Satellite-detected fluorescence reveals global physiology of ocean phytoplankton

Phytoplankton photosynthesis links global ocean biology and climate-driven fluctuations in the physical environment. These interactions are largely expressed through changes in phytoplankton physiology, but physiological status has proven extremely challenging to characterize globally. Phytoplankton fluorescence does provide a rich source of physiological information long exploited in laboratory and field studies, and is now observed from space. Here we evaluate the physiological underpinnings of global variations in satellite-based phytoplankton chlorophyll fluorescence. The three dominant factors influencing fluorescence distributions are chlorophyll concentration, pigment packaging effects on light absorption, and light-dependent energy-quenching processes. After accounting for these three factors, resultant global distributions of quenching-corrected fluorescence quantum yields reveal a striking consistency with anticipated patterns of iron availability. High fluorescence quantum yields are typically found in low iron waters, while low quantum yields dominate regions where other environmental factors are most limiting to phytoplankton growth. Specific properties of photosynthetic membranes are discussed that provide a mechanistic view linking iron stress to satellite-detected fluorescence. Our results present satellite-based fluorescence as a valuable tool for evaluating nutrient stress predictions in ocean ecosystem models and give the first synoptic observational evidence that iron plays an important role in seasonal phytoplankton dynamics of the Indian Ocean. Satellite fluorescence may also provide a path for monitoring climate-phytoplankton physiology interactions and improving descriptions of phytoplankton light use efficiencies in ocean productivity models.

The use of Raman microscopy to determine and localize vitamin E in biological samples

Alpha-tocopherol (aT), the predominant form of vitamin E in mammals, is thought to prevent oxidation of polyunsaturated fatty acids. In the lung, aT is perceived to be accumulated in alveolar type II cells and secreted together with surfactant into the epithelial lining fluid. Conventionally, determination of aT and related compounds requires extraction with organic solvents. This study describes a new method to determine and image the distribution of aT and related compounds within cells and tissue sections using the light-scattering technique of Raman microscopy to enable high spatial as well as spectral resolution. This study compared the nondestructive analysis by Raman microscopy of vitamin E, in particular aT, in biological samples with data obtained using conventional HPLC analysis. Raman spectra were acquired at spatial resolutions of 2-0.8 microm. Multivariate analysis techniques were used for analyses and construction of corresponding maps showing the distribution of aT, alpha-tocopherol quinone (aTQ), and other constituents (hemes, proteins, DNA, and surfactant lipids). A combination of images enabled identification of colocalized constituents (heme/aTQ and aT/surfactant lipids). Our data demonstrate the ability of Raman microscopy to discriminate between different tocopherols and oxidation products in biological specimens without sample destruction. By enabling the visualization of lipid-protein interactions, Raman microscopy offers a novel method of investigating biological characterization of lipid-soluble compounds, including those that may be embedded in biological membranes such as aT.

Atomistic Insights into Rhodopsin Activation from a Dynamic Model

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.

Monte Carlo calculations of quantum yield in inhomogeneous PtSi/p-Si Schottky barriers

Monte Carlo calculations of quantum yield in PtSi/p-Si infrared detectors are carried out taking into account the presence of a spatially distributed barrier potential. In the 1-4 mu m wavelength range it is found that the spatial inhomogeneity of the barrier has no significant effect on the overall device photoresponse. However, above lambda = 4.0 mu m and particularly as the cut-off wavelength (lambda approximate to 5.5 mu m) is approached, these calculations reveal a difference between the homogeneous and inhomogeneous barrier photoresponse which becomes increasingly significant and exceeds 50% at lambda = 5.3 mu m. It is, in fact, the inhomogeneous barrier which displays an increased photoyield, a feature that is confirmed by approximate analytical calculations assuming a symmetric Gaussian spatial distribution of the barrier. Furthermore, the importance of the silicide layer thickness in optimizing device efficiency is underlined as a trade-off between maximizing light absorption in the silicide layer and optimizing the internal yield. The results presented here address important features which determine the photoyield of PtSi/Si Schottky diodes at energies below the Si absorption edge and just above the Schottky barrier height in particular.

