Stopping power dependence of nitrogen sputtering yields in copper nitride films under swift-ion irradiation: Exciton model approach

Nitrogen sputtering yields as high as 104 atoms/ion, are obtained by irradiating N-rich-Cu3N films (N concentration: 33 ± 2 at.%) with Cu ions at energies in the range 10?42 MeV. The kinetics of N sputtering as a function of ion fluence is determined at several energies (stopping powers) for films deposited on both, glass and silicon substrates. The kinetic curves show that the amount of nitrogen release strongly increases with rising irradiation fluence up to reaching a saturation level at a low remaining nitrogen fraction (5?10%), in which no further nitrogen reduction is observed. The sputtering rate for nitrogen depletion is found to be independent of the substrate and to linearly increase with electronic stopping power (Se). A stopping power (Sth) threshold of ?3.5 keV/nm for nitrogen depletion has been estimated from extrapolation of the data. Experimental kinetic data have been analyzed within a bulk molecular recombination model. The microscopic mechanisms of the nitrogen depletion process are discussed in terms of a non-radiative exciton decay model. In particular, the estimated threshold is related to a minimum exciton density which is required to achieve efficient sputtering rates.

Kinetics of amorphization induced by swift heavy ions in α-quartz

The kinetics of amorphization in crystalline SiO2 (α-quartz) under irradiation with swift heavy ions (O+1 at 4 MeV, O+4 at 13 MeV, F+2 at 5 MeV, F+4 at 15 MeV, Cl+3 at 10 MeV, Cl+4 at 20 MeV, Br+5 at 15 and 25 MeV and Br+8 at 40 MeV) has been analyzed in this work with an Avrami-type law and also with a recently developed cumulative approach (track-overlap model). This latter model assumes a track morphology consisting of an amorphous core (area σ) and a surrounding defective halo (area h), both being axially symmetric. The parameters of the two approaches which provide the best fit to the experimental data have been obtained as a function of the electronic stopping power Se. The extrapolation of the σ(Se) dependence yields a threshold value for amorphization, Sth ≈ 2.1 keV/nm; a second threshold is also observed around 4.1 keV/nm. We believe that this double-threshold effect could be related to the appearance of discontinuous tracks in the region between 2.1 and 4.1 keV/nm. For stopping power values around or below the lower threshold, where the ratio h/σ is large, the track-overlap model provides a much better fit than the Avrami function. Therefore, the data show that a right modeling of the amorphization kinetics needs to take into account the contribution of the defective track halo. Finally, a short comparative discussion with the kinetic laws obtained for elastic collision damage is given.

Banco de ensayos para el control de calidad de paneles solares fotovoltaicos

El objetivo principal del presente Proyecto Fin de Carrera es el de dotar a la Escuela Universitaria de Ingenieros Técnicos de Telecomunicación – Universidad Politécnica de Madrid (EUITT-UPM) de un banco de medida donde poder caracterizar los módulos fotovoltaicos en condiciones reales de operación. Es necesario comprobar el funcionamiento de los módulos para asegurarse de que está acorde a lo indicado en las especificaciones anunciadas por los fabricantes. A lo largo del texto daremos una introducción al concepto de energía solar fotovoltaica y una descripción de los sistemas tanto aislados como los conectados a la red eléctrica de distribución. Hablaremos sobre el fenómeno fotovoltaico y describiremos los módulos fotovoltaicos para ver las partes de las que está compuesto un módulo. Finalmente nos centraremos en el banco de ensayo y acabaremos explicando el caso práctico realizado en la EUITT. A través de la medida de la curva I-V del módulo fotovoltaico en condiciones reales de operación y la extrapolación de los resultados obtenidos a las Condiciones Estándar de Medida (CEM) comprobaremos lo que se ajustan los valores dados por los fabricantes de los módulos solares. ABSTRACT. The main aim of this project is to provide the EUITT-UPM a measure workbench to characterize photovoltaic (PV) modules in real test conditions (RTC). It is necessary to check the PV modules operations to assure that its characteristics are close to the ones given by the manufacturers. I will introduce the concept of photovoltaic solar energy and describe remote systems as well as network-connected systems. I will talk about the photovoltaic phenomenon and describe the PV modules in order to know the parts making up a module. Finally, I shall describe the measure workbench explaining the practical case carried out at the university. By measuring the I-V curve of PV modules in real test conditions and the later extrapolation of the results to the standard test conditions (STC), manufacturers’ data can be compared to the data obtained within this study.

Effects of conservation interventions on the archaeological Roman site of Merida (Spain). Advance of research.

Research on the assessment of the effects of conservation/restoration treatments on stone material has been significant in recent years, with focus on the early observation of decay caused by the application of these treatments. However, in the case of archaeological sites, research is still scarce and few studies on the subject have been published. Restoration, as everything else, has changed according to trends, mainly guided by the release of new products and technologies, an experimental field where scientific assessment of suitability, efficacy and durability pre-evaluations of treatments are not always conducted. Some efforts have been made to solve this problem in the architectural field, where functional needs and technical requirements force to set clear standards. Unfortunately, archaeological sites, unlike historic buildings, have specific features that preclude the extrapolation of these results. A critical review of the methodologies, products and restoration materials is necessary, coupled with deeper research on degradation mechanisms caused by these treatments in the mid- and long-term. The aim of this paper is to introduce the research on the above issues using Merida as a case study.

