Temporal biomass dynamics of an Arctic plankton bloom

Ocean acidification and carbonation, driven by anthropogenic emissions of carbon dioxide (CO2), have been shown to affect a variety of marine organisms and are likely to change ecosystem functioning. High latitudes, especially the Arctic, will be the first to encounter profound changes in carbonate chemistry speciation at a large scale, namely the under-saturation of surface waters with respect to aragonite, a calcium carbonate polymorph produced by several organisms in this region. During a CO2 perturbation study in 2010, in the framework of the EU-funded project EPOCA, the temporal dynamics of a plankton bloom was followed in nine mesocosms, manipulated for CO2 levels ranging initially from about 185 to 1420 ?atm. Dissolved inorganic nutrients were added halfway through the experiment. Autotrophic biomass, as identified by chlorophyll a standing stocks (Chl a), peaked three times in all mesocosms. However, while absolute Chl a concentrations were similar in all mesocosms during the first phase of the experiment, higher autotrophic biomass was measured at high in comparison to low CO2 during the second phase, right after dissolved inorganic nutrient addition. This trend then reversed in the third phase. There were several statistically significant CO2 effects on a variety of parameters measured in certain phases, such as nutrient utilization, standing stocks of particulate organic matter, and phytoplankton species composition. Interestingly, CO2 effects developed slowly but steadily, becoming more and more statistically significant with time. The observed CO2 related shifts in nutrient flow into different phytoplankton groups (mainly diatoms, dinoflagellates, prasinophytes and haptophytes) could have consequences for future organic matter flow to higher trophic levels and export production, with consequences for ecosystem productivity and atmospheric CO2.