Multiphysics Simulation of Nanostructured Semiconductor Devices

Thesis (Ph.D.)--University of Washington, 2013

Nanotech thin film photovoltaics

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia de Electrónica e Telecomunicações

Fonctionnalisation covalente des nanotubes de carbone : propriétés, réversibilité et applications dans le domaine de l'électronique

Le sujet général de cette thèse est l’étude de la fonctionnalisation covalente des nanotubes de carbone (CNT) et son application en électronique. Premièrement, une introduction au sujet est présentée. Elle discute des propriétés des CNT, des différentes sortes de fonctionnalisation covalente ainsi que des principales techniques de caractérisation utilisées au cours de la thèse. Deuxièmement, les répercussions de la fonctionnalisation covalente sur les propriétés des nanotubes de carbone monoparoi (SWNT) sont étudiées. Deux types de fonctionnalisation sont regardés, soit le greffage de groupements phényles et le greffage de groupements dichlorométhylènes. Une diminution de l’absorption optique des SWNT dans le domaine du visible-proche infrarouge est observée ainsi qu’une modification de leur spectre Raman. De plus, pour les dérivés phényles, une importante diminution de la conductance des nanotubes est enregistrée. Troisièmement, la réversibilité de ces deux fonctionnalisations est examinée. Il est montré qu’un recuit permet de résorber les modifications structurales et retrouver, en majorité, les propriétés originales des SWNT. La température de défonctionnalisation varie selon le type de greffons, mais ne semble pas affectée par le diamètre des nanotubes (diamètre examinés : dérivés phényles, Ømoyen= 0,81 nm, 0,93 nm et 1,3 nm; dérivés dichlorométhylènes, Ømoyen = 0,81 nm et 0,93 nm). Quatrièmement, la polyvalence et la réversibilité de la fonctionnalisation covalente par des unités phényles sont exploitées afin de développer une méthode d’assemblage de réseaux de SWNT. Celle-ci, basée sur l’établissement de forces électrostatiques entre les greffons des SWNT et le substrat, est à la fois efficace et sélective quant à l’emplacement des SWNT sur le substrat. Son application à la fabrication de dispositifs électroniques est réalisée. Finalement, la fonctionnalisation covalente par des groupements phényles est appliquée aux nanotubes de carbone à double paroi (DWNT). Une étude spectroscopique montre que cette dernière s’effectue exclusivement sur la paroi externe. De plus, il est démontré que la signature électrique des DWNT avant et après la fonctionnalisation par des groupements phényles est caractéristique de l’agencement nanotube interne@ nanotube externe.

Polymères de coordination et éponge cristalline : de nouveaux matériaux pour la conversion de l’énergie solaire et la résolution de la structure cristalline de composés huileux.

