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Dissertations / Theses on the topic 'Optical and molecular fingerprints'

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Published: 25 May 2024

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1

Wong, Zilla Yin Har. "Molecular analysis of human minisatellites." Thesis, University of Leicester, 1990. http://hdl.handle.net/2381/34372.

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Tandem-repetitive hypervariable minisatellites detected in a DNA fingerprint provide highly informative genetic markers. To identify and localize specific loci represented in a DNA fingerprint, it is necessary to clone individual minisatellites. This thesis is concerned with the characterization of single locus minisatellite probes cloned from DNA fingerprints. Seven single locus human minisatellite probes have been cloned by screening ? libraries with DNA fingerprint probes 33.6 and 33.15. Each locus consists of a minisatellite, with repeat units ranging in length from 9 to 47 base pairs depending on the locus. These autosomal loci are amongst the most variable loci characterized to date. The heterozygosity values of D1S7, D1S8, D5S43, D7S21, D7S22 and D12S11 range from 85% to >99%. Clustering of minisatellites was initially detected at the D12S11 locus. This observation led to the subsequent discovery of minisatellites showing close physical linkage as well as a tendency for minisatellites to be localized in proterminal chromosomal regions. An association of a minisatellite with a dispersed repetitive element was identified when studying the organization of cloned D7S22. This phenomenon was later found to be common amongst minisatellites. Pedigree analysis revealed a high level of instability of the locus detected by D1S7. This manifestation of detectable mutant alleles demonstrated the feasibility of direct estimation of mutation rates at minisatellite loci. The hypervariability of loci detected by minisatellites and their sensitivity in blot hybridizations make minisatellites a powerful tool in genetic analysis. These probes have already proved instrumental in many genetic and clinical studies. The high degree of individual specificity and the relatively simple banding pattern generated make these probes invaluable in forensic medicine. D1S7 and D7S21 were used in the first example of DNA-based identification in a rape and murder enquiry. One minisatellite probe was found to detect two loci, DNF21S1 and DNF21S2, on chromosomes 6 and 16 respectively. The 39 base pair repeat unit of this minisatellite is itself repetitive. The heterozygosity values of DNF21S1 and DNF21S2 are 61% and 16% respectively. Genomic mapping and sequence analyses revealed close similarity between these loci. Human population and pedigree studies showed that some individuals carry two alleles at DNF21S2, some carry one allele, some carry a duplicated allele while some are devoid of this locus. A model of duplication of a large proterminal segment of chromosome 6 DNA containing a minisatellite and transposition into an interstitial region of chromosome 16 in some human individuals is suggested. This is, to my knowledge, the first report of a human DNA polymorphism arising via transposition of DNA. The duplication unit on chromosome 16 is large (>15 kb) and has inserted into a member of a target site family present in 5-10 copies per genome. This sequence family represents a novel class of human repetitive DNA.
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2

Costa, Henrique Sérgio Gutierrez da. "Biometric identification with 3D fingerprints acquired through optical coherence tomography." reponame:Repositório Institucional da UFPR, 2016. http://hdl.handle.net/1884/44486.

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Orientador : Prof. Dr. Luciano Silva
Coorientador : Profª. Olga Regina Pereira Bellon
Tese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa: Curitiba, 28/06/2016
Inclui referências : f. 75-82
Área de concentração
Resumo: Um método para se obter impressões digitais 3D da derme e da epiderme a partir de imagens em alta resolução adquiridas utilizando Tomografia de Coerência Ótica (OCT) é proposto neste trabalho. Este método, resolve limitações das técnicas de reconstrução 3D de impressões digitais que empregam múltiplas câmeras/triangulação ou iluminação estruturada, tais como variações de resolução do centro para as bordas das impressões digitais 3D causadas por erros de reconstrução, sensibilidade a baixa iluminação e contraste insuficiente. Uma técnica de busca e identificação baseados em padrões inovativos, os "mapas KH " (usados para a segmentação de regiões de superfície em imagens de intensidade e de profundidade), extraídos computando as curvaturas Gaussiana (K) e média (H) de uma região de interesse na vizinhança das minúcias (denominada nuvem de minúcia), é apresentada. Grandes bases de mapas KH, uma para cada nuvem de minúcia identificada, podem ser construídos com essa técnica. A estratégia de busca e identificação, em duas etapas, baseia-se primeiro em padrões locais de gradientes (LGP) dos mapas KH, para reduzir o espaço de busca dentro da base, seguidos de uma comparação que utiliza uma medida de similaridade, a correlação cruzada normalizada dos padrões pré-selecionados com o LGP com os que se quer identificar. A acuracidade do método e sua compatibilidade com os métodos correntes, comparável ou superior à dos métodos 2D, é verificada através da identificação biométrica de impressões digitais 3D utilizando duas bases de imagens, uma adquirida através da tecnologia OCT e a outra gentilmente cedida pela Universidade Politécnica de Hong Kong. A base de imagens OCT, a primeira adquirida com essa tecnologia, é composta de imagens coletadas de onze voluntários em duas sessões de escaneamento e contém imagens de dedos de pessoas com diferentes idades, gênero e etnias e contém casos de cicatrizes, calos e alterações, tais como abrasão e arranhões. Uma base de impressões digitais 2D, obtida dos mesmos voluntários através de um leitor regular de impressões digitais, foi adquirida para permitir uma comparação da técnica proposta com os métodos de identificação tradicionais. A aplicabilidade do método proposto à identificação de impressões digitais alteradas, deterioradas acidentalmente ou intencionalmente, é investigada. Nesses casos, a impressão digital 3D extraída da derme e compatível com a da epiderme é empregada. A identificação destas impressões 3D alteradas é testada utilizando a base de imagens adquiridas com OCT. A acuracidade da técnica é comparada com a obtida utilizando os métodos tradicionais 2D usando os gráficos de taxas de Falsa Aceitação e Falsa Rejeição (FAXxFRR) e de Características Cumulativas de Identificação (CMC). Impressões digitais 2D, extraídas a partir das impressões digitais 3D simulando o rolamento do dedo durante a aquisição (rolamento virtual), foram geradas e sua compatibilidade com as bases de imagens 2D foi testada. Um conjunto de medidas de avaliação de qualidade foram aplicados às bases de imagens de impressões digitais 3D e sua correspondência aos escores de identificação foi analisada para determinar aqueles que podem contribuir para melhorar a acuracidade da identificação. Palavras-chave: Impressões digitais 3D. Identificação Biométrica. Tomografia de Coerência Ótica.
Abstract: A method to obtain epidermal and dermal 3D fingerprints from high-resolution images acquired using Optical Coherence Tomography (OCT) is proposed. This method addresses limitations of current 3D reconstruction techniques that employ multiple cameras/triangulation or structured illumination such as depth and resolution variations from the center to the borders of the fingerprint caused by reconstruction errors, sensitivity to low illumination and poor contrast. The availability of these 3D fingerprints allowed the creation of new matching methods that benefit from the rich information available in 3D. A 3D fingerprint matching technique based on novel patterns, the KH maps (used to surface region segmentation in range and intensity images), extracted by computing the Gaussian and mean curvatures (SILVA; BELLON; GOTARDO, 2001) from a region of interest around the minutiae, named minutiae clouds is presented. Large databases of KH maps, one for each identified minutiae cloud can be built. The matching strategy, a two-step approach, relies on local gradient patterns (LGP) of the KH maps to narrow the search space, followed by a similarity matching, the normalized cross correlation of patterns being matched. The accuracy and matching compatibility, comparable or improved in relation to the 2D matching methods, is verified through matching 3D fingerprints from two databases one acquired using OCT and a public database gently made available by the Hong Kong Polytechnic University. The OCT database, the first 3D database acquired using Optical Coherence Tomography, to our knowledge, is made of images collected from eleven volunteers in two scanning sessions and contains images of people of different ages, genders and ethnicities and also cases of scars, calluses and alterations as abrasion and scratches. A 2D fingerprint database, scanned from the same volunteers using a regular fingerprint reader was also obtained for comparison with traditional matching methods. We investigate the applicability of our method to the identification of altered fingerprints, damaged unintentionally or accidentally. In these cases, the 3D dermal fingerprint, compatible with the epidermis fingerprint, is employed. Matching with 3D dermal and epidermal fingerprints is tested in the OCT database. Matching accuracy is compared with the obtained using traditional matching 2D methods by using False Acceptance and False rejection rate (FARxFRR) and Cumulative Matching Characteristics (CMC) graphs. Unwrapped fingerprints, 2D fingerprints extracted from 3D fingerprints by virtual unrolling were generated and tested for compatibility with 2D databases. A set of quality evaluation measures were employed to the 3D fingerprint databases and their correspondence to the matching scores was analyzed to identify those that can contribute to improve the matching accuracy. Key-words: 3D Fingerprints. Biometric identification. Optical Coherence Tomography.
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3

Adelantado, Sánchez Carlos. "Use of aspartic acid racemization in fingerprints as a molecular clock." Master's thesis, Instituto Superior de Ciências da Saúde Egas Moniz, 2014. http://hdl.handle.net/10400.26/6716.

