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<p> In this thesis, two inner shell excitation spectroscopy techniques, inner shell electron energy loss spectroscopy (ISEELS) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy, were used to measure the C ls, N ls and 0 ls spectra of the amino acids, glycine, alanine, cysteine, phenylalanine, proline, threonine, tryptophan and the peptides, Gly-Ala, Lys-Trp-Lys (KWK), and Arg-Gly-Asp (RGD). The spectra are analysed with the aide of ab initio computations using the GSCF3 method. The characteristic spectral features of the specific side chains of amino acids are identified. Differences in the spectra of the gas and solid are related to differences between the neutral gas phase molecule and the zwitterionic solid form. A rationalization of observations of high degree of variability in theN ls spectra of amino acids is proposed. The characteristic spectral signatures of peptide bonds have been identified further by comparing the spectra of small peptides to the spectra of their subunit amino acids. A modified "building block" approach is showed to be very useful in modeling the inner shell excitation spectra of peptides through linear combinations of the spectra of the amino acids residues and peptide bonds. </p> / Thesis / Master of Science (MSc)

THz spinduliuotės generavimas iš puslaidininkių paviršiaus turi didelį potencialą puslaidininkių fizikinėms savybėms tirti. Šis darbas skiriamas puslaidininkių tyrimams generuojant THz impulsus iš jų paviršių, apšviestų femtosekundiniais lazerio impulsais. THz spinduliuotė iš puslaidininkių paviršių gali būti generuojama dėl visos eilės fizikinių mechanizmų: paviršinio lauko ekranavimo, foto-Demberio efekto, optinio lyginimo, elektriniu lauku indukuoto optinio lyginimo, plazminių svyravimų, koherentinių fononų ir plazmonų. Tiriant THz spinduliuotės generacijos mechanizmus galima išmatuoti daug svarbių puslaidininkių parametrų, tokių kaip lūžio rodiklis, judris, krūvininkų gyvavimo trukmė, aukštesniųjų laidumo slėnių padėtys. Darbo metu tirti THz spinduliuotės generacijos puslaidininkio paviršiuje mechanizmai keičiant žadinimo sąlygas: aplinkos temperatūrą, magnetinį lauką, žadinančio lazerio bangos ilgį ir intensyvumą, bei impulso trukmę. Ištyrus visą eilę įvairių puslaidininkių nustatyta, kad geriausias THz spinduliuotės emiteris žadinant 800 nm bangos ilgio spinduliuote yra p-InAs. Pirmą kartą THz žadinimo spektroskopijos metodu tiesiogiai išmatuoti tarpslėniniai atstumai InxGa1-xAs , InAs ir InSb bandiniuose. / Generation of terahertz radiation from semiconductor surfaces has great potential for investigation of physical properties of semiconductors. This work focuses on the semiconductor research when generating terahertz pulses from a variety of semiconductor surfaces. THz radiation from semiconductor surfaces can be generated on a whole range of physical mechanisms: the surface field screening, photo-Dember effect, the optical rectification, electric field induced optical rectification, plasma oscillations, coherent phonons and plasmons. A number of important semiconductor parameters such as refractive index, mobility, carrier relaxation time and higher conductivity valley positions can be measured using THz generation from semiconductor surface technique. In this work THz radiation generation mechanisms were investigated when changing excitation conditions: ambient temperature, magnetic field, laser wavelength and intensity, pulse duration. After tests with variety different semiconductors it was found that p-InAs is the best surface emitter when excitation laser wavelength is 800 nm. Using THz excitation spectroscopy the intervalley distances were measured directly, for the first time, in two InxGa1-xAs, InAs and InSb samples.

