Thesis (PhD)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: The generation of ultrafast light pulses and the development of time resolved spectroscopic techniques, such as the femtosecond pump probe spectroscopy technique, have facilitated the study of ultrafast energy transfer in the photosynthetic systems of green plants and photodynamic therapy drugs. It has allowed the investigation of biological and chemical processes that take place on the ultrafast timescale and has allowed us to obtain spectral and kinetic information on energy transfer. In addition, it has allowed time resolved experiments in which the transient absorption of species under investigation was observed and has elucidated molecular dynamics. In the present work this was done with a temporal resolution of approximately 200 fs and covering a pump-to-probe delay range of 300 fs to 2 ns. The main aims of this study were to characterise the femtosecond pump probe spectroscopy system, to investigate the energy transfer in the natural light harvesting complex II (LHC II) in view of future expansion to the study of synthesized arti cial functional light harvesting complexes and nally to study ultrafast processes in zinc phthalocyanine (ZnPc) systems. In photosynthetic organisms, LHC II is the most abundant light harvesting complex and it plays an important role in light harvesting and photoprotection. The light energy is absorbed by light harvesting complexes and transferred to a reaction centre (RC) in an ultrafast timescale. Phthalocyanines are a new class of photosensitiser used for photodynamic therapy. These drugs are used to treat small and super cial tumours. The energy transfer from the singlet excited state to the triplet excited state occurs on an ultrafast timescale. However, recent work done on zinc phthalocyanine has proved that the determination of the ultrafast component remains a challenge. Several ultrafast studies carried out on ZnPc in solvents have been not only unsuccessful to give a clear picture of the ultrafast dynamics but have also produced divergent results. In this study, a characterisation of the femtosecond pump probe spectroscopy setup was done. The samples under investigation were probed by a white light continuum. The generation of the white light continuum introduced chirp, which in uenced the temporal evolution of the transient absorption results. The technique used to correct the chirp introduced by white light generation is discussed in detail. Our femtosecond pump probe spectroscopy setup was benchmarked by using a well known dye, namely malachite green. In addition, the investigation of the transient absorption change of LHC II, an active component in photosynthesis, as extracted from spinach leaves and the ultrafast dynamics of a promising photosensitiser ZnPc in dimethyl sulfoxide (DMSO) as well as in dimethyl formamide (DMF) was done. The spectral and dynamic results obtained using these three samples are described and exponential ts to the absorbance decay curves used to estimate the timescales of the energy transfer processes are presented. In this experiment, the dynamics and measured time constants related to the energy transfer between the different types of chlorophyll in LHC II was monitored, whereas with ZnPc, the dynamics and the measured time constants associated with solvation dynamics and vibrational relaxation was examined. / AFRIKAANSE OPSOMMING: Die vorming van ultravinnige lig pulse en die ontwikkeling van tyd opgelosde spektroskopiese tegnieke, soos die femtosekonde pomp proef spektroskopie tegniek, het die studie van ultravinnige energie oordrag in fotosintetiese stelsels van groen plante en chemiese prosesse gefasiliteer, wat kan plaasvind op die ultravinnige tyd skaal en laat dit toe om spektrale en kinetiese informasie oor die energie oordrag te kan bepaal. Dit het ook dit moontlik gemaak om tyd opgelosde eksperimente te kan doen waarin ons veranderlike absorbsie van die monster kon ondersoek en die molekulere dinamika kon ontrafel. In hierdie werk is dit gedoen met n tyd resolusie van omtrent 200 fs termyl 'n pomp-tot-proef tydvertraging van 300 fs tot 2 ns gebruik is. Die hoof doelwitte van hierdie werk was om 'n femtosekonde pomp proef spektroskopie stelsel te karakteriseer, die energie oordrag in die