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Dissertação de Erasmus Mundus para obtenção do grau de mestre em Técnicas Laboratoriais Forenses
Aspartic acid is the chemical, amongst amino acids, whose racemization process is considered to be the fastest and the most reliable way to conduct an ageing study in some living-being tissues. Racemization is a natural-occurring event in which L-stereoisomer of aspartic acid is converted into D-stereoisomer in an equilibrium dependent on factors namely pH, environmental conditions and, most critically, on temperature.
The main objective of the current study is to assess the influence of temperature on kinetics of aspartic acid racemization and to implement this methodology in fingermarks. The hypothesis is that different starting points of deposition of a biological specimen will give rise to significant differences in L-/D- racemization after the sample has been heated, allowing to determine time since deposition of a fingerprint. In this way, it would be possible to find the time since build a molecular clock for fingerprints, consisting of time since deposition of fingermarks based on racemization degree of aspartic acid.
Firstly, a calibration curve was built within the concentrations range expected to be quantified in actual samples both with L-aspartic acid (L-Asp) and D-aspartic acid (D-Asp) separately, Gas Chromatography - Flame Ionization Detector (GC-FID) being the chosen technique and detection mode to set up the calibration experiments. Secondly, L-aspartic acid standards were treated at different temperatures during different time periods and were analyzed by GC-FID with a chiral column, aimed for detecting D- isomer, providing with information about racemization rate of aspartic acid.
Eventually a downward trend was observed for L-Asp but not for D-Asp and a pseudo-rate constant could be calculated for the former, demonstrating that temperature degrades this chemical. Fingerprints study was not successful to determine aspartic acid racemization but a simple handling of them and an adequate, sensitive response of the chromatographic system could quantify racemization degree.
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4

Grubbs, Garry Smith II. "Investigating Molecular Structures: Rapidly Examining Molecular Fingerprints Through Fast Passage Broadband Fourier Transform Microwave Spectroscopy." Thesis, University of North Texas, 2011. https://digital.library.unt.edu/ark:/67531/metadc67988/.

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Microwave spectroscopy is a gas phase technique typically geared toward measuring the rotational transitions of Molecules. The information contained in this type of spectroscopy pertains to a molecules structure, both geometric and electronic, which give insight into a molecule's chemistry. Typically this type of spectroscopy is high resolution, but narrowband ≤1 MHz in frequency. This is achieved by tuning a cavity, exciting a molecule with electromagnetic radiation in the microwave region, turning the electromagnetic radiation o, and measuring a signal from the molecular relaxation in the form of a free induction decay (FID). The FID is then Fourier transformed to give a frequency of the transition. "Fast passage" is defined as a sweeping of frequencies through a transition at a time much shorter (≤10 s) than the molecular relaxation (≈100 s). Recent advancements in technology have allowed for the creation of these fast frequency sweeps, known as "chirps", which allow for broadband capabilities. This work presents the design, construction, and implementation of one such novel, high-resolution microwave spectrometer with broadband capabilities. The manuscript also provides the theory, technique, and motivations behind building of such an instrument. In this manuscript it is demonstrated that, although a gas phase technique, solids, liquids, and transient species may be studied with the spectrometer with high sensitivity, making it a viable option for many molecules wanting to be rotationally studied. The spectrometer has a relative correct intensity feature that, when coupled with theory, may ease the difficulty in transition assignment and facilitate dynamic chemical studies of the experiment. Molecules studied on this spectrometer have, in turn, been analyzed and assigned using common rotational spectroscopic analysis. Detailed theory on the analysis of these molecules has been provided. Structural parameters such as rotational constants and centrifugal distortion constants have been determined and reported for most molecules in the document. Where possible, comparisons have been made amongst groups of similar molecules to try and get insight into the nature of the bonds those molecules are forming. This has been achieved the the comparisons of nuclear electric quadrupole and nuclear magnetic coupling constants, and the results therein have been determined and reported.
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5

Boukra, Mohamed-Amine. "Caractérisation intégrée de la matière organique dissoute : recherche d'empreintes physico-chimiques pour tracer les sources de pollutions anthropiques." Electronic Thesis or Diss., Lyon 1, 2023. http://www.theses.fr/2023LYO10094.

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Les activités anthropiques à l'échelle d'un bassin-versant peuvent être très nombreuses (e.g. pratiques agricoles, industries, transport et tourisme). Ces activités engendrent des pressions qui se manifestent par l'apport de polluants vers les cours d'eau (e.g. éléments majeurs, micropolluants organiques, métaux traces). L'identification de ces sources de polluants dans les cours d'eau, et plus particulièrement les sources diffuses, reste un réel défi à ce jour. La matière organique dans sa fraction dissoute (MOD) constitue un mélange complexe de molécules dont la composition et les propriétés physicochimiques dépendent de son origine qu'elle soit naturelle ou anthropique, terrigène ou autochtone, diffuse ou ponctuelle. Du fait de son ubiquité, la MOD présente dans les cours d'eau pourrait ainsi être utilisée comme traceur des activités anthropiques et donc des sources de polluants à l'échelle d'un bassin versant. Dans ce contexte, l'objectif de cette thèse est de mettre en évidence des marqueurs basées sur des propriétés physico-chimiques de la MOD (e.g. distribution en poids moléculaire, aromaticité, famille de composés…) qui soient caractéristiques de sources naturelles (e.g. apports terrigènes, production autochtone) et anthropiques (e.g. rejets de stations de traitement des eaux usées STEU, ruissellement urbain, activités d'agriculture et d'élevage) à l'échelle de bassins versants. Pour cela, une base de données originale a été construite avec plus de 130 échantillons d'eau représentatifs de ces différentes sources et analysés avec un large panel de techniques analytiques (dosage du carbone organique dissous, analyse par spectroscopie UV-Visible et excitation-émission de fluorescence, analyse par chromatographie d'exclusion stérique couplée à la détection UV et fluorescence - HPSEC/UV-fluorescence - , et analyse moléculaire par chromatographie liquide couplée à la spectrométrie de masse haute résolution - LC-HRMS - ). L'exploitation de la base de données a tout d'abord permis d'améliorer la caractérisation de la MOD avec l'identification de nouveaux indicateurs optiques (HPSEC/UV-fluorescence) et moléculaires (LC-HRMS). Un protocole de traitement des données complexes issues de l'analyse LC-HRMS non-ciblée a été développé et validé à l'aide de contrôle qualité afin d'extraire les composés moléculaires les plus pertinents pour différencier les sources de MOD. Ces travaux ont également servi à valider une méthodologie d'échantillonnage spécifique aux sources diffuses terrigènes en lien avec l'occupation des sols. Finalement, l'approche intégrée multi-analytique et multi-sources développée dans le cadre de la thèse a contribué à la construction d'empreintes spécifiques des sources de MOD sélectionnées apriori (naturelles, anthropiques, diffuses, ponctuelles). Les résultats de ces travaux permettent clairement d'envisager la MOD comme traceur de l'origine des masses d'eaux et des pollutions associées dans les cours d'eau
Anthropogenic activities at the scale of a watershed can be very numerous (e.g. agricultural practices, industries, transport, and tourism). These activities generate pressures that result in the input of pollutants to the watercourse (e.g. major elements, organic micropollutants, trace metals). The identification of these sources of pollutants in watercourses remains a challenge to date. Organic matter in its dissolved fraction (DOM) constitutes a complex mixture of molecules whose composition and physicochemical properties depend on its origin, whether natural or anthropogenic, terrigenous or autochthonous, diffuse or point source. Because of its ubiquity, the DOM present in the rivers could be used as a tracer of the anthropic activities and thus of the sources of pollutants at the scale of a catchment. In this context, the objective of this thesis is to identify markers based on physico-chemical properties of DOM (that are characteristic of natural (e.g. terrigenous inputs, autochthonous production) and anthropogenic (e.g. wastewater treatment plant discharges, urban runoff, agriculture and livestock activities) sources at the watershed scale. For this purpose, an original database was built with more than 130 water samples representative of these different sources and analyzed with a wide range of analytical techniques (dissolved organic carbon determination, analysis by UV-Visible spectroscopy and fluorescence excitation-emission, analysis by steric exclusion chromatography coupled with UV and fluorescence detection - HPSEC/UV-fluorescence - , and molecular analysis by liquid chromatography coupled with high resolution mass spectrometry - LC-HRMS - ). The exploitation of the database allowed to improve the characterization of DOM with the identification of new optical (HPSEC/UV-fluorescence) and molecular (LC-HRMS) indicators. A protocol for processing complex data from non-targeted LC-HRMS analysis was developed and validated using quality control in order to extract the most relevant molecular compounds to differentiate DOM sources. This work also validated a sampling methodology specific to land-based diffuse sources in relation to land use to build their footprints at the watershed scale. Finally, the integrated multi-analytical and multi-source approach developed in the framework of the thesis allowed the construction of specific fingerprints of the selected sources of DOM (natural, anthropogenic, diffuse, point). The results of this work clearly show that DOM can be considered as a tracer of the origin of the water masses and the associated pollutions in the rivers
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6

Jakobs, Stefan [Verfasser], Matthias [Akademischer Betreuer] Wuttig, and Uwe [Akademischer Betreuer] Klemradt. "Exploring the limits of metavalent bonding : optical and structural fingerprints / Stefan Jakobs ; Matthias Wuttig, Uwe Klemradt." Aachen : Universitätsbibliothek der RWTH Aachen, 2019. http://d-nb.info/1210929104/34.

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7

Landmann, Marc [Verfasser]. "Fingerprints of order and disorder : the electronic structure and optical response of crystalline and amorphous materials / Marc Landmann." Paderborn : Universitätsbibliothek, 2020. http://d-nb.info/121429555X/34.

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8

Apitz, Dirk. "Molecular orientation in optical polymer films." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=980148804.

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9

Cong, Alexander Xiao. "Reconstruction Methods for Optical Molecular Tomography." Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/19253.

