En els últims anys la importància de la polarització en les comunicacions òptiques ha crescut notablement com resultat de tres grans desenvolupaments:1. L'aparició de l'amplificació òptica ha fet que es produeixi un gran increment en les longituds dels enllaços de fibra monomode, així com en el nombre de dispositius òptics que ha de travessar la llum sense regenerar-se. Com a resultat d'això, petits efectes com la diferència de retards entre els modes amb polaritzacions ortogonals, o petites diferències entre les pèrdues d'inserció per a aquests modes, poden acumular-se a causa de la gran distància a recórrer, esdevenint un paràmetre a considerar en el disseny dels sistemes.2. La possibilitat de la detecció coherent en la qual el receptor és sensible al batut de dos feixos de llum i no només a la potència del feix, ha dut també a haver de considerar el tractament de la polarització com un dels punts d'investigació importants.3. L'última raó per la qual la polarització s'ha convertit en un tema fonamental és l'impressionant increment que s'ha donat en les velocitats de transmissió, que de nou duu que petits efectes es tornin importants per l'extremadament petit temps de bit.L'estructura no perfectament cilíndrica de la fibra òptica durà a les diferents components transversals dels camps a veure índexs de refracció lleugerament diferents, amb el que es produirà acoblament d'energia d'un mode a l'ortogonal i diferències de retard entre els modes. Les imperfeccions de la fibra no són predictibles (les seves causes van des de la pròpia fabricació fins als esforços als que es vegi sotmesa després de la seva instal·lació) pel que es fa difícil una caracterització del problema. Es tractarà d'un fenomen estadístic pel que no es pot solucionar de forma determinista. Aquest treball s'emmarca dintre de l'àmbit de la recerca de solucions als efectes provocats per la polarització en els sistemes de comunicacions per fibra òptica. Els objectius marcats inicialment es van circumscriure a la detecció coherent. L'objectiu fonamental era l'estudi de les diverses tècniques per a solucionar els esvaïments per desadaptació de les polaritzacions en aquest tipus de receptors. No obstant això, en el treball que es presenta s'han inclòs també realitzacions encaminades als sistemes MI-DD, cap a les quals s'han bolcat els nostres esforços durant el període de durada del mateix. Encara que es tracta de filosofies totalment distintes, pràcticament totes les realitzacions pensades per als sistemes coherents podran aplicar-se també als sistemes MI-DD pel que no ha de pensar-se en aplicacions excloents.Les parts en que es divideix el treball són: · Estudi analític de la variació de la polarització de la llum en fibres òptiques. Dintre d'aquesta part s'oferixen resultats que es corresponen amb mesures realitzades sobre fibra i simulacions del comportament de la mateixa, i representen la justificació de tot el treball posterior.· Estudi de les diferents solucions al problema de la polarització en els receptors coherents. Es presenten aquí tots els dispositius dissenyats i construïts així com els diferents algorismes proposats per al control de la polarització. S'exposen tanmateix les mesures realitzades per a la caracterització d'aquests dispositius i la seva integració en un receptor coherent real.· Estudi dels efectes de la polarització en els sistemes MI-DD d'última generació i aplicació dels dispositius dissenyats en aquest tipus de sistemes. En aquesta part s'oferixen algunes prediccions sobre els valors que pot prendre la dispersió deguda a la polarització en enllaços reals. Així mateix es proposa un aleatorizador de la polarització amb aplicació en sistemes amb amplificació òptica. / El trabajo desarrollado en esta tesis doctoral se enmarca dentro del ámbito de la búsqueda de soluciones a los efectos provocados por la polarización en los sistemas de comunicaciones por fibra óptica tanto Coherentes como de Modulación de Intensidad y Detección Directa. El objetivo fundamental es el estudio de diversas técnicas para solucionar los problemas que los efectos de la polarización provocan en dichos sistemas como por ejemplo, los desvanecimientos por desadaptación de las polarizaciones en receptores de detección coherente o la dispersión debida a la polarización (PMD) en los sistemas MI-DD de última generación.Las partes en que se divide el trabajo son:- Estudio analítico de la variación de la polarización de la luz en fibras ópticas.Dentro de esta parte se ofrecen resultados que se corresponden con medidas realizadas sobre fibra y simulaciones del comportamiento de la misma y representan la justificación de todo el trabajo posterior.