harmonic radiation. It is shown that with this setup it is possible to generate isolated AS pulses with outstanding spatial and temporal structure, but with an intensity of orders of magnitude smaller than in standard gas harmonic arrangements. In the second part, an experimental technique for the imaging of surface plasmonic excitations on nanostructured surfaces is proposed, where AS pulses are used to probe the surface field by means of photoionization. The concept constitutes an extension of the attosecond streak camera to ``Attosecond Photoscopy'', which allows space- and time-resolved imaging of the plasmon dynamics during the excitation process. It is numerically demonstrated that the relevant parameters of the plasmonic resonance buildup phase can be determined with subfemtosecond precision. Finally, the method used for the numerical solution of the Maxwell's equations is discussed, with particular attention to the problem of absorbing boundary conditions. New insights into the mathematical formulation of the absorbing boundary conditions for Maxwell's equations are provided.
Attosekundenpulse sind ultrakurze extrem-ultraviolette (XUV) Pulse, die durch einen nicht-linearen, von einer nah-infraroten (NIR) Laserquelle stimulierten Anregungsprozess erzeugt werden. Attosekundenpulse können verwendet werden, um die Elektronendynamik eines ultraschnellen Prozesses durch die ``Attosecond Streaking'' Technik zu messen, mit einer Auflösung auf der Attosekundenskala. In dieser Dissertation wird gezeigt, dass sowohl die Erzeugung von Attosekundenpulsen als auch die Messung ultraschneller Prozesse mittels Attosekundenpulse auf Fälle erweitert werden können, bei denen die Anregungs- und Streakingsfelder von Oberflächenplasmonen generiert werden, welche bei nahinfraroten Wellenlängen auf Nanostrukturen angeregt werden. Oberflächenplasmonen sind optische Moden, die aus einer kollektiven Schwingung der Elektronen an der Oberfläche in Resonanz mit einer externen Quelle entstehen. Im ersten Abschnitt dieser Dissertation wird das Konzept der High Harmonic Generation (HHG) in plasmonisch erhöhten Feldern durch numerische Simulationen analysiert. Ein NIR Puls wird mit einem Oberflächenplasmon, das sich in einem konischen, mit Edelgas gefüllten, Hohlleiter ausbreitet, gekoppelt. Die Intensität des plasmonischen Feldes steigt mit der Verringerung des Durchmessers des Hohlleiters, sodass die Felderhöhung an seiner Spitze groß genug wird, um hohe harmonische Strahlung zu generieren. Es wird nachgewiesen, dass die Herstellung von isolierten Attosekundenpulsen mit außergewöhnlichen Zeit- und Raumstrukturen möglich ist. Trotzdem ist deren Intensität um mehrere Größenordnungen niedriger als die, die in Experimenten mit fokussierten Laserpulsen erreicht werden kann. Im zweiten Abschnitt wird eine experimentelle Technik für die Abbildung plasmonischer Oberflächenanregungen vorgeschlagen, wobei Attosekundenpulse verwendet werden, um das Feld an der Oberfläche mittels ``Momentum Streaking'' der photoionisierten Elektronen zu messen. Dieses Konzept ist eine Erweiterung der ``Attosecond Streak Camera'', welches ich ``Attosecond Photoscopy'' nenne. Es ermöglicht die Abbildung eines Plasmons in Zeit und Raum während des Anregungsprozesses. Anhand von numerischen Simulationen wird es gezeigt, dass die wesentlichen Parameter des plasmonischen Resonanzaufbaus mit subfemtosekunden-Präzision bestimmt werden können. Zuletzt wird die Methode für die numerische Lösung der Maxwell-Gleichungen diskutiert, mit Fokus auf das Problem der absorbierenden Randbedingungen. Neue Einsichten in die mathematische Formulierung der Randbedingungen der Maxwell-Gleichungen werden vorgestellt.

Fifty three Staphylococcus aureus isolates were obtained from three centres, two hospitals and a private pathology laboratory, and studied for susceptibility to bacteriophages, resistance to antimicrobial agents and plasmid contents.Results of bacteriophage typing revealed that they belonged to a variety of phage types. Eighteen were untypable by any of the International Set of Phages, 16 belonged to phage group 111, nine to group I, four to group 11, two to group IV and two to the miscellaneous group.The isolates were resistant to one or more of methicillin (Mc), benzyl penicillin (Pc), gentamicin (Gm) , kanamycin (Km) , neomycin (Nm) , streptomycin (Sm) , trimethoprim (Tp), sulphonamides (Su), tetracycline (Tc), minocycline (Mn), chloramphenicol (Cm), novobiocin (Nb) and fusidic acid (Fa). Resistance to Pc was due to the production of beta-lactamase (Bla). No resistance to vancomycin, spectinomycin and erythromycin was detected. Resistance was also found to heavy metals such as cadmium (Cd), mercury (Hg), phenyl mercuric acetate (Pma), arsenate (Asa) and to the nucleic-acid binding compounds propamidine isethionate (Pi) and ethidium bromide (Eb).All but one of the isolates harboured plasmids. The number of plasmids the isolates carried varied from one to six and their sizes ranged from < 1.0 kb to c.48 kb.Location of the resistance determinants was ascertained by curing and transfer experiments. Loss of resistance was tested after growth at 43.5°C and transfer of resistance determinants was attempted by transduction, mixed-culture transfer and conjugation. The results revealed that resistance to Mc, Gm, Tp, Mn and Fa was chromosomal in all the resistant isolates and in some isolates Bla and resistance to Sm and Cd were chromosomal as well as plasmid encoded. In the majority of cases Bla and resistance to Km, Nm, Sm, Tc, Cin, Cd, Hg, Asa, Pma, Pi and Eb was encoded by plasmids.Conjugation experiments led to the isolation of three unique conjugative plasmids which have not been found to confer resistance to antimicrobials or to produce haemolysins or diffusible pigment (Dip). The three plasmids, pWBG620, pWBG637 and pWBG661, were indistinguishable by restriction endonuclease analysis and DNA-DNA hybridisation. However pWBG620, unlike pWBG637 and pWBG661, was not detected in the cytoplasm of its host and was only detected in transconjugants after it mobilised a non-conjugative Sm-resistance (SmR) plasmid. Further analysis indicated that it is integrated into the chromosome of its host, excises during conjugation and mobilises the SmR plasmid.These plasmids were studied further using pWBG637 as a representative. It was compared with representatives of the two groups of conjugative plasmids which have been reported in the staphylococci. These are the plasmids which encode resistance to Gm, Km and Nm and those which code for the production of diffusible pigment. The three types of conjugative plasmids were compared by restriction endonuclease analysis and DNA- DNA hybridisation and were found to be different. A preliminary restriction map of pWBG637 has also been constructed.However since pWBG637 has no resistance phenotype direct selection for it was not possible in transfer experiments and for incompatibility (Inc.). To study it further it was necessary to construct resistant derivatives which could be selected for in transfer experiments. This was achieved by labelling pWBG637 with resistance transposons to generate two conjugative plasmids, pWBG636 carrying an insert of Tn3851 (Gm- resistance) and pWBG642 carrying an insert of Tn551 (hn- resistance). It was found that transposon labelling had not changed the incompatibility of pWBG637 and therefore pWBG636 and pWBG642 were used in further experiments in place of pWBG637. Inc. tests with the pWBG637 derivatives revealed that the pWBG637 type of plasmid is not only different from the other two types of conjugative plasmids but is different from any of the described staphylococcal Inc. groups and therefore the pWBG637 type of plasmids represent a new Inc. group 15. The pWBG637 type of plasmids were studied further using plasmids pWBG636 and pWBG642. They were able to transfer conjugatively to a capsulated S.aureus strain either by the polyethylene glycol method or on filter membranes. They also transferred by conjugation to S. epidermidis and Streptococcus faecalis and were able to transfer back from these strains to S.aureus indicating that they also replicate in these hosts. Consequently they have been used to mobilise non-conjugative plasmids from S.epidermidis and non phage typable S.aureus. Both plasmids failed to transfer conjugatively to Bacillus subtilis and Escherichia coli.pWBG637 transferred non-conjugative plasmids by mobilising them in a manner similar to mobilisation (donation) in E.coli or by recombining with them to form new resistance plasmids. In one case, pWBG628 which encodes Bla and resistance to Cd, Km, Nm and Sm and has no homology with pWBG637 recombined with it during conjugation to produce three new conjugative plasmids pWBG629, pWBG630 and pWBG631 carrying resistance determinants from pWBG628. One of these plasmids, pWBG629, was found to be pWBG637 which had acquired a 4.5 kb element encoding resistance to Km, Nm and Sm. This element was shown to be transposable in both rec+ and rec- backgrounds and has been designated Tn3854. It expressed Sm resistance in E.coli and differs on this account from the Gram-negative transposon Tn5 which expresses resistance to Km, Nm and Sm in non-enteric bacteria but only resistance to Km and Nm in E. coli.Where possible the non-conjugative plasmids encoding resistance to antimicrobial agents were compared with phenotypically similar plasmids isolated from other parts of the world. It was found that the Tc and Sm resistance plasmids were closely related to other plasmids with the same phenotype whereas the Cm resistance plasmids were different.Although the majority of the Bla plasmids belonged to Inc. group 1 they demonstrated significant restriction enzyme fragment length polymorphism when compared with other Bla plasmids.This study has provided the first data on the genetics of antimicrobial resistance in Nigerian S.aureus. Although many of the plasmids studied were found to be similar to those previously described the isolates also contained some unique and previously undescribed plasmids.

Thesis (MScMedSc)--Stellenbosch University, 2001.
ENGLISH ABSTRACT: The plasmid pAL5000 is a mycobacterial plasmid isolated from Mycobacterium fortuitum. It is a low copy number plasmid, which replicates in both fast growing (e.g. M. smegmatis) and slow growing (e.g. M. bovis BCG) mycobacteria. Most mycobacterial-E. coli shuttle vectors utilise the pAL5000 origin of replication. The minimum replicon consists of ORF1 (RepA), ORF2 (RepB) and the origin of replication. Dr W.R. Bourn created an E. coli-mycobacterial vector based on the pAL5000 origin of replication (pORI) and then subjected it to semi-random mutagenesis. A high copy number mutant was identified (pHIGH) and the causative mutation was tentatively identified as a 3bp deletion situated just upstream of repB. This work describes the further characterisation of the mutant plasmid. Firstly, it was shown by retransforming M. smegmatis with both the original and mutant plasmids (pORI and pHIGH), that the mutation causing the increased copy number was plasmid-encoded and not on the chromosome. Following this, it was demonstrated by simple subcloning of the region that carries the 3 bp deletion, that other pAL5000-based vectors could be converted to high copy number. In addition to this, the subcloned region was sequenced and the nature of the mutations was confirmed. The subcloning experiment confirmed that the 3bp deletion caused the high copy number phenotype. Following this, the exact copy number of pHIGH and the relative increase in copy number was determined. From this, the copy number of pORI could also be determined. The plasmid pHIGH has a copy number of approximately 54, compared to the 8 of pORI (a relative increase by a factor of 7). Because it is important for researchers to know the characteristics of the vectors that they use, especially the influence it will have on its host, stability tests and growth curves were also performed. It was seen that the higher copy number did not markedly increase the stability, however, this is because pORI is already extremely, and unexpectedly, stable in the host M. smegmatis. According to the growth curves, the increased copy number has little effect on the growth of the host M. smegmatis. Possible mechanisms for the increased copy number were then investigated. By using a promoter probe vector, the possible existence of a promoter situated between the two open reading frames of pAL5000 (repA and repB) was investigated. It was thought that the mutation might have created, or changed an existing promoter, situated between repA and repB. The results showed, however, that in both pORI and pHIGH there might be a very weak promoter upstream of repB, but the mutation did not cause any change that was measurable by the method that was used. A further possibility was that the mutation caused a change in the RNA secondary structure, which might then have an effect on the translational efficiency of RepB. It was found that the 3bp deletion in pHIGH causes a change in the local RNA secondary structure around the ribosomal binding site and the start codon, when compared to pORI (wild type). This change may cause the translation initiation rate of RepB to be different between pHIGH and pORI. Ultimately it would lead to a different ratio of RepA and RepB in the cell.
AFRIKAANSE OPSOMMING: Die plasmied pAL5000 is ‘n mikobakteriele plasmied wat vanuit Mycobacterium fortuitum gei'soleer is. Dit is ‘n lae kopie-getal plasmied wat in beide vinnig groeiende (bv. M. smegmatis) en stadig groeiende (bv. M. bovis BCG) mikobakteriee kan repliseer. Die meeste mikobakteriele-E. coli shuttle vektore gebruik die pAL5000 oorsprong van replisering. Die minimum replikon bestaan uit ORF1 (RepA), ORF2 (RepB) en die oorsprong van replisering. Dr. W.R. Bourn het ‘n E. coli-mikobakteriele vektor gemaak wat gebaseer is op die pAL5000 oorsprong van replisering (pORI), en dit onderwerp aan semi-random mutagenese. ‘n Hoë kopie-getal mutant is gei'dentifiseer (pHIGH) en die mutasie hiervoor verantwoordelik was tentatief gei'dentifiseer as ‘n 3bp delesie, net stroomop van repB. Die projek beskryf die verdere karakterisering van die mutante plasmied. Eerstens, deur M. smegmatis te hertransformeer met die plasmied DNA (pORI en pHIGH), is dit bewys dat dit mutasie wat die toename in kopie-getal veroorsaak, deur die plasmied gekodeer word, en dat dit nie ‘n mutasie op die chromosoom is nie. Hierna is dit deur eenvoudige subklonering bewys dat die gedeelte wat die 3bp delesie dra, ander pAL5000-gebaseerde vektore ook kan verander in ‘n hoër kopie-getal. Die sub-klonerings eksperiment het ook bewys dat die 3 bp delesie die oorsaak is vir die hoë kopie-getal fenotipe. Volgende is die presiese kopie-getal van pHIGH en die relatiewe toename in kopiegetal bepaal. Die kopie-getal van pORI kon vanaf hierdie data bepaal word. Die plasmied pHIGH het ‘n kopie-getal van ongeveer 54 in M. smegmatis, in vergelyking met die 8 van pORI (‘n relatiewe toename met ‘n faktor van 7). Aangesien dit vir navorsers belangrik is om die eienskappe van die vektore wat hulle gebruik, te ken, en veral die invloed wat dit op die gasheer sal hê, is stabiliteits toetse, en groeikurwes gedoen. Die hoër kopie-getal het nie die stabiliteit werklik verbeter nie, maar dit is omdat pORI alreeds uiters stabiel is in die gasheer M. smegmatis. Volgens die groeikurwes het die toename in kopie-getal ‘n minimale effek op die groei van die gasheer M. smegmatis. Moontlike meganismes vir die hoër kopie-getal is ook ondersoek. Die moontlike bestaan van ‘n promoter tussen die twee oop-leesrame van pAL5000 (repA en repB) is ondersoek deur gebruik te maak van ‘n “promoter probe” vektor. Die mutasie kon moontlik ‘n promoter geskep het, of ‘n bestaande een tussen repA en repB verander het. Die resultate het gewys dat daar in beide pORI en pHIGH moontlik ‘n baie swak promoter stroomop van repB is, maar die mutasie het nie enige veranderinge veroorsaak wat meetbaar was met die metode wat gebruik is nie. ‘n Verdere moontlikheid was dat die mutasie ‘n verandering in die RNA sekondere struktuur kon veroorsaak het, en dit mag ‘n effek hê op die translasie effektiwiteit van RepB. Daar is gevind dat, in vergelyking met pORI, het die 3bp delesie in pHIGH ‘n verandering in die lokale RNA sekondere struktuur rondom die ribosomale bindings posisie en die begin-kodon veroorsaak. Die verandering mag veroorsaak dat die translasie inisiasie tempo van RepB verskillend is vir pORI en pHIGH. Uiteindelik sal dit lei tot ‘n heeltemal ander verhouding van RepA en RepB in die sel.