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Molecular imaging plays an important role for development of systems biomedicine, which non-invasively extracts pictorial information on physiological and pathological activities at the cellular and molecular levels. Optical molecular tomography is an emerging area of molecular imaging. It locates and quantifies a 3D molecular probe distribution in vivo from data measured on the external surface of a small animal around the visible and infrared range. This approach can facilitate or enable preclinical applications such as cancer studies, involving angiogenesis, tumor growth, cell motility, metastasis, and interaction with a micro-environment. The reconstruction of diffuse light sources is the central task of optical molecular tomography, and generally ill-posed and rather complex. The key element of optical molecular tomography includes the geometrical model, tissue properties, photon characteristics, transport model, and reconstruction algorithm.

This dissertation focuses mainly on the development optical molecular tomography methods based on bioluminescence/fluorescence probes to solve some well-known challenges in this field. Our main results are as follows. We developed a new algorithm for estimation of optical parameters based on the phase-approximation model.  Our iterative algorithm takes advantage of both the global search ability of the differential evolution algorithm and the ef"ciency of the conjugate gradient method. We published the first paper on multispectral bioluminescence tomography (BLT). The multispectral BLT approach improves the accuracy and stability of the BLT reconstruction even if data are highly noisy. We established a well-posed inverse source model for optical molecular tomography. Based on this model, we proposed a differential evolution-based reconstruction algorithm to determine the source locations and strengths accurately and reliably. Furthermore, to enhance the spatial resolution of fluorescence molecular tomography, we proposed fluorescence micro-tomography to image cells in a tissue scaffold based on Monte Carlo simulation on a massive parallel processing architecture. Each of these methods shows better performance in numerical simulation, phantom experiments, and mouse studies than the conventional methods.

Ph. D.
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10

Lubian, Elisa. "Porphyrin Derivatives as Optical Molecular Sensors." Doctoral thesis, Università degli studi di Padova, 2011. http://hdl.handle.net/11577/3427495.

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In this Doctorate Thesis project, a small library of four structurally related melamine-bridge bis(porphyrin-ZnII) receptors, was synthesized The coordination properties of these porphyrin derivatives has been investigated by UV-vis spectroscopy for a series of aliphatic diamines of general formula H2N (CH2)n NH2 (n = 4-8). A marked colour variation occours due to a favourable host-guest ditopic interaction. The binding constants, higher than 10e7 M-1, make these receptors excellent candidates for the development of sensor devices for continuous flow analyses, in which the porphyrin derivatives are covalently supported onto appropriate solid materials. These dimeric metalloporphyrin hosts (molecular tweezers), have also been successfully exploited as chirality probes for determination of the absolute configuration (AC) for a wide variety of chiral molecules (diamines, amino esters, amino amides, amino alcohols and secondary monoalcohols) by using circular dichroism spectroscopy, in collaboration with Prof. Nina Berova of Columbia University. The deposition of porphyrin derivatives on different matrices was also investigated. Characterizations of substrates were carried out by scanning electron microscopy (SEM), atomic force microscopy (AFM) and scanning tunneling microscopy. These results show promising potential in the synthesis of highly ordered networks of surface-supported functional materials for sensing and solar energy applications.
Il progetto di ricerca di questa Tesi di Dottorato ha riguardato la sintesi, la caratterizzazione e lo studio delle proprietà di ricognizione molecolare di nuovi derivati bis-porfirinici contenenti un ponte triazinico. Studi di spettroscopia UV-vis hanno permesso di determinare l’affinità di tali recettori nei confronti delle diammine lineari di formula generale H2N(CH2)nNH2, con n = 4-8. Le costanti di formazione dei complessi host-guest sono molto grandi, fino a 10e7 M-1, grazie all’effetto ditopico realizzato dai due centri porfirinici. La coordinazione delle diammine al dimero porfirinico è associata ad una variazione marcata del colore e questo fatto ha favorito l’impiego di tali derivati in ambito sensoristico. A tal proposito, è stata messa a punto una procedura per supportare i dimeri porfirinici su materiali polimerici per la costruzione di sensori da utilizzare per l’analisi in flusso continuo. Questi derivati sono stati anche utilizzati come pinze molecolari (tweezers) per la determinazione della configurazione assoluta di molecole chirali (diammine, ammino esteri, ammino ammidi e ammino alcoli, monoalcoli secondari) mediante l’impiego della spettroscopia di dicroismo circolare (CD), in collaborazione con la Prof. Berova della Columbia University. Parallelamente, sono stati realizzati studi di deposizione di derivati porfirinici su superfici in vista di applicazioni di tipo sensoristico e in campo energetico (fotovoltaico). La caratterizzazione dei substrati è stata condotta mediante misure di microscopia elettronica a scansione (SEM), microscopia a forza atomica (AFM) e microscopia a scansione ad effetto tunnel (STM). Questi studi di deposizione hanno dimostrato come, scegliendo le opportune condizioni di deposizione, sia possibile costruire dei sistemi ordinati a lungo raggio, su superfici di diversa natura, rendendo questi sistemi candidati ideali per lo sviluppo di nuovi materiali ad alto contenuto tecnologico.
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11

Mendolia, Isabella. "Deep neural networks leveraging different arrangements of molecular fingerprints to define a novel embedding for virtual screening procedure." Doctoral thesis, Università degli Studi di Palermo, 2022. https://hdl.handle.net/10447/554696.

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Winkler, Amy. "OPTICAL METHODS FOR MOLECULAR SENSING: SUPPLEMENTING IMAGING OF TISSUE MICROSTRUCTURE WITH MOLECULAR INFORMATION." Diss., The University of Arizona, 2010. http://hdl.handle.net/10150/195176.

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More and more researchers and clinicians are looking to molecular sensing to predict how cells will behave, seeking the answers to questions like "will these tumor cells become malignant?" or "how will these cells respond to chemotherapy?" Optical methods are attractive for answering these questions because optical radiation is safer and less expensive than alternative methods, such as CT which uses X-ray radiation, PET/SPECT which use gamma radiation, or MRI which is expensive and only available in a hospital setting. In this dissertation, three distinct optical methods are explored to detect at the molecular level: optical coherence tomography (OCT), laser-induced fluorescence (LIF), and optical polarimetry. OCT has the capability to simultaneously capture anatomical information as well as molecular information using targeted contrast agents such as gold nanoshells. LIF is less useful for capturing anatomical information, but it can achieve significantly better molecular sensitivity with the use of targeted fluorescent dyes. Optical polarimetry has potential to detect the concentration of helical molecules, such as glucose. All of these methods are noninvasive or minimally invasive.The work is organized into four specific aims. The first is the design and implementation of a fast, high resolution, endoscopic OCT system to facilitate minimally invasive mouse colon imaging. The second aim is to demonstrate the utility of this system for automatically identifying tumor lesions based on tissue microstructure. The third is to demonstrate the use of contrast agents to detect molecular expression using OCT and LIF. The last aim is to demonstrate a new method based on optical polarimetry for noninvasive glucose sensing.
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13

Robertson, John Michael. "Nonlinear optical properties of absorbing molecular systems." Thesis, University of Essex, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390961.

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Nichols, Alexander J. "Optical Molecular Sensing in Complex Biological Environments." Thesis, Harvard University, 2014. http://nrs.harvard.edu/urn-3:HUL.InstRepos:14226087.

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Although techniques in molecular imaging have advanced considerably over the past several decades, there remain numerous categories of biological molecular targets that are refractory to straightforward imaging. Among these is molecular oxygen, which is vital to a host of physiological as well as pathological processes, as well as the amorphous pigment pheomelanin, which may play a formerly unappreciated role in melanoma carcinogenesis. This thesis describes two related bodies of work that advance techniques in oxygen and pheomelanin imaging, respectively. First, inspired by a desire to understand how hypoxia affects cancer chemotherapy on a cellular level, we designed and synthesized a novel oxygen-sensitive, dendritic nanoconstruct that is capable of spontaneously penetrating through hundreds of microns of multiple cellular layers. After demonstrating our nanoconjugate's oxygen sensitivity using time-domain phosphorescence lifetime measurements, we demonstrate that it retains its oxygen sensitivity in a 3D spheroid in vitro model of ovarian cancer through the use of a custom-made, near infrared-optimized confocal phosphorescence imaging system. Drawing from this approach, we then describe the fabrication and calibration of a separate oxygen-sensing bandage platform for use in wound-healing applications, and demonstrate its use in ex vivo and in vivo animal systems. The second body of work describes the use of non-linear four-wave mixing techniques to facilitate straightforward imaging of the molecular pigment pheomelanin. Recent findings suggest that pheomelanin may play a previously unappreciated role in melanoma carcinogenesis, even in the complete absence of an ultraviolet light insult. However, due to its pale color, pheomelanin is difficult to visualize against a skin background, making its study challenging. After constructing a femtosecond-pulsed coherent anti-Stokes Raman scatter (CARS) microscopy imaging system, we use imaging and spectroscopy to provide proof-of-concept that pheomelanin can be imaged through a combination of CARS microscopy and electronically-enhanced four-wave mixing. We then use our non-linear imaging system to specifically observe pheomelanin in isolated "redhead" mouse melanocytes, and show through an siRNA gene knock-down strategy that our system can be used to observe changes in pheomelanin signal upon modification of biological pathways known to affect pheomelanin synthesis.
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15

Azarm, Ali, Paul Corkum, and Pavel Polynkin. "Optical gain in rotationally excited nitrogen molecular ions." AMER PHYSICAL SOC, 2017. http://hdl.handle.net/10150/626190.