Geotechnical Analysis of Contaminated Sand by Light Non-Aquous Phase Liquids

Contaminated soil reuse was investigated, with higher profusion, throughout the early 90’s, coinciding with the 1991 Gulf War, when efforts to amend large crude oil releases began in geotechnical assessment of contaminated soils. Isolated works referring to geotechnical testing with hydrocarbon ground contaminants are described in the state-of-the-art, which have been extended to other type of contaminated soil references. Contaminated soils by light non-aquous phase liquids (LNAPL) bearing capacity reduction has been previously investigated from a forensic point of view. To date, all the research works have been published based on the assumption of constant contaminant saturation for the entire soil mass. In contrast, the actual LNAPLs distribution plumes exhibit complex flow patterns which are subject to physical and chemical changes with time and distance travelled from the release source. This aspect has been considered along the present text. A typical Madrid arkosic soil formation is commonly known as Miga sand. Geotechnical tests have been carried out, with Miga sand specimens, in incremental series of LNAPL concentrations in order to observe the soil engineering properties variation due to a contamination increase. Results are discussed in relation with previous studies and as a matter of fact, soil mechanics parameters change in the presence of LNAPL, showing different tendencies according to each test and depending on the LNAPL content, as well as to the specimen’s initially planned relative density, dense or loose. Geotechnical practical implications are also commented on and analyzed. Variation on geotechnical properties may occur only within the external contour of contamination distribution plume. This scope has motivated the author to develop a physical model based on transparent soil technology. The model aims to reproduce the distribution of LNAPL into the ground due to an accidental release from a storage facility. Preliminary results indicate that the model is a potentially complementary tool for hydrogeological applications, site-characterization and remediation treatment testing within the framework of soil pollution events. A description of the test setup of an innovative three dimensional physical model for the flow of two or more phases, in porous media, is presented herein, along with a summary of the advantages, limitations and future applications for modeling with transparent material. En los primeros años de la década de los años 90, del siglo pasado, coincidiendo con la Guerra del Golfo en 1991, se investigó intensamente sobre la reutilización de suelos afectados por grandes volúmenes de vertidos de crudo, fomentándose la evaluación geotécnica de los suelos contaminados. Se describen, en el estado del arte de esta tésis, una serie de trabajos aislados en relación con la caracterización geotécnica de suelos contaminados con hidrocarburos, descripción ampliada mediante referencias relacionadas con otros tipos de contaminación de suelos. Existen estudios previos de patología de cimentaciones que analizan la reducción de la capacidad portante de suelos contaminados por hidrocarburos líquidos ligeros en fase no acuosa (acrónimo en inglés: LNAPL de “Liquid Non-Aquous Phase Liquid”). A fecha de redacción de la tesis, todas las publicaciones anteriores estaban basadas en la consideración de una saturación del contaminante constante en toda la extensión del terreno de cimentación. La distribución real de las plumas de contaminante muestra, por el contrario, complejas trayectorias de flujo que están sujetas a cambios físico-químicos en función del tiempo y la distancia recorrida desde su origen de vertido. Éste aspecto ha sido considerado y tratado en el presente texto. La arena de Miga es una formación geológica típica de Madrid. En el ámbito de esta tesis se han desarrollado ensayos geotécnicos con series de muestras de arena de Miga contaminadas con distintas concentraciones de LNAPL con el objeto de estimar la variación de sus propiedades geotécnicas debido a un incremento de contaminación. Se ha realizado una evaluación de resultados de los ensayos en comparación con otros estudios previamente analizados, resultando que las propiedades mecánicas del suelo, efectivamente, varían en función del contenido de LNAPL y de la densidad relativa con la que se prepare la muestra, densa o floja. Se analizan y comentan las implicaciones de carácter práctico que supone la mencionada variación de propiedades geotécnicas. El autor ha desarrollado un modelo físico basado en la tecnología de suelos transparentes, considerando que las variaciones de propiedades geotécnicas únicamente deben producirse en el ámbito interior del contorno de la pluma contaminante. El objeto del modelo es el de reproducir la distribución de un LNAPL en un terreno dado, causada por el vertido accidental de una instalación de almecenamiento de combustible. Los resultados preliminares indican que el modelo podría emplearse como una herramienta complementaria para el estudio de eventos contaminantes, permitiendo el desarrollo de aplicaciones de carácter hidrogeológico, caracterización de suelos contaminados y experimentación de tratamientos de remediación. Como aportación de carácter innovadora, se presenta y describe un modelo físico tridimensional de flujo de dos o más fases a través de un medio poroso transparente, analizándose sus ventajas e inconvenientes así como sus limitaciones y futuras aplicaciones.

Phase transition in the countdown problem

We present a combinatorial decision problem, inspired by the celebrated quiz show called Countdown, that involves the computation of a given target number T from a set of k randomly chosen integers along with a set of arithmetic operations. We find that the probability of winning the game evidences a threshold phenomenon that can be understood in the terms of an algorithmic phase transition as a function of the set size k. Numerical simulations show that such probability sharply transitions from zero to one at some critical value of the control parameter, hence separating the algorithm's parameter space in different phases. We also find that the system is maximally efficient close to the critical point. We derive analytical expressions that match the numerical results for finite size and permit us to extrapolate the behavior in the thermodynamic limit.

Electrooptic effect in cholesteric blue phases with small positive dielectric anisotropy

An electrooptic effect in the blue phase of the cholesteric mixture S811-and the nematic mixture N5 is reported. To demonstrate this effect ac voltages (ƒ = 1000 Hz) between 0 and 150 νwere applied. Wavelength shifts of 70 nm were obtained.

Effects of forage type on diversity in bacterial pellets isolated from liquid and solid phases of the rumen content in sheep and goats.