Cette thèse contribue, par différents aspects, morphologiques, moléculaires et phylogénétiques, à une meilleure connaissance de la diversité des parasites de l’ordre des Haemosporidia chez les vertébrés des classes des oiseaux, reptiles et mammifères dans deux hot spots de biodiversité, à Madagascar et au Cambodge. Un atlas des Haemosporidia de la faune sauvage de Madagascar et du Cambodge a été constitué pour mettre à disposition nos données. L’aspect moléculaire a concerné la caractérisation et l’identification avec quatre marqueurs moléculaires (cyt b, tufA, ldh et cox 1) des parasites. L’utilisation de différents marqueurs moléculaires a permis de comparer leurs degrés d’informations phylogénétiques et de montrer que les gènes mitochondriaux, cyt b et cox 1 permettaient une meilleure résolution des constructions phylogénétiques que celles réalisées avec le gène de l’apicoplaste tufA ou le gène nucléaire ldh. Les analyses phylogénétiques, ont permis de mettre en évidence des évènements de capture d’hôte entre deux classes de vertébrés, les oiseaux et les mammifères (chauves-souris). Un scénario de coévolution hôte parasite a été proposé pour les Plasmodium des primates (incluant P. Falciparum chez l’homme) et la famille d’hôte des Hominidae. Une estimation de la datation de l’apparition de P. Falciparum entre 7 et 9 millions d’années a été déduite de ce scénario. P. Ovale partagerait un ancêtre commun le plus récent avec un Plasmodium de chimpanzé. Enfin, les grands singes africains se sont révélés de potentiels réservoirs pour trois des quatre espèces plasmodiales infectant l’homme (P. Falciparum, P. Ovale et P. Malariae)
This thesis contributes, in using morphological, molecular and phylogenetic aspects to a better understanding of the Haemosporidian parasite diversity in vertebrate classes of birds, reptiles and mammals in two biodiversity hot spots, Madagascar and Cambodia. An atlas of Haemosporidia in wildlife of Madagascar and Cambodia has been realised to make available these data for public use. The parasites isolated have been characterized and identified with four molecular markers (cyt b, tufA, ldh and cox 1). The phylogenetic signal of each molecular marker has been evaluated. The mitochondrial genes, cyt b and cox 1 could carry a phylogenetic signal sufficient to conduct phylogenetic tree analyses comparing to tufA apicoplaste gene and ldh nuclear gene. The phylogenetic analyses highlighted host switches events between two vertebrate host classes, birds and mammals (bats). A co-evolutionary host parasite scenario bas been proposed for primate Plasmodium (including P. Falciparum in human) and Hominidae host family. A estimation of the emergence of P. Falciparum between 7 and 9 millions years has been deduced from this evolutionary scenario. P. Ovale would share a most recent common ancestor with a chimpanzee Plasmodium. Finally, greats apes could appear as a potential reservoirs for three of the four human Plasmodium (P. Falciparum, P. Ovale et P. Malariae)

L'objectif de ce travail de thèse est d'étudier le couplage plasmon-émetteur dans des structures plasmoniques hybrides, visant à renforcer l’interaction lumière-matière à l'échelle nanométrique. Contrairement aux cavités optiques dont le volume de modes est limité par la diffraction, les cavités plasmoniques offrent un unique avantage d’efficacité du confinement sub-longueur d'onde. Cela peut conduire à l’accroissement de la fluorescence des émetteurs placés dans leur voisinage. Pour cela, nous proposons comme dispositif de focalisation une structure intégrée d’un réseau annulaire avec des nanoantennes afin de garantir une meilleure efficacité. Ce dispositif bénéficie du couplage entre des plasmons polaritons de surface (SPP) qui se propagent à partir du réseau et des plasmons localisés de surface (LSP) localisés aux niveaux des nanoantennes afin de parvenir à une augmentation de champ plus élevée. Nous présentons une étude de caractérisation de la plate-forme plasmonique constitué du réseau de diffraction métallique annulaire, d’une nanoantenne en étoile, et la structure intégrée réseau/nanoantenne. Nous montrons comment cette structure peut conduire à une plus grande émission des molécules de colorants ainsi que de centre SiV du diamant. La combinaison du confinement sub-longueur d'onde des LSP et l'énergie élevé des SPP dans notre structure conduit à une focalisation précise qui peut être mis en œuvre pour étudier le couplage plasmon-émetteur dans les régimes de couplage faibles et forts
There is a growing interest nowadays in the study of strong light-matter interaction at the nanoscale, specifically between plasmons and emitters. Researchers in the fields of plasmonics, nanooptics and nanophotonics are constantly exploring new ways to control and enhance surface plasmon launching, propagation, and localization. Moreover, emitters placed in the vicinity of metallic nanoantennas exhibit a fluorescence rate enhancement due to the increase in the electromagnetic field confinement. However, numerous applications such as optical electronics, nanofabrication and sensing devices require a very high optical resolution which is limited by the diffraction limit. Targeting this problem, we introduce a novel plasmonic structure consisting of nanoantennas integrated in the center of ring diffraction gratings. Propagating surface plasmon polaritons (SPPs) are generated by the ring grating and couple with localized surface plasmons (LSPs) at the nanoantennas exciting emitters placed in the gap. We provide a thorough characterization of the optical properties of the simple ring grating structure, the double bowtie nanoantenna, and the integrated ring grating/nanoantenna structure, and study the coupling with an ensemble of molecules as well as single SiV centers in diamond. The combination of the sub-wavelength confinement of LSPs and the high energy of SPPs in our structure leads to precise nanofocusing at the nanoscale, which can be implemented to study plasmon-emitter coupling in the weak and strong coupling regimes

Sinusoidally patterned metallic surfaces, known as plasmonic gratings, constitute one of the principal structures which allow to achieve the coupling between an incident light beam and a Surface Plasmon Polariton mode. A variety of phenomena are available when the grating is rotated of an azimuthal angle with respect to the incidence plane. Aim of this work is a comprehensive investigation of the propagation properties of the surface mode under this configuration, correlating the role of the anisotropy introduced by the grating to the position and shape of the plasmonic resonance dip in the reflectance spectra. Analytical models and physical interpretations are provided; both experimental and computational means are exploited in order to validate the models, including the observation of innovative effects. Thin-film coupled modes, the Long Range and Short Range Surface Plasmon Polaritons, are studied and experimentally observed in the azimuthally rotated configuration. Special attention is paid to the role of the plasmon radiative losses, due to the scattering by the grating. Their dependence on the grating amplitude and the plasmon propagation direction is unraveled, and correlated to the width of the observed plasmonic resonances. The outcomes of these analyses lead to the evaluation of the sensitivity and Figure of Merit achievable when the considered configurations are exploited in the framework of Surface Plasmon Resonance sensing. The developed concepts and methods are proved to be valuable tools to predict and understand the response of actual plasmonic structures applied as sensing devices against gaseous analytes. Experimental tests of the plasmonic platforms as TNT, hydrogen and aromatic compounds sensors are reported, giving promising results. A particularly remarkable experiment is the combined exploitation of Long Range modes and azimuthally rotated configuration to sensibly enhance the performance of a xylene sensor
Superfici metalliche con modulazione sinusoidale, note come grating plasmonici, costituiscono una delle principali strutture che permettono di ottenere l’accoppiamento tra un fascio di luce incidente e un Plasmone Polaritone di Superficie. Una varietà di fenomeni sono accessibili quando il grating viene ruotato di un angolo azimutale rispetto al piano di incidenza. Scopo di questo lavoro è uno studio approfondito delle proprietà di propagazione del modo di superficie in questa configurazione, correlando il ruolo dell’anisotropia introdotta dal grating con la posizione e forma del dip di risonanza plasmonica negli spettri in riflettanza. Vengono presentati modelli analitici e interpretazioni fisiche; metodi sia sperimentali che computazionali vengono impiegati per validare i modelli, includendo l’osservazione di nuovi effetti. I modi accoppiati di film sottile, ovvero i Plasmoni Long Range e Short Range, vengono studiati e osservati sperimentalmente nella configurazione ad azimuth ruotato. Una particolare attenzione è dedicata al ruolo delle perdite radiative del plasmone, dovute allo scattering da parte del grating. La loro dipendenza dall’ampiezza del grating e dalla direzione di propagazione del plasmone è spiegata, e correlata con la larghezza delle risonanze plasmoniche osservabili. I risultati di queste analisi conducono alla valutazione delle sensibilità e Figura di Merito che si possono ottenere quando le configurazioni considerate sono sfruttate nell’ambito della sensoristica a Risonanza Plasmonica di Superficie. I concetti e metodi sviluppati si dimostrano strumenti di valore per predire e interpretare la risposta di strutture plasmoniche reali, applicate come dispositivi di sensing verso analiti allo stato gassoso. Le piattaforme plasmoniche vengono testate come sensori per TNT, idrogeno e composti aromatici, con risultati promettenti. Un esperimento particolarmente interessante è l’uso combinato dei modi Long Range e della configurazione ad azimuth ruotato per incrementare notevolmente le performance di un sensore di xylene

Les nanoparticules plasmoniquespossèdent des propriétés intéressantes grâce àla résonance de plasmon de surface localisé. Enplus de leur grande efficacité de conversionphotothermique due au plasmon, leconfinement de l’échauffement peut êtremodulé par le type de source lumineuseutilisée (impulsionnelle ou continue). Cespropriétés font des nanoparticulesplasmoniques une solution potentielle pour lathérapie contre le cancer par hyperthermie.Afin de développer une telle applicationbiomédicale, il est nécessaire d'optimiserl'absorption de l'énergie lumineuse et le ciblagedes nanoparticules sur la tumeur considérée.Dans cette thèse, l'influence des électronschauds photo-générés sur l'absorptiond’impulsions laser ultracourtes par lesnanoparticules est d'abord étudiée. Ensuite, untravail effectué avec des chimistes, biologisteset médecins pour l'application desnanoparticules d’or irradiées par impulsionslaser ultracourtes à la thérapie contre le cancerest présenté. Enfin, nous présentons une étudepréliminaire sur la photoluminescence denanoparticules plasmoniques, dont l'origine estencore controversée, en appliquant un modèleprenant en compte la nature non thermale dela distribution d’électrons chauds
Plasmonic nanoparticles possessinteresting properties thanks to the localizedsurface plasmon resonance. In addition totheir high photothermal conversion efficiency,the heat release confinement can bemodulated by the type of light source used(pulsed or continuous laser). These propertiesmake the plasmonic nanoparticles a potentialsolution for cancer therapy by hyperthermia.In order to develop such a biomedicalapplication, it is necessary to optimize theabsorption of light energy and the targeting ofnanoparticles on the tumor considered.In this thesis, the influence of the photogeneratedhot electrons on the absorption ofultrashort laser pulses by nanoparticles is firststudied. Then, a work carried out withchemists, biologists and physicians for theapplication of gold nanoparticles irradiated byultrashort laser pulses to cancer therapy isdescribed. Finally, we present a preliminarystudy on the photoluminescence of plasmonicnanoparticles, the origin of which is stillcontroversial, by applying a model accountingfor the non-thermal nature of the hot electrondistribution

