Properties of seawater (partial pressure of carbon dioxide (pCO2)) from a ProOceanus CO2-Pro sensor mounted on the continuous surface water sampling system during the Tara Oceans expedition 2009-2013

The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set provides continuous measurements of partial pressure of carbon dioxide (pCO2), using a ProOceanus CO2-Pro instrument mounted on the flowthrough system. This automatic sensor is fitted with an equilibrator made of gas permeable silicone membrane and an internal detection loop with a non-dispersive infrared detector of PPSystems SBA-4 CO2 analyzer. A zero-CO2 baseline is provided for the subsequent measurements circulating the internal gas through a CO2 absorption chamber containing soda lime or Ascarite. The frequency of this automatic zero point calibration was set to be 24 hours. All data recorded during zeroing processes were discarded with the 15-minute data after each calibration. The output of CO2-Pro is the mole fraction of CO2 in the measured water and the pCO2 is obtained using the measured total pressure of the internal wet gas. The fugacity of CO2 (fCO2) in the surface seawater, whose difference with the atmospheric CO2 fugacity is proportional to the air-sea CO2 fluxes, is obtained by correcting the pCO2 for non-ideal CO2 gas concentration according to Weiss (1974). The fCO2 computed using CO2-Pro measurements was corrected to the sea surface condition by considering the temperature effect on fCO2 (Takahashi et al., 1993). The surface seawater observations that were initially estimated with a 15 seconds frequency were averaged every 5-min cycle. The performance of CO2-Pro was adjusted by comparing the sensor outputs against the thermodynamic carbonate calculation of pCO2 using the carbonic system constants of Millero et al. (2006) from the determinations of total inorganic carbon (CT ) and total alkalinity (AT ) in discrete samples collected at sea surface. AT was determined using an automated open cell potentiometric titration (Haraldsson et al. 1997). CT was determined with an automated coulometric titration (Johnson et al. 1985; 1987), using the MIDSOMMA system (Mintrop, 2005). fCO2 data are flagged according to the WOCE guidelines following Pierrot et al. (2009) identifying recommended values and questionable measurements giving additional information about the reasons of the questionability.

Advances in the Simultaneous Multiple Surface optical design method for imaging and non-imaging applications