Generation of terahertz radiation from semiconductor surfaces has great potential for investigation of physical properties of semiconductors. This work focuses on the semiconductor research when generating terahertz pulses from a variety of semiconductor surfaces. THz radiation from semiconductor surfaces can be generated on a whole range of physical mechanisms: the surface field screening, photo-Dember effect, the optical rectification, electric field induced optical rectification, plasma oscillations, coherent phonons and plasmons. A number of important semiconductor parameters such as refractive index, mobility, carrier relaxation time and higher conductivity valley positions can be measured using THz generation from semiconductor surface technique. In this work THz radiation generation mechanisms were investigated when changing excitation conditions: ambient temperature, magnetic field, laser wavelength and intensity, pulse duration. After tests with variety different semiconductors it was found that p-InAs is the best surface emitter when excitation laser wavelength is 800 nm. Using THz excitation spectroscopy the intervalley distances were measured directly, for the first time, in two InxGa1-xAs, InAs and InSb samples. / THz spinduliuotės generavimas iš puslaidininkių paviršiaus turi didelį potencialą puslaidininkių fizikinėms savybėms tirti. Šis darbas skiriamas puslaidininkių tyrimams generuojant THz impulsus iš jų paviršių, apšviestų femtosekundiniais lazerio impulsais. THz spinduliuotė iš puslaidininkių paviršių gali būti generuojama dėl visos eilės fizikinių mechanizmų: paviršinio lauko ekranavimo, foto-Demberio efekto, optinio lyginimo, elektriniu lauku indukuoto optinio lyginimo, plazminių svyravimų, koherentinių fononų ir plazmonų. Tiriant THz spinduliuotės generacijos mechanizmus galima išmatuoti daug svarbių puslaidininkių parametrų, tokių kaip lūžio rodiklis, judris, krūvininkų gyvavimo trukmė, aukštesniųjų laidumo slėnių padėtys. Darbo metu tirti THz spinduliuotės generacijos puslaidininkio paviršiuje mechanizmai keičiant žadinimo sąlygas: aplinkos temperatūrą, magnetinį lauką, žadinančio lazerio bangos ilgį ir intensyvumą, bei impulso trukmę. Ištyrus visą eilę įvairių puslaidininkių nustatyta, kad geriausias THz spinduliuotės emiteris žadinant 800 nm bangos ilgio spinduliuote yra p-InAs. Pirmą kartą THz žadinimo spektroskopijos metodu tiesiogiai išmatuoti tarpslėniniai atstumai InxGa1-xAs , InAs ir InSb bandiniuose.

As the global population approaches 11 billion people, demands for sustainable food, energy, and water (FEW) are approaching unprecedented levels. Current technology places sustainable FEW production methods in direct competition with one another for global surface area, such as land area for agriculture versus photovoltaic farms. This is because current installation methods for solar modules create deep shading that suppresses plant growth. The field of agrivoltaics (AgPV) addresses this issue directly by optimizing coproduction strategies for FEW and developing systems where competition is reduced; however, previous work has seen reductions in agricultural output. AgPV, where module architecture is also modified and agricultural output is minimally impacted, requires novel multi-level experimental design and characterization. In my proposed thesis, I will address the following two aspects of the project: (1) a farm-level experimental analysis of existing PV and (2) a device-level analysis of new and emerging PV material candidates. To establish the plausibility of this work, I designed and implemented an agrivoltaic system with two treatments that was successfully farmed this year. In my thesis, I will demonstrate a fully characterized utility scale AgPV array through several steps. First, I will validate the prior simulation work on the constructed AgPV array. Then I will experimentally correlate crop growth underneath the AgPV experiment. Next, the effects of the shadowing from the array on crop growth will be quantified. I will optimize the tracking algorithm for the array to maximize crop growth during the summer and power production during other seasons. Finally, I will investigate a platform for evaluation of novel PV materials and devices tailored for AgPV systems using Photoluminescence Excitation Spectroscopy (PLE) where I redesigned, constructed, and validated a new experimental design.

Biological invasion has become a major threat to economy, ecology, global biodiversity and ecosystem function of aquatic ecosystems. The main aim of the thesis was to study the effects of the zebra mussel (Dreissena polymorpha), a versatile invasive species, on phytoplankton dynamics and ecosystem function of lakes. In a first attempt, I compared the density of Dreissena and the physicochemical data of ecosystems that it invaded among North American and European lakes to identify important factors in its invasion success. Secondly, I investigated the impact of zebra mussels on phytoplankton community composition in a natural lake. Thirdly, I evaluated whether zebra mussel feeding behavior were affected by the presence of predatory waterborne cues. Finally, I examined the effect of Dreissena on seston stoichiometry. A Generalized Additive Model revealed that a joint effect of surface area, mean depth, total phosphorus and calcium concentrations can explain the variability in Dreissena density. Selective grazing by zebra mussels varied in relation to seasonal phytoplankton dynamics. Risk cues released by predators affected both feeding rate and prey selection of the mussels and had cascading indirect effects on phytoplankton biomass and community structure. I found that the flux in nutrients caused by differences in zebra mussel consumption lead to a variation in phytoplankton nutrient limitation. The flexibility of zebra mussel feeding behavior and variation in susceptibility among phytoplankton groups to mussel ingestion indicate that invading zebra mussels could alter phytoplankton community composition of lakes and have important ecosystem consequences. The results of this thesis contribute to the growing evidence that predators indirectly affect resource dynamics and food web structure through their non-lethal effects on consumers. The results suggested that zebra mussel can indirectly both reduce and increase the energy transfer efficiency from primary producers to upper trophic levels in the pelagic and benthic food webs, respectively.