Surface plasmon waves are transverse magnetic electromagnetic waves propagating along a dielectric-metal interface. These waves can be excited by resonant absorption of electromagnetic radiation leading to surface plasmon resonance (SPR) at the interface. The resonance is characterised by a reduction in the intensity of the reflected light at the interface due to strong coupling of incident optical radiation to surface plasmons. This gives rise to a minimum at a sharply defined angle of incidence, referred to as SPR angle or plasmon angle. The phenomenon of SPR has been extensively used in the past to develop reflective type optical devices for sensing applications on account of the high dielectric function dependent sensitivity of the SPR angle. Basically, devices which exhibit this phenomenon have a structure consisting of a metal film sandwiched between two dielectrics. The reflectivity of such a device is theoretically modelled based on either theory of thin films (Fresnel's model) or theory of resonance (Lorentzian model). These models have very effectively predicted the behaviour of such devices based on the shift in SPR angle due to the dielectric function variations. We have been investigating the SPR device for intensity based metrological applications utilising its high angular sensitive reflectivity, with fixed SPR angle. In these intensity based applications or measurements, direct and simple expressions connecting intensity variation to angular change are unavailable in the literature and quantitative estimation or data inversion is based on either curve fitting or iterative methods. Fresnel and Lorentzian models have commonly been used in the experiments but data inversion through the Fresnel model is computationally complex and the Lorentzian model, although less complicated, gives erroneous results due to its approximate nature. In order to obtain a simple expression between intensity variation and the angular change, we have re-looked at the two existing models in order to derive an expression which has the simplicity of the Lorentzian model and the accuracy of the Fresnel model in the experiments with fixed plasmon angles. These efforts have been particularly directed to understand the relationship between intensity variation and meteorologically important properties of such devices. This thesis is an attempt to summarize the computational results which have led us to some novel experimental methodologies which have been used to exploit these devices for inverse type, illumination specific, SPR based applications. The work presented in this thesis is organised in six chapters. Chapter 1, gives an overview of optical sensing, theory of surface plasmons, excitation schemes for surface plasmons, development of the SPR device and its characterisation. It also includes a brief literature review in the area of surface plasmon resonance, covering both the theoretical and experimental aspects. The objectives of the work and the scope of the thesis are also presented. Chapter 2 presents the existing models of SPR device, based on Fresnel's and the Lorentzian models. These models allow reflectance calculations from knowledge of either the optical parameters that describe the layers or the parameters of the waves that propagate through them. Using these models, the inverse problem of estimating either the angle of incidence or the optical constants of the layers of the sensors utilizing the intensity based measurements is generally difficult. In order to solve this problem where the plasmon angles are fixed, a modified formalism for the angle scanned SPR spectrum of a three-layered SPR sensor is presented in this chapter. The new formalism regroups the wave vector parameters of Lorentzian resonance theory into a set of non-dimensional parameters 1, 4K and R. The new reflectivity index (1), which is the ratio of reflectance to the absorptance, has been introduced to help explain the physical processes underlying the device operation in the high sensitivity region of the characteristics. The parameter 4Kis a constant of the device and it depends on the dielectric constants of the device. This is a new SPR index and is identified at a point where reflectance and absorptance match. Parameter R is related to the loss mechanisms in the device and will be explained in detail in Chapter 3. This simple model links the new reflectivity index (1) to the angular detune from SPR angle (ΔƟ) and it brings out a parabolic variation of ΔƟ with 1. In this chapter the mathematical derivation of the proposed model is presented and the significance of the new parameters 1, 4Kand Rare discussed. Chapter 3 evaluates the characteristic nature of errors associated with the predictions from the proposed model and presents methods for neutralizing them. It is demonstrated with the help of the function K which is linearly dependant on 1, that the proposed model predicts the reflectance from the wave vector parameters as accurately as the Fresnel's model. This R parameter explains the slowly varying nature of the radiative loss with the angle of incidence and this variation contributes significantly to the SPR characteristics. As a consequence, it is found that the SPR characteristics can be represented as a sum of two primary functions which are parabolic and linear, respectively, and this leads to the easy explanation of the SPR characteristics. The present chapter also discusses a new observation that the angle-scanned SPR spectrum can be accurately described using a straight line in intercept form. The intercept value depends on 4Kand the slope depends on K. In addition to this, this chapter discusses practical methods for estimation of the intercept and the slope of such a straight line which are functions of the key wave vector parameters. A detailed discussion on the proposed model highlighting its advantages for inverse type, illumination specific, SPR-based applications with fixed SPR angle is also presented. Chapter 4 describes the applications of the proposed model for optical constant measurements. The first part highlights a new approach for the determination of the dielectric constants of the metal film used for the optimised- or nearly-optimised SPR sensors using the proposed model. In the complex dielectric constant, the real part is calculated from the SPR angle and the imaginary part from 4K. A discussion on the dielectric constant study of silver and gold metal film is presented. The advantages of the proposed approach such as its simplicity and direct methodology are then discussed. The second part of the chapter also proposes a new approach to carry out measurements on the absorbance of the medium with enhanced sensitivity utilising the parameter 4K It describes a computational study on the variation of 4K values with the dielectric function and highlights the relationship of 4K variation due to the imaginary part of the dielectric function (absorption) of the samples. The physical processes causing a change in the value of 4Kdue to absorption is also discussed along with some computational results. Chapter 5 reports the study carried out to bring out the importance of the new index,4K in metrological applications. Based on the new model, the effect of the laser beam divergence on SPR curve is studied. This chapter first of all discusses the design of the SPR device and the new methods for the development and characterisation of such a device. Details of the experimental procedure for laser divergence evaluation are proposed along with some of the significant computational results. Furthermore, a few applications such as focal length measurement of optical lenses, micro-displacement measurement based on the divergence of the laser beam are also reported. Since the SPR characteristics can be represented easily using the new model, the angular dependent intensity variation can be utilised for some metrological applications with simple data processing. In this context, the high angular sensitivity of the SPR device is studied and some applications such as micro-displacement measurement, pressure measurement and optical wedge angle measurement are included to highlight the above advantages. The last chapter, Chapter 6, gives a summary and conclusions of the work presented in the thesis. The scope for future investigations is also included in this chapter.

Cette etude constitue la premiere evaluation de la diversite genetique et de la structure de population de plasmodium falciparum, au venezuela, par analyse rapd et par pcr des sequences polymorphes des genes codant pour les proteines msp-1, msp-2, resa et csp. Par ailleurs, nous avons realise la caracterisation moleculaire des mutations dans les genes de la dihydrofolate reductase (dhfr) et dihydropteroate synthetase (dhps), supposees etre associees a l'echec des traitements a la pyrimethamine-sulfadoxine (ps) au venezuela. L'analyse rapd a montre une variabilite considerable dans les souches collectees pendant les mois de mai et juillet (epoque de haute transmission) par rapport a celles qui ont ete collectees en novembre (epoque de faible transmission). Un desequilibre de liaison tres significatif (p<104) a ete detecte dans les populations naturelles de p. Falciparum au venezuela. Ceci suggere que la propagation clonale des genotypes joue un role important dans la structure des populations de ce parasite au venezuela, ce qui peut etre explique par de forts taux d'autofecondation. Cependant, la structuration occasionnee par la propagation clonale est clairement moins accentuee que pour d'autres especes parasitaires telles que trypanosoma cruzi. L'analyse phylogenetique de la variabilite rapd montre clairement le caractere monophyletique de p. Falciparum, qui peut etre caracterise par plusieurs caracteres rapd specifiques (tags). Cette etude a trouve en haute proportion des mutations simultanees sur les genes dhfr et dhps. L'effet cumulatif de ces mutations pourrait etre un mecanisme important dans l'emergence d'une resistance elevee a la ps dans cette region. La haute prevalence et diffusion rapide de genotypes resistants pourrait etre une consequence directe de la clonalite et de l'autofecondation, lesquelles peuvent diffuser avec plus de rapidite le mecanisme de multi-resistance aux drogues antipaludiques, comme c'est le cas au venezuela.

Le paludisme, une maladie qui affecte non seulement les humains mais également divers autres vertébrés, est causé par un protozoaire du genre Plasmodium. Chez l'homme, l'espèce Plasmodium falciparum est responsable de la forme la plus grave de la maladie. Les lipides membranaires comptent parmi les éléments les plus critiques pour son développement intraérythrocytaire, et pour assurer sa prolifération. Les phospholipides (PLs), les principaux constituants membranaires, sont synthétisés de novo par la machinerie enzymatique du parasite. En préambule, nous présentons dans deux revues les voies de synthèse des glycérophospholipides chez les procaryotes et les eucaryotes en général, et faisons un examen détaillé de celles présentes dans différentes espèces de Plasmodium. Les majeurs PLs structuraux, la phosphatidylcholine (PC) et la phosphatidylethanolamine (PE), sont synthétisés par de nombreuses voies métaboliques, très similaires à celles de la levure et des plantes. Le premier travail de thèse a porté sur le large éventail de voies métaboliques chez diverses espèces de Plasmodium. Des études in silico et des expériences de marquage métabolique ont révélé des différences marquées concernant le type de voies métaboliques dans les espèces de Plasmodium infectant les rongeurs. Ces résultats ouvrent le débat sur l'origine évolutive des parasites du paludisme humain. Dans une deuxième partie, nous avons eu pour objectifs de déterminer le caractère essentiel ou non pour la survie du parasite, des voies de synthèse de novo de PC et PE (voies de Kennedy). Des études génétiques chez le parasite de rongeur P. Berghei indiquent que les deux voies de Kennedy sont nécessaires au stade érythrocytaire. Ainsi, Plasmodium diffère de la levure où ces voies métaboliques sont auxiliaires et non essentielles. En parallèle, d'autres points ont été abordés concernant les enzymes clefs impliquées dans la synthèse des PLs qui sont absents chez l'hôte humain et/ou qui présentent des caractéristiques particulières par rapport à leurs homologues eucaryotes. D'autres études sont nécessaires pour caractériser plus en détail le métabolisme des PLs, incluant d'autres enzymes, leur régulation, et leur caractère essentiel, ceci tant d'un point de vue fondamental, que pour des retombées possibles en pharmacologie anti-paludique
Malaria, a disease affecting not only humans but also various other vertebrates, is caused by a protozoon of the genus Plasmodium. The Plasmodium falciparum species is responsible for the most severe form of malaria in humans. At the intraerythrocytic stage of its complex life cycle, lipids are among the most critical components to be required for parasite growth and proliferation. Phospholipids (PLs), the main membrane constituents, mostly originate from the enzymatic machinery of the parasite. Foremost, in the form of two detailed reviews, we compare the PL synthetic pathways of prokaryotes and eukaryotes in general, to those of Plasmodium species. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE), the major structural PLs of the parasite, are synthesized in P. Falciparum through a bewildering number of routes, greatly similar to those of yeast and plants. The first asked question concerned the occurrence of this wide range of metabolic pathways among diverse Plasmodium species. In silico and metabolic labelling studies revealed marked differences in PL synthesis between rodent and non-rodents parasite species. These findings relaunch the debate on the evolutionary origin of the human malaria parasites. As a second issue, the essential nature for parasite survival of the de novo PC and PE synthetic pathways, i. E. The Kennedy pathways, was questioned. Genetic studies in the rodent Plasmodium berghei parasite indicated that both Kennedy pathways are required at the erythrocytic stage. Thus, P. Berghei differs from yeast, in which these routes are auxiliary and not crucial. In parallel, other issues were addressed concerning key enzymes involved in PL synthesis, that are absent in the human host and/or that exhibit particular features compared to eukaryotic counterparts. Further studies in P. Falciparum are needed to characterize in greater detail the PL metabolism – i. E. Individual enzymes, regulation and cruciality – from a fundamental point of view and for antimalarial purposes

As visual display technologies move closer to producing true three dimensional displays, pixel technologies need to be ever smaller and more functional to keep pushing the boundaries. Plasmonic metasurfaces have been shown to control the phase, amplitude and/or polarisation of incoming electromagnetic radiation. Nano-fabrication advancements have resulted in the fabrication of the building blocks of such metasurfaces at nano-scale dimensions, allowing the surfaces to interact with visible light, opening up applications in visual displays. As pixel sizes shrink, smaller colour filters will be required. The excitation of plasmonic resonances in metallic nano-structure arrays have resulted in colour filters an order of magnitude smaller than what is currently commercially available. As colour filters, plasmonic metasurfaces offer numerous advantages over pigment-based colour filters used in modern commercial liquid crystal (LC) displays, including environmental, size and longevity factors. Furthermore, exploiting the wavelength and polarisation dependant scattering of nano-structures, optical components, including lenses, waveplates and holograms containing sub-wavelength pixels have been demonstrated in the visible wavelength spectrum. The metasurfaces are able to mould optical wavefronts into arbitrary shapes with sub-wavelength resolution by introducing spatial variations in the optical response of the light scatterers. The applications demonstrated so far are, on the whole, static devices, that is to say their optical properties may not be altered post fabrication. To realise the full potential of plasmonic metasurfaces to visual applications the devices must be made active. By activating structural colour surfaces, not only may pixel densities potentially be increased simply by removing the need for separate red, green and blue filters, but a new class of high definition ultra-thin display devices may be accessible, whilst the dynamic manipulation of the wavelength and polarisation properties of nano-scattering elements would open up the possibilities to create sub-wavelength holographic pixels. This thesis investigates ways to activate static metasurfaces for colour, flat optic, and holographic applications. First, methods of dynamic control of the structural colour of plasmonic nano-hole arrays are investigated. By combining nano-hole arrays with liquid crystals, transmissive electrically tunable LC-nanohole pixels operating across the visible spectrum with un-polarised input light are experimentally demonstrated. An output analyser in combination with a nematic LC layer enables pixel colour to be electronically controlled through an applied voltage across the device, where LC re-orientation leads to tunable mixing of the relative contributions from the plasmonic colour input. Furthermore, exploiting the strong surface anchoring effects between an aluminium surface and LC molecules a twisted nematic LC cell, using a metallic grating as a combined colour filter, electrode and alignment layer, was shown to act a variable amplitude colour filter. The colour of these pixels was improved greatly utilising a grating-insulator-grating structure unique to this work. Second, a new process for fabricating aluminium nano-rod structures embedded in an elastomeric medium, with high spatial accuracy, is presented. The process is used to create nano-rod plasmonic resonator arrays whose optical properties may be altered by mechanical deformation. The pattern transfer process is further utilised to create dynamic optical elements, including nano-rod arrays for colour filters, tunable focal length Fresnel zone plates and photon sieves, and stretchable holograms with dynamic replay fields.