Classical imaging optics has been developed over centuries in many areas, such as its paraxial imaging theory and practical design methods like multi-parametric optimization techniques. Although these imaging optical design methods can provide elegant solutions to many traditional optical problems, there are more and more new design problems, like solar concentrator, illumination system, ultra-compact camera, etc., that require maximum energy transfer efficiency, or ultra-compact optical structure. These problems do not have simple solutions from classical imaging design methods, because not only paraxial rays, but also non-paraxial rays should be well considered in the design process. Non-imaging optics is a newly developed optical discipline, which does not aim to form images, but to maximize energy transfer efficiency. One important concept developed from non-imaging optics is the “edge-ray principle”, which states that the energy flow contained in a bundle of rays will be transferred to the target, if all its edge rays are transferred to the target. Based on that concept, many CPC solar concentrators have been developed with efficiency close to the thermodynamic limit. When more than one bundle of edge-rays needs to be considered in the design, one way to obtain solutions is to use SMS method. SMS stands for Simultaneous Multiple Surface, which means several optical surfaces are constructed simultaneously. The SMS method was developed as a design method in Non-imaging optics during the 90s. The method can be considered as an extension to the Cartesian Oval calculation. In the traditional Cartesian Oval calculation, one optical surface is built to transform an input wave-front to an out-put wave-front. The SMS method however, is dedicated to solve more than 1 wave-fronts transformation problem. In the beginning, only 2 input wave-fronts and 2 output wave-fronts transformation problem was considered in the SMS design process for rotational optical systems or free-form optical systems. Usually “SMS 2D” method stands for the SMS procedure developed for rotational optical system, and “SMS 3D” method for the procedure for free-form optical system. Although the SMS method was originally employed in non-imaging optical system designs, it has been found during this thesis that with the improved capability to design more surfaces and control more input and output wave-fronts, the SMS method can also be applied to imaging system designs and possesses great advantage over traditional design methods. In this thesis, one of the main goals to achieve is to further develop the existing SMS-2D method to design with more surfaces and improve the stability of the SMS-2D and SMS-3D algorithms, so that further optimization process can be combined with SMS algorithms. The benefits of SMS plus optimization strategy over traditional optimization strategy will be explained in details for both rotational and free-form imaging optical system designs. Another main goal is to develop novel design concepts and methods suitable for challenging non-imaging applications, e.g. solar concentrator and solar tracker. This thesis comprises 9 chapters and can be grouped into two parts: the first part (chapter 2-5) contains research works in the imaging field, and the second part (chapter 6-8) contains works in the non-imaging field. In the first chapter, an introduction to basic imaging and non-imaging design concepts and theories is given. Chapter 2 presents a basic SMS-2D imaging design procedure using meridian rays. In this chapter, we will set the imaging design problem from the SMS point of view, and try to solve the problem numerically. The stability of this SMS-2D design procedure will also be discussed. The design concepts and procedures developed in this chapter lay the path for further improvement. Chapter 3 presents two improved SMS 3 surfaces’ design procedures using meridian rays (SMS-3M) and skew rays (SMS-1M2S) respectively. The major improvement has been made to the central segments selections, so that the whole SMS procedures become more stable compared to procedures described in Chapter 2. Since these two algorithms represent two types of phase space sampling, their image forming capabilities are compared in a simple objective design. Chapter 4 deals with an ultra-compact SWIR camera design with the SMS-3M method. The difficulties in this wide band camera design is how to maintain high image quality meanwhile reduce the overall system length. This interesting camera design provides a playground for the classical design method and SMS design methods. We will show designs and optical performance from both classical design method and the SMS design method. Tolerance study is also given as the end of the chapter. Chapter 5 develops a two-stage SMS-3D based optimization strategy for a 2 freeform mirrors imaging system. In the first optimization phase, the SMS-3D method is integrated into the optimization process to construct the two mirrors in an accurate way, drastically reducing the unknown parameters to only few system configuration parameters. In the second optimization phase, previous optimized mirrors are parameterized into Qbfs type polynomials and set up in code V. Code V optimization results demonstrates the effectiveness of this design strategy in this 2-mirror system design. Chapter 6 shows an etendue-squeezing condenser optics, which were prepared for the 2010 IODC illumination contest. This interesting design employs many non-imaging techniques such as the SMS method, etendue-squeezing tessellation, and groove surface design. This device has theoretical efficiency limit as high as 91.9%. Chapter 7 presents a freeform mirror-type solar concentrator with uniform irradiance on the solar cell. Traditional parabolic mirror concentrator has many drawbacks like hot-pot irradiance on the center of the cell, insufficient use of active cell area due to its rotational irradiance pattern and small acceptance angle. In order to conquer these limitations, a novel irradiance homogenization concept is developed, which lead to a free-form mirror design. Simulation results show that the free-form mirror reflector has rectangular irradiance pattern, uniform irradiance distribution and large acceptance angle, which confirm the viability of the design concept. Chapter 8 presents a novel beam-steering array optics design strategy. The goal of the design is to track large angle parallel rays by only moving optical arrays laterally, and convert it to small angle parallel output rays. The design concept is developed as an extended SMS method. Potential applications of this beam-steering device are: skylights to provide steerable natural illumination, building integrated CPV systems, and steerable LED illumination. Conclusion and future lines of work are given in Chapter 9. Resumen La óptica de formación de imagen clásica se ha ido desarrollando durante siglos, dando lugar tanto a la teoría de óptica paraxial y los métodos de diseño prácticos como a técnicas de optimización multiparamétricas. Aunque estos métodos de diseño óptico para formación de imagen puede aportar