Le premier volet de ce travail portera sur l’expérience acquise lors d’un stage d’étude à Tokyo, au Japon, dans le groupe de recherche du Pr. Makoto Fujita, une sommité d’envergure internationale dans le domaine de l’auto-assemblage. En continuité avec les plus récents travaux du Pr. Fujita, des systèmes poreux auto-assemblés présentant des cavités fonctionnalisées ont été développés dans le but d’encapsuler des acides gras afin d’en déterminer la structure cristalline. Ces éponges ont été caractérisées par des techniques courantes telles que la spectroscopie à résonance magnétique nucléaire 1H, 13C{1H} et Cosy, la spectrométrie de masse, l’analyse élémentaire, la microscopie optique infrarouge ainsi que la diffraction des rayons X. Une autre approche employée pour obtenir de meilleures propriétés spectroscopiques fut la synthèse de dendrimères métalliques de génération 0. Un nouveau ligand de type 1,3,5-triazine a été synthétisé par une réaction typique de cyclisation de nitrile en présence catalytique d’hydrure de sodium. Des espèces mono-, bis- et trinucléaire de Ru(II) furent synthétisés ainsi que deux espèces hétérométalliques de Ru(II)/Pt(II) et de Ru(II)/Os(II). Tous les complexes obtenus furent caractérisés par spectroscopie à résonance magnétique nucléaire (1H, 13C{1H} et Cosy) à l’état liquide, par spectroscopie de masse à haute résolution et par analyse élémentaire. La génération de dihydrogène à partir de l’espèce hétérométallique a été étudiée. Les propriétés optiques et électroniques ont été analysées par spectroscopie UV-Vis, par analyse de la luminescence, du temps de vie de luminescence, par des analyses de rendement quantique ainsi que par des analyses de voltampérométrie cyclique à balayage. Finalement, dans le but d’améliorer les propriétés spectroscopiques d’absorption de complexes métalliques, nous avons synthétisé une série de polymères homo- et hétérométalliques, intégrant des ligands de type bis(2,2’:6,2’’-terpyridine). Les complexes générés furent caractérisés par diverses techniques tel que la spectroscopie à résonance magnétique nucléaire (1H, 13C{1H} et Cosy) à l’état liquide, par spectroscopie de masse à haute résolution ainsi que par analyse élémentaire. Les propriétés optiques et électroniques ont été analysées par spectroscopie UV-Vis, par analyse de la luminescence, du temps de vie de luminescence, par des analyses de rendement quantique ainsi que par des analyses de voltampérométrie cyclique à balayage.

Studies on Chemical Bath Deposited Semiconducting Copper Selenide and Iron Sulfide Thin Films Useful For Photovoltaic Applications

Chemical bath deposition (CBD)is one of the simplest, very convient and probably the cheapest method for thin film preparation. Photovoltaic is the cleanest and the most efficient mode of conversion of energy to electrical power. Silicon is the most popular material in this field. The present study on chemical bath deposited semiconducting copper selenide and iron sulfide thin films useful for photovoltaic applications. Semiconducting thin films prepared by chemical deposition find applications as photo detectors, solar control coatings and solar cells. Copper selenide is a p-type semiconductor that finds application in photovolitics. Several heterojunction systems such as Cu2-xSe/ZnSe (for injection electro luminescence), Cu2Se/AgInSe2 and Cu2Se/Si (for photodiodes), Cu2-xSe/CdS, Cu2-xSe/CdSe, CuxSe/InP and Cu2-xSe/Si for solar cells are reported. A maximum efficiency of 8.3% was achieved for the Cu2-xSe/Si cell, various preparation techniques are used for copper selenide like vacuum evaporation, direct reaction, electrodeposition and CBD. Instability of the as-prepared films was investigation and is accounted as mainly due to deviation from stoichiometry and the formation of iron oxide impurity. A sulphur annealing chamber was designed and fabricated for this work. These samples wee also analysed using optical absorption technique, XPS (X-ray Photoelectron Spectroscopy) and XRD.(X-Ray Diffraction).The pyrite films obtained by CBD technique showed amorphous nature and the electrical studies carried out showed the films to be of high resistive nature. Future work possible in the material of iron pyrite includes sulphur annealing of the non-stochiometric iron pyrite CBD thin films in the absence of atmospheric oxygen

Atomistic-continuum modeling of ultrafast laser-induced melting of silicon targets