- Estudio de las diferentes soluciones al problema de la polarización en los receptores coherentes. Se presentan aquí todos los dispositivos diseñados y construidos así como los diferentes algoritmos propuestos para el control de la polarización. Se exponen asimismo las medidas realizadas para la caracterización de los mismos y su integración en un receptor coherente real.- Estudio de los efectos de la polarización en los sistemas MI-DD de última generación y aplicación de los dispositivos diseñados a su solución. En esta parte se ofrecen algunas predicciones sobre los valores que puede tomar la dispersión debida a la polarización en enlaces reales. Asimismo se propone un aleatorizador de la polarización con aplicación en sistemas con amplificación óptica. / Polarization related topics have gained momentum during last years in the optical communications field, due to the advent of three main developments:1. Optical amplification has allowed a great increase in the singlemode fiber lengths, as well as in the number of optical devices that the light must cross without being regenerated. As a result, small effects like the difference of propagation delays between the orthogonal modes, or the small differences between the insertion losses for those modes, can be accumulated due to the great distance, becoming a parameter to consider in the systems design.2. The optical coherent detection, where the receiver is sensitive to the beat of two light beams and not only to the optical power level, has also lead to take into account the light polarization as an increasingly important topic of research, as a mismatch in beams polarizations implies no signal found after the coherent detection.3. Last reason for the high importance of polarization stems from the impressive increase in bit rates that optical communications have experienced. This implies that small effects which could be neglected at lower bit rates appear now as important due to the extremely low bit periods.Therefore, it is clear that in the present and future systems the problems related to the polarization are one of the stumbling blocks to save. The origin of the polarization effects in fibers resides in their non-ideal performance. The not perfectly cylindrical structure of the optical fiber will lead the orthogonal components of the fields to see slightly different refractive indices, and so coupling of energy between modes, as well as different delays will take place. The imperfections of the fiber are not predictable (their causes go from the own manufacture to the stress applied after its installation) reason why a characterization of the problem becomes difficult. It is a statistical phenomenon, so it is not possible to be solved in a deterministic form.This work focuses on the search of solutions to the effects brought about the polarization in optical fiber communications systems. The objectives were initially confined to coherent detection systems. The main target was the study of the diverse techniques to solve the fadings by polarizations mismatch in this type of receivers. Nevertheless, solutions focusing on IM-DD systems have also been included in this work. Even considering that the approaches are very different, the different solutions thought for coherent systems can find their place in IM-DD systems.This work is divided in three parts:· Analytical study of the variation of the light polarization in optical fibers. Within this part results are offered that correspond to measures and simulations realised on fibers characterizing their behaviour. These results give reason for the remaining work.· Study of the different solutions about the polarization problem in coherent receivers. All the devices designed and constructed, as well as the different algorithms proposed for the control of the polarization are presented in this part. The measures realised for their characterization and their integration in an actual coherent receiver are also shown.· Study of the polarization effects in advanced MI-DD systems, and application of the devices designed to overcome polarization related problems. In this part some predictions are offered on the values that can take the dispersion due to the polarization in real links. Also a polarization scrambler to be used in systems with optical amplification has been designed, constructed and tested.