soluciones elegantes a muchos problemas convencionales, siguen apareciendo nuevos problemas de diseño óptico, concentradores solares, sistemas de iluminación, cámaras ultracompactas, etc. que requieren máxima transferencia de energía o dimensiones ultracompactas. Este tipo de problemas no se pueden resolver fácilmente con métodos clásicos de diseño porque durante el proceso de diseño no solamente se deben considerar los rayos paraxiales sino también los rayos no paraxiales. La óptica anidólica o no formadora de imagen es una disciplina que ha evolucionado en gran medida recientemente. Su objetivo no es formar imagen, es maximazar la eficiencia de transferencia de energía. Un concepto importante de la óptica anidólica son los “rayos marginales”, que se pueden utilizar para el diseño de sistemas ya que si todos los rayos marginales llegan a nuestra área del receptor, todos los rayos interiores también llegarán al receptor. Haciendo uso de este principio, se han diseñado muchos concentradores solares que funcionan cerca del límite teórico que marca la termodinámica. Cuando consideramos más de un haz de rayos marginales en nuestro diseño, una posible solución es usar el método SMS (Simultaneous Multiple Surface), el cuál diseña simultáneamente varias superficies ópticas. El SMS nació como un método de diseño para óptica anidólica durante los años 90. El método puede ser considerado como una extensión del cálculo del óvalo cartesiano. En el método del óvalo cartesiano convencional, se calcula una superficie para transformar un frente de onda entrante a otro frente de onda saliente. El método SMS permite transformar varios frentes de onda de entrada en frentes de onda de salida. Inicialmente, sólo era posible transformar dos frentes de onda con dos superficies con simetría de rotación y sin simetría de rotación, pero esta limitación ha sido superada recientemente. Nos referimos a “SMS 2D” como el método orientado a construir superficies con simetría de rotación y llamamos “SMS 3D” al método para construir superficies sin simetría de rotación o free-form. Aunque el método originalmente fue aplicado en el diseño de sistemas anidólicos, se ha observado que gracias a su capacidad para diseñar más superficies y controlar más frentes de onda de entrada y de salida, el SMS también es posible aplicarlo a sistemas de formación de imagen proporcionando una gran ventaja sobre los métodos de diseño tradicionales. Uno de los principales objetivos de la presente tesis es extender el método SMS-2D para permitir el diseño de sistemas con mayor número de superficies y mejorar la estabilidad de los algoritmos del SMS-2D y SMS-3D, haciendo posible combinar la optimización con los algoritmos. Los beneficios de combinar SMS y optimización comparado con el proceso de optimización tradicional se explican en detalle para sistemas con simetría de rotación y sin simetría de rotación. Otro objetivo importante de la tesis es el desarrollo de nuevos conceptos de diseño y nuevos métodos en el área de la concentración solar fotovoltaica. La tesis está estructurada en 9 capítulos que están agrupados en dos partes: la primera de ellas (capítulos 2-5) se centra en la óptica formadora de imagen mientras que en la segunda parte (capítulos 6-8) se presenta el trabajo del área de la óptica anidólica. El primer capítulo consta de una breve introducción de los conceptos básicos de la óptica anidólica y la óptica en formación de imagen. El capítulo 2 describe un proceso de diseño SMS-2D sencillo basado en los rayos meridianos. En este capítulo se presenta el problema de diseñar un sistema formador de imagen desde el punto de vista del SMS y se intenta obtener una solución de manera numérica. La estabilidad de este proceso se analiza con detalle. Los conceptos de diseño y los algoritmos desarrollados en este capítulo sientan la base sobre la cual se realizarán mejoras. El capítulo 3 presenta dos procedimientos para el diseño de un sistema con 3 superficies SMS, el primero basado en rayos meridianos (SMS-3M) y el segundo basado en rayos oblicuos (SMS-1M2S). La mejora más destacable recae en la selección de los segmentos centrales, que hacen más estable todo el proceso de diseño comparado con el presentado en el capítulo 2. Estos dos algoritmos representan dos tipos de muestreo del espacio de fases, su capacidad para formar imagen se compara diseñando un objetivo simple con cada uno de ellos. En el capítulo 4 se presenta un diseño ultra-compacto de una cámara SWIR diseñada usando el método SMS-3M. La dificultad del diseño de esta cámara de espectro ancho radica en mantener una alta calidad de imagen y al mismo tiempo reducir drásticamente sus dimensiones. Esta cámara es muy interesante para comparar el método de diseño clásico y el método de SMS. En este capítulo se presentan ambos diseños y se analizan sus características ópticas. En el capítulo 5 se describe la estrategia de optimización basada en el método SMS-3D. El método SMS-3D calcula las superficies ópticas de manera precisa, dejando sólo unos pocos parámetros libres para decidir la configuración del sistema. Modificando el valor de estos parámetros se genera cada vez mediante SMS-3D un sistema completo diferente. La optimización se lleva a cabo variando los mencionados parámetros y analizando el sistema generado. Los resultados muestran que esta estrategia de diseño es muy eficaz y eficiente para un sistema formado por dos espejos. En el capítulo 6 se describe un sistema de compresión de la Etendue, que fue presentado en el concurso de iluminación del IODC en 2010. Este interesante diseño hace uso de técnicas propias de la óptica anidólica, como el método SMS, el teselado de las lentes y el diseño mediante grooves. Este dispositivo tiene un límite teórica en la eficiencia del 91.9%. El capítulo 7 presenta un concentrador solar basado en un espejo free-form con irradiancia uniforme sobre la célula. Los concentradores parabólicos tienen numerosas desventajas como los puntos calientes en la zona central de la célula, uso no eficiente del área de la célula al ser ésta cuadrada y además tienen ángulos de aceptancia de reducido. Para poder superar estas limitaciones se propone un novedoso concepto de homogeneización de la irrandancia que se materializa en un diseño con espejo free-form. El análisis mediante simulación demuestra que la irradiancia es homogénea en una región rectangular y con mayor ángulo de aceptancia, lo que confirma la viabilidad del concepto de diseño. En el capítulo 8 se presenta un novedoso concepto para el diseño de sistemas afocales dinámicos. El objetivo del diseño es realizar un sistema cuyo haz de rayos de entrada pueda llegar con ángulos entre ±45º mientras que el haz de rayos a la salida sea siempre perpendicular al sistema, variando únicamente la posición de los elementos ópticos lateralmente. Las aplicaciones potenciales de este dispositivo son varias: tragaluces que proporcionan iluminación natural, sistemas de concentración fotovoltaica integrados en los edificios o iluminación direccionable con LEDs. Finalmente, el último capítulo contiene las conclusiones y las líneas de investigación futura.