Nanopartículas de Fe3O4 e Fe2O3 foram sintetizadas a partir da rota de coprecipitação, em atmosfera de N2, mantendo-se o pH entre 9 e 14 na temperatura ambiente e utilizando como precursores o FeCl2 e FeCl3. Após a síntese, as nanopartículas foram tratadas termicamente a 250, 500 e 800 oC. Para obtenção de um sistema híbrido, foram sintetizadas nanopartículas de ouro sobre as nanopartículas de óxido previamente tratadas em diferentes temperaturas. As amostras foram caracterizadas por UV-Vis, difratometria de Raios-X (DRX), microscopia eletrônica de transmissão (MET), microscopia eletrônica de transmissão de alta resolução (MET-AR), espectroscopia no na região do infravermelho (FTIR), magnometria de amostra vibrante (VSM) e espectroscopia Mossbauer (EM), e aplicadas para produção de hidrogênio promovendo a decomposição da hidrazina. Os resultados mostram a síntese de nanopartículas de óxido de ferro com diâmetro médio de cerca de 7 nm. Quando aquecidas a 250 oC o tamanho médio aumentou para ca. de 11 nm e foi observado uma pequena mudança no comportamento óptico e estrutural, mantendo o comportamento superparamagnetico. Quando aquecidas a 500 oC o tamanho médio aumenta para ca. de 50nm e são observadas mudanças significativas nas propriedades ópticas, morfológicas, estruturais. Adicionalmente observa-se transição de comportamento superparamagnetico para paramagnético. Quando aquecidas a 800 oC os efeitos nas propriedades dos materiais são ainda mais significativos; as partículas apresentam tamanho médio de 200 nm, o espectro de absorção no UV-Vis muda significativamente e as partículas passam a ter comportamento pagamagnético. Os resultados obtidos pelas diferentes técnicas e somadas ao Mossbauer sugerem que as amostras sintetizadas são uma mistura de Fe3O4 e -Fe2O3, quando aquecido a 250 e 500 oC uma mistura de -Fe2O3 e -Fe2O3 e a 800 oC somente -Fe2O3. As nanopartículas de ouro sintetizadas sobre as amostras de oxido de ferro apresentaram tamanho médio de 6,0 nm e não afetaram as propriedades magnéticas dos oxidos. As amostras de óxido com nanopartículas de ouro promoveram a decomposição da hidrazina por rota completa, levando a formação de hidrogênio com seletividade de até 33%.
Fe3O4 and Fe2O3 nanoparticles were synthesized by coprecipitation route carried out under N2 atmosphere, maintaining the pH between 9 and 14 at room temperature and using FeCl2 and FeCl3 as precursors. After synthesis the iron oxide nanoparticles were thermally treated at 250, 500 and 800 oC. To obtain a hybrid system, gold nanoparticles were synthesized on the thermally treated oxide nanoparticles. The samples were analyzed by UV-Vis, X-ray diffraction (XRD), transmission electron microscopy (TEM), high resolution transmission electron microscopy (MET-AR), spectroscopy in the region of Infrared (FTIR), vibrating sample magnitude (VSM) and Mossbauer, and applied to produce H2 through hydrazine decomposition. The results show the synthesis of Fe3O4 nanoparticles with average diameter of about 7 nm. When heated to 250 oC the average size increased to about 11 nm and a small change in the optical and structural behavior was observed, while the superparamegnetic behaviour was maintained. When heated to 500 °C, the average particle size increase to ca 51nm, significant changes in the optical, morphological and structural properties are observed, in addition to a transition from superparamegnetic to paramagnetic behaviour. When heated to 800 oC the effects on the properties are even more significant; the nanoparticles increase to ca. 200 nm, the absorption spectrum in UV-Vis changes significantly and the particles present paramagnetic behaviour. The results suggest that when heated to 250 and 500 oC a mixture of -Fe2O3 e -Fe2O3 is obtained, after heating at 800 oC only -Fe2O3 is observed. The gold nanoparticles synthesized on the iron oxides present average size of 6.0 nm, and did not affect the magnetic properties of the oxides. The iron oxides/gold nanoparticle samples were efficiently applied to produce hydrogen, promoting the decomposition of hydrazin. The selectivity to hydrogen reached up to 33%.

Fifty three Staphylococcus aureus isolates were obtained from three centres, two hospitals and a private pathology laboratory, and studied for susceptibility to bacteriophages, resistance to antimicrobial agents and plasmid contents.Results of bacteriophage typing revealed that they belonged to a variety of phage types. Eighteen were untypable by any of the International Set of Phages, 16 belonged to phage group 111, nine to group I, four to group 11, two to group IV and two to the miscellaneous group.The isolates were resistant to one or more of methicillin (Mc), benzyl penicillin (Pc), gentamicin (Gm) , kanamycin (Km) , neomycin (Nm) , streptomycin (Sm) , trimethoprim (Tp), sulphonamides (Su), tetracycline (Tc), minocycline (Mn), chloramphenicol (Cm), novobiocin (Nb) and fusidic acid (Fa). Resistance to Pc was due to the production of beta-lactamase (Bla). No resistance to vancomycin, spectinomycin and erythromycin was detected. Resistance was also found to heavy metals such as cadmium (Cd), mercury (Hg), phenyl mercuric acetate (Pma), arsenate (Asa) and to the nucleic-acid binding compounds propamidine isethionate (Pi) and ethidium bromide (Eb).All but one of the isolates harboured plasmids. The number of plasmids the isolates carried varied from one to six and their sizes ranged from < 1.0 kb to c.48 kb.Location of the resistance determinants was ascertained by curing and transfer experiments. Loss of resistance was tested after growth at 43.5°C and transfer of resistance determinants was attempted by transduction, mixed-culture transfer and conjugation. The results revealed that resistance to Mc, Gm, Tp, Mn and Fa was chromosomal in all the resistant isolates and in some isolates Bla and resistance to Sm and Cd were chromosomal as well as plasmid encoded. In the majority of cases Bla and resistance to Km, Nm, Sm, Tc, Cin, Cd, Hg, Asa, Pma, Pi and Eb was encoded ++
by plasmids.Conjugation experiments led to the isolation of three unique conjugative plasmids which have not been found to confer resistance to antimicrobials or to produce haemolysins or diffusible pigment (Dip). The three plasmids, pWBG620, pWBG637 and pWBG661, were indistinguishable by restriction endonuclease analysis and DNA-DNA hybridisation. However pWBG620, unlike pWBG637 and pWBG661, was not detected in the cytoplasm of its host and was only detected in transconjugants after it mobilised a non-conjugative Sm-resistance (SmR) plasmid. Further analysis indicated that it is integrated into the chromosome of its host, excises during conjugation and mobilises the SmR plasmid.These plasmids were studied further using pWBG637 as a representative. It was compared with representatives of the two groups of conjugative plasmids which have been reported in the staphylococci. These are the plasmids which encode resistance to Gm, Km and Nm and those which code for the production of diffusible pigment. The three types of conjugative plasmids were compared by restriction endonuclease analysis and DNA- DNA hybridisation and were found to be different. A preliminary restriction map of pWBG637 has also been constructed.However since pWBG637 has no resistance phenotype direct selection for it was not possible in transfer experiments and for incompatibility (Inc.). To study it further it was necessary to construct resistant derivatives which could be selected for in transfer experiments. This was achieved by labelling pWBG637 with resistance transposons to generate two conjugative plasmids, pWBG636 carrying an insert of Tn3851 (Gm- resistance) and pWBG642 carrying an insert of Tn551 (hn- resistance). It was found that transposon labelling had not changed the incompatibility of pWBG637 and therefore pWBG636 and pWBG642 were used in further experiments in place of pWBG637. Inc. ++
tests with the pWBG637 derivatives revealed that the pWBG637 type of plasmid is not only different from the other two types of conjugative plasmids but is different from any of the described staphylococcal Inc. groups and therefore the pWBG637 type of plasmids represent a new Inc. group 15. The pWBG637 type of plasmids were studied further using plasmids pWBG636 and pWBG642. They were able to transfer conjugatively to a capsulated S.aureus strain either by the polyethylene glycol method or on filter membranes. They also transferred by conjugation to S. epidermidis and Streptococcus faecalis and were able to transfer back from these strains to S.aureus indicating that they also replicate in these hosts. Consequently they have been used to mobilise non-conjugative plasmids from S.epidermidis and non phage typable S.aureus. Both plasmids failed to transfer conjugatively to Bacillus subtilis and Escherichia coli.pWBG637 transferred non-conjugative plasmids by mobilising them in a manner similar to mobilisation (donation) in E.coli or by recombining with them to form new resistance plasmids. In one case, pWBG628 which encodes Bla and resistance to Cd, Km, Nm and Sm and has no homology with pWBG637 recombined with it during conjugation to produce three new conjugative plasmids pWBG629, pWBG630 and pWBG631 carrying resistance determinants from pWBG628. One of these plasmids, pWBG629, was found to be pWBG637 which had acquired a 4.5 kb element encoding resistance to Km, Nm and Sm. This element was shown to be transposable in both rec+ and rec- backgrounds and has been designated Tn3854. It expressed Sm resistance in E.coli and differs on this account from the Gram-negative transposon Tn5 which expresses resistance to Km, Nm and Sm in non-enteric bacteria but only resistance to Km and Nm in E. coli.Where possible the non-conjugative plasmids encoding resistance to ++
antimicrobial agents were compared with phenotypically similar plasmids isolated from other parts of the world. It was found that the Tc and Sm resistance plasmids were closely related to other plasmids with the same phenotype whereas the Cm resistance plasmids were different.Although the majority of the Bla plasmids belonged to Inc. group 1 they demonstrated significant restriction enzyme fragment length polymorphism when compared with other Bla plasmids.This study has provided the first data on the genetics of antimicrobial resistance in Nigerian S.aureus. Although many of the plasmids studied were found to be similar to those previously described the isolates also contained some unique and previously undescribed plasmids.

Surface plasmon polaritons are highly localised field oscillations that propagate along interfaces between a dielectric and a metal. Their localised fields make them potential signal carriers between integrated circuits, replacing electronic signals, to allow wider bandwidths and less power dissipation. End-fire coupling is a simple, compact method for exciting surface plasmon polaritons with potential for high coupling efficiency. However, the parameters that determine the mechanism's optimisation are not well understood. We present a semi-analytical model of the end-fire mechanism, in which a free-space incident beam excites a surface plasmon polariton in a configuration with a single transverse dimension. We first model coupling into a surface plasmon polariton on an air-lossless metal interface. Our projection method, a key modelling component, uses an energy conservation expression which includes contributions from both propagating and evanescent fields, which become significant for near-field sources. By optimising the incident beam width and position, we find maximum coupling efficiencies of up to ~90% over the wavelength range of λ∈[0.5,1.8] μm, averaging ~80%. We also find that each excitation produces not only the primary surface plasmon polariton, but also a transversely propagating secondary surface plasmon polariton. We then adapt our method to simulate lossy plasmonic materials, replacing the lossless metal with silver, gold, titanium nitride and zirconium nitride using their values from literature. By optimising the incident beam parameters, we find that the coupling efficiencies of all four materials reach 87% over the range λ∈[0.38,2] μm. These high coupling efficiencies are explained using an impedance-matching argument, concluding that most of the surface plasmon polariton field is in the dielectric, not the plasmonic material. Using a simple analytical model, we show that there is a universal relationship between the optimum beam width and position.