natuurlike ligoes kompleks II te ondersoek met die toekomstige uitbreiding van die studie na sintetiese lig-oes komplekse as oogmerk en laastens om ultravinnige prosesse in Sink Ftalosianiene stelsels te ondersoek. In fotosintetiese organismes, is lig oes kompleks II die mees volop lig oes kompleks en speel 'n belangrike rol in lig oes en foto skerming. Die lig energie word geabsorbeer deur lig oes komplekse en dan oorgedra na reaksie middelpunte in 'n ultravinnige tydskaal. Ftalosianiene is 'n nuwe klas fotosensiteerder wat gebruik word in fotodinamiese terapie. Hierdie dwelms word gebruik om klein en oppervlakkige gewasse te behandel. Die energie oordrag van die opgewekte singlet tot die triplet toestand vind plaas op die ultravinnige tydskaal. Onlangse navorsingswerke het getoon dat die bepaling van die ultravinnige komponent 'n uitdaging bly. Verskeie vorige ondersoeke is gedoen op Sink Ftalosianiene in verskeie oplosmiddels, en nie net het hierdie studies nie 'n helder prentjie verskaf van die ultravinnige dinamika nie, maar het ook divergerende resultate opgelewer. In hierdie werk word 'n karakterisering van die femtosekonde pomp proef spektroskopie stelsel gedoen. Die monsters is ondersoek met 'n wit lig kontinuum proef. Die vorming van die wit lig kontinuum het tjirp veroorsaak, wat die tyd evolusie van die veranderlike absorbsie resultate beinvloed het. Die tegniek wat gebruik was om die tjirp te korregeer word bespreek. Ons femtosekonde pomp proef spektroskopie stelsel is gestandardiseer deur die welbekende kleurstof malachiet groen. Ons het ook die veranderlike absorbsie van lig oes kompleks II ondersoek, 'n aktiewe komponent in fotosintese, soos dit onttrek is uit spinasie blare, asook die ultravinnige dinamika van die belowende photosensitizer Sink Ftalosianiene in DMSO asook DMF. Die spektrale en dinamiese resultate verkry vanaf hierdie drie monsters word beskryf en eksponensiele passings aan die absorbsie verval kurwes is gebruik om die tydskale van die energie oordrag prosesse te skat. In hierdie eksperiment is dinamika en gemete tydkonstantes waargeneem wat toegeskryf kan word aan die energie oordrag tussen verskillende soorte chloro l in lig oes kompleks II. In die Sink Ftalosianien eksperimente is dinamika en gemete tydkonstantes waargeneem wat toegeskryf kan word aan solverings dinamika asook vibrasionele ontspanning.

In this thesis experimental samples of multiple quantum wells in the InGaN/GaN structures will be compared using methods of laser spectroscopy. In particular, the optical properties of the samples will be investigated. The samples were prepared under different conditions; therefore one of the aims is to compare them. The knowledge of the influence of preparation enables utilization not only for fundamental research, but also for the construction of radiation sources or scintillation detectors. Measurements of absorption and photoluminescence will be carried out and their dynamic properties will be measured as well. There will be examined the effect of different excitation power and different excitation wavelength on the intensity of photoluminescence. From dynamic properties there will be examined the effect of different excitation wavelength on the lifetime of the absorption and how does temperature influence the lifetime of the photoluminescence. Individual quantities will be compared amongst samples and their suitability for further applications will be discussed.

In the main part of this thesis I study the relaxation mechanisms of charge carriers in silicon nanocrystals in SiO2 matrix. One of the potential applications of these structures lies in photovoltaics, specifically in construction of all-silicon tandem solar cells. I studied the dynamics of carriers in these structures by methods of ultrafast spectroscopy which helped to unravel the microscopic behaviour of carriers, their transport, localization etc. Furthermore I investigated the doping of such structures as the technology of doping is crucial for manufacture of pn- junctions which are the core component of solar cells. At the end I delve into the dissipative Jaynes-Cummings model by mathematical modeling and theoretical calculations which describes among others microlasers and as such comes under a field of cavity quantum electrodynamics.