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We pump low-pressure nitrogen gas with ionizing femtosecond laser pulses at 1.5 mu m wavelength. The resulting rotationally excited N-2(+) 2 molecular ions generate directional, forward-propagating stimulated and isotropic spontaneous emissions at 428 nmwavelength. Through high-resolution spectroscopy of these emissions, we quantify rotational population distributions in the upper and lower emission levels. We show that these distributions are shifted with respect to each other, which has a strong influence on the transient optical gain in this system. Although we find that electronic population inversion exists in our particular experiment, we show that sufficient dissimilarity of rotational distributions in the upper and lower emission levels could, in principle, lead to gain without net electronic population inversion.
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16

Korobenko, Aleksey. "Control of molecular rotation with an optical centrifuge." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/58640.

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The major purpose of this work is the experimental study of the applicability of an optical centrifuge - a novel tool, utilizing non-resonant broadband laser radiation to excite molecular rotation - to produce and control molecules in extremely high rotational states, so called molecular "super rotors", and to study their optical, magnetic, acoustic, hydrodynamic and quantum mechanical properties.
Science, Faculty of
Physics and Astronomy, Department of
Graduate
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17

Fulton, Ray. "Atomic and molecular manipulation in pulsed optical fields." Thesis, Heriot-Watt University, 2006. http://hdl.handle.net/10399/125.

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18

Qureshi, Faisal. "The nonlinear optical properties of conjugated molecular materials." Thesis, University of Sheffield, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264642.

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19

Gerakis, A. "Controlling and probing molecular motion with optical lattices." Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1436072/.

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This thesis describes the further improvement of an already developed by our group laser system capable of delivering high energy, frequency agile, flat-top pulses and its uses in non-resonant molecular scattering diagnostics in the form of coherent Rayleigh-Brillouin scattering, as well as for optical Stark deceleration of neutral H2 molecules. This laser system is capable of delivering two computer controlled flat-top pulses of variable duration (20~1000 ns) with energies up to 700 mJ per pulse and with linearly chirped frequencies up to 1.5 GHz. With the use of constant velocity lattices driven by this system we were able to accurately obtain coherent Brillouin scattering spectra of purified air in the hydrodynamic regime where, for the first time, we observed additional spectral peaks to the main Brillouin peak, as well as up to 40% reduction of the peak due to the interaction of the laser driven electrostrictive grating with the acoustic which was launched in the gas due to its thermalisation by the optical field. Furthermore, by utilising chirped frequency optical lattices, we were able to obtain accurate coherent Rayleigh-Brillouin spectra with signal-to-noise ratios in excess of 100, in a single laser shot ( 140ns) thus reducing the acquisition times needed for such spectra by ten orders of magnitude, rendering the technique ideal for combustion and transient flow diagnostics. Finally, we report on the use of this laser system as a tool for optical Stark deceleration of neutral H2 molecules, where through a Raman tagging scheme of the interacting molecules we are proposing an efficient way to monitor the interactions occurring within the decelerating optical lattice. We hope that this technique will pave the way for the production of narrow velocity spread molecular ensembles to be used in cold collisional studies as well as sympathetic cooling.
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20

Zhang, Yuan. "Optical spectra of molecular complexes and molecular junctions coupled to metal nano-particles." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät, 2015. http://dx.doi.org/10.18452/17356.

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Diese Arbeit präsentiert eine vollständige quantenmechanische Beschreibung eines Systems bestehend aus einem Molekül und einem metallischem Nanopartikel (MNP) in der Gegenwart eines Strahlungsfeldes. Zuerst wird ein System aus einem Molekül und einem Gold-MNP betrachtet. Das Emissionsund Absorptionsspektrum zeigt viele scharfe molekulare Schwingungssatelliten auf einem breiten Plasmonmaximum. Eine Verstärkung der Schwingungssatelliten um drei Größenordnungen ist auf effiziente Absorption und Emission durch die MNP zurückzuführen. Dann wird ein System aus einer molekularen Kette mit einem Gold-MNP untersucht. Alle zuvor genannten Phänomene treten auch hier auf, jedoch werden die Schwingungssatelliten durch das Exzitonenband der molekularen Kette ersetzt. Anschließend wird ein Nano-Laser aus vielen Molekülen und einem Gold-MNP betrachtet. Die Moleküle werden durch inkohärentes optisches Pumpen angeregt. Dabei wird eine starke Plasmonanregung durch die gemeinsame Kopplung an die Moleküle erreicht. Die Photonenemission des Lasers zeigt, dass die Intensität ansteigt, während die Linienbreite schmaler wird. Die Korrelationsfunktion in zweiter Ordnung für die Photonen in Verbindung mit der schmaler Emission könnte dabei sogar einen Hinweis auf Lasing geben. Zuletzt wird eine Nanoverbindung aus einem Molekül und zwei sphärischen metallischen Elektroden betrachtet. Das Molekül wird durch den sequentiellen Ladungstransfer angeregt. Durch die Kopplung an die Moleküle werden die Elektrodenplasmonen angeregt. Die Photonenemission der Verbindung zeigt, dass die scharfen molekularen Schwingungssatelliten um das Tausendfache verstärkt werden. Anschließend ist ein System aus zwei pyramidalen Elektroden, die seitlich von zwei Gold-MNP eingeschlossen werden, untersucht. Hier können die Schwingungssatelliten einzeln verstärkt werden, indem der Abstand zwischen den MNP variiert wird. Wir zeigen auch, dass das Lasing in einer Verbindung aus vielen Molekülen theoretisch möglich ist.
This thesis presents a unified quantum description of the combined molecule-metal nano-particle system in the presence of a radiation field. Firstly, a single molecule coupled to a gold nano-sphere is investigated. The emission and absorption spectrum show many sharp molecular vibrational satellites over one broad plasmon peak. The three orders of magnitude enhancement of the vibrational satellites is due to the great ability of the sphere to absorb and emit photons. Secondly, a molecular chain coupled to a gold nano-sphere is investigated. All the phenomena mentioned above appear also for such system, except that the vibrational satellites are replaced by the Frenkel exciton band of the molecular chain. Thirdly, a plasmonic nano-laser consisting of many dye molecules and a gold nano-sphere is considered. The molecules are initially excited by incoherent optical pump. The strong plasmon excitation of the sphere is achieved due to the concerted coupling with the molecules. The emission of the laser shows that the intensity is enlarged while the line-width is reduced. The second-order correlation function of photons together with the emission narrowing can be utilized to determine lasing operation. Finally, a nano-junction formed by a molecule and two spherical metallic leads is investigated. The molecule is excited through sequential electron transfer. The lead plasmons get excited due to the coupling with the excited molecule. The emission of the junction shows that the molecular vibrational satellites are about one thousand times enhanced by the lead plasmons. Then, a junction with two pyramidal metallic leads sandwiched by two gold nano-spheres is investigated. The simulations show that the molecular vibrational satellites can be selectively enhanced by varying the inter-sphere distance. It is also proved that the lasing can be realized by a junction with many molecules.
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21

Soattin, Marica. "The use of molecular markers for analyzing genes and genomes of livestock." Doctoral thesis, Università degli studi di Padova, 2008. http://hdl.handle.net/11577/3425494.

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The present thesis has been developed considering three different livestock species such as chicken, cattle and sheep. The aim of the study was the evaluation of the application of molecular makers in order to assay the genetic population structure on seven local breeds of chicken, to evaluate the applicability of candidate genes as support of conventional breeding on Piedmontese cattle breed and to detect new SNPs on a sheep population. The first two researchs were carried out at Department of Animal Science of University of Padova while the last one at Reprogen (Faculty of Veterinary Science, University of Sydney, NSW, AUS).
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22

Huxley, Allen John McAllister. "Switches based on molecular recognition processes." Thesis, Queen's University Belfast, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.322948.

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23

Olivindo, Cellyneude de Souza. "DetecÃÃo de microorganismos utilizando a tÃcnica de pcr em sequÃncias palindrÃmicas extragÃnicas repetidas (REP-PCR) no monitoramento da qualidade do leite de cabra em sala de ordenha." Universidade Federal do CearÃ, 2008. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=1704.

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CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior
O presente estudo foi realizado, com o objetivo de aplicar a tÃcnica de PCR em seqÃÃncias palindrÃmicas extragÃnicas repetidas (REP-PCR) no monitoramento da qualidade do leite de cabra, atravÃs da detecÃÃo de Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa e Streptococcus spp., em amostras de mÃos de ordenhadores, tetos das cabras, leite, ordenhadeira e Ãgua, para o futuro estabelecimento e implantaÃÃo do sistema de AnÃlise de Perigos e Pontos CrÃticos de Controle (APPCC). Verificou-se vÃrios fingerprints de todos os isolados coletados das diferentes fontes estudadas (mÃos de ordenhadores, tetos das cabras, leite, ordenhadeira e Ãgua). Observou-se comportamentos muito similares das bandas indicando que os isolados podem ser relatados como clones epidemiolÃgicos. A Ãgua sem tratamento, utilizada para a lavagem das mÃos dos ordenhadores, caracterizou-se como um ponto crÃtico de controle (PCC), pois se destaca como iniciador de contaminaÃÃo nas amostras Streptococcus spp., Escherichia coli e Pseudomonas aeruginosa,. Outro PCC seria as mÃos do ordenhador, pois nas amostras de Staphylococcus aureus, aparece tambÃm como indicador de contaminaÃÃo. A tÃcnica demonstrou ser eficiente para a anÃlise da similaridade entre indivÃduos da mesma espÃcie, no caso, do Staphylococcus aureus, Streptococcus spp., Escherichia coli e Pseudomonas aeruginosa, sendo, portanto, uma ferramenta Ãtil para investigaÃÃo de falhas no manejo e consequentemente, na busca de um controle mais eficiente para evitar ou minimizar a disseminaÃÃo de microrganismos patogÃnicos causadores de sÃrias enfermidades em humanos e animais, que muitas vezes podem ser transmitidas atravÃs de produtos como o leite e seus derivados.
The present study was carried out, with the objective of applying the PCR technique in repetitive extragenic palindromic (REP-PCR) sequences in the monitoring of the quality of goat milk, through the detection of Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Streptococcus spp., in samples of milking handlers, goats teats, milk, milk machine and water, for the future establishment and implantation of the system of Hazard Analysis Critical Control Points (HACCP). Several fingerprints was verified of all the isolates collected of the different studied sources (milking handlers, goats teats, milk, milk machine and water). It was observed very similar behaviors of the bands indicating that the isolates can be related as epidemic clones. The water without treatment, used for the wash milking handlers, it was characterized as a critical point of control (PCC), because stands out as starter contamination in the Streptococcus spp., Escherichia coli and Pseudomonas aeruginosa samples. Another PCC would be the hands of the milking handlers, because in the Staphylococcus aureus samples, it is also appears as initial point of contamination. The technique demonstrated to be efficient for the similarity analysis among individuals of the same species, in case, of the Staphylococcus aureus, Streptococcus spp., Escherichia coli and Pseudomonas aeruginosa, being, therefore, an useful tool for investigation of fails on management and consequently, in the search of more efficient control to avoid or to minimize the spread of pathogenic microorganisms that cause serious illnesses in humans and animals, and can be transmitted through products as the milk and your products.
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24