Pour la première fois, en associant un microscope à effet tunnel (STM) et un microscope optique inversé,nous avons imagé les plasmons de surface excités électriquement sur un film d'or avec la pointe d'un STM.Par microscopie de fuite radiative, en observant l'image de l'interface air/or et celle du plan de Fourierassocié, nous avons distingué les plasmons propagatifs des plasmons localisés sous la pointe. Les plasmonspropagatifs sont caractérisés par une distance de propagation et une direction d'émission en accord aveccelles de plasmons propagatifs créés par excitation laser sur des films d'or de mêmes épaisseurs. Les fuitesradiatives des plasmons localisés s'étalent jusqu'à l'angle maximum d'observation. Plasmons propagatifs etlocalisés ont une large bande spectrale dans le visible. Si la pointe est plasmonique (en argent), lesplasmons localisés ont une composante supplémentaire due au couplage associé. Pour différents types depointe, nous avons déterminé les intensités relatives des plasmons localisés et propagatifs. Nous trouvonsque chaque mode plasmon (propagatif ou localisé) peut être préférentiellement sélectionné en modifiant lematériau de la pointe et sa forme. Une pointe en argent produit une intensité élevée de plasmons localisés,tandis qu'une pointe fine de tungstène (rayon de l'apex inférieur à 100 nm) produit essentiellement desplasmons propagatifs. Nous avons étudié la cohérence spatiale des plasmons propagatifs excités par la pointe du STM. Avec un film d'or opaque (épaisseur 200 nm) percé de paires de nanotrous nous avons réalisé une expérienceanalogue à celle des fentes d'Young. Des franges d'interférences sont observées. La mesure de leurvisibilité en fonction de la distance des nanotrous donne une longueur de cohérence des plasmons de 4.7±0.5 μm. Cette valeur, très proche de la valeur 3.7± 1.2 μm déduite de la largeur de la distribution spectraledes plasmons, indique que l'élargissement spectral des plasmons propagatifs est homogène.Nous avons aussi étudié la diffusion des plasmons propagatifs excités par la pointe du STM par desnanoparticules d'or déposées sur un film d'épaisseur 50 nm. Nous observons une diffusion élastique et unediffusion radiative. Des franges d'interférences sont observées dans la région d'émission lumineuseinterdite du plan de Fourier, dont la période est inversement proportionnelle à la distancepointe-nanoparticule d'or avec un facteur de proportionnalité égal à la longueur d'onde moyenne desplasmons. Il y a donc interférence entre la radiation des plasmons localisés et la radiation provenant de ladiffusion des plasmons propagatifs sur les nanoparticules d'or. Ceci indique que les plasmons localisés etpropagatifs excités électriquement par la pointe du STM sont différentes composantes du plasmon uniqueproduit par effet tunnel inélastique avec la pointe du STM. Ces résultats originaux sur les plasmons créés sur film d'or par un effet tunnel inélastique localisé à l'échelle atomique (i) élargissent la compréhension du processus et (ii) offrent des perspectives intéressantes pour une association de la nanoélectronique et de la nanophotonique.

La plasmonique vise à utiliser des nanostructures métalliques très petites devant la longueur d’onde pour manipuler la lumière. Les structures métalliques sont particulières parce qu’elles contiennent un plasma d’électrons libres qui conditionne complètement leur réponse optique. Notamment, lorsque la lumière se propage à proximité des métaux, sous forme de mode guidés comme les plasmons et les gap-palsmons, elle est souvent lente, présentant une vitesse de groupe faible. Dans ce travail, nous présentons une analyse physique qui permet de comprendre cette faible vitesse en considérant le fait que l’énergie se déplace à l’opposé de la lumière dans les métaux. Nous montrons que la vitesse de groupe est égale à la vitesse de l’énergie pour ces modes guidés, et proposons la notion de ralentissement plasmonique. Finalement, nous étudions comment cette « trainée plasmonique » rend une structure aussi simple qu’un coupleur à prisme sensible à la répulsion entre les électrons du plasma
The field of plasmonics aims at manipulating light using deeply subwavelength nanostructures. Such structures present a peculiar optical response because of the free electron plasma they contain. Actually, when light propagates in the vicinity of metals, usually under the form of a guided mode, it presents a low group velocity. Such modes, like plasmons and gap-plasmons, are said to be slow. In this work we present a general physical analysis of this phenomenon by studying how the energy propagates in metals in a direction that is opposite to the propagation direction of the mode. We show that the group velocity and the energy velocity are the same, and finally introduce the concept of plasmonic drag. Finally, we study how slow guided modes make structures as simple as prism couplers sensitive to the repulsion between electrons inside the plasma

The diploma thesis deals with plasmonic nanostructures for visible eventually near-infrared region of electromagnetic spectrum. At first, there are discussed basic terms which are necessary for description of plasmonic nanostructures and their properties. Then the resonant properties of gold nanoantennas on a fused silica substrate and in proximity of nanocrystalline diamond are addressed. FDTD simulations are used for an assesment of resonant properties and local electric field enhancement of these nanostructures. Possible manufacturing methods of the antennas and techniques for the measurement of their properties are mentioned at the end of the thesis.

Thesis (M. S.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2008.
Committee Chair: El-Sayed, Mostafa A.; Committee Member: Lyon, L. Andrew; Committee Member: Sherrill, C. David; Committee Member: Wang, Zhong Lin; Committee Member: Whetten, Robert L.

Els plasmidis són molècules d’ADN circular extracromosòmiques amb capacitat de replicació autònoma i, són descrits com els principals promotors de la disseminació de gens de resistència a antimicrobians. Escherichia coli i Klebsiella pneumoniae, són freqüents agents causals d’infeccions, importants pel seu caràcter multirresistent. En aquests bacteris, les betalactamases constitueixen un dels mecanismes de resistència més difosos mitjançant plasmidis. Mitjançant l’estudi i comparació del contingut plasmídic en bacteris d’individus sans i de pacients, l’objectiu va ser determinar les diferències o similituds d’aquests plasmidis entre les dues poblacions, per tal d’inferir en el seu origen i evolució en els soques causants d’infecció. Per a això, es van aïllar soques d’E. coli (n = 244) i K. pneumoniae (n = 115) de 150 mostres fecals d’individus sans i de 202 pacients amb bacterièmia. Es va realitzar un estudi de sensibilitat a antimicrobians mitjançant disc difusió, es van identificar les soques multirresistents i es van caracteritzar, per PCR i seqüenciació, els gens codificants de BLEE, AmpC i carbapenemases. L’estudi de plasmidis es va realitzar utilitzant la tècnica de PBRT i, es van subtipificar els plasmidis IncF, IncI1 i IncN mitjançant pMLST per a la seva diferenciació dins d’un mateix grup d’incompatibilitat. La localització dels gens de resistència i la definició de la fórmula FAB dels plasmidis IncF, es va realitzar mitjançant la tècnica de Southern-blot i hibridació. Un 29,2% de les soques de mostra clínica front d’un 10,8% en individus sans van resultar multirresistents. La prevalença de soques d’E. coli clíniques productores de BLEE va ser de 17,2% i 5% d’AmpC i, en K. pneumoniae, de 16,5% i 1%, respectivament, a més a més d’un 1,9% de carbapenemases . D’altra banda, es va observar una prevalença del 4,7% de portadors sans d’E. coli productores de BLEE i un 2,7% d’AmpC. Ambdues poblacions han sofert un augment en la detecció de soques productores d’aquests enzims sent també, en ambdós casos, la CTX-M-15 i la CMY-2 les betalactamases més freqüents. Els resultats del PBRT van mostrar com el contingut plasmídic de les dues poblacions seguia una mateixa tendència sense diferències significatives destacables. L’excepció es va observar en els replicons L, M, A/C i N, els quals només es van detectar en les soques de mostra clínica. A més, alguns d’aquests plasmidis amb replicó L o N van ser detectats en associació a gens blaBLEE. La subtipificació dels plasmidis, ens va permetre observar l’existència d’una gran diversitat de secuenciotips dins d’un mateix grup d’incompatibilitat. Dins dels plasmidis IncI1 es va observar una gran diferència entre els ST identificats en les soques d’individus sans i pacients. Només els ST12 i ST36 es van identificar en ambdues poblacions d’E. coli, i tots els ST12 en associació amb el gen blaCMY-2. Per contra, tot i que també es va detectar una gran diversitat de RST entre els plasmidis IncF, aquells detectats amb més freqüència, van estar presents en ambdues poblacions i, no es va identificar cap fórmula FAB destacable per la seva associació a gens bla. En conclusió, el contingut plasmídic en la població de soques clíniques és un reflex del contingut en soques d’individus sans però, certs plasmidis, només es detecten en soques causants d’infecció, suggerint una millor adaptació a ambients sotmesos a pressió selectiva. Secuenciotips IncI1 com el ST12, poden ser considerats plasmidis epidèmics per la seva alta prevalença i freqüència en associació amb gens blaCMY-2. En canvi, els plasmidis IncF semblen haver adquirit diferents gens de resistència a antimicrobians de forma aleatòria, suggerint que tota la família de plasmidis IncF és potencialment susceptible a adquirir i disseminar gens de resistència.
Los plásmidos son moléculas de ADN circular extracromosómicas con capacidad de replicación autónoma y, se describen como principales promotores de la diseminación de genes de resistencia a antimicrobianos. Escherichia coli y Klebsiella pneumoniae, son frecuentes agentes causales de infecciones, importantes por su carácter multirresistente. En estas bacterias, las betalactamasas constituyen uno de los mecanismos de resistencia más difundidos mediante plásmidos. Mediante el estudio y comparación del contenido plasmídico en bacterias de individuos sanos y de pacientes, el objetivo fue determinar las diferencias o similitudes de estos plásmidos entre ambas poblaciones, con el fin de inferir en su origen y evolución en las cepas causantes de infección. Para ello, se aislaron cepas de E. coli (n=244) y K. pneumoniae (n=115) de 150 muestras fecales de individuos sanos y de 202 pacientes con bacteriemia. Se realizó un estudio de sensibilidad a antimicrobianos mediante disco difusión, se identificaron las cepas multirresistentes y se caracterizó, por PCR y secuenciación, los genes codificantes de BLEE, AmpC y carbapenemasas. El estudio de plásmidos se realizó utilizando la técnica de PBRT y, se subtipificaron los plásmidos IncF, IncI1 e IncN mediante pMLST para su diferenciación dentro de un mismo grupo de incompatibilidad. La localización de los genes de resistencia y la definición de la fórmula FAB de los plásmidos IncF, se realizó mediante la técnica de Southern-blot e hibridación. Un 29,2% de las cepas de muestra clínica frente a un 10,8% en individuos sanos resultaron multirresistentes. La prevalencia de cepas de E. coli clínicas productoras de BLEE fue de 17,2% y 5% de AmpC y, en K. pneumoniae, de 16,5% y 1%, respectivamente, además de un 1,9% de carbapenemasas. Por otro lado, se observó una prevalencia del 4,7% de portadores sanos de E. coli productoras de BLEE y un 2,7% de AmpC. Ambas poblaciones han sufrido un aumento en la detección de cepas productoras de estas enzimas siendo también, en ambos casos, la CTX-M-15 y la CMY-2 las betalactamasas más frecuentes. Los resultados del PBRT mostraron como el contenido plasmídico de ambas poblaciones seguía una misma tendencia sin diferencias significativas destacables. La excepción se observó en los replicones L, M, A/C y N, los cuales solo se detectaron en las cepas de muestra clínica. Además, algunos de estos plásmidos con replicón L o N fueron detectados en asociación a genes blaBLEE. La subtipificación de los plásmidos, nos permitió observar cómo dentro de un mismo grupo de incompatibilidad existe una gran diversidad de secuenciotipos. Dentro de los plásmidos IncI1 se observó una gran diferencia entre los ST identificados en las cepas de individuos sanos y pacientes. Solo los ST12 y ST36 se identificaron en ambas poblaciones de E. coli, y todos los ST12 en asociación con el gen blaCMY-2. Por el contrario, a pesar de que también se detectó una gran diversidad de RST entre los plásmidos IncF, aquellos detectados con mayor frecuencia, estuvieron presentes en ambas poblaciones y, no se identificó ninguna fórmula FAB destacable por su asociación a genes bla. En conclusión, el contenido plasmídico en la población de cepas clínicas es un reflejo del contenido en cepas de individuos sanos, pero hay ciertos plásmidos, que solo se detectan en cepas causantes de infección, sugiriendo una mejor adaptación a ambientes sometidos a presión selectiva. Secuenciotipos IncI1 como el ST12 pueden ser considerados plásmidos epidémicos por su alta prevalencia y frecuencia en asociación con genes blaCMY-2. En cambio, los plásmidos IncF parecen haber adquirido distintos genes de resistencia a antimicrobianos de forma aleatoria, sin ningún RST destacable por ello; sugiriendo que toda la familia de plásmidos IncF es potencialmente susceptible a adquirir y diseminar genes de resistencia.
Plasmids are extracromosomal circular DNA molecules that can replicate autonomously. They are globally described as primary promoters for the dissemination of antimicrobial resistance genes. Escherichia coli and Klebsiella pneumoniae have been described as critical propriety microorganisms due to their increasing detection as multiresistant bacteria. In these bacteria, beta-lactamases constitute one of the most disseminated resistance-providing mechanisms through plasmids. Through the study and comparison of the plasmid content in the commensal microbiota from healthy individuals and patients with bacteriemia, the aim was to determine the differences and similarities of the plasmid content between these two populations, with the purpose to shed light on the origin and evolution of bacteria-causing infection. To achieve that goal, E. coli (n=244) and K. pneumoniae (n=115) strains from 150 faecal samples from healthy individuals and 202 patients with bacteraemia where isolated. An antimicrobial susceptibility testing was performed through the disc diffusion technique, the multiresistant strains were identified and, the blaESBL, blaAmpC and blacarbapenemase genes were characterised by PCR and sequencing approaches. The plasmid study was performed by using the PBRT technique. Plasmids IncF, Incl1 and IncN plasmids, were subtyped by pMLST, to differentiate each of them within the same incompatibility group. The location of the resistance genes was performed by using the Southern blot and hybridisation techniques. The same methodology was used to generate the FAB formula of the IncF plasmids. From the clinical samples, 29.2% of the strains turned out to be multiresistant against 10.8% from healthy individuals. The prevalence of clinical ESBL-producing and AmpC-producing E. coli strains was 17.2% and 5%, respectively. The prevalence of clinical ESBL-producing, AmpC-producing and carbapenemase-producing K. pneumoniae strains was 16.5%, 1% and 1.9%, respectively. Furthermore, 4.7% of the healthy individuals were carriers of ESBL-producing E. coli and 2.7% were carriers of AmpC-producing E. coli. Both populations have suffered an increased detection of strains that produce those enzymes and, in both cases, the beta-lactamases CTX-M-15 and CMY-2 were the most frequent. The PBRT results showed how the plasmid content in both populations kept the same trend without significant differences. The exception was observed in the replicons L, M, A/C and N, which were only detected in strains from clinical samples. What is more, some of these plasmids with L or N repliclon were detected in association with blaESBL genes. The plasmid subtyping, allowed us to observe a great diversity of sequence types (ST) within the same group of incompatibility. Within the Incl1-plasmids, a huge difference between the identified ST in healthy individuals and patient strains was observed. Only ST12 and ST36 were identified in both populations of E. coli. Noticeably, all the ST12 were found in association with the blaCMY-2 gene. In contrast, even though a great diversity of RSTs was detected within the IncF plasmids, those detected at higher rates were present in both populations. Furthermore, no formula was distinguishable by its association with bla genes. In conclusion, the replicon content of clinical strains mirrored that of comensal strains. Nevertheless, there are certain plasmids only detected in infection-causing strains, suggesting a better adaptation to an enviroment subjected to selective presure. IncI1 sequencetypes such as ST12 can be considered epidemic plasmids due to their high prevalence and frequency in association with blaCMY-2. On the other hand, the IncF plasmids have acquired multiple antimicrobial resistace genes randomly, with no evidence that the persitance of a single IncF is responsible for their dissemination. Therfore, the entire IncF family of plasmids is potentially capable of acquiring and propagating resitance genes.