L’étude présentée dans ce manuscrit s’inscrit dans le domaine du magnétisme de surface, qui a connu de grands développements ces dernières années grâce au microscope à effet tunnel (STM). Elle a pour but de montrer qu’une molécule simple, le nickelocène [Ni(C5H5)2], peut être attachée au sommet d’une pointe STM afin de produire une pointe-sonde magnétique, qui, dans le cadre de l’imagerie magnétique, présente des avantages indéniables comparés à des pointes conventionnelles. À la différence d’autres systèmes moléculaires étudiés avec le STM, nous montrons que les propriétés magnétiques du nickelocène en phase gazeuse sont préservées en présence d’un métal, même lorsque la molécule est attachée au sommet d’une pointe STM. Nous présentons trois résultats marquants avec cette pointe-sonde moléculaire: 1) Nous montrons que l’on peut contrôler le spin du nickelocène, activant à souhait un effet Kondo ; 2) Nous produisons à l’aide du courant tunnel des excitations entre les états de spin du nickelocène, que nous pouvons aisément identifier au travers de la conductance moléculaire. Ces états sont sensibles à toute perturbation magnétique extérieure au nickelocène; 3) Au travers de ces excitations, nous sondons alors le magnétisme de surface. Nous montrons qu’en couplant magnétiquement la pointe-sonde moléculaire avec des atomes, soit isolés soit dans une surface ferromagnétique, nous pouvons mesurer leur polarisation de spin, ainsi que le couplage d’échange nickelocène-atome. Ce dernier permet d’obtenir un contraste magnétique en imagerie STM à l’échelle atomique. / The study presented in this manuscript is part of the field of surface magnetism, which has undergone major developments in recent years thanks to the scanning tunneling microscope (STM). It aims to show that a single molecule, nickelocene [Ni(C5H5)2], can be attached to the tip of a STM to produce a magnetic probe-tip, which, in the context of magnetic imaging, has undeniable advantages compared to conventional tips. Unlike other molecular systems studied with STM, we show that the magnetic properties of nickelocene in the gas phase are preserved in the presence of a metal, even when the molecule is attached to the tip of a STM. We present three remarkable results with this molecular probe-tip: 1) We show that we can control the spin of nickelocene, activating at will a Kondo effect; 2) We monitor the spin states of nickelocene by producing electrically-driven excitations, which we can easily identify through the molecular conductance. These states are sensitive to the magnetic environment surrounding nickelocene; 3) We use these states to probe surface magnetism. We show that by magnetically coupling the molecular probe tip with single atoms, either isolated or in a ferromagnetic surface, we can measure their spin polarization, as well as the nickelocene-atom exchange coupling. By monitoring this coupling it is possible to obtain a magnetic contrast in the STM images with atomic-scale resolution.

<p>Biological invasion has become a major threat to economy, ecology, global biodiversity and ecosystem function of aquatic ecosystems. The main aim of the thesis was to study the effects of the zebra mussel <i>(Dreissena polymorpha)</i>, a versatile invasive species, on phytoplankton dynamics and ecosystem function of lakes. </p><p>In a first attempt, I compared the density of <i>Dreissena</i> and the physicochemical data of ecosystems that it invaded among North American and European lakes to identify important factors in its invasion success. Secondly, I investigated the impact of zebra mussels on phytoplankton community composition in a natural lake. Thirdly, I evaluated whether zebra mussel feeding behavior were affected by the presence of predatory waterborne cues. Finally, I examined the effect of <i>Dreissena</i> on seston stoichiometry.</p><p>A Generalized Additive Model revealed that a joint effect of surface area, mean depth, total phosphorus and calcium concentrations can explain the variability in <i>Dreissena</i> density. Selective grazing by zebra mussels varied in relation to seasonal phytoplankton dynamics. Risk cues released by predators affected both feeding rate and prey selection of the mussels and had cascading indirect effects on phytoplankton biomass and community structure. I found that the flux in nutrients caused by differences in zebra mussel consumption lead to a variation in phytoplankton nutrient limitation.</p><p>The flexibility of zebra mussel feeding behavior and variation in susceptibility among phytoplankton groups to mussel ingestion indicate that invading zebra mussels could alter phytoplankton community composition of lakes and have important ecosystem consequences. The results of this thesis contribute to the growing evidence that predators indirectly affect resource dynamics and food web structure through their non-lethal effects on consumers. The results suggested that zebra mussel can indirectly both reduce and increase the energy transfer efficiency from primary producers to upper trophic levels in the pelagic and benthic food webs, respectively. </p>