Coherent imaging is a promising method in the field of x-ray microscopy allowing for the nondestructive determination of the interior structure of radiation-hard samples with a spatial resolution that is only limited by the fluence on the sample and the scattering strength of the sample. Ultimately, the achievable spatial resolution is limited by the wavelength of the incoming x-ray radiation. Combining coherent imaging with scanning microscopy to a method called ptychography enables one to also probe extended objects. In this method, a sample is scanned through a defined coherent x-ray beam and at each scan point a diffraction pattern is recorded with a diffraction camera located in the far field of the sample. Neighboring illuminated areas must have a certain overlap to guarantee the collection of sufficient information about the object for a subsequent successful and unique computational reconstruction of the object. Modern ptychographic reconstruction algorithms are even able to reconstruct the complex-valued transmission function of the sample and the complex illumination wave field at the same time. Once the 2D transmission function of a sample is known, it is an obvious step forward to combine ptychography with tomographic techniques yielding the 3D internal structure of an object with unprecedented spatial resolution. Here, projections at varying angular positions of the sample are generated via ptychographic scans and are subsequently used for the tomographic reconstruction. In this thesis the development of 3D ptychography is described. It includes the description of the required experimental environment, the numerical implementation of ptychographic phase retrieval and tomographic reconstruction routines, and a detailed analysis of the performance of 3D ptychography using an example of an experiment carried out at beamline P06 of PETRA III at DESY in Hamburg. In that experiment the investigated object was a Mo/UO2 thin film, which is a simplified model for spent nuclear fuel from nuclear power plant reactors. Such models find application in systematic scientific investigations related to the safe disposal of nuclear waste. We determined the three-dimensional interior structure of this sample with an unprecedented spatial resolution of at least 18 nm. The measurement of the fluorescence signal at each scan point of the ptychograms delivers the two- and three-dimensional elemental distribution of the sample with a spatial resolution of 80 nm. Using the fluorescence data, we assigned the chemical element to the area of the corresponding phase shift in the ptychographic reconstruction of the object phase and to the corresponding refractive index decrement in the tomographic reconstruction. The successful demonstration of the feasibility of the 3D ptychography motivates further applications, for instance, in the field of medicine, of material science, and of basic physical research. / Kohärente Bildgebung ist eine vielversprechende Methode der Röntgenmikroskopie. Sie ermöglicht die zerstörungsfreie Bestimmung der inneren Struktur von strahlenharten Untersuchungsobjekten mit einer räumlichen Auflösung, die im Prinzip nur von der integralen Anzahl der Photonen auf der Probe sowie deren Streukraft abhängt. Letztendlich stellt die Wellenlänge der verwendeten Röntgenstrahlung eine Grenze für die erreichbare räumliche Auflösung dar. Die Kombination der kohärenten Bildgebung mit der Rastermikroskopie zur sogenannten Ptychographie eröffnet die Möglichkeit, auch ausgedehnte Objekte mit hoher Auflösung zu untersuchen. Dabei wird die Probe mit einem räumlich begrenzten, kohärenten Röntgenstrahl abgerastert und an jedem Rasterpunkt ein Beugungsbild von einer im Fernfeld platzierten Beugungskamera registriert. Die Beleuchtungen benachbarter Rasterpunkte müssen dabei zu einem bestimmten Prozentsatz überlappen, um genügend Informationen für eine anschließende computergestützte und eindeutige Rekonstruktion des Objektes sicherzustellen. Moderne Rekonstruktionsalgorithmen ermöglichen sogar die gleichzeitige Rekonstruktion der Transmissionsfunktion des Objektes und der Beleuchtungsfunktion des eintreffenden Röntgenstrahls. Die Verknüpfung der Ptychographie mit der Tomographie zur 3D-Ptychographie ist der nahe liegende Schritt, um nun auch die dreidimensionale innere Struktur von Objekten mit hoher räumlicher Auflösung zu bestimmen. Die Projektionen an den verschiedenen Winkelpositionen der Probe werden dabei mittels ptychographischer Abrasterung der Probe erzeugt und anschließend der tomographischen Rekonstruktion zugrunde gelegt. In dieser Arbeit wird die Entwicklung der 3D-Ptychographie beschrieben. Das beinhaltet die Beschreibung der experimentellen Umgebung, der numerischen Implementierung des ptychographischen und des tomographischen Rekonstruktionsalgorithmus als auch eine detaillierte Darstellung der Durchführung der 3D-Ptychographie am Beispiel eines Experiments, welches unter Verwendung des modernen Nanoprobe-Aufbaus des Strahlrohres P06 am PETRA III Synchrotronring des DESY in Hamburg durchgeführt wurde. Als Untersuchungsobjekt diente dabei ein dünner Mo/UO2-Film, der ein vereinfachtes Modell für die in Reaktoren von Atomkraftwerken verbrauchten Brennstäbe darstellt und deshalb im Bereich des Umweltschutzes Anwendung findet. Die dreidimensionale Struktur der Probe wurde mit einer - für diese Methode bisher einmaligen - räumlichen Auflösung von 18 nm bestimmt. Die Messung des von der Probe kommenden Fluoreszenz-Signals an jedem Rasterpunkt der Ptychogramme ermöglichte zusätzlich die Bestimmung der zwei- und dreidimensionalen Elementverteilung innerhalb der Probe mit einer räumlichen Auflösung von 80 nm. Anhand der Fluoreszenzdaten konnte sowohl den Bereichen verschiedener Phasenschübe in den ptychographischen Rekonstruktionen der Objektphase als auch den verschiedenen Werten des Dekrementes des Brechungsindex in der tomographischen Rekonstruktion, das entsprechende chemische Element zugeordnet werden. Die erfolgreiche Demonstration der Durchführbarkeit der 3D-Ptychographie motiviert weitere zukünftige Anwendungen, z. B. auf dem Gebiet der Medizin, der Materialforschung und der physikalischen Grundlagenforschung.