Dans ce travail de these, nous étudions comment des nano-structures métalliques modifient le processus d'émission spontannée d'objets fluorescents et jouent ainsi un rôle d'antenne. Ces structures supportent des modes optiques confinés aux interfaces metal-diélectrique: ce sont des modes plasmoniques.De par leur fort confinement, ces modes modifient la densité locale d'états optiques et permettent notamment d'accélérer le processus d'émission spontannée (facteur de Purcell). Nous étudions le cas d'une structure planaire metal-isolant-métal de type patch couplée à un ensemble de nanocristaux colloïdaux fluorescents. Nos mesures, soutenues par des calculs numériques, montrent une acceleration de l'émission fluorescente d'un facteur 80 ainsi qu'une augmentation de la directivité de l'émission. Nous décrivons ensuite le procedé de fabrication d'une structure patch metal-semiconducteur-métal pour laquelle la source fluorescente est un puits quantique émettant dans le proche infra-rouge. Nous montrons que l'antenne permet d'augmenter l'extraction fluorescente d'un facteur 8. Enfin, nous considérons le cas d'une structure sphérique composée d'un unique nanocristal fluorescent au centre d'une bille de silice entourée par une fine coquille métallique. Cette structure plasmonique accélère l'émission d'une facteur 10 et permet de supprimer le scintillement caractéristique de l'émission des nanocristaux. La coquille métallique permet également d'isoler chimiquement le nanocristal de l'environnement, assurant ainsi une grande photostabilité et une toxicité réduite. L'émetteur ainsi obtenu est donc un candidat prometteur pour des applications de marquage de fluorescence in-vivo.

Les réponses optiques d'agrégats de métaux nobles sont caractérisées par une absorption intense, situées dans le domaine UV-Visible, et appelée plasmon de surface localisé. Pour des particules de plusieurs nanomètres de diamètre, le phénomène de plasmon peut être interprété par des modèles semi-classiques ou classiques comme la théorie de Mie, mais ces modèles trouvent leur limite lorsque la taille du système diminue. La théorie de la fonctionnelle de la densité dépendante du temps (TDDFT) est une approche entièrement quantique qui permet d'appréhender le phénomène de plasmon en reproduisant la réponse optique de petits agrégats d'argent, composés de quelques atomes à quelques centaines d'atomes. Dans ce contexte, nous avons réalisé des calculs TDDFT avec une fonctionnelle de type Range-Separated-Hybrid (RSH) sur des agrégats contenant entre 8 et 147 atomes d'argent. Les spectres obtenus sont en excellent accord avec les données expérimentales et les réponses optiques calculées perme ttent de retrouver les prédictions du modèle en couches. Nous présentons des outils permettant d'identifier et de caractériser les excitations plasmoniques dans le formalisme de la TDDFT. Les effets de l'environnement sur la réponse optique des agrégats sont également étudiés, avec notamment la présentation d'une méthodologie permettant de reproduire les spectres mesurés sur des agrégats d'argent piégés dans des matrices de gaz rare. Les effets de l'oxydation et les effets induits par une matrice de silice sur la réponse optique des agrégats sont également étudiés
Optical responses of noble metal clusters are characterized by a strong absorption in the UV-Visible range called localized surface plasmon. For clusters of several nanometers, the plasmon phenomenon can be interpreted by semi-classical or classical model, as the Mie theory, but those models can not describe the optical response of small-size clusters. The time dependent density functional theory (TDDFT) is a quantum method that allow to understand the plasmon phenomenon by reproducing the optical response of small silver cluster, made of a few tens or hundreds atoms. In this context, we performed TDDFT calculation using Range-Separated Hybrid (RSH) functionals over cluster containing between 8 and 147 silver atoms. The obtained spectra are in excellent agreement with the experimental ones and the calculated optical response allows to recover the shell model prediction. We present some tools that allow to identify and characterize plasmonic excitations within the TDDFT framework. The effect of the surrounding medium over the optical response of clusters are studied, in particular we will present a methodology that allow to reproduce spectra measured over clusters trapped in rare gas matrix. The effects of the oxidation and the effects induced by a silica matrix over the optical response of clusters are also studied

Une étape cruciale dans le cycle de Plasmodium, parasite causal du paludisme est sa transmission de l'hôte vertébré au moustique vecteur. Seuls les stades sanguins sexués sont capables de se développer dans le moustique. Chez le moustique, le nouvel environnement déclenche une cascade de signalisation conduisant à la gamétogenèse. Les travaux de thèse ont pour objectifs d'élucider cette cascade de signalisation qui joue un rôle clé dans la transmission du paludisme. Des approches pharmacologiques biochimiques et génétiques ainsi que des études d'imagerie ont été utilisées et fournissent de multiples évidences d'une implication de la phospholipase C (PLC) au cours de la gamétogenèse mâle de Plasmodium berghei. Les études pharmacologiques impliquent le récepteur à la ryanodine pour un premier signal calcique qui active la PLC. Un marquage métabolique du PIP2 et des mesures d'inositol tris phosphate (IP3) montre la chronologie de l'activité PLC. Les données biochimiques ont été corroborées par imagerie des gamétocytes exprimant une protéine fluorescente liant PIP2 et IP3, et suggèrent que l'activation de la PLC agit comme amplificateur du signal calcique. En outre, nous avons développé une nouvelle méthode pour analyser la gamétogenèse mâle, basée sur le marquage radioactif de l'ADN nouvellement synthétisé. Cette méthode a donné de nouvelles informations sur la cinétique de la réplication de l'ADN au cours de la gamétogenèse. La méthode a été validée pour l'identification de composés qui interfèrent avec la gamétogenèse et éventuellement bloquerait la transmission du paludisme
A crucial step in the life cycle of Plasmodium, the causative agent of malaria, is its transmission from vertebrate host to mosquito vector. Only sexual blood stages, termed gametocytes, are capable to develop within the mosquito. Upon ingestion by a mosquito, cues from the new environment trigger an intracellular signalling cascade within the gametocytes leading to gametogenesis, the first developmental step in the mosquito. This study aimed to further our understanding of this signalling cascade, as it plays a key role in malaria transmission. Genetic, biochemical, pharmacological, and live cell imaging approaches were employed and provide multiple lines of evidence for phospholipase C (PLC) involvement in the signalling events during male gametogenesis of Plasmodium berghei. Pharmacological evidence suggests that ryanodine receptors mediate an initial release of calcium that activates PLC. Metabolic labelling of PIP2 was used in combination with sensitive IP3 detection and allowed to deduce a timeline of PLC activity during gametogenesis. Biochemical data were confirmed by live cell microscopy of gametocytes expressing a fluorescent reporter protein binding to PIP2 and IP3, and suggest that PLC acts as calcium signal amplifier. Furthermore, we developed a new method to analyse male gametogenesis, based on radioactive labelling of newly synthesised DNA. This method provided new insight into the kinetics of DNA replication during Plasmodium gametogenesis. This assay can now be used to identify compounds that interfere with gametogenesis and potentially block malaria transmission

Applications of surface plasmon polaritons (SPPs) have thus far emphasized visible and near-infrared wavelengths. Extension into the long-wave infrared (LWIR) has numerous potential advantages for biosensors and waveguides, which are explored in this work. A surface plasmon resonance (SPR) biosensor that operates deep into the infrared (3-11 µm wavelengths) is potentially capable of biomolecule recognition based on both selective binding and characteristic vibrational modes. The goal is to operate such sensors at wavelengths where biological analytes are strongly differentiated by their IR absorption spectra and where the refractive index is increased by dispersion, which will provide enhanced selectivity and sensitivity. Potentially useful IR surface plasmon resonances are investigated on lamellar gratings formed from various materials with plasma frequencies in the IR wavelength range including doped semiconductors, semimetals, and conducting polymers. One outcome of this work has been the demonstration of a simple analytic formula for calculating the SPP absorption resonances in the angular reflectance spectra of gratings. It is demonstrated for Ag lamellar gratings in the 6-11 µm wavelength range. The recipe is semi-empirical, requiring knowledge of a surface-impedance modulation amplitude, which is found here by comparison to experiment as a function of the grating groove depth and the wavelength. The optimum groove depth for photon-to-SPP energy conversion was found by experiment and calculation to be ~10-15% of the wavelength. Hemicylindrical prism couplers formed from Si or Ge were investigated as IR surface plasmon couplers for the biosensor application. Strong Fabry-Perot oscillations in the angular reflectance spectra for these high index materials suggest that grating couplers will be more effective for this application in the LWIR. A variety of materials having IR plasma frequencies were investigated due to the tighter SPP mode confinement anticipated in the IR than for traditional noble metals. First doped-Si and metal silicides (Ni, Pd, Pt and Ti) were investigated due to their inherent CMOS compatibility. Rutherford backscattering spectroscopy, x-ray diffraction, scanning electron microscopy, secondary ion mass spectrometry and four point probe measurements complemented the optical characterization by ellipsometry. Calculation of propagation length and mode confinement from measured permittivities demonstrated the suitability for these materials for LWIR SPP applications. Semimetals were also investigated since their plasma frequencies are intermediate between those of doped silicon and metal silicides. The semimetal antimony, with a plasma frequency ~80 times less than that of gold was characterized. Relevant IR surface plasmon properties, including the propagation length and penetration depths for SPP fields, were determined from optical constants measured in the LWIR. Distinct resonances due to SPP generation were observed in angular reflection spectra of Sb lamellar gratings in the wavelength range of 6 to 11 µm. Though the real part of the permittivity is positive in this range, which violates the usual condition for the existence of bound SPP modes, calculations based on experimental permittivity showed that there is little to distinguish bound from unbound SPP modes for this material. The SPP mode decays exponentially away from the surface on both sides of the permittivity sign change. Water is found to broaden the IR plasmon resonances significantly at 9.25 micron wavelength where aqueous extinction is large. Much sharper resonances for water based IR SPR biosensor can be achieved in the 3.5 to 5.5 µm range. Nano-structured Au films (Au-black) were investigated as IR absorbers and possible solar cell enhancers based on surface plasmon resonance. The characteristic length scales of the structured films vary considerably as a function of deposition parameters, but the absorbance is found to be only weakly correlated with these distributions. Structured Au-black with a broad range of cluster length scales appear to be able to support multiple SPP modes with incident light coupling to the corrugated surface as seen by photoelectron emission microscopy (PEEM) and SPR experiments, supporting the hypothesis that Au-black may be a suitable material for plasmon-resonance enhancement solar-cell efficiency over the broad solar spectrum.
Ph.D.
Department of Physics
Sciences
Physics PhD

The trivalent (arsenite) and pentavalent (arsenate) forms of arsenic are introduced into the environment through the use of arsenic in herbicides, pesticides, fertilizers, and the smelting of arsenic-bearing ores. Bacteria resistant to arsenic are readily isolated from surface waters, sewage, and clinical infections. Although some bacterial resistance is provided by inducible phosphate transport systems that discriminate against arsenate, marked resistance is carried on bacterial plasmids. A 6.9 kilobase fragment previously derived from one such plasmid, R45, and containing the genes for inducible resistance to arsenite and arsenate was ligated into the cloning vectors puce and pUC9 in opposite orientations and transformed into Escherichia coli JM 105. Insertion into the multiple cloning site of the pUC vectors places the inserted fragment under the inducible control of the lac operon promoter. An attempt was made to determine the direction of transcription in the fragment by growth in 10-3 M isopropyl-β-D-thiogalactoside prior to challenge with arsenite.