Benchmarking of calculation schemes in Apollo2 and COBAYA3 for VVER lattices

This paper presents solutions of the NURISP VVER lattice benchmark using APOLLO2, TRIPOLI4 and COBAYA3 pin-by-pin. The main objective is to validate MOC based calculation schemes for pin-by-pin cross-section generation with APOLLO2 against TRIPOLI4 reference results. A specific objective is to test the APOLLO2 generated cross-sections and interface discontinuity factors in COBAYA3 pin-by-pin calculations with unstructured mesh. The VVER-1000 core consists of large hexagonal assemblies with 2mm inter-assembly water gaps which require the use of unstructured meshes in the pin-by-pin core simulators. The considered 2D benchmark problems include 19-pin clusters, fuel assemblies and 7-assembly clusters. APOLLO2 calculation schemes with the step characteristic method (MOC) and the higher-order Linear Surface MOC have been tested. The comparison of APOLLO2 vs.TRIPOLI4 results shows a very close agreement. The 3D lattice solver in COBAYA3 uses transport corrected multi-group diffusion approximation with interface discontinuity factors of GET or Black Box Homogenization type. The COBAYA3 pin-by-pin results in 2, 4 and 8 energy groups are close to the reference solutions when using side-dependent interface discontinuity factors.

Calculation of the spatial distribution of photovoltaic field by arbitrary 2D ilumination patterns en LiNbO3; application to photovoltaic particle trapping.

Patterns of evanescent photovoltaic field induced by illumination on a surface of lithium niobate (LN) have been calculated and compared with the experimental patterns of nano- and microparticles trapped by dielectrophoretic forces. A tool for this calculation has been developed. Calculo de distribución espacial de campo por efecto fotovoltaico con patrones arbitrarios de iluminación, en LiNbO3

Calculation of dielectrophoretic potential generated under illumination patterns on x- and z-cut LiNbO3 : application to photovoltaic particle trapping

The dielectrophoretic potential generated near the surface of a z-cut LiNbO3 by photovoltaic charge transport has been calculated for first time. The procedure and results are compared with the ones corresponding to x-cut. Diferences in the position, sharpness and time evolution are reported, and their implication on particle trapping are discussed.