Two sheep and two goats, fitted with a ruminal cannula, received two diets composed of 30% concentrate and 70% of either alfalfa hay (AL) or grass hay (GR) as forage in a two-period crossover design. Solid and liquid phases of the rumen were sampled from each animal immediately before feeding and 4 h post-feeding. Pellets containing solid associated bacteria (SAB) and liquid associated bacteria (LAB) were isolated from the corresponding ruminal phase and composited by time to obtain 2 pellets per animal (one SAB and one LAB) before DNA extraction. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S ribosomal DNA was used to analyze bacterial diversity. A total of 78 and 77 bands were detected in the DGGE gel from sheep and goats samples, respectively. There were 18 bands only found in the pellets from sheep fed AL-fed sheep and 7 found exclusively in samples from sheep fed the GR diet. In goats, 21 bands were found only in animals fed the AL diet and 17 were found exclusively in GR-fed ones. In all animals, feeding AL diet tended (P < 0.10) to promote greater NB and SI in LAB and SAB pellets compared with the GR diet. The dendrogram generated by the cluster analysis showed that in both animal species all samples can be included in two major clusters. The four SAB pellets within each animal species clustered together and the four LAB pellets grouped in a different cluster. Moreover, SAB and LAB clusters contained two clear subclusters according to forage type. Results show that in all animals bacterial diversity was more markedly affected by the ruminal phase (solid vs. liquid) than by the type of forage in the diet.

Phase transitions in number theory: from the birthday problem to Sidon sets

In this work, we show how number theoretical problems can be fruitfully approached with the tools of statistical physics. We focus on g-Sidon sets, which describe sequences of integers whose pairwise sums are different, and propose a random decision problem which addresses the probability of a random set of k integers to be g-Sidon. First, we provide numerical evidence showing that there is a crossover between satisfiable and unsatisfiable phases which converts to an abrupt phase transition in a properly defined thermodynamic limit. Initially assuming independence, we then develop a mean-field theory for the g-Sidon decision problem. We further improve the mean-field theory, which is only qualitatively correct, by incorporating deviations from independence, yielding results in good quantitative agreement with the numerics for both finite systems and in the thermodynamic limit. Connections between the generalized birthday problem in probability theory, the number theory of Sidon sets and the properties of q-Potts models in condensed matter physics are briefly discussed

Consideration of Multi-Phase Criterion in the Differential Protection Algorithm for High-Impedance Grounded Synchronous Generators

The generator differential protection is one of the most important electrical protections of synchronous generator stator windings. Its operation principle is based on the comparison of the input current and output current at each phase winding. Unwanted trip commands are usually caused by CT saturation, wrong CT selection, or the fact that they may come from different manufacturers. In generators grounded through high impedance, only phase-to-phase or three-phase faults can be detected by the differential protection. This kind of fault causes differential current to flow in, at least, two phases of the winding. Several cases of unwanted trip commands caused by the appearance of differential current in only one phase of the generator have been reported. In this paper multi-phase criterion is proposed for generator differential protection algorithm when applied to high impedance grounded generators.

Analysis of single and binary phases in cerium doped sodium bismuth titanate -Na0.5Bi0.5TiO3 materials

The pure and cerium doped sodium bismuth titanate inorganic powders were synthesized by solid state reaction method. The presence of rhombohedral phase was observed in cerium doped NBT compounds. At 1200 ºC, the 5% of cerium doped NBT compound forms single perovskite phase. The samples of x = 0.10 and 0.15 were heat treated to 1350 ºC, the binary phases with cerium and bismuth oxides were observed. The X-ray diffraction, fourier transform infrared spectroscopy, reflectance spectra, differential thermal analysis and thermo gravimetric analysis were used to analyze the various properties of samples. Moreover, the effects of cerium doping and calcining temperature on NBT samples were investigated. In this work we present our recent results on the synthesis and characterization of Ce doped sodium bismuth titanate materials.