Thesis (DSc)--Stellenbosch University, 2014.
ENGLISH ABSTRACT: Plasmids belonging to the IncQ family have an exceptionally broad host-range and are highly mobilizable in the presence of the self-transmissible IncP plasmids. All IncQ plasmids identified to date have certain features in common. The feature that distinguishes them most from all other plasmids is that they have a unique mechanism of replication. Their replicons consist of repA, repB and repC genes encoding a replicase, primase and DNA-binding proteins respectively. All IncQ plasmids contain at least three 22-bp iterons (or 20-bp iterons with 2-bp spacers) that are identical in sequence and to which the RepC DNA-binding protein binds. They replicate by means of a unique strand-displacement mechanism that is considered to place a limit on their size. Replication proceeds by a partially single-stranded intermediate that is believed to result in an increased likelihood of structural instability with an increase in plasmid size. The most compact backbone of IncQ plasmids is approximately 5.9-kb and the largest natural IncQ plasmid reported is 14.2-kb. Although the mobilization regions of IncQ plasmids are not as unique as the replicons, they are all characterized by the primase of the replicon being fused to the relaxase of the mobilization genes. The remainder of the mobilization genes may vary substantially in number and sequence between plasmids and have been subdivided into at least four distinct lineages. This dissertation consists of twenty one manuscripts published during the period 1984 to 2012. The focus is almost entirely on the IncQ plasmid subfamily known as IncQ2. Most of the earlier work was on determining the nature and extent of the replicons, mobilization genes and the toxin-antitoxin plasmid stability system. A strong theme in the latter work focussed on using the natural variation among the IncQ2 plasmids as a means to understand IncQ plasmid evolution. The collection of articles comprises a combination of original research and reviews.
AFRIKAANSE OPSOMMING: Plasmiede wat aan die IncQ familie behoort kom ‘n uitsonderlike wye gasheerselreeks voor en is hoogs mobiliseerbaar deur middel van die selfoordraagbaar IncP plasmiede. Alle IncQ plasmiedes wat tot datum identifiseer is het sekere gemeenskaplike eienskappe. Die eienskap wat hulle van alle ander plasmiedes onderskei is hul unieke dupliseringsmeganisme. Hul dupliseringsmeganisme bestaan uit repA, repB en repC gene wat onderskeidlik ‘n helikase, ‘n ‘primase’ en ‘n DNSbindingsproteïen enkodeer. Die IncQ plasmiede het ten minste drie 22-bp iterone (of 20-bp iterone met 2-bp skeidingsnukleotiede) met ‘n identiese nukleotiedvolgorde en waaraan die RepCbindingsproteïen bind. Hulle dupliseer deur middel van ‘n unieke DNA-string-vervangingsmeganisme wat ‘n beperking op hul grootte plaas. Tydens replikasie word ‘n intermediêre struktuur gevorm wat gedeeltelik enkelstring is en dit is blykbaar die rede vir ‘n verhoging in strukturële onstabilitiet as die plasmied groter word. Die kleinste ruggraat onder die IncQ plasmiede is min of meer 5.9-kb en die grootste natuurlike IncQ plasmied wat gerapporteer is, is 14.2-kb. Alhoewel die mobiliseringsgebied van die IncQ plasmiede nie so duidelik uitkenbaar as die replikons nie, hierdie gebied is gekenmerk deur ‘n ‘primase’ wat aan ‘n ‘relaxase’ in die mobiliseringsgene gekoppel is. Die oorblywende mobiliseringsgene verskil in beide getal en nukleotiedvolgorde tussen plasmiede en is gebruik om die plasmiede in vier duidelike oorsponggroepe in te deel. Hierdie proefskrif bestaan uit een-en-twintig artikels wat tussen 1984 en 2012 gepubliseer is. Die fokus is hoofsaaklik op die IncQ plasmiedsubfamilie wat as IncQ2 bekend is. Baie van die vroeër werk het oor die aard en omvang van die duplisering en mobiliseringsgene asook die toksienteentoksien plasmiedstabiliseringsmeganisme hanteer. ‘n Sterk tema in die latere werk was om die natuurlike variasie onder die IncQ2 plasmiede te bestudeer ten einde IncQ plasmiedevolusie te verstaan. Die publikasie versameling bestaan uit ‘n kombinasie van oorspronklike navorsing en oorsigartikels.

Les objectifs de ce travail étaient d’évaluer qualitativement et quantitativement l’effet d’antipaludiques « classiques » (primaquine, Malarone®, amino-4-quinoléines) et « d’avenir » (artésunate, ferroquine, seuls ou associés) sur les formes hépatiques et les stades sexués du parasite responsable de la transmission du paludisme. Le modèle expérimental comprend des souris swiss femelle infestées par Plasmodium yoelii et Anopheles stephensi comme moustique vecteur. L’action de la Malarone® (proguanil-atovaquuone) sur les stades hépatiques est quasi totale et plus importante que celle, incomplète, de la primaquine, de la ferroquine ou de l’artésunate. Si les molécules précédentes (ferroquine, artésunate), prescrites à doses subcuratives, entraînent souvent une augmentation de la gamétocytogénèse, elles altèrent certains stades de gamétocytes et inhibent statistiquement chez le moustique la formation d’oocystes et leur nombre et, par là même, interviennent négativement dans la transmission du parasite
The objective of this study is to evaluate qualitatively and quantitatively the effect of "classic" (primaquine, Malarone®, amino-4-quinoline) and "future" (artesunate, ferroquine, alone or associated) antimalarials on the liver forms and sexual stages of the parasite responsible for malaria transmission. The experimental model was : swiss mouse female infected with Plasmodium yoelii and Anophelesstephensi as the vector. The action of Malarone® (proguanil-atovaquuone) on liver stages is almost complete and more than that, incomplete, primaquine, the ferroquine or artesunate. If the previous molecules (ferroquine, artesunate), prescribed at subcurative doses, often lead to an increase in gametocytogenesis, they alter certain stages of gametocytes and statistically inhibit the formation of oocysts in the mosquito; hence, their number involve negatively in the transmission of the parasite

Malgré leurs contribution dans plusieurs domaines, les biopuces à lecture plasmonique conventionnelles basées sur l'utilisation d’un film métallique plan d'or, sont limitées en terme de sensibilité surtout quand il s'agit de détecter des molécules de faible masse molaire à l’état de trace.Dans ce cadre, nous étudions numériquement et expérimentalement le potentiel de détection d’interactions biomoléculaires d’une nouvelle génération de biopuces à lecture plasmonique intégrant un film métallique micro-nano-structurée en réseau rectangulaire 1D. L’étude numérique développée met en œuvre une méthode hybride, basée sur la combinaison de deux méthodes classiques : la méthode des éléments finis et la méthode modale de Fourier. Grâce à ce nouvel outil numérique, nous présentons une cartographie exhaustive du potentiel de détection d’une couche biologique, en variant les paramètres de la structuration liés aux dimensions du réseau. La réponse de la biopuce à l’accrochage de biomolécules est ensuite interprétée théoriquement par les différents phénomènes plasmoniques notamment les «points chauds» et les bandes plasmoniques interdites. Nos calculs soulignent l'importance de l’exploitation du confinement de la lumière à travers la structuration sub-longueur d’onde des surfaces plasmoniques. Ceci permet non seulement d’optimiser les paramètres géométriques afin d’améliorer la sensibilité vis-à-vis de la réponse d’une biopuce conventionnelle, mais aussi de mettre en évidence la transition entre le régime où les plasmons propagatifs dominent et le régime où les plasmons localisés dominent. De nouvelles figures de mérite sont introduites pour évaluer les performances des biopuces structurées.Cette étude montre également que de nouvelles opportunités pour améliorer davantage la bio-sensibilité sont offertes, si la localisation de biomolécules peut être effectuée dans les régions où le champ électrique est amplifié et confiné
Surface plasmons resonance imaging with continuous thin metallic films have become a central tool for the study of biomolecular interactions. However, in order to extend the field of applications of surface plasmons resonance systems to the trace detection of biomolecules having low molecular weight, a change in the plasmonic sensing methodology is needed. In this study, we investigate theoretically and experimentally the sensing potential of 2D nano- and micro- ribbon grating structuration on the surface of Kretschmann-based surface plasmon resonance biosensors when they are used for detection of biomolecular binding events. Numerical simulations were carried out by employing a fast and novel model based on the hybridization of two classical methods, the Fourier Modal Method and the Finite Element Method. Our calculations confirm the importance of light manipulation by means of structuration of the plasmonic thin film surfaces on the nano- and micro- scales. Not only does it highlight the geometric parameters that allow the sensitivity enhancement, and associated figures of merit, compared with the response of the conventional surface plasmon resonance biosensor based on a flat surface, but it also describes the transition from the regime where the propagating surface plasmon mode dominates to the regime where the localized surface plasmon mode dominates. An exhaustive mapping of the biosensing potential of the nano- and micro- structured biosensors surface is presented, varying the structural parameters related to the ribbon grating dimensions. New figures of merit are introduced to evaluate the performance of the structured biosensors. The structuration also leads to the creation of regions on biosensor chips that are characterized by strongly enhanced electromagnetic fields. New opportunities for further improving the bio-sensitivity are offered if localization of biomolecules can be carried out in these regions of high electromagnetic fields enhancement and confined

Lors de mes travaux de thèse je me suis intéressée à l’invasion des hépatocytes par Plasmodium. Bien que certains récepteurs cellulaires mis en jeu aient déjà été identifiés tels que CD81 et SR-B1, les facteurs parasitaires restaient à identifier. J’ai testé différents facteurs parasitaires grâce à un protocole de test d’invasion de cellules HepG2 et HepG2/CD81 par des parasites complémentés avec différentes protéines. Suite à l’identification de la protéine P36 comme déterminant du choix de la voie d’entrée dans les hépatocytes, j’ai étudié les déterminants structuraux de cette protéine nécessaires à la détermination de la voie d’entrée. Pour cela j’ai complémenté des parasites délétés pour P36 avec des protéines chimériques exprimant les domaines d’un parasite utilisant à la fois les récepteurs CD81 et SR-B1 et des domaines d’un parasites ne pouvant utiliser que la voie CD81. J’ai identifié le second domaine à 6 cystéine de P36 comme déterminant du choix de la voie d’invasion. Afin d’étudier les interactions de P36 avec d’éventuels récepteurs cellulaires, j’ai produit cette protéine en système bactérien. Les protéines ont été utilisées pour réaliser des tests d’interactions (ELISA et SPR) avec des récepteurs d’intérêt : CD81, SR-B1, CD36, LIMPII et EphA2 qui n’ont malheureusement pas permis d’identifier le ligand de P36. Des anticorps sont également en cours de production, dans le but d’une part de tester s’ils sont capables de bloquer l’invasion des hépatocytes par Plasmodium et d’autre part de localiser la protéine chez le parasite. Enfin, j’ai étudié les polymorphismes des protéines P36 de parasites infectant l’homme
During my thesis, I was interested in the study of the hepatocyte invasion by Plasmodium. Several cellular receptors are involved, such as CD81 and SRB1, but the parasitic factors required were unknown until now. I tested different parasitic factors thanks to an invasion test of HepG2 or HepG2/CD81 cells with parasites complemented with different proteins. Following the identification of the 6 cystein protein P36 as a determinants of the entry pathway, I studied the structural determinants of this protein which are involved in the hepatocytes’ entry pathway. To this end, I complemented parasites knock-out for P36 with chimeric proteins constituted of domains of a parasite using both CD81 and SRB1, and domains from a parasite using only CD81. I showed that the second 6 cystein domain of P36 is decisive in the entry pathway choice.In order to study the P36 interactions with potential cellular receptors, I developed a production protocol of this protein in bacteria. I used the recombinant protein to test the interactions (ELISA and SPR) with potential receptors: CD81, SRB1, CD36, LIMP2, Epha2. Unfortunately, no interaction has been detected. Antibodies are in production, in order to test whether they are capable to block the hepatocyte invasion by Plasmodium. They will also be used to localize the protein in the parasite. In the end, I studied the polymorphisms of P36 in human parasites

Les phénomènes de résistance des Plasmodium aux médicaments sont impliqués dans l'extension du paludisme, ainsi que les variations de production des gamétocytes (stade responsable de la transmission) en présence de chimiothérapie médicamenteuse. Afin de mieux comprendre ces mécanismes, nous avons réalisé l'étude suivante sur des Plasmodium de muridés africains transmis à la souris blanche. Dans la première partie, nous avons étudié les différences schizogoniques induites par pression de chloroquine sur deux souches de Plasmodium, P. Berghei NK 65 et P. Berghei ANKA. Les deux souches, pourtant très proches, réagissent de façon distincte à cette pression médicamenteuse et les résultats obtenus pour la synchronicité et la chimiorésistance sont très différents en raison de l'affinité propre de chaque souche pour les réticulocytes, et de l'action de la chloroquine, qui favorise une augmentation de la synchronicité en détruisant les stades parasitaires autres que les mérozoi͏̈tes. Dans le deuxième partie, nous avons étudié l'effet d'une pression infracurative de chloroquine sur la production de gamétocytes de quatre souches de Plasmodium de chloroquinosensibilité différente. Dans les quatre cas, on observe une augmentation significative de la production de gamétocytes dans le lot traité. Il n'y a pas de corrélation entre le niveau de chimiorésistance naturelle et la quantité de gamétocytes produits, que ce soit sous l'effet ou non de la chloroquine : elle modifie la quantité de gamétocytes produits par rapport au lot témoin mais le nombre de gamétocytes produits semble respecter un classement par espèce et ce classement n'est pas modifié par le médicament.