In this work, we present an atomistic-continuum model for simulations of ultrafast laser-induced melting processes in semiconductors on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with MD method on the atomic level, whereas the laser light absorption, strong generated electron-phonon nonequilibrium, fast heat conduction, and photo-excited free carrier diffusion are accounted for with a continuum TTM-like model (called nTTM). First, we independently consider the applications of nTTM and MD for the description of silicon, and then construct the combined MD-nTTM model. Its development and thorough testing is followed by a comprehensive computational study of fast nonequilibrium processes induced in silicon by an ultrashort laser irradiation. The new model allowed to investigate the effect of laser-induced pressure and temperature of the lattice on the melting kinetics. Two competing melting mechanisms, heterogeneous and homogeneous, were identified in our big-scale simulations. Apart from the classical heterogeneous melting mechanism, the nucleation of the liquid phase homogeneously inside the material significantly contributes to the melting process. The simulations showed, that due to the open diamond structure of the crystal, the laser-generated internal compressive stresses reduce the crystal stability against the homogeneous melting. Consequently, the latter can take a massive character within several picoseconds upon the laser heating. Due to the large negative volume of melting of silicon, the material contracts upon the phase transition, relaxes the compressive stresses, and the subsequent melting proceeds heterogeneously until the excess of thermal energy is consumed. A series of simulations for a range of absorbed fluences allowed us to find the threshold fluence value at which homogeneous liquid nucleation starts contributing to the classical heterogeneous propagation of the solid-liquid interface. A series of simulations for a range of the material thicknesses showed that the sample width we chosen in our simulations (800 nm) corresponds to a thick sample. Additionally, in order to support the main conclusions, the results were verified for a different interatomic potential. Possible improvements of the model to account for nonthermal effects are discussed and certain restrictions on the suitable interatomic potentials are found. As a first step towards the inclusion of these effects into MD-nTTM, we performed nanometer-scale MD simulations with a new interatomic potential, designed to reproduce ab initio calculations at the laser-induced electronic temperature of 18946 K. The simulations demonstrated that, similarly to thermal melting, nonthermal phase transition occurs through nucleation. A series of simulations showed that higher (lower) initial pressure reinforces (hinders) the creation and the growth of nonthermal liquid nuclei. For the example of Si, the laser melting kinetics of semiconductors was found to be noticeably different from that of metals with a face-centered cubic crystal structure. The results of this study, therefore, have important implications for interpretation of experimental data on the kinetics of melting process of semiconductors.

Detection of matchings in a sequence of underwater images through texture analysis

This paper presents an approach to ameliorate the reliability of the correspondence points relating two consecutive images of a sequence. The images are especially difficult to handle, since they have been acquired by a camera looking at the sea floor while carried by an underwater robot. Underwater images are usually difficult to process due to light absorption, changing image radiance and lack of well-defined features. A new approach based on gray-level region matching and selective texture analysis significantly improves the matching reliability

Black carbon measurements in the boundary layer over western and northern Europe

Europe is a densely populated region that is a significant global source of black carbon (BC) aerosol, but there is a lack of information regarding the physical properties and spatial/vertical distribution of rBC in the region. We present the first aircraft observations of sub-micron refractory BC (rBC) aerosol concentrations and physical properties measured by a single particle soot photometer (SP2) in the lower troposphere over Europe. The observations spanned a region roughly bounded by 50° to 60° N and from 15° W to 30° E. The measurements, made between April and September 2008, showed that average rBC mass concentrations ranged from about 300 ng m−3 near urban areas to approximately 50 ng m−3 in remote continental regions, lower than previous surface-based measurements. rBC represented between 0.5 and 3% of the sub-micron aerosol mass. Black carbon mass size distributions were log-normally distributed and peaked at approximately 180 nm, but shifted to smaller diameters (~160 nm) near source regions. rBC was correlated with carbon monoxide (CO) but had different ratios to CO depending on location and air mass. Light absorption coefficients were measured by particle soot absorption photometers on two separate aircraft and showed similar geographic patterns to rBC mass measured by the SP2. We summarize the rBC and light absorption measurements as a function of longitude and air mass age and also provide profiles of rBC mass concentrations and size distribution statistics. Our results will help evaluate model-predicted regional rBC concentrations and properties and determine regional and global climate impacts from rBC due to atmospheric heating and surface dimming.