Les protéines modifiées ont suscité un grand intérêt en raison de leur taille extrêmement petite par rapport à l'anticorps entier. Ces petites protéines de liaison ont démontré de nombreux avantages tels qu'une bio distribution rapide, une bonne pénétration dans le tissu tumoral et une élimination rapide du sérum et des tissus non-infectés. Ainsi, ces protéines devraient être d'excellentes alternatives aux anticorps pour les applications cliniques. Cette thèse présente le développement de biocapteurs basés sur des anticorps synthétiques et le transfert d'énergie par résonance de type Förster (FRET) résolu en temps par la détection de biomarqueurs. Les tests immunologiques à base de FRET sont établis en utilisant des complexes de terbium (Tb) comme donneurs de FRET et des boîtes quantiques semi-conducteurs (QDs) comme accepteurs de FRET. Les propriétés photophysiques exceptionnelles de ce couple de FRET Tb-QD permettent une détection quantitative ultrasensible. Des anticorps monocaténaires (single-domain antibody, sdAb) et des petites protéines d’affinité synthétiques (albumin-binding domain-derived affinity protein, ADAPT) sont utilisés pour étudier différentes stratégies de conjugaison d'anticorps, et quantifier des biomarqueurs cliniques (EGFR, HER2). Ce travail peut être considéré comme une condition préalable à l’utilisation des QDs en diagnostic clinique. / Engineered affinity proteins have raised great interest due to their extremely small size compared to full length antibodies. Such small binding proteins have demonstrated many advantages such as quick biodistribution, good penetration into tumor tissue, and fast elimination from serum and nondiseased tissues. Thus, they are expected to be excellent alternatives to antibodies for clinical applications. This thesis focuses on the development of biosensors based on engineered antibodies and time-resolved Förster resonance energy transfer (FRET) through biological recognition of biomarkers. FRET-based immunoassays are established using terbium complexes (Tb) as FRET donors and semiconductor quantum dots (QDs) as FRET acceptors. The exceptional photophysical properties of the Tb-QD FRET pair allow for ultrasensitive quantitative biosensing. Single-domain antibodies (sdAb) and small engineered scaffold antibodies (ADAPT) are used to investigate different antibody-conjugation strategies for quantifying human epidermal growth factor receptors (EGFR, HER2) as clinical biomarkers. This work can be considered as a prerequisite to implementing QDs into applied clinical diagnostics.

The rapid progress on developing new and improved multifunctional materials, for optoelectronic and spin based phenomena/devices, have increased the importance of the fundamental understanding of their coherent states and nonlinear optical properties. This study is aimed at characterizing, modeling, and controlling the fundamental electronic, phononic, and spin properties of several classes of materials through nonequilibrium and nonlinear light-matter interactions, coupled with a novel design of the material phases, interfaces, and heterostructures. This research directly addresses the Grand Challenges identified in the Basic Energy Sciences Advisory Committee report "Directing Matter and Energy: Five Challenges for Science and the Imagination" (Hemminger, 2007) [1], in particular, the area: "Matter far beyond equilibrium" and addresses the questions, "How do remarkable properties of matter emerge from complex correlations of the atomic or electronic constituents and how can we control these properties?" and "How do we design and perfect atom- and energy-efficient synthesis of revolutionary new forms of matter with tailored properties?". The knowledge gained from these fundamental studies can provide new information for a broad community to provide concepts for the next generation of multifunctional materials and devices, and resulted in several publications and conference presentations. The materials studied in this dissertation included multiferroic BaTiO3-BiFeO3 [2], ferroelectric Pb0.52Zr0.48TiO3 (PZT), InAs/AlAsSb multi-quantum-well [3], lead halide perovskite [4], n-type InAsP films [5, 6], and nanolaminate plasmonic crystals [7]. Probing multiferroics, which are materials that can exhibit ferromagnetic, ferroelectric, and ferroelastic orders simultaneously in a single phase, was a main focus of this study. BiFeO3 (BFO) is the most widely investigated multiferroic due to its high Neel and Curie temperatures and has antiferromagnetic and ferroelectric properties [8]. An inherent drawback of BFO is its large leakage currents. In this project, (1 − x)BaTiO3-(x)BiFeO3, x = 0.725 (BTO-BFO) heterostructures were investigated [9], where the