We have developed a general theory of the plasmonic enhancement of many-body phenomena resulting in a closed expression for the surface plasmon-dressed Coulomb interaction. It is shown that this interaction has a resonant nature. We have also demonstrated that renormalized interaction is a long-ranged interaction whose intensity is considerably increased compared to bare Coulomb interaction over the entire region near the plasmonic nanostructure. We illustrate this theory by re-deriving the mirror charge potential near a metal sphere as well as the quasistatic potential behind the so-called perfect lens at the surface plasmon (SP) frequency. The dressed interaction for an important example of a metal–dielectric nanoshell is also explicitly calculated and analyzed. The renormalization and plasmonic enhancement of the Coulomb interaction is a universal effect, which affects a wide range of many-body phenomena in the vicinity of metal nanostructures: chemical reactions, scattering between charge carriers, exciton formation, Auger recombination, carrier multiplication, etc. We have described the nanoplasmonic-enhanced Förster resonant energy transfer (FRET) between quantum dots near a metal nanoshell. It is shown that this process is very efficient near high-aspect-ratio nanoshells. We have also obtained a general expression for the force exerted by an electromagnetic field on an extended polarizable object. This expression is applicable to a wide range of situations important for nanotechnology. Most importantly, this result is of fundamental importance for processes involving interaction of nanoplasmonic fields with metal electrons. Using the obtained expression for the force, we have described a giant surface-plasmoninduced drag-effect rectification (SPIDER), which exists under conditions of the extreme nanoplasmonic confinement. Under realistic conditions in nanowires, this giant SPIDER generates rectified THz potential differences up to 10 V and extremely strong electric fields up to 10^5-10^6 V/cm. It can serve as a powerful nanoscale source of THz radiation. The giant SPIDER opens up a new field of ultraintense THz nanooptics with wide potential applications in nanotechnology and nanoscience, including microelectronics, nanoplasmonics, and biomedicine. Additionally, the SPIDER is an ultrafast effect whose bandwidth for nanometric wires is 20 THz, which allows for detection of femtosecond pulses on the nanoscale.

Natural transformation is the process by which cells take up DNA from the surrounding medium under physiological conditions, altering the genotype in a heritable fashion. This occurs without chemical or physical treatment of the cells. Certain Acinetobacter strains exhibit a strong tendency to incorporate homologous DNA into their chromosomes by natural transformation. Transformation in Acinetobacter exhibits several unique properties that indicate this system's superiority as a model for transformation studies or studies which benefit from the use of transformation as an experimental method of gene manipulation. Pseudomonas putida is the natural host of TOL plasmids, ranging between 50 kbp and 300 kbp in size and encoding genes for the catabolism of toluene, meta-toluate, and xylene. These very large, single-copy plasmids are difficult to isolate, manipulate, or modify in vitro. In this study, the TOL plasmid pDKR1 was introduced into Acinetobacter calcoaceticus strains and genetically engineered utilizing natural transformation as part of the process. Following engineering by transformation, the recombinant DNA molecule was returned to the native genetic background of the original host P. putida strain. Specific parameters for the successful manipulation of large plasmids by natural transformation in Acinetobacter were identified and are outlined. The effects of growth phase, total transforming DNA concentration, transforming DNA conformation, and gene dosage on transformation efficiency are presented. Addition of Acinetobacter plasmid DNA sequences to the manipulated constructs did not have an effect on transformation rates. Results suggest that a broadly applicable and efficient method to carry out site-directed genetic manipulations of large plasmids has been identified. The ability to easily reintroduce the recombinant DNA molecules back into the original host organism was maintained.

Group- III nitride based semiconductors have emerged as the leading material for short wavelength optoelectronic devices. The InGaN alloy system forms a continuous and direct bandgap semiconductor spanning ultraviolet (UV) to blue/green wavelengths. An ideal and highly efficient light-emitting device can be designed by enhancing the spontaneous emission rate. This thesis deals with the design and fabrication of a visible light-emitting device using GaN/InGaN single quantum well (SQW) system with enhanced spontaneous emission. To increase the emission efficiency, layers of different metals, usually noble metals like silver, gold and aluminum are deposited on GaN/InGaN SQWs using metal evaporator. Surface characterization of metal-coated GaN/InGaN SQW samples was carried out using atomic force microscopy (AFM) and scanning electron microscopy (SEM). Photoluminescence is used as a tool for optical characterization to study the enhancement in the light emitting structures. This thesis also compares characteristics of different metals on GaN/InGaN SQW system thus allowing selection of the most appropriate material for a particular application. It was found out that photons from the light emitter couple more to the surface plasmons if the bandgap of former is close to the surface plasmon resonant energy of particular metal. Absorption of light due to gold reduces the effective mean path of light emitted from the light emitter and hence quenches the quantum well emission peak compared to the uncoated sample.

Thesis (M. S.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009.
Committee Chair: Mostafa A. El-Sayed; Committee Member: Adegboyega K. Oyelere; Committee Member: Bridgette Barry; Committee Member: Joseph W. Perry; Committee Member: Mark R. Prausnitz.

Different types of plasmonic nanostructures are proposed and examined experimentally and theoretically, with a view towards sensing applications. First, a self-assembly approach was developed to create arrays of well-ordered glass-supported gold nanoparticles (AuNPs) with controllable particle size and inter-particle spacing. Then, a periodic array of gold nano-disks (AuNDs) supported by a Bragg reflector was proposed and examined in a search for Fano resonances in its optical response. Arrays of heptamer-arranged nanoholes (HNH) in a thin gold film were also proposed and explored theoretically and experimentally, revealing a very rich spectrum of resonances, several exhibiting a Fano lineshape. A commercial implementation of the vectorial finite element method (FEM) was used to model our plasmonic structures. Taking advantage of the periodic nature of the structures, a unit cell containing a single element was modelled. The transmittance, reflectance or absorbance spectra were computed, and the associated electromagnetic fields were obtained by solving the vector wave equations for the electromagnetic field vectors throughout the structures, subject to the applicable boundary conditions, and the applied source fields. The sensing performance of the structures, based on the bulk sensitivity, surface sensitivity and figure of merit (FOM) was calculated. First, a novel bottom-up fabrication approach was applied (by our collaborators) to form a periodic array of AuNPs with controllable size over large areas on SiO2 substrates. In this method, self-assembly of block copolymer micelles loaded with metal precursors was combined with a seeding growth route to create ordered AuNPs of desired size. It was shown that this new fabrication method offers a new approach to tune the AuNP size and edge-to-edge inter-particle spacing while preserving the AuNP ordering. The optical characteristics of the AuNP arrays, such as their size, interparticle spacing, localized surface plasmon resonance (LSPR) wavelength, and bulk sensitivity, were examined, numerically and experimentally. This proposed novel fabrication method is applicable for low-cost mass-production of large-area arrays of high-quality AuNPs on a substrate for sensing applications. Then, we proposed and examined the formation of Fano resonances in a plasmonic-dielectric system consisting of uncoupled gold nano-disk (AuND) arrays on a quarter-wave dielectric stack. The mechanism behind the creation of Fano resonances was explained based on the coherent interference between the reflection of the Bragg stack and the LSPPs of the AuNDs. Fano parameters were obtained by fitting the computational data to the Fano formula. The bulk sensitivities and figure of merit of the Fano resonances were calculated. This plasmonic structure supports Fano resonances with a linewidth around 9 nm which is much narrower than the individual AuND LSPP bandwidth ( 80 nm) and the Bragg stack bandwidth ( 100 nm). Supporting Fano resonances with such a narrow linewidth, the structure has a great potential to be used for sensing applications. Also, this metallic-dielectric nanostructure requires no near-field coupling between AuNDs to generate the Fano resonances. So, the AuNDs can be located far enough from each other to simplify the potential fabrication process. The optical properties of HNH arrays on an SiO2 substrate were investigated, numerically and experimentally. Helium focused ion beam (HeFIB) milling was applied (by Dr. Choloong Hahn) to fabricate well-ordered and well-defined arrays of HNHs. Transmittance spectra of the structures were obtained as the optical response, which exhibits several Fano resonances. Then, the mechanism behind the formation of the Fano resonances was explained, and the sensing performance of the structure was inspected by measuring the bulk sensitivities. This array of nanohole cluster is exciting because it supports propagating SPPs and LSPPs, and also Wood’s anomaly waves, which makes the optical response very rich in excitations and spectral features. Also, as a periodic array of sub-wavelength metallic nanoholes, the system produces extraordinary optical transmission - highly enhanced transmission through (otherwise) opaque metallic films at specific wavelengths, facilitating measurement acquisition in transmission.

La découverte de la photoluminescence du silicium sous sa forme nanométrique a ouvert la voie de l’utilisation du silicium dans les composants optoélectroniques. Cependant cette photoluminescence reste trop peu efficace et de nombreuses recherches portent aujourd’hui sur l’amélioration des propriétés optiques du silicium. Ce travail de thèse s’intéresse particulièrement à l’utilisation de plasmons de surface localisés afin d’améliorer les propriétés optiques de nanocristaux de silicium. Grâce au contrôle de tous les paramètres géométriques des nanocristaux de silicium et des nanoparticules métalliques lors de la fabrication des échantillons, il a été possible d’étudier les phénomènes physiques du couplage entre ces deux objets. Une modification de l’émission des nanocristaux de silicium en fonction de la distance, de la taille et de la nature des nanoparticules métalliques a été étudiée. Grâce au développement de différentes techniques de caractérisation optique, il a été possible de montrer que la photoluminescence des nanocristaux de silicium était modifiée à la fois spectralement et spatialement par les plasmons de surface localisés. Ce travail montre que grâce aux plasmons de surface localisés il est possible de grandement améliorer la photoluminescence des nanocristaux de silicium et ainsi il est possible d’imaginer de nouveaux composants optoélectroniques à base de silicium et de plasmons
The discovery of photoluminescence of nanometric silicon paves the way to use silicon in optoelectronic devices. However this photoluminescence remains low and a lot of works aim at improving silicon optical properties. In this dissertation we study localized surface plasmons to improve optical properties of silicon nanocrystals. Thanks to the control of all geometrical parameters of silicon nanocrystals and metallic nanoparticles during the fabrication process, the coupling process between these two objects has been studied. The modification of silicon nanocrystals emission as a function of the distance, the size and the nature of metallic nanoparticles has been investigated. Thanks to the development of experimental optical characterization techniques we showed that silicon nanocrystals photoluminescence is modified both spectrally and spatially by localized surface plasmons. This work shows that it’s possible to enhance silicon’s optical properties and thus to devise optoelectronic devices with silicon and plasmons

With the development of ultra-fast laser technology, several new imaging techniques have pushed optical resolution past the diffraction limit for traditional light-based optics. Advancements in lithography have enabled the straightforward creation of micron- and nanometer-sized optical devices. Exposing metal-dielectric structures to light can result in surface plasmon excitation and propagation along the transition interface, creating a surface plasmon polariton (SPP) response. Varying the materials or geometry of the structures, the plasmonic response can be tailored for a wide range of applications.

Photoemission electron microscopy (PEEM) has been used to image excitations in micron-sized plasmonic devices. With PEEM, optical responses can be characterized in detail, aiding in the development of new types of plasmonic structures and their applications. We show here that in thin, triangular gold platelets SPPs can be excited and concentrated within specific regions of the material (thickness ~50 nm); resulting in localized photoemission in areas of high electric field intensity. In this regard, the platelets behave as receiver antennas by converting the incident light into localized excitations in specific regions of the gold platelets. The excited areas can be significantly smaller than the wavelength of the incident light (λ ≤ 1 µm). By varying the wavelength of the light, the brightness of the excited spots can be changed and by varying the polarization of the light, the brightness and position can be changed, effectively switching the photoemission on or off for a specific region within the triangular gold structure.

In this work, the spatial distribution of surface plasmons and the imaging results from photoemission electron microscopy are reproduced in simulation using finite element analysis (FEA). In addition, we show that electromagnetic theory and simulation enable a detailed and quantitative analysis of the excited SPP modes, an explanation of the overall optical responses seen in PEEM images, and prediction of new results.

Plasmonics is a recently emerged technology that enables the compression of electromagnetic waves into miniscule metallic structures, thus enabling the focusing and routing of light on the nanoscale. Plasmonic waveguides can be used to miniaturise the size of integrated chip circuits while increasing the data transmission speed. Plasmonic waveguides are used to route the plasmons around a circuit and are a major focus of this thesis. Also, plasmons are highly sensitive to the surrounding dielectric environment. Using this property we have experimentally realised a refractive index sensor to detect refractive index change in solutions.

This project is to develop a series of new photocatalyst for fine organic synthesis in irradiation of visible light under mild conditions. To achieve this goal, the detailed study of photocatalytic properties of plasmonic metal nanoparticles supported on zirconium dioxide was carried out, including the catalyst synthesis, characterization and application in redox reactions with high activity. The discovery of these new plasmonic metal nanoparticle photocatalyst may inspire further studies on other efficient photocatalysts and enhance the potential to utilize sunlight via a controlled and environmentally friendly process.