McEwan, Kennneth John. "Mechanisms for non-linear optical behaviour in molecular fluids." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.305473.

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25

Fisher, Shari Powell. "Fabrication of advanced optical devices by molecular beam deposition." Thesis, Heriot-Watt University, 1992. http://hdl.handle.net/10399/808.

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26

van, Kleef Eduard Hendrik. "Optical preparation of reagent states in molecular dynamics investigations." Thesis, University of Nottingham, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.357947.

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27

Verlet, Jan Raf Rogier. "Controlling electronic and molecular dynamics using optical pulse sequences." Thesis, King's College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.397922.

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28

Pilizota, Teuta. "A programmable optical angle clamp for rotary molecular motors." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670185.

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29

Ngo, Ndimba Alphonsine L. "Photoactive molecular assemblies for optical limiting and bio-imaging." Thesis, Rennes 1, 2020. http://www.theses.fr/2020REN1S103.

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Dans cette thèse, nous ciblons de nouveaux absorbeurs biphotoniques pour la bio-imagerie et la limitation optique. Nous nous sommes intéressés plus précisément à des octupôles, structures connues pour posséder des propriétés intéressantes en optique non-linéaire et plus particulièrement en absorption à deux photons. Ainsi, les cœurs isocyanurate et 1,3,5-triazine, connus comme étant des accepteurs, mènent à des octupôles bidimensionnels lorsqu’ils sont substitués de façon symétrique. Pour lors, les isocyanurates ont été peu étudiés pour l’optique non linéaire tandis que les triazines ont déjà été étudiées dans ce cadre et sont connues pour avoir de bonnes propriétés en absorption à deux photons. Dans un premier temps, nous nous sommes intéressés à la synthèse d’isocyanurates organiques et à l’étude de leurs propriétés optiques. Nous avons plus particulièrement étudié l’effet de la planarisation et de l’extension du système conjugué. Dans un deuxième temps, nous nous sommes intéressés à la synthèse et à l’étude des propriétés optiques des tristyryltriazines afin de comparer celles-ci à leurs analogues tristyrylisocyanurates et d’étudier l’influence du cœur sur les propriétés en sachant que la triazine est un cœur plus électroattracteur que l’isocyanurate. Puis, nous nous sommes intéressés à la synthèse de complexes ruthénium-alkynyl trinucléaires à cœurs isocyanurates et triazines, car le ruthénium est un métal d6 connu pour améliorer les propriétés en optique non linéaire. Enfin, nous avons synthétisé des dérivés hydrosolubles de composés organiques qui présentaient les propriétés optiques les plus prometteuses pour la bio-imagerie. En collaboration avec le Dr. Gary-Bobo, nous avons pu confirmer le potentiel de ces molécules pour de telles applications
In this work, new biphotonic absorbers were targeted for applications in bio-imaging and optical limiting. We have investigated the synthesis of octupoles since these multipolar structures were often shown to lead to interesting optical properties, especially two-photon absorption. The structures studied were isocyanurate- or 1,3,5-triazine-cored star-shaped derivatives. Both cores are known to be electron-accepting units and to give rise to two-dimensional octupoles when symmetrically substituted. So far, isocyanurates have not often been studied in nonlinear optics, whereas triazines have already been screened and were shown to have good two-photon absorption properties. We first focused on the synthesis of organic isocyanurates and on the study of their optical properties. We started by studying the planarization effect of the extension of the peripheral arms on the optical properties. We then focused on the synthesis and study tristyryltriazines analogous to the previous tristyrylisocyanurates. New structure/property relationships were thus established since the triazine is more electron-attracting than the isocyanurate core. We next synthesized ruthenium-alkynyl trinuclear complexes with isocyanurate and triazine cores, since ruthenium is a d6 metal known to enhance the nonlinear optical properties. We finally studied water-soluble derivatives for bio-imaging. In collaboration with Dr. Gary-Bobo we confirmed their potential for such applications
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30

Augulis, Ramūnas. "Molecular aggregates, dendrimers, and motors optical dynamics and control /." [S.l. : [Groningen : s.n.] ; University Library Groningen] [Host], 2008. http://irs.ub.rug.nl/ppn/.

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31

BARBAGLIA, ANDREA. "ELECTRO-TUNABLE OPTICAL DEVICES FOR MOLECULAR AND CELLULAR STUDIES." Doctoral thesis, Università degli studi di Genova, 2020. http://hdl.handle.net/11567/1001750.

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In the present scenario of information technology, researchers are looking for new systems able to deal more efficiently with the increasing amount of information produced by modern society. Nowadays, these tasks are accomplished by CMOS transistors and FLASH memories. Despite their wide implementation, these devices are facing serious issues along their road of development, mainly related to stable operation and power dissipation managing. Advancements in this field could boost the application of artificial intelligence and Big Data analysis, as well as enable new data communication protocols. By taking inspiration from the brain, a very powerful system characterized by low power consumption and high interconnectivity, new proposed devices, such as RRAM memories, aim at overcoming these issues. Properly engineered systems of this typology could act moreover as platforms for more precise and comprehensive biomedical studies. In this thesis, a new class of electro-tunable optical devices is presented in the framework of next-generation memory systems. The model device possesses very favorable characteristics, such as high density and interconnectivity. Moreover, the optical readout, performed by a camera, enables parallel operation. Two realizations of this device concept were studied. The first one is a new configuration for Zero-Mode Waveguides (ZMWs), a well-known nanophotonic system used to perform studies on fluorophore dispersion at the single molecule level. In the proposed device, the interplay of an electric voltage allows to control fluorophore concentration and residence time inside the ZMWs. The light intensity coming from the ZMWs gives information about these two parameters. In the second realization, the developed ZMWs platform is used to perform an optical detection of cardiomyocytes action potentials (APs). The cells are cultured on a thin substrate placed above the fluorophore dispersion. The substrate features an array of pass-through electrodes, which allow the electric APs to be transferred from the cells to the fluorophore dispersion. APs were successfully measured with high SNR. Moreover, the device proved able to detect the effects of a drug administered to the cell culture. This device could find application as a new system for in-vitro electrophysiology, including drugs cardiotoxicity studies. Due to the optical readout scheme, it promises to offer very high spatial resolution, orders of magnitude higher than conventional multi-electrode arrays systems.
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32

Snelling, Michael. "Optical orientation in quantum wells." Thesis, University of Southampton, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.305526.

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33

Li, Weiyao. "Chemical structure and optical functions of synthetic melanin." University of Akron / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=akron1627042724510547.

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34

Fasihi, Amer Zia. "Measurement of chlorocarbons using quenching of molecular fluorescence." Thesis, Cranfield University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.309837.

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35

Thomas, Philip Robert. "The molecular properties of zwitterionic, non-linear optical molecules and their evolution with molecular environment." Thesis, Durham University, 1998. http://etheses.dur.ac.uk/4998/.

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The concepts involved with the experimental techniques of Electric Field Induced Second Harmonic generation (EFISH), dipole moment measurement, and solvatochromism, are introduced with particular application to the properties of organic molecules. A number of organic chromophores are introduced, but emphasis is applied to the study of tetracyanoquinodimethane (TCNQ) derivatives which are expected to possess large dipole moments (µ) and large hyperpolarisabilities (β). Furthermore, the behaviour of and with respect to the local environment of the molecule is discussed where a novel evolution is predicted from theoretical calculations. The measurement of µ, is discussed with particular reference to the geometry of the local field factor and the size of the molecule. Consequently, the choice of local field is found to be critical when dipole moments are large, as is the case with the TCNQ derivatives. The EFISH experimental technique is introduced where the calibration of the experiment is discussed. The measurement of the molecular figure of merit, µβ at 1.064 µm and 1.907 µm in chloroform and dichloromethane is presented for the TCNQ derivatives, again paying attention to the geometry of the local field factor. µβ is found to be moderate for most of the compounds, but β is found to be unexpectedly small. This is partly due to the fact that µ is large. A novel evolution of the transition frequency with solvent polarity is found for three of the chromophores under study, where the solvatochromic shift reverses. Solvatochromism experiments are conducted with binary solvent mixtures to ascertain the position of the cyanine limit (β=0) with respect to reaction field. It is found that the materials reside close to the cyanine limit in chloroform and dichloromethane. This is attributed as a reason for the low β measurements. Comparisons of µ and β are also made with Sum-Over-State calculations. A better correlation is found for ellipsoidal local field factors.
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36

Barry, Judith Anne. "Optical and infrared spectra of some unstable molecules." Thesis, University of British Columbia, 1987. http://hdl.handle.net/2429/28619.