Atomistic modeling of Ge damage accumulation, amorphization and solid phase epitaxial regrowth

En los últimos años, el Ge ha ganado de nuevo atención con la finalidad de ser integrado en el seno de las existentes tecnologías de microelectrónica. Aunque no se le considera como un canddato capaz de reemplazar completamente al Si en el futuro próximo, probalemente servirá como un excelente complemento para aumentar las propiedades eléctricas en dispositivos futuros, especialmente debido a su alta movilidad de portadores. Esta integración requiere de un avance significativo del estado del arte en los procesos de fabricado. Técnicas de simulación, como los algoritmos de Monte Carlo cinético (KMC), proporcionan un ambiente atractivo para llevar a cabo investigación y desarrollo en este campo, especialmente en términos de costes en tiempo y financiación. En este estudio se han usado, por primera vez, técnicas de KMC con el fin entender el procesado “front-end” de Ge en su fabricación, específicamente la acumulación de dañado y amorfización producidas por implantación iónica y el crecimiento epitaxial en fase sólida (SPER) de las capas amorfizadas. Primero, simulaciones de aproximación de clisiones binarias (BCA) son usadas para calcular el dañado causado por cada ión. La evolución de este dañado en el tiempo se simula usando KMC sin red, o de objetos (OKMC) en el que sólamente se consideran los defectos. El SPER se simula a través de una aproximación KMC de red (LKMC), siendo capaz de seguir la evolución de los átomos de la red que forman la intercara amorfo/cristalina. Con el modelo de amorfización desarrollado a lo largo de este trabajo, implementado en un simulador multi-material, se pueden simular todos estos procesos. Ha sido posible entender la acumulación de dañado, desde la generación de defectos puntuales hasta la formación completa de capas amorfas. Esta acumulación ocurre en tres regímenes bien diferenciados, empezando con un ritmo lento de formación de regiones de dañado, seguido por una rápida relajación local de ciertas áreas en la fase amorfa donde ambas fases, amorfa y cristalina, coexisten, para terminar en la amorfización completa de capas extensas, donde satura el ritmo de acumulación. Dicha transición ocurre cuando la concentración de dañado supera cierto valor límite, el cual es independiente de las condiciones de implantación. Cuando se implantan los iones a temperaturas relativamente altas, el recocido dinámico cura el dañado previamente introducido y se establece una competición entre la generación de dañado y su disolución. Estos efectos se vuelven especialmente importantes para iones ligeros, como el B, el cual crea dañado más diluido, pequeño y distribuido de manera diferente que el causado por la implantación de iones más pesados, como el Ge. Esta descripción reproduce satisfactoriamente la cantidad de dañado y la extensión de las capas amorfas causadas por implantación iónica reportadas en la bibliografía. La velocidad de recristalización de la muestra previamente amorfizada depende fuertemente de la orientación del sustrato. El modelo LKMC presentado ha sido capaz de explicar estas diferencias entre orientaciones a través de un simple modelo, dominado por una única energía de activación y diferentes prefactores en las frecuencias de SPER dependiendo de las configuraciones de vecinos de los átomos que recristalizan. La formación de maclas aparece como una consecuencia de esta descripción, y es predominante en sustratos crecidos en la orientación (111)Ge. Este modelo es capaz de reproducir resultados experimentales para diferentes orientaciones, temperaturas y tiempos de evolución de la intercara amorfo/cristalina reportados por diferentes autores. Las parametrizaciones preliminares realizadas de los tensores de activación de tensiones son también capaces de proveer una buena correlación entre las simulaciones y los resultados experimentales de velocidad de SPER a diferentes temperaturas bajo una presión hidrostática aplicada. Los estudios presentados en esta tesis han ayudado a alcanzar un mejor entendimiento de los mecanismos de producción de dañado, su evolución, amorfización y SPER para Ge, además de servir como una útil herramienta para continuar el trabajo en este campo. In the recent years, Ge has regained attention to be integrated into existing microelectronic technologies. Even though it is not thought to be a feasible full replacement to Si in the near future, it will likely serve as an excellent complement to enhance electrical properties in future devices, specially due to its high carrier mobilities. This integration requires a significant upgrade of the state-of-the-art of regular manufacturing processes. Simulation techniques, such as kinetic Monte Carlo (KMC) algorithms, provide an appealing environment to research and innovation in the field, specially in terms of time and funding costs. In the present study, KMC techniques are used, for the first time, to understand Ge front-end processing, specifically damage accumulation and amorphization produced by ion implantation and Solid Phase Epitaxial Regrowth (SPER) of the amorphized layers. First, Binary Collision Approximation (BCA) simulations are used to calculate the damage caused by every ion. The evolution of this damage over time is simulated using non-lattice, or Object, KMC (OKMC) in which only defects are considered. SPER is simulated through a Lattice KMC (LKMC) approach, being able to follow the evolution of the lattice atoms forming the amorphous/crystalline interface. With the amorphization model developed in this work, implemented into a multi-material process simulator, all these processes can be simulated. It has been possible to understand damage accumulation, from point defect generation up to full amorphous layers formation. This accumulation occurs in three differentiated regimes, starting at a slow formation rate of the damage regions, followed by a fast local relaxation of areas into the amorphous phase where both crystalline and amorphous phases coexist, ending in full amorphization of extended layers, where the accumulation rate saturates. This transition occurs when the damage concentration overcomes a certain threshold value, which is independent of the implantation conditions. When implanting ions at relatively high temperatures, dynamic annealing takes place, healing the previously induced damage and establishing a competition between damage generation and its dissolution. These effects become specially important for light ions, as B, for which the created damage is more diluted, smaller and differently distributed than that caused by implanting heavier ions, as Ge. This description successfully reproduces damage quantity and extension of amorphous layers caused by means of ion implantation reported in the literature. Recrystallization velocity of the previously amorphized sample strongly depends on the substrate orientation. The presented LKMC model has been able to explain these differences between orientations through a simple model, dominated by one only activation energy and different prefactors for the SPER rates depending on the neighboring configuration of the recrystallizing atoms. Twin defects formation appears as a consequence of this description, and are predominant for (111)Ge oriented grown substrates. This model is able to reproduce experimental results for different orientations, temperatures and times of evolution of the amorphous/crystalline interface reported by different authors. Preliminary parameterizations for the activation strain tensors are able to also provide a good match between simulations and reported experimental results for SPER velocities at different temperatures under the appliance of hydrostatic pressure. The studies presented in this thesis have helped to achieve a greater understanding of damage generation, evolution, amorphization and SPER mechanisms in Ge, and also provide a useful tool to continue research in this field.