Different approaches to grounding resistance. Calculation for thin wire structures at low frequency energization

The present paper deals with the calculation of grounding resistance of an electrode composed of thin wires, that we consider here as perfect electric conductors (PEC) e.g. with null internal resistance, when buried in a soil of uniform resistivity. The potential profile at the ground surface is also calculated when the electrode is energized with low frequency current. The classic treatment by using leakage currents, called Charge Simulated Method (CSM), is compared with that using a set of steady currents along the axis of the wires, here called the Longitudinal Currents Method (LCM), to solve the Maxwell equations. The method of moments is applied to obtain a numerical approximation of the solution by using rectangular basis functions. Both methods are applied to two types of electrodes and the results are also compared with those obtained using a thirth approach, the Average Potential Method (APM), later described in the text. From the analysis performed, we can estimate a value of the error in the determination of grounding resistance as a function of the number of segments in which the electrodes are divided.

Evaluation of the surface free energy of plant surfaces: toward standardizing the procedure

Plant surfaces have been found to have a major chemical and physical heterogeneity and play a key protecting role against multiple stress factors. During the last decade, there is a raising interest in examining plant surface properties for the development of biomimetic materials. Contact angle measurement of different liquids is a common tool for characterizing synthetic materials, which is just beginning to be applied to plant surfaces. However, some studies performed with polymers and other materials showed that for the same surface, different surface free energy values may be obtained depending on the number and nature of the test liquids analyzed, materials' properties, and surface free energy calculation methods employed. For 3 rough and 3 rather smooth plant materials, we calculated their surface free energy using 2 or 3 test liquids and 3 different calculation methods. Regardless of the degree of surface roughness, the methods based on 2 test liquids often led to the under- or over-estimation of surface free energies as compared to the results derived from the 3-Liquids method. Given the major chemical and structural diversity of plant surfaces, it is concluded that 3 different liquids must be considered for characterizing materials of unknown physico-chemical properties, which may significantly differ in terms of polar and dispersive interactions. Since there are just few surface free energy data of plant surfaces with the aim of standardizing the calculation procedure and interpretation of the results among for instance, different species, organs, or phenological states, we suggest the use of 3 liquids and the mean surface tension values provided in this study.

Pattern formation of parametrically driven surface waves induced by vibration

Esta tesis se centra en la generación de ondas superficiales subarmónicas en fluidos sometidos a vibración forzada en el régimen gravitatorio capilar con líquidos de baja viscosidad. Tres problemas diferentes han sido estudiados: un contenedor rectangular con vibración horizontal, la misma geometría pero con una combinación de vibración vertical y horizontal y un obstáculo completamente sumergido vibrado verticalmente en un contenedor grande. Se deriva una ecuación de amplitud desde primeros principios para describir las ondas subarmónicas con forzamiento parámetrico inducido por la vibración. La ecuación es bidimensional mientras que el problema original es tridimensional y admite un forzamiento espacial no uniforme. Usando esta ecuación los tres sistemas han sido analizados, centrándose en calcular la amplitud crítica, la orientación de los patrones y el carácter temporal de los patrones espaciotemporales, que pueden ser estrictamente subarmónicos o cuasiperiodicos con una frecuencia de modulación temporal. La dependencia con los parámetros adimensionales también se considera. La teoría será comparada con los experimentos disponibles en la literatura. Abstract This thesis focus on the generation of subharmonic surface waves on fluids subject to forced vibration in the gravity-capillary regime with liquids of small viscosity. Three different problems have been considered: a rectangular container under horizontal vibration; the same geometry but under a combination of horizontal and vertical vibration; and a fully submerged vertically vibrated obstacle in a large container. An amplitude equation is derived from first principles that fairly precisely describes the subharmonic surfaces waves parametrically driven by vibration. That equation is two dimensional while the underlying problem is three-dimensional and permits spatially nonuniform forcing. Using this equation, the three systems have been analyzed, focusing on the calculation of the threshold amplitude, the pattern orientation, and the temporal character of the spatio-temporal patterns, which can be either strictly subharmonic or quasi-periodic, showing an additional modulation frequency. Dependence on the non-dimensional parameters is also considered. The theory is compared with the experiments available in the literature.