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Some unstable gaseous molecules, cobalt oxide (CoO), niobium nitride (NbN) and aminoborane (NH₂BH₂), were studied by high resolution optical spectroscopy. A portion of the "red" system of CoO, from 7000 Å to 5800 Å, was measured using laser induced fluorescence techniques. Three bands of the system, with origins at 6338 Å, 6411 Å and 6436 Å, were rotationally analyzed. The lower levels of these parallel bands are the Ω = 7/2 and 5/2 spin-orbit components of a ⁴∆i electronic state. Available evidence indicates that this is the ground state of the molecule; its bond length is 1.631 Å. This work completes the determination of the ground state symmetries for the entire series of first row diatomic transition metal oxides. The hyperfine structure in the ground state is very small, supporting a σ²δ³π² electron configuration. The upper state, assigned as σδ³π²σ*, has large positive hyperfine splittings that follow a case (aβ) pattern; it is heavily perturbed, both rotationally and vibrationally. The sub-Doppler spectrum of the ³Φ₋³∆ system of NbN was measured by intermodulated fluorescence techniques, and the hyperfine structure analyzed. Second order spin-orbit interactions have shifted the ³Φ₃₋³∆₂ subband 40 cm⁻¹ to the blue of its central first order position. The perturbations to the spin-orbit components were so extensive that five hyperfine constants, rather than three, were required to fit the data to the case (a) Hamiltonian. The ³∆₋³Φ system of NbN is the first instance where this has been observed. The magnetic hyperfine constants indicate that all components of the ³∆ and ³Φ spin orbit manifolds may be affected, though the ³∆ state interacts most strongly, presumably by the coupling of the ³∆₂ component with the ¹∆ state having the same configuration. The Fermi contact interactions in the ³∆ substates are large and positive, consistent with a σ¹δ¹ configuration. In the ³Φ state the (b + c) hyperfine constants are negative, as expected from a π¹δ¹ configuration. The ³∆ and ³Φ bond lengths are 1.6618 Å and 1.6712 Å, respectively, which are intermediate between those of ZrN and MoN. The Fourier transform infrared spectrum of the V7 BH₂ wagging fundamental of NH₂BH₂ was rotationally analyzed. A set of effective rotational and centrifugal distortion constants was determined, but the band shows extensive perturbations by Coriolis interactions with the nearby V5 and V11 fundamentals. A complete analysis could not be made without an analysis of the V5-V7-V11 Coriolis interactions, which is currently not possible because the very small dipole derivative of the V5 vibration has prevented its analysis.
Science, Faculty of
Chemistry, Department of
Graduate
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37

Langsner, Robert James. "Optical contrast agents to visualize molecular expression in breast cancer." Thesis, Rice University, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3577602.

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38

Schäffer, Erik. "Hydrodynamic resonance in optical traps & friction of molecular machines." Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-179472.

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39

Judkewitz, B. "Optical and molecular techniques for the study of neuronal networks." Thesis, University College London (University of London), 2010. http://discovery.ucl.ac.uk/20175/.

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A central goal of systems neuroscience is to understand how brain function can be explained by the activity of intricate neuronal circuits. A major hurdle towards addressing this question has been the lack of appropriate techniques to specifically manipulate individual neurons within functioning networks and to measure their connectivity at single cell resolution. Here I present a new technique, two-photon guided single-cell electroporation, to perform genetic manipulations of individual neurons in the intact mammalian brain in vivo. I demonstrate how stable transgene expression can reliably be induced with high success rates both in single neurons as well as in spatially defined groups of neurons in the cerebral cortex of mice. Furthermore, I demonstrate how single-cell electroporation can be used in combination with retrograde viral tracing techniques to label the microcircuit impinging on a single postsynaptic target neuron. Using this approach, I present the first data of monosynaptic neuronal tracing at single-cell resolution in intact networks in vivo. These complementary techniques will provide researchers with a new approach to manipulate the function of single neurons within intact networks and to link the function of a neuronal network to the underlying circuitry.
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40

Craven, Thomas Henry John. "Resolving uncertainty in acute respiratory illness using optical molecular imaging." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/29507.

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Ventilator associated pneumonia (VAP) and acute respiratory distress syndrome (ARDS) are two respiratory conditions unique to mechanically ventilated patients. The diagnosis of these conditions, and therefore any subsequent treatment, are befuddled by uncertainty. VAP rates vary considerably according to the diagnostic or surveillance criteria used. The pathogenesis of ARDS is well understood but when the internationally agreed consensus criteria are employed, the histological hallmarks are absent about half the time, indicating a disconnection between the clinical diagnosis and what is known about the biology of this condition. It is argued that tests of biological function should be considered in addition to clinical characteristics in order to improve the utility of diagnosis. Given that the pathological sequelae of both VAP and ARDS are driven by an over exuberant host neutrophil response, the activated neutrophil was selected as a potential biological imaging target. Optical molecular imaging uses visible and near visible wavelengths from the electromagnetic spectrum to derive or visualize information based on the optical properties of the target tissue. Optical wavelengths are safe and cheap to work with, producing much higher resolution images than those relying on x-rays or gamma radiation. The imaging modality can be coupled with exogenously applied chemistry to identify specific biological targets or processes. The hypothesis that optical molecular imaging could be used to detect activated neutrophils in real time in the alveolar region of patients was tested. A bespoke optical molecular imaging agent called Neutrophil Activation Probe (NAP), designed in-house, was used to test the hypothesis. NAP is a dendrimeric compound delivered to the alveolar region of a patient in microdoses (≤100 micrograms), becoming fluorescent only on contact with activated neutrophils, and can be detected by optical endomicroscopy. Both the imaging agent and the endomicroscope are delivered to the distal lung via routine bronchoscopy. The agent was tested extensively in the laboratory to demonstrate function, specificity, and safety. Ex vivo testing took place using human and ovine lungs. A regulated dose escalation Phase I clinical trial of investigational medicinal product (CTIMP) in healthy volunteers, patients with bronchiectasis, and mechanically ventilated patients with a pulmonary infiltrate on chest radiography (NCT01532024) was designed and conducted. The aim of the Phase I study was to demonstrate the safety of the technique and to confirm proof of concept. In order to support the requirement for a technique that interrogates alveolar neutrophils two supplementary clinical studies were performed. Firstly, two VAP surveillance techniques (CDC surveillance and HELICS European VAP surveillance) were compared with clinically diagnosed VAP across consecutive admissions in two large tertiary centres for one year. Secondly, the utility of circulating neutrophils to permit discrimination between acute respiratory illnesses was examined. Blood samples from mechanically ventilated patients with and without ARDS underwent flow cytometric assessment using eight clusters of differentiation and internal markers of activation to determine neutrophil phenotype. All clinical studies received the appropriate regulatory, ethical, and/or Caldicott guardian approval prior to commencement. NAP became fluorescent only in the presence of three processes specific to neutrophil activation: active pinocytosis, progressive alkalinization of the phagolysosome, and the activity of human neutrophil elastase. High optical signal was detected following the application of NAP in the alveolar regions of explanted lungs from patients with cystic fibrosis, known to be rich in activated neutrophils. Using an ex vivo ovine lung ventilation and perfusion model optical signal was demonstrated following segmental lung injury. The safety and specificity of the technique in a small cohort of healthy volunteers and mechanically ventilated patients was demonstrated. The technique was tested on a small cohort of patients with bronchiectasis, which provided the first opportunity to obtain broncho-alveolar lavage samples for laboratory correlation. Fluorescent signal was shown in the lavaged neutrophils, labeling that could only have taken place in the alveolar region. The supportive clinical studies found the concordance between actual VAP events was virtually zero even though the reported VAP rates were similar. Furthermore, the rate at which clinicians initiate antibiotics for VAP was approximately five times higher than either surveillance VAP rate. The study of circulating neutrophils from the blood of healthy volunteers and mechanically ventilated patients with and without ARDS indicated circulating neutrophil activation phenotype was not capable of discriminating between clinically diagnosed ARDS and other acute respiratory illnesses. In summary, an ambitious programme of work was completed to develop and support an optical molecular imaging technique that meets the rigorous requirements for human application and can be applied at the bedside to yield immediate visual results. The spatiotemporal relationship of neutrophil activation in real time both in the laboratory and in volunteers and patients was visualized. The visualization of neutrophil activation at such a resolution has never been achieved before in humans, healthy or unhealthy. The Phase I study was not powered to determine utility but recruitment has begun to a Phase II CTIMP (NCT02804854) to investigate the utility, accuracy, and precision of the imaging technique in a large cohort of mechanically ventilated patients. Ultimately, it is proposed that the technique will facilitate diagnosis, stratify patients for treatment and monitor treatment response using this technique.
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41

Schäffer, Erik. "Hydrodynamic resonance in optical traps & friction of molecular machines." Diffusion fundamentals 20 (2013) 11, S. 1, 2013. https://ul.qucosa.de/id/qucosa%3A13533.

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42

Selvam, Sangeetha. "Molecular Population Dynamics of DNA Tetraplexes using Magneto-Optical Tweezers." Kent State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=kent1516742116760289.