Lung carcinoma is the most prevalent type of cancer in the world, considered to be a relentlessly progressive disease, with dismal mortality rates to patients. Recent advances in targeted therapy hold the premise for the delivery of better, more effective treatments to lung cancer patients, that could significantly enhance their survival rates. Optimizing care delivery through targeted therapies requires the ability to effectively identify and diagnose lung cancer along with identifying the lung cancer cell type specific to each patient, \textit{small cell carcinoma}, \textit{adenocarcinoma}, or \textit{squamous cell carcinoma}. Label free optical imaging techniques such as the \textit{Coherent anti-stokes Raman Scattering microscopy} have the potential to provide physicians with minimally invasive access to lung tumor sites, and thus allow for better cancer diagnosis and sub-typing. To maximize the benefits of such novel imaging techniques in enhancing cancer treatment, the development of new data analysis methods that can rapidly and accurately analyze the new types of data provided through them is essential. Recent studies have gone a long way to achieving those goals but still face some significant bottlenecks hindering the ability to fully exploit the diagnostic potential of CARS images, namely, the streamlining of the diagnosis process was hindered by the lack of ability to automatically detect cancer cells, and the inability to reliably classify them into their respective cell types. More specifically, data analysis methods have thus far been incapable of correctly identifying and differentiating the different non-small cel lung carcinoma cell types, a stringent requirement for optimal therapy delivery. In this study we have addressed the two bottlenecks named above, through designing an image processing framework that is capable of, automatically and accuratly, detecting cancer cells in two and three dimensional CARS images. Moreover, we built upon this capability with a new approach at analyzing the segmented data, that provided significant information about the cancerous tissue and ultimately allowed for the automatic differential classification of non-small cell lung carcinoma cell types, with superb accuracies.

Orthogonal Frequency Division Multiplexing (OFDM) is a multicarrier modulation technique which is robust against multipath fading and very easy to implement in transmitters and receivers using the inverse fast Fourier transform and the fast Fourier transform. A guard interval using cyclic prefix is inserted in each OFDM symbol to avoid the inter-symbol interference. This guard interval should be at least equal to, or longer than the maximum delay spread of the channel to combat against inter-symbol interference properly.<p> In coherent detection, channel estimation is required for the data detection of OFDM systems to equalize the channel effects. One of the popular techniques is to insert pilot tones (reference signals) in OFDM symbols. In conventional method, pilot tones are inserted into every OFDM symbols. Channel capacity is wasted due to the transmission of a large number of pilot tones. To overcome this transmission loss, incoherent data detection is introduced in OFDM systems, where it is not needed to estimate the channel at first. We use differential modulation based incoherent detection in this thesis for the data detection of OFDM systems. Data can be encoded in the relative phase of consecutive OFDM symbols (inter-frame modulation) or in the relative phase of an OFDM symbol in adjacent subcarriers (in-frame modulation). We use higher order differential modulation for in-frame modulation to compare the improvement of bit error rate. It should be noted that the single differential modulation scheme uses only one pilot tone, whereas the double differential uses two pilot tones and so on. Thus overhead due to the extra pilot tones in conventional methods are minimized and the detection delay is reduced. It has been observed that the single differential scheme works better in low SNRs (Signal to Noise Ratios) with low channel taps and the double differential works better at higher SNRs. Simulation results show that higher order differential modulation schemes don¡¯t have any further advantages. For inter-frame modulation, we use single differential modulation where only one OFDM symbol is used as a reference symbol. Except the reference symbol, no other overhead is required. We also perform channel estimation using differential modulation. Channel estimation using differential modulation is very easy and channel coefficients can be estimated very accurately without increasing any computational complexity. Our simulation results show that the mean square channel estimation error is about ¡¼10¡½^(-2) at an SNR of 30 dB for double differential in-frame modulation scheme, whereas channel estimation error is about ¡¼10¡½^(-4) for single differential inter-frame modulation. Incoherent data detection using classical DPSK (Differential Phase Shift Keying) causes an SNR loss of approximately 3 dB compared to coherent detection. But in our method, differential detection can estimate the channel coefficients very accurately and our estimated channel can be used in simple coherent detection to improve the system performance and minimize the SNR loss that happens in conventional method.