Negative electrostatic surface potential of protein sites specific for anionic ligands.

Determination of the crystal structure of an "open" unliganded active mutant (T141D) form of the Escherichia coli phosphate receptor for active transport has allowed calculation of the electrostatic surface potential for it and two other comparably modeled receptor structures (wild type and D137N). A discovery of considerable implication is the intensely negative potential of the phosphate-binding cleft. We report similar findings for a sulfate transport receptor, a DNA-binding protein, and, even more dramatically, redox proteins. Evidently, for proteins such as these, which rely almost exclusively on hydrogen bonding for anion interactions and electrostatic balance, a noncomplementary surface potential is not a barrier to binding. Moreover, experimental results show that the exquisite specificity and high affinity of the phosphate and sulfate receptors for unions are insensitive to modulations of charge potential, but extremely sensitive to conditions that leave a hydrogen bond donor or acceptor unpaired.

Real-time 3D semi-local surface patch extraction using GPGPU

Feature vectors can be anything from simple surface normals to more complex feature descriptors. Feature extraction is important to solve various computer vision problems: e.g. registration, object recognition and scene understanding. Most of these techniques cannot be computed online due to their complexity and the context where they are applied. Therefore, computing these features in real-time for many points in the scene is impossible. In this work, a hardware-based implementation of 3D feature extraction and 3D object recognition is proposed to accelerate these methods and therefore the entire pipeline of RGBD based computer vision systems where such features are typically used. The use of a GPU as a general purpose processor can achieve considerable speed-ups compared with a CPU implementation. In this work, advantageous results are obtained using the GPU to accelerate the computation of a 3D descriptor based on the calculation of 3D semi-local surface patches of partial views. This allows descriptor computation at several points of a scene in real-time. Benefits of the accelerated descriptor have been demonstrated in object recognition tasks. Source code will be made publicly available as contribution to the Open Source Point Cloud Library.

Calculation of paleoproductivity during the Eocene-Oligocene transition of ODP Site 113-689

High-resolution records of carbon and oxygen isotopes and benthic foraminiferal accumulation rates for the Eocene-Oligocene section at Ocean Drilling Program Site 689 (Maud Rise, Weddell Sea; paleodepth about 1500 m) were used to infer variations in paleoproductivity in relation to changes in climate and ventilation of the deeper-water column. The benthic foraminiferal abundance and isotope records show short-term fluctuations at periodicities of 100 and 400 ka, implying orbitally driven climatic variations. Both records suggest that intermediate-depth water chemistry and primary productivity changed in response to climate. During the Eocene, productivity increased during cold periods and during cold-to-warm transitions, possibly as a result of increased upwelling of nutrient-rich waters. In the Oligocene, in contrast, productivity maxima occurred during intervals of low delta18O values (presumably warmer periods), when a proto-polar front moved to the south of the location of Site 689. This profound transition in climate-productivity patterns occurred around 37 Ma, coeval with rapid changes toward increasing variability of the oxygen and carbon isotope and benthic abundance records and toward larger-amplitude delta18O fluctuations. Therefore, we infer that, at this time, temperature fluctuations increased and a proto-polar front formed in conjunction with the first distinct pulsations in size of the Antarctic ice sheet. We speculate that this major change might have resulted from an initial opening of the Drake Passage at 37 Ma, at least for surface- and intermediate-water circulation.

(Table 1) Age determination of surface sediment samples from the North Atlantic

Most seafloor sediments are dated with radiocarbon, and the sediment is assumed to be zero-age (modern) when the signal of atmospheric testing of nuclear weapons is present (Fraction modern (Fm) > 1). Using a simple mass balance, we show that even with Fm > 1, half of the planktonic foraminifera at the seafloor can be centuries old, because of bioturbation. This calculation, and data from four core sites in the western North Atlantic indicate that, first, during some part of the Little Ice Age (LIA) there may have been more Antarctic Bottom Water than today in the deep western North Atlantic. Alternatively, bioturbation may have introduced much older benthic foraminifera into surface sediments. Second, paleo-based warming of Sargasso Sea surface waters since the LIA must lag the actual warming because of bioturbation of older and colder foraminifera.