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43

Döringshoff, Klaus. "Optical frequency references based on hyperfine transitions in molecular iodine." Doctoral thesis, Humboldt-Universität zu Berlin, 2018. http://dx.doi.org/10.18452/19156.

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Diese Arbeit beschäftigt sich mit der Entwicklung und Untersuchung von optischen Absolutfrequenzreferenzen basierend auf rovibronischen Übergängen in molekularen Jod. Dabei werden Methoden der Doppler-freien Sättigungsspektroskopie angewendet, um einzelne Übergänge der Hyperfeinstruktur mit Linienbreiten unterhalb von 1 MHz im B-X System von molekularem Iod bei 532 nm, der zweiten harmonischen des Nd:YAG-Laser, aufzulösen. Elektronische Regelungstechniken ermöglichen eine präzise Stabilisierung der optischen Frequenz auf die Linienmitte der Übergänge mit einer Auflösung von Teilen in 10^5. Mit dem Ziel einer weltraumtauglichen Absolutfrequenzreferenz für zukünftige Weltraummissionen, wurden zwei Spektroskopiemodule konzipiert und in quasi-monolithischen Glaskeramik-Aufbauten, als sogenanntes elegant breadboard model und engineering model, realisiert. Diese Jodfrequenzreferenzen wurden im Detail in Bezug auf ihre Frequenzstabilität und Reproduzierbarkeit untersucht und Letzteres wurde für die angestrebte Weltraumqualifizierung ersten Umwelttests, sowohl vibrations- als auch thermischen Belastungstests, unterzogen. Für die Untersuchung der Frequenzstabilität dieser Jodreferenzen wurde ein auf einen optischen Resonator hoher Güte stabilisiertes Lasersystem für direkte Frequenzvergleiche bei 1064 nm realisiert. Die Analyse der Frequenzstabilität der Jod Referenzen zeigt eine Frequenzstabilität von 6x10^−15 bei 1 s, und weniger als 2x10^−15 bei 100 s Integrationszeit, was der bis heute besten veröffentlichten Frequenzstabilität entspricht die mit Jod Referenzen erreicht wurde. Mit der erreichten Frequenzstabilität ermöglichen diese Absolutfrequenzreferenzen präzise Lasersysteme für zukünftige Weltraummissionen wie z.B. zur Detektion von Gravitationswellen, zur Vermessung des Gravitationsfelds der Erde oder für Präzisionstest fundamentaler Theorien der Physik.
This thesis deals with the development and investigation of optical absolute frequency references based on rovibronic transitions in molecular iodine. Doppler-free saturation spectroscopy methods are employed to resolve individual transitions of the hyperfine structure with linewidths below 1 MHz in the B-X system of molecular iodine at 532 nm with the second harmonic of Nd:YAG lasers. Electronic feedback control systems are employed for laser frequency stabilization to the line center of the optical transitions with a line splitting of 10^5. With the goal of a space qualified optical absolute frequency reference for future laser-interferometric space missions, two spectroscopy setups were designed and realized in quasi-monolithic, glass-ceramic setups as so called elegant bread board model and engineering model. These iodine references were characterized in detail with respect to their frequency stability and reproducibility and the engineering model was subject to environmental tests, including vibrations and thermal cycling to verify its applicability in future space missions. For the investigation of the frequency instability of these iodine references, a frequency stabilized laser system was realized based on a temperature controlled high Finesse ULE cavity for direct frequency comparisons at 1064 nm. Analysis of the frequency stability of the iodine references revealed exceptionally low fractional frequency instability of 6x10^−15 at 1 s, averaging down to less than 2×10^−15 at 100 s integration time, constituting the best reported stability achieved with iodine references to date. With the demonstrated performance, these absolute frequency references enable precision laser systems required for future space missions that are dedicated to, e.g., the detection of gravitational waves, mapping of the Earth’s gravitational field or precision test of fundamental physics.
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44

MOCCI, PAOLA. "Electronic an Optical Properties of 2D molecular systems - Paola Mocci." Doctoral thesis, Università degli Studi di Cagliari, 2020. http://hdl.handle.net/11584/284138.

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This Thesis presents and explores the attractive landscape of the reduced dimensionality systems world, focusing in particular, on 2D materials. We analyze the effects of partial/complete atomic substitution and specific chemical functionalization on the electronic and optical properties of nanometric portions of 2D compounds, that are of interest for both fundamental research and potential use in technological devices and applications. In particular, we considered the class of PAHs, concentrating our attention on the Circumacenes molecules. For these systems we studied the effects induced by different substitutions: insertions of Si atoms, total substitutions of B and N to form the Boron-Nitride (BN) counterpart and total replacement of peripheral H atoms with F atoms on several physical properties. In the first part of this Thesis we report a systematic comparative study of Coronene and Ovalene molecules analyzing the effects of Si-atoms substitutions (single, double and triple insertions) on the ground-state electronic and optical properties of these systems. We performed all electrons density functional theory (DFT) and time-dependent DFT (TDDFT) calculations to quantify the effects of morphology and chemical modifications on different physical observables. For this part of the work we used the hybrid exchange-correlation functional B3LYP in combination with a gaussian localized basis-set. This adopted union functional/basis-set has proven to produce good results for PAHs and their derivatives. Globally, for this first part of the work we have used NWChem computational code. In the second part, using the same theoretical framework (DFT and TDDFT), we study the electronic and optical properties of the BN counterparts of the five first members of the Circumacenes. In addition, we also select the case of the smallest molecule of the cluster to deepen the perfluorination effects on the same observables. We investigate in a comparative approach the molecular properties of these compounds, presenting the trend for different physical observables and comparing with the corresponding results for the C-made original parents, as well as with the available data from the literature. For this part of the Thesis we used an all-electrons gaussian-based computational package, namely Gaussian-16. In the last part of this Thesis, we present a comparative study focused on the C-made linear Acenes and their Si/Ge-based counterparts. We quantified the effects of complete substitution on the electronic and optical properties of these systems, showing the behavior of the above mentioned observables as a function of the molecular size for each cluster and the differences among clusters of different atomic type at fixed molecular size. In this last part of the work we implemented DFT and TDDFT calculations through Gaussian computational code. In conclusion, using state-of-the-art computational techniques, this Thesis presents original results on key molecular properties of different Polycyclic Aromatic Hydrocarbons, considered as nanometric portions of their infinite successful counterparts. We performed a systematic comparative investigation to evaluate, from a quantitative point-of-view, the effects of different chemical modifications (partial/total substitutions of different atomic types or perfluorination) on the electronic, optical and structural properties of different systems which are the building blocks of materials widely employed in molecular electronics. Our findings can be possibly used to select tailored chemical modifications to specific compounds for future electronic and optical applications.
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45

Gilbertson, Steve. "Double optical gating." Diss., Manhattan, Kan. : Kansas State University, 2010. http://hdl.handle.net/2097/4250.

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46

Wood, Emma Louise. "Optical mode study of liquid crystal layers." Thesis, University of Exeter, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.332498.

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47

Zhao, Yu. "Growth and optical characterization of Sb-based materials on InP for optical telecommunication." Thesis, Rennes, INSA, 2014. http://www.theses.fr/2014ISAR0002/document.

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Ce travail de thèse porte sur la croissance et sur la caractérisation optique de nanostructures à base d’antimoine sur substrats InP, en vue d’applications dans le domaine des télécommunications optiques. La transition inter-sous-bande est un processus ultrarapide qui permet la modulation de la lumière dans les réseaux de télécommunication optique. Durant cette thèse, une absorption inter-sous-bande dans le proche-infrarouge provenant de puits quantiques Ga0.47In0.53As/AlAs0.56Sb0.44 a été observée pour la première fois au laboratoire. Les analyses par microscopie électronique à effet tunnel sur la face clivée montrent cependant de nombreux déviations à l’idéalité de nos structures : mélange à l’échelle atomique aux interfaces entre GaInAs et AlAsSb, inhomogénéité de l’alliage GaInAs, incorporation non-intentionnel d’antimoine dans le GaInAs. Les puits quantiques InAs/AlAs0.56Sb0.44 sont potentiellement des objets de choix pour la réalisation de composants intersous- bande travaillant à 1,55 μm. Des puits quantiques InAs/AlAs0.56Sb0.44 contraint, exempt de défauts ont été obtenus par croissance assistée par effet surfactant de Sb. En symétrisant la contrainte induite par le dépôt d’InAs par l’insertion de couches nanométriques de AlAs dans les barrières, des multi-puits InAs/AlAs0.56Sb0.44 sans contrainte macroscopique ont été réalisés. L’effet de l’antimoine en surface sur la croissance de structure InAs/GaAs0.51Sb0.49 a également été étudié. En présence d’antimoine sur substrats InP d’orientation (001), le dépôt d’InAs conduit à la formation de puits quantiques. Par contre sur ceux orientés suivant (113)B des boites quantiques sont formées suivant le mode de croissance Volmer-Weber. Ces résultats sont discutés en termes d’effets cinétiques ou énergétiques de l’antimoine en surface. La modification de l’anisotropie de l’énergie de surface induite par l’antimoine permet d’interpréter nos résultats sur substrats (100) et (113) B
This PhD work presents molecular beam epitaxy growth and optical studies on several Sb-nanostructures on InP substrate, for their potential use in optical telecommunication. Inter-subband transition in Ga0.47In0.53As/AlAs0.56Sb0.44 quantum well is a useful physical process for implementing ultrafast fulloptical modulations. Near-infrared inter-subband transition in this material was achieved and microscopic studies on this structure has revealed that the intermixing at GaInAs/AlAsSb interface, unintentional Sb incorporation in GaInAs layer and the inhomogeneity within GaInAs layer could prevent Ga0.47In0.53As/ AlAs0.56Sb0.44 multiple quantum wells from achieving intersubband transition in 1.55 μm optical telecommunication band. The strained InAs/AlAs0.56Sb0.44 quantum well is another material that has potential use in 1.55 μm full-optical modulation. 2 nm-thick defect-free InAs/AlAs0.56Sb0.44 was obtained under Sb surfactant-mediated growth, and by using strain compensation techniques, InAs/AlAs0.56Sb0.44 multiple quantum wells with zero net-strain were realized. The study of Sb-mediated growth is also carried on to InAs/GaAs0.51Sb0.49 nanostructures. The growths of such structures on InP (001) substrate has led to the formation of flat InAs layer, while high-density InAs/GaAs0.51Sb0.49 quantum dots were obtained on InP (113)B substrates under Volmer-Weber growth mode. We attribute such phenomena to the surfaceorientation dependent surfactant effect of Sb. Emission wavelength close to 2 μm was achieved with only 5 ML of InAs deposition, which makes these quantum dots attractive to InPbased mid-wave applications
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48