<p>An important problem in the analysis of gene expression data is the identification of groups of features that are coherently expressed. For example, one often wishes to know whether a group of genes, clustered because of correlation in one data set, is still highly co-expressed in another data set. For some microarray platforms there are many, relatively short, probes for each gene of interest. In this case, it is possible that a given probe is not measuring its targeted transcript, but rather a different gene with a similar region (called cross-hybridization). Similarly, the incorrect mapping of short nucleotide sequences to a target gene is a common issue related to the young technology producing RNA-Seq data. The expression pattern across samples is a valuable source of information, which can be used to address distinct problems through the application of factor models. Our first study is focused on the identification of the presence/absence status of a gene in a sample. We compare our factor model to state-of-the-art detection methods; the results suggest superior performance of the factor analysis for detecting transcripts. In the second study, we apply factor models to investigate gene modules (groups of coherently expressed genes). Variation in the number of copies of regions of the genome is a well known and important feature of most cancers. Copy number alteration is detected for a group of genes in breast cancer; our goal is to examine this abnormality in the same chromosomal region for other types of tumors (Ovarian, Lung and Brain). In the third application, the expression pattern related to RNA-Seq count data is evaluated through a factor model based on the Poisson distribution. Here, the presence/absence of coherent patterns is closely associated with the number of incorrect read mappings. The final study of this dissertation is dedicated to the analysis of multi-factor models with linear and non-linear structure of interactions between latent factors. The interaction terms can have important implications in the model; they represent relationships between genes which cannot be captured in an ordinary analysis.</p> / Dissertation

A negative index material (NIM), which possesses simultaneously negative permittivity and permeability, is an emerging material that has caught many researchers attention after it was first demonstrated in 2001. It has been shown that electromagnetic waves propagating in NIMs have some remarkable properties such as negative phase velocities and negative refraction and hold enormous promise for applications in imaging and optical communications. This dissertation is centered on investigating the unique aspects of the radiative properties of NIMs. Photon tunneling, which relies on evanescent waves to transfer radiative energy, has important applications in thin-film structures, microscale thermophotovoltaic devices, and scanning thermal microscopes. With multilayer thin-film structures, photon tunneling is shown to be greatly enhanced using NIM layers. The enhancement is attributed to the excitation of surface or bulk polaritons, and depends on the thicknesses of the NIM layers according to the phase matching condition. A new coherent thermal emission source is proposed by pairing a negative permittivity (but positive permeability) layer with a negative permeability (but positive permittivity) layer. The merits of such a coherent thermal emission source are that coherent thermal emission occurs for both s- and p-polarizations, without use of grating structures. Zero power reflectance from an NIM for both polarizations indicates the existence of the Brewster angles for both polarizations under certain conditions. The criteria for the Brewster angle are determined analytically and presented in a regime map. The findings on the unique radiative properties of NIMs may help develop advanced energy conversion devices. Motivated by the recent advancement in scanning probe microscopy, the last part of this dissertation focuses on prediction of the radiation heat transfer between two closely spaced semi-infinite media. The objective is to investigate the dopant concentration of silicon on the near-field radiation heat transfer. It is found that the radiative energy flux can be significantly augmented by using heavily doped silicon for the two media separated at nanometric distances. Large enhancement of radiation heat transfer at the nanoscale may have an impact on the development of near-field thermal probing and nanomanufacturing techniques.