Effect of water-soluble polymers, polyethylene glycol and poly(vinylpyrrolidone),on the gelation of aqueous micellar solutions of Pluronic copolymer F127

The micellization of F127 (E98P67E98) in dilute aqueous solutions of polyethylene glycol (PEG6000 and PEG35000) and poly(vinylpyrrolidone) (PVP K30 and PVP K90) is studied. The average hydrodynamic radius (rh,app) obtained from the dynamic light scattering technique increased with increase in PEG concentration but decreased on addition of PVP, results which are consistent with interaction of the micelles with PEG and the formation of micelles clusters, but no such interaction occurs with PVP. Tube inversion was used to determine the onset of gelation. The critical concentration of F127 for gelation increased on addition of PEG and of PVP K30 but decreased on addition of PVP K90. Small-angle X-ray scattering (SAXS) was used to show that the 30 wt% F127 gel structure (fcc) was independent of polymer type and concentration, as was the d-spacing and so the micelle hard-sphere radius. The maximum elastic modulus (G0 max) of 30 wt% F127 decreased from its value for water alone as PEG was added, but was little changed by adding PVP. These results are consistent with the packed-micelles in the 30 wt% F127 gel being effectively isolated from the polymer solution on the microscale while, especially for the PEG, being mixed on the macroscale.

Influence of pH on the phototransformation process of PhotogemA (R)

PhotogemA (R) is a hematoporphyrin derivative that has been used as a photosensitizer in experimental and clinical Photodynamic Therapy (PDT) in Brazil. Photosensitizers are degraded under illumination. This process, usually called photobleaching, can be monitored by decreasing in fluorescence intensities and includes the following photoprocesses: photodegradation, phototransformation, and photorelocalization. Photobleaching of hematoporphyrin-type sensitizers during illumination in aqueous solution is related not only to photodegradation but is also followed by the formation of photoproducts with a new fluorescence band at around 640-650 nm and with increased light absorption in the red spectral region at 640 nm. In this study, the influence of pH on the phototransformation process was investigated. PhotogemA (R) solutions, 40 mu g/ml, were irradiated at 514 nm with intensity of 100 mW/cm(2) for 20 min with different pH environments. The controls were performed with the samples in the absence of light. The PhotogemA (R) photodegradation is dependent on the pH. The behavior of photodegradation and photoproducts formation (monitored at 640 nm) is distinct and depends on the photosensitizer concentration. The processes of degradation and photoproducts formation were monitored with Photogemin the concentration of 40 mu g/mL since that demonstrated the best visualization of both processes. While below pH 5 the photodegradation occurred, there was no detectable presence of photoproducts. The increase of pH led to increase of photoproducts formation rate with photodegradation reaching the highest value at pH 10. The increase of photoproducts formation and instability of PhotogemA (R) from pH 6 to pH 10 are in agreement with the desired properties of an ideal photosensitizer since there are significant differences in pH between normal (7.0 < pH < 8.6) and tumor (5.8 < pH < 7.9) tissues. It is important to know the effect of pH in the process of phototransformation (degradation and photoproduct formation) of the molecule since low pH values promotes increase in the proportion of aggregates species in solution and high pH values promotes increase in the proportion of monomeric species. There must be an ideal pH interval which favors the phototransformation process that is correlated with the singlet oxygen formation responsible by the photodynamic effect. These differences in pH between normal and tumor cells can explain the presence of photosensitizers in target tumor cells, making PDT a selective therapy.

Spectrophotometric determination of zinc in pharmaceutical and biological samples with di-2-pyridyl ketone benzoylhydrazone: A simple, fast, accurate and sensitive method

A simple, fast, accurate, and sensitive spectrophotometric method was developed to determine zinc(II). This method is based on the reaction of Zn(II) with di-2-pyridyl ketone benzoylhydrazone (DPKBH), at pH=5.5 and 50% (v/v) ethanol. Beers law was obeyed in the range 0.020-1.82 mu g mL(-1) with a molar apsorptivity of 3.64 x 10(4) L mol(-1) cm(-1), and a detection limit (3) of 2.29 mu g L-1. The action of some interfering ions was verified and the developed method applied to pharmaceutical and biological samples. The results were then compared with those obtained by using a flame atomic absorption technique.