Ding, Li. "Optical Anisotropy and Molecular Orientation of CuPc Films and Optical Properties of Ultra-thin High-k Films." Doctoral thesis, Universitätsbibliothek Chemnitz, 2012. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-qucosa-97100.

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In the thesis CuPc thin films were investigated by (in situ) SE and RAS, which are employed to determine the out-of-plane and in-plane optical anisotropy and molecular orientation, respectively. CuPc is a promising candidate of organic semiconductors used in organic field effect transistors, organic light emitting diodes and organic solar cells. Vicinal Si(111) substrates are interesting due to the in-plane anisotropy caused by the steps and terraces on the surface. The strength of in-plane anisotropy of vicinal Si(111) is dependent on the offcut angle. The influence of offcut angle on out-of-plane and in-plane molecular orientation in CuPc thin films is explored. The in situ investigation of CuPc films suggests that structural changes occur during film growth. In addition, two different surface modification layers were utilized to examine the effect on CuPc molecular orientation: OTS monolayer with upright standing molecules and PTCDA layers with flat lying molecules. Metal-organic interface plays an important role in organic electronic devices. In-CuPc is chosen to be an example system investigated employing in situ SE and RAS. When In was thermally evaporated onto CuPc film, In atoms firstly diffuse into the CuPc film underneath and then aggregate to form clusters on top. Hafnium dioxide (HfO2) is currently a hot topic to replace the conventionally used SiO2 as gate dielectrics in order to minimize leakage current when further scaling down microelectronic devices. Since HfO2 films are often crystalline, in order to obtain amorphous films which are beneficial to minimize leakage current, aluminum oxide (Al2O3) (k value: 9) which stays amorphous at much higher temperatures are combined to overcome this difficulty. Two series of ultra-thin samples were deposited by atomic layer deposition: mixed layers HfxAl1-xOz and bilayers HfO2 on Al2O3. Optical constants and bandgap are determined using SE in the energy range of 0.7-10 eV. It is found that the (effective) optical bandgap of both mixed layer and bilayer structures can be tuned by the film composition. Aging effect of high-k films was observed after storage of samples in air for two months, which is attributed to further oxidation of the dielectric films caused by the oxygen diffusion from ambient air to high-k films
In dieser Arbeit werden dünne Schichten aus Kupferphthalozyanin (CuPc) mittels spektroskopischer (in-situ) Ellipsometrie (SE) und (in-situ) Reflektions-Anisotropie-Spektroskopie (RAS) untersucht, um die optische Anisotropie in einer Ebene parallel und senkrecht zur Schichtoberfläche und die molekulare Orientierung zu bestimmen. CuPc ist ein aussichtsreicher Kandidat als organischer Halbleiter in organischen Feldeffekt-Transistoren, organischen Leuchtdioden und organischen Solarzellen. Vizinale Si(111)-Substrate sind wegen der Anisotropie in der Substratebene interessant, die durch die Treppen und Terrassen auf der Oberfläche verursacht wird. Die Stärke der Anisotropie der vizinalen Si(111)-Oberfläche ist vom Schnittwinkel (Offcut) abhängig. Es wird der Einfluss des Offcut-Winkels auf die molekulare Orientierung in dünnen CuPc-Schichten parallel und senkrecht zur Substratoberfläche untersucht. Die in-situ Untersuchungen von CuPc-Schichten weisen darauf hin, dass strukturelle Veränderungen beim Wachstum auftreten. Darüber hinaus wurden zwei unterschiedliche Oberflächenmodifizierungsschichten, um deren Wirkung auf die molekulare Orientierung von CuPc zu untersuchen, verwendet: eine OTS-Monoschicht mit aufrecht stehenden Molekülen und PTCDA-Schichten mit flach liegenden Molekülen. Metall-organische Grenzflächen spielen eine wichtige Rolle in organischen elektronischen Bauelementen. In-CuPc wird als Beispiel für ein Metall-organisches System durch in-situ SE und RAS untersucht. Wenn In thermisch auf eine CuPc-Schicht aufgedampft wird, diffundieren In-Atome zunächst in die darunterliegende CuPc-Schicht und bilden dann Cluster auf der Schicht. Hafniumdioxid (HfO2) ist ein heißer Kandidat für das Ersetzen des herkömmlich als Gate-Dielektrikum verwendeten SiO2 mit dem Ziel, die Leckströme bei der weiteren Verkleinerung mikroelektronischer Bauelemente zu minimieren. Um amorphe Schichten, die vorteilhaft zur Minimierung der Leckströme sind, zu erhalten, werden die HfO2-Schichten, die oft kristallin sind, mit Aluminiumoxid (Al2O3) (k-Wert: 9) kombiniert, das bei wesentlich höheren Temperaturen amorph bleibt. Zwei Serien von ultra-dünnen Proben wurden durch Atomlagenabscheidung hergestellt: Mischschichten HfxAl1-xOz und Doppelschichten HfO2 auf Al2O3. Die optischen Konstanten und Bandlücken wurden mittels SE im Energiebereich von 0,7 bis 10 eV bestimmt. Es hat sich gezeigt, dass die (effektive) Bandlücke der Misch- und Doppelschichten durch die Komposition abgestimmt werden kann. Nach Lagerung der High-k-Schichten für zwei Monate an Luft konnte ein Alterungseffekt beobachtet werden. Dieser wird auf die weitere Oxidation der dielektrischen Schichten, die durch Sauerstoffdiffusion aus der Umgebungsluft in die High-k-Schichten ermöglicht wird, zurückgeführt
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49

Goeders, James E. "Resolved sideband spectroscopy for the detection of weak optical transitions." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/49082.

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This thesis reports on the setup of a new ion trap apparatus designed for experiments with single ⁴⁰Ca⁺ ions to perform molecular spectroscopy. The calcium ion is laser cooled, allowing for sympathetic cooling of the nonfluorescing molecular ion. The aim of these experiments is to explore loading and identifying molecular ions in RF-Paul traps, as well as developing new spectroscopic tools to measure transitions of molecular ions via the fluorescence of co-trapped ⁴⁰Ca⁺ ions. Ground state cooling of a mixed ion pair is implemented as a first step towards increasing the sensitivity of our technique to the level necessary to measure transitions with low scattering rates (like those present in molecular ions). Doppler cooling on the S(1/2)->P(1/2) transition of the calcium ion results in the formation of a Coulomb crystal, the behavior of which may be used to infer properties of the molecular ion. Following cooling, sideband spectroscopy on the narrow S(1/2)->D(5/2) quadrupole transition of calcium may be used to identify the mass of single molecular ions. This method is verified via a non-destructive measurement on ⁴⁰CaH⁺ and ⁴⁰Ca¹⁶O⁺. The normal modes of the Coulomb crystal can also be used to extract information from the target ion to the control ion. By driving the blue side of a transition, laser induced heating can be put into the two ion system, which leads to changes in fluorescence of the ⁴⁰Ca⁺ ion, first demonstrated with two Ca⁺ isotopes. Increasing the sensitivity of this technique requires ground state cooling of both the ⁴⁰Ca⁺ ion and the ion of interest, enabling the transfer of the ion's motional state into the ground state with high probability. This thesis demonstrates ground state cooling of the atomic ion and sympathetic cooling of a second ion (⁴⁴Ca⁺). Once in the ground state, heating of the Coulomb crystal by scattering photons off of the spectroscopy ion can be measured by monitoring the resolved motional sidebands of the S(1/2)->D(5/2) transition of ⁴⁰Ca⁺, allowing for spectral lines to be inferred. Future experiments will investigate this technique with molecular ions.
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50

Ekström, Ulf. "Time-dependent molecular properties in the optical and x-ray regions." Doctoral thesis, Linköpings universitet, Beräkningsfysik, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-10125.

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Time-dependent molecular properties are important for the experimental characterization of molecular materials. We show how these properties can be calculated, for optical and x-ray frequencies, using novel quantum chemical methods. For xray absorption there are important relativistic effects appearing, due to the high velocity electrons near the atomic nuclei. These effects are treated rigorously within the four-component static exchange approximation. We also show how electron correlation can be taken into account in the calculation of x-ray absorption spectra, in time-dependent density functional theory based on the complex polarization propagator approach. The methods developed have been applied to systems of experimental interest|molecules in the gas phase and adsorbed on metal surfaces. The effects of molecular vibrations have been take into account both within and beyond the harmonic approximation.
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