conductivity of the solid solution can be reduced by adding another perovskite material, BaTiO3 [2]. We aimed to study optically induced coherent states in our BTO-BFO structures. Time resolved pumpprobe spectroscopic measurements were performed at room temperature as well as at low temperature (100 K) up to 10 T. Coherent acoustic phonons were observed both in a film and nanorods, resulting in coherent phonon frequencies of 27 and 33 GHz, respectively [2]. Coherent phonon spectroscopy is a sensitive tool to characterize the interfaces and can be employed as an effective ultrasensitive quantum sensor [10]. Furthermore, in the nanorods arrays of BTO-BFO, an additional oscillation with frequency in the range of 8.1 GHz was observed. This frequency is close to a theoretically predicted magnon frequency which could indicate the coexistence of coherent phonons and magnons in the nanorods arrays [2]. In an analogy to photonics which relies on electromagnetic waves, magnonics utilizes spin waves to carry and process information, offering several advantages such as an operation frequency in the THz range. Recently, "a quantum tango" [11] was reported where coupled coherent magnon and phonons modes were formed on a surface patterned ferromagnet. Furthermore, BTO-BFO heterostructures were probed using transient birefringence and magneto-optical Kerr effect spectroscopy. The results demonstrated that the magnetic field dependence of coherent phonons, measured by these two techniques, exhibits more sensitivity to the external magnetic fields compared to the differential reflectivity technique [2]. Moreover, nonlinear optical properties of this structure were investigated via second harmonic generation spectroscopy, where wavelength and polarization dependence of this nonlinear observation will be discussed in this dissertation. As part of this study, another class of multiferroic materials, with strong ferroelectric and piezoelectric properties, Pb0.52Zr0.48TiO3 (PZT) was studied [12]. In this project, the nonlinear optical properties of PZT nanorod arrays were investigated. Clear signatures of second harmonic generations from 490-525 nm (2.38-2.53 eV) at room temperature, were observed. Furthermore, time resolved differential reflectivity measurements were performed to study dynamical properties in the range of 690-1000 nm where multiphoton processes were responsible for the photoexcitations. We compared this excitation scheme, which is sensitive mainly to the surface states, to when the photoexcited energy (∼ 3.1 eV) was close to the bandgap of the nanorods. Our results offer promises for employing these nanostructures in nonlinear photonic applications. Furthermore, the established techniques during my research provided new insights on optical properties of InAs/AlAsSb multi-quantum-well [3], lead halide perovskite [4], n-type InAsP films [5, 6], and nanolaminate plasmonic crystals [7], and the results will be briefly presented in this dissertation. / Doctor of Philosophy / My research activities have explored multifunctional materials and heterostructures with strongly enhanced coupled electric and magnetic orders and optical properties. In particular, pursuing novel heterostructure designs such as multiferroics can provide control over electric and magnetic ordering in mixed dimensionality. This, together with control at the level from lattice structure to electron spin states can give rise to improved or even qualitatively new and robust materials properties. For example, a better understanding of the phenomena associated with the spin degree of freedom of electrons allows for advancement in spintronic device applications such as storage, logic, and sensors, which are associated with quantum computers and quantum communications [13, 14, 15]. Overarching questions and goals of my activities included: What are the microscopic origins and mechanisms of nonlinear response in strongly coupled nanostructured materials and its relationship to electronic, spin, and lattice degrees of freedom? (2) What are the effects of dimensionality and quantum confinement on optical properties? (3) How do we control and manipulate the coherent states, such as coherent phonons and magnons using external and internal fields, material composition, and morphology to achieve maximal efficiency and tunability? Addressing many of the challenges in the fast-paced technological world requires continued developments of new materials with enhanced optical properties. The knowledge gained from my fundamental studies can provide new information for the next generation of multifunctional materials and devices with advanced optical properties and resulted in several publications and conference presentations.