Two-dimensional infrared spectroscopy of peptides by phase-controlled femtosecond vibrational photon echoes

Two-dimensional infrared spectra of peptides are introduced that are the direct analogues of two- and three-pulse multiple quantum NMR. Phase matching and heterodyning are used to isolate the phase and amplitudes of the electric fields of vibrational photon echoes as a function of multiple pulse delays. Structural information is made available on the time scale of a few picoseconds. Line narrowed spectra of acyl-proline-NH2 and cross peaks implying the coupling between its amide-I modes are obtained, as are the phases of the various contributions to the signals. Solvent-sensitive structural differences are seen for the dipeptide. The methods show great promise to measure structure changes in biology on a wide range of time scales.

Phase identity of the maize leaf is determined after leaf initiation

The vegetative development of the maize shoot can be divided into juvenile and adult phases based on the types of leaves produced at different times in shoot development. Models for the regulation of phase change make explicit predictions about when the identity of these types of leaves is determined. To test these models, we examined the timing of leaf type determination in maize. Clones induced in transition leaf primordia demonstrated that the juvenile and adult regions of these leaves do not become clonally distinct until after the primordium is 700 μm in length, implying that these cell fates were undetermined at this stage of leaf development. Adult shoot apices were cultured in vitro to induce rejuvenation. We found that leaf primordia as large as 3 mm in length can be at least partially rejuvenated by this treatment, and the location of rejuvenated tissue is correlated with the maturation pattern of the leaf. The amount and distribution of juvenile tissue in rejuvenated leaves suggests that rejuvenation occurs nearly simultaneously in all leaf primordia. In vitro culture rejuvenated existing leaf primordia and the P0 primordium, but did not change the identity of subsequent primordia or the total number of leaves produced by the shoot. This result suggests that leaf identity can be regulated independently of the identity of the shoot apical meristem, and it implies that vegetative phase change is not initiated by a change in the identity of the shoot apical meristem.