In recent years, the requirement of application such as wireless sensor networks and short-range wireless controllers caused the growing of ZigBee technology. ZigBee is a communication technology developed specifically for short-range, low rate, low-cost wireless transmission.There are some characteristic such as short-range, low rate, low cost, and low power. The ZigBee Aliance group developed the specifications of software, and IEEE 802.15.4 group developed the specifications of hardware. IEEE 802.15.4a impulse radio UWB physical layer is one of the ZigBee physical layers. In our study, we designed a baseband signal processing algorithm meeting the specifications of IEEE 802.15.4a. The data processing flow in transmitter followed the specifications. In receiver, we designed baseband algorithms based-on the non-coherent energy detection scheme. Our algorithm including packet detection, synchronization and demodulation, and considering the implementation of algorithm, reducing the complexity of hardware as possible and improving the efficiency. Finally, the system performance is 3.9dB better than the receiver sensitivity.

This paper studies is considered the problem of coherent re ection of an acoustic plane wave from a rough seabed with a randomly inhomogeneous sediment layer overlying a uniform elastic basement. The randomness of the sound eld is attributable to the rough- ness of the seabed and the sound-speed perturbation in the sediment layer, resulting in a joint rough surface and volume scattering problem. An approach based upon perturbation theory, combined with a derived Green's function for a slab bounded above and below by a uid and an elastic half space, respectively, is employed to obtain an analytic solution for the coherent eld in the sediment layer. Furthermore, a boundary perturbation the- ory developed by Kuperman and Schmidt [22] is applied to treat the problem of rough surface scattering. A linear system is then established to facilitate the computation of the coherent re ection eld. The coherent re ection coe cients for various surface roughness, sediment randomness, frequency, sediment thickness, and basement elasticity have been generated numerically and analyzed. It was found that the higher/larger size of surface and/or medium randomness, frequency, thickness, and shear-wave speed, the lower the coherent re ection. Physical interpretations of the various results are provided.

As the demand for high performance small electronic devices has increased, heat removal from these devices for space use is approaching critical limits. A heat pipe is a promising device to enhance the heat removal performance due to the phase change phenomena for space thermal management system. Even though a heat pipe has a big potential to remove the thermal energy from a high heat flux source, the heat removal performance of heat pipes cannot be predicted well since the first principle of evaporation has not been established. The purpose of this study is to establish a method to apply the evaporation model based on the statistical rate theory for engineering application including vapor-liquid-structure intermolecular effect. The evaporation model is applied to the heat pipe performance analysis through a pressure balance and an energy balance in the loop heat pipe.

In this work, interference and coherence phenomena, appearing in atomic and molecular ensembles interacting with coherent light sources, as electromagnetically induced transparency (EIT), coherent population trapping (CPT), and slow group velocity of light are investigated. The goal of the project is to make the steps towards various applications of these phenomena, first, by studying them in solid media (which are the most advantageous for applications), second, by suggesting some novel applications such as CPT-based plasma diagnostics, and realization of new types of solid-state lasers (based on suppression of excited-state absorption via EIT). The third goal of the project is extension of coherence and interference effects well-known in optics to the gamma-ray range of frequencies and, correspondingly, from atomic to nuclear transitions. A particular technique of chirped pulse compression applied to M??ossbauer transitions is considered and the possibility of compression of M??ossbauer radiation into ultrashort gamma-ray pulses is analyzed. The theoretical treatment of the interference and coherence effects is based on the semiclassical description of atom-light interaction, which is sufficient for correct analysis of the phenomena considered here. Coherent media are considered in two-, three-, and four-level approximations while their interaction with light is studied both analytically and numerically using the Maxwell-Bloch set of equations.