No description available.

Nature uses sunlight either as energy source or as information carrier. Photoreception is achieved by two groups of specialised proteins: photo-enzymes that catalyse photoreactions and photosensors that initiate physiological functions. In the present work mechanistic studies were conducted on one representative of each group by using site-directed mutagenesis as well as stationary and time-resolved spectroscopy. The photo-enzyme NADPH:Protochlorophyllide Oxidoreductase (POR) catalyses the light-dependent C17-C18 double bond reduction of protochlorophyllide, including a hydride and a proton transfer, to produce chlorophyllide, the immediate precursor of chlorophyll. POR provides a unique opportunity to study the hydride transfer mechanism in detail. Three distinct intermediates, prior to product formation, were observed that were interpreted as electron and proton-coupled electron transfer reactions from NADPH indicating a sequential hydride transfer mechanism. An active-site mutant, POR-C226S, yields distinct different intermediates compared to POR wild type but ends in the same chlorophyllide stereoisomer most likely due to an altered protochlorophyllide binding. This work provides the first direct observation of a stepwise hydride transfer mechanism in a biological system. Cryptochromes (CRY) are so far defined as flavoprotein blue-light photosensors that regulate the circadian clock throughout nature and are suggested as the candidate magnetoreceptor in animals. Animal CRY are subdivided into two classes of proteins: the light-responsive Type I (invertebrates) and the light-independent Type II (mainly vertebrates). The molecular basis of their different roles in the circadian clock is still unknown. Animal Type I CRY are suggested to undergo conformational changes - required for induction of subsequent signalling cascades - induced by the change in the FAD redox state due to light absorption. The study shows that in contrast to Type I animal Type II CRY do not bind tightly FAD as a cofactor due to the lack of structural features and therefore provide the molecular basis for their different biological roles ruling out a direct photomagnetoreceptor function. Further, detailed studies on a fruit fly (Dm)CRY reveal that it does not undergo a photocycle as FAD release and Trp decomposition were observed. Thus, it is suggested that light is a negative regulator of DmCRY stability linking the initial photochemistry to subsequent dark processes leading to signal transduction on a molecular level.

Στην παρούσα Ειδική Ερευνητική Εργασία μελετόνται οι φωτοφυσικές ιδιότητες γνωστών χρωμοφόρων μορίων. Συγκεκριμένα μελετάται η Coumarin 30, η Fluorescein Isothiocyanate και η Dichlorofluorescein, τόσο με φασματοσκοπία σταθερής κατάστασης όσο και με φασματοσκοπία χρονικής ανάλυσης μέσω της τεχνικής Time Correlated Single Photon Counting. Η διερεύνηση γίνεται με τα μόρια αυτά να βρίσκονται σε μορφή διαλυμάτων με στόχο τον προσδιορισμό της συμπεριφοράς τους όταν αυτά βρισκονται σε διαφορετικά περιβάλλοντα (διαλύτες). Επιπλέον ερευνώνται οι αλληλεπιδράσεις των μορίων αυτών μέσω της φασματοσκοπίας σταθερής κατάστασης και χρονικής ανάλυσης όταν βρίσκονται σε μορφή μειγμάτων. / In this Master Thesis, the phophysical properties of chromophrores are investigated. Specifically, Coumarin 30, Fluorescein Isothiocyanate and Dichlorofluorescein are studied with steady – state spectroscopy as well as with time – resolved spectroscopy via the technique of Time Correlated Single Photon Counting. The study of these molecules focuses also on solvent – solute effects. Finally, interactions between them are also studied through steady – state spectroscopy and time resolved spectroscopy.