From patterns to processes: Phase and density dependencies in the Canadian lynx cycle

Across the boreal forest of North America, lynx populations undergo 10-year cycles. Analysis of 21 time series from 1821 to the present demonstrates that these fluctuations are generated by nonlinear processes with regulatory delays. Trophic interactions between lynx and hares cause delayed density-dependent regulation of lynx population growth. The nonlinearity, in contrast, appears to arise from phase dependencies in hunting success by lynx through the cycle. Using a combined approach of empirical, statistical, and mathematical modeling, we highlight how shifts in trophic interactions between the lynx and the hare generate the nonlinear process primarily by shifting functional response curves during the increase and the decrease phases.

Two Genetically Separable Phases of Growth Inhibition Induced by Blue Light in Arabidopsis Seedlings1

High fluence-rate blue light (BL) rapidly inhibits hypocotyl growth in Arabidopsis, as in other species, after a lag time of 30 s. This growth inhibition is always preceded by the activation of anion channels. The membrane depolarization that results from the activation of anion channels by BL was only 30% of the wild-type magnitude in hy4, a mutant lacking the HY4 BL receptor. High-resolution measurements of growth made with a computer-linked displacement transducer or digitized images revealed that BL caused a rapid inhibition of growth in wild-type and hy4 seedlings. This inhibition persisted in wild-type seedlings during more than 40 h of continuous BL. By contrast, hy4 escaped from the initial inhibition after approximately 1 h of BL and grew faster than wild type for approximately 30 h. Wild-type seedlings treated with 5-nitro-2-(3-phenylpropylamino)-benzoic acid, a potent blocker of the BL-activated anion channel, displayed rapid growth inhibition, but, similar to hy4, these seedlings escaped from inhibition after approximately 1 h of BL and phenocopied the mutant for at least 2.5 h. The effects of 5-nitro-2-(3-phenylpropylamino)-benzoic acid and the HY4 mutation were not additive. Taken together, the results indicate that BL acts through HY4 to activate anion channels at the plasma membrane, causing growth inhibition that begins after approximately 1 h. Neither HY4 nor anion channels appear to participate greatly in the initial phase of inhibition.

Cellular expression of human centromere protein C demonstrates a cyclic behavior with highest abundance in the G1 phase.

Centromere proteins are localized within the centromere-kinetochore complex, which can be proven by means of immunofluorescence microscopy and immunoelectron microscopy. In consequence, their putative functions seem to be related exclusively to mitosis, namely to the interaction of the chromosomal kinetochores with spindle microtubules. However, electron microscopy using immune sera enriched with specific antibodies against human centromere protein C (CENP-C) showed that it occurs not only in mitosis but during the whole cell cycle. Therefore, we investigated the cell cycle-specific expression of CENP-C systematically on protein and mRNA levels applying HeLa cells synchronized in all cell cycle phases. Immunoblotting confirmed protein expression during the whole cell cycle and revealed an increase of CENP-C from the S phase through the G2 phase and mitosis to highest abundance in the G1 phase. Since this was rather surprising, we verified it by quantifying phase-specific mRNA levels of CENP-C, paralleled by the amplification of suitable internal standards, using the polymerase chain reaction. The results were in excellent agreement with abundant protein amounts and confirmed the cyclic behavior of CENP-C during the cell cycle. In consequence, we postulate that in addition to its role in mitosis, CENP-C has a further role in the G1 phase that may be related to cell cycle control.