Optical microcavities exhibit high resonance quality, so that, they are of key interest for the design of low-threshold lasers or for achieving strong coupling regime. But, such systems support modes whose the volume remain diffraction limited.In this manuscript, we are interested in their plasmonic counterparts because they support confined modes at the sub-wavelength scale. First, we study an in-plane plasmonic cavity which is the transposition of 1D optical cavity to surface wave. We characterize the cavity by measuring the fluorescence lifetime of dye molecules deposited inside.Then, we are interested in 3-dimension mode confinement achieved by spherical metal nanoparticles. We discuss on the definition of the mode volume used in cavity quantum electrodynamic and based on the calculation of energy confinement around the particle. We also simulate the fluorescence enhancement of rare-earth ions embedded inside core-shell plasmonic particles. Finally, we disturb the photodynamic emission of a single-photon source by puttingthe extremity of a plasmonic tip nearby the emitter

Η φύση της οπτικής διέγερσης και ο βαθμός της ενδομοριακής μεταφοράς του φορτίου (Intramolecular Charge Transfer, ICT), καθώς επίσης η δυναμική των διεγερμένων στάθμεων, σε δύο νέες οργανικές δομές μορίων , D-π-A (γραμμικό μόριο) και DΑ3 (δενδριμερές - αστεροειδές μόριο με επίκεντρο τον δότη ηλεκτρονίων) έχουν διερευνηθεί με femtosecond φασματοσκοπία χρονικής ανάλυσης (απόσβεση του φθορισμού τους) σε δύο διαφορετικούς διαλύτες, το τολουόλιο (με ασθενή πολικότητα) και το τετραϋδροφουράνιο (με μέτρια πολικότητα). Τα πειραματικά αποτελέσματα με βάση τη σύγκριση των μορίων της ίδιας δομής (DA ή DA3) με προοδευτική αλλαγή των αποδεκτών ηλεκτρονίων (από τους ασθενέστερους προς τους ισχυρότερους) στον ίδιο διαλύτη έδειξαν ότι οι οργανικές δομές με υποκαταστάτες τους ισχυρότερους αποδέκτες ηλεκτρονίων είχαν γρηγορότερη απόσβεση του φθορισμού τους και συνεπώς ισχυρότερη ενδομοριακή μεταφορά του φορτίου. Επιπλέον, η σύγκριση των δύο δομών έδειξε ότι τα δενδριμερή μόρια γενικά παρουσίαζαν ισχυρότερη ενδομοριακή μεταφορά του φορτίου. Επίσης τα πειραματικά αποτελέσματα έδειξαν ότι κατά τη σύγκριση των δύο διαλυτών οι αλληλεπιδράσεις διπόλου - διπόλου μεταξύ της διαλυμένης ουσίας και του διαλύτη επιδρά στις φασματικές ιδιότητες των μορίων μειώνοντας την ενέργεια της διεγερμένης στάθμης αφού παρατηρήθηκε ερυθρή μετατόπιση Stoke (red shift Stoke) των φασμάτων φθορισμού των μορίων και ακολούθως οι δομές με τους ισχυρότερους αποδέκτες ηλεκτρονίων παρουσίαζαν μεγαλύτερη απόσβεση του φθορισμού. / The optic excitement and the degree of Intramolecular Charge Transfer (ICT), as well as the dynamics of excited states, two new organic structures of molecules, D-pi-A (linear molecule) and DA3 (dendrimers – molecule with center an electron donor) have been investigated with femtosecond time resolved spectroscopy in two different solvents, toluene (with weak polarity) and tetrahydrofuran (moderate polarity). The experimental results by comparing the molecules of the same structure (DA or DA3) with gradual change of electrons acceptors (from weakest to strongest) in the same solvent showed that the organic structures with strongest electron acceptors had faster decay of the fluorescence and hence a stronger intramolecular charge transfer. Moreover, the comparison of the two structures showed that the dendrimers molecules generally showed stronger intramolecular charge transfer. Also the experimental results showed that when the solvent effect ( interactions dipole – dipole) on spectral properties of molecules by reducing the energy of the excited levels (red shift Stoke) of the fluorescence spectra of molecules and then the structures with the strongest electron acceptors had faster decay of the fluorescence