Characterization of spontaneous combustuion tendency of dried sewage sludge

The general purpose of this study was the determination of the safety conditions to avoid the presence of explosive atmospheres in the wastewater industry. Eight Spanish plants located in Madrid, Barcelona and Málaga were considered and several sludge samples were taken in different seasons. The base for the assessment of the spontaneous ignition behaviour of dust accumulations is the experimental determination of the self-ignition temperature under isothermal conditions. Self-ignition temperatures at four volumes were obtained for one sample of sewage sludge, allowing their extrapolation to large storage facilities. A simple test method, based also on an isothermal study of samples, is the UN classification of substances liable to spontaneous combustion. Two different samples were so tested, obtaining unlike results if transported in packages of different volumes. By means of thermogravimetric techniques it is possible to analyse the thermal susceptibility of dried sewage sludge. Apparent activation energy can be obtained from the rate of weight loss. It is also applied to the study of self-ignition susceptibility by modifying test conditions when oxygen stream is introduced. As a consequence of this oxidant contribution, sample behaviour can be very different during testing and a step drop or sudden loss of weight is observed at a characteristic temperature for every substance, associated to a rapid combustion. Plotting both the activation energy and the characteristic temperature, a map of self-ignition risk was obtained for 10 samples, showing different risk levels for samples taken in different locations and at different seasons. A prediction of the self-ignition risk level can be also determined.

Assessing the potential of hybrid fossil–solar thermal plants for energy policy making: Brayton cycles

This paper proposes a first study in-depth of solar-fossil hybridization from a general perspective. It develops a set of useful parameters for analyzing and comparing hybrid plants, it studies the case of hybridizing Brayton cycles with current solar technologies and shows a tentative extrapolation of the results to integrated combined cycle systems (ISCSS). In particular, three points have been analyzed: the technical requirements for solar technologies to be hybridized with Brayton cycles, the temperatures and pressures at which hybridization would produce maximum power per unit of fossil fuel, and their mapping to current solar technologies and Brayton cycles. Major conclusions are that a hybrid plant works in optimum conditions which are not equal to those of the solar or power blocks considered independently, and that hybridizing at the Brayton cycle of a combined cycle could be energetically advantageous.

Una arquitectura en el territorio. Naturaleza de los tipos de la edificación vernácula española: la casa tradicional soriana

La presente Tesis Doctoral trata de ofrecer el primer estudio monográfico global que se dedica a cierta arquitectura vernácula, de un territorio situado en el centro–norte de la Península Ibérica. Asentada a horcajadas entre la Meseta septentrional castellana y la depresión mediterránea del río Ebro, y repartida en comarcas vinculadas a la España del norte y áreas de aspecto más meridional, la provincia de Soria presenta una notable superposición de tradiciones culturales, que se reúnen para generar desarrollos edificatorios diversos. En relación con esa variedad esencial, algunos datos contenidos en este trabajo, y muchos resultados de sus análisis, podrían extrapolarse, sin excesivos forzamientos, a fenómenos constructivos paralelos, correspondientes a amplias regiones del país. Tras enunciar brevemente las razones y objetivos de la investigación, junto con sus planteamientos de partida y determinados principios metodológicos, se han presentado unos elementos preliminares: apartados en los que se describe el medio físico y el marco humano, dentro de los cuales la arquitectura tradicional se desarrolla. Seguidamente, da comienzo la monografía referida a una realidad construida compleja, cuya explicación se ha dividido, por causas instrumentales, en dos partes diferenciadas. En el primer desarrollo, de género esencialmente analítico, se presentan los objetos edificados desde la perspectiva de la realidad material y constructiva de sus partes componentes; o desde el punto de vista de las técnicas que, en su día, sirvieron para definir elementos edificatorios, y sistemas generales de ellos. En la sección segunda, de naturaleza algo más sintética, se muestran otros aspectos de las arquitecturas, tomadas ya globalmente, o asociadas en grandes agrupaciones y conjuntos. Describiendo, de modo conciso, los territorios y ambientes urbanos tradicionales, en los que unos u otros tipos comparecen. Y pasando después a exponer, ya in extenso, los rasgos comunes o más específicos de estos y aquellos modelos arquitectónicos, así como sus recíprocas vinculaciones o procesos tipológicos corrientes. A modo de discusión final, se incluyen determinadas conclusiones, deducidas de cuanto se ha expuesto a lo largo del texto. Tales resultados, de índole algo más teórica, nos ayudan a comprender cuál es la efectiva naturaleza de los tipos individuados en las construcciones populares sorianas, particularmente en aquéllas de uso doméstico. Carácter compartido, sin duda, con otros modelos que, para territorios de mayor dimensión, podrían llegar a describirse. Así, el fenómeno constructivo referenciado se contempla, más allá de su concreto alcance local, como una muestra representativa de realidades más vastas, de orden real y también conceptual, que se regirían principios análogos. ABSTRACT The present Dissertation brings the first monographic study dedicated to certain vernacular architecture located in the territory of Soria, at the Center-North of the Iberian Peninsula. Seated between the Northern Castilian Plateau and the Ebro River Mediterranean Depression, and spread into regions linked to Northern Spain and areas of more southern characteristics, the province of Soria presents a remarkable overlap of cultural traditions providing several building developments. That essential variety is widely shown throughout this work, where the information recovered and the analysis’ reports allow a feasable extrapolation that explain the constructive phenomena all over broad regions of the Spanish country. After stating briefly the aim of the research and its background, along with its methodological process, this work starts its task introducing some preliminary elements: the physical environment and the human context where traditional architecture takes place. Afterwards the text focuses on the different vernacular constructions in all their complexity, which exposure has been divided in two parts: the first one, analytic, shows the built objects from the point of view of the materials and each constructive element; or, in another way, the constructive techniques that define building elements in the overall constructive systems. The second section, more synthetic, shows other aspects of this kind of architecture considering all cases, attempting to a theoretical classification and describing the territory and the urban environments where these architectures are placed. As follows, common and specific features of the architectural types studied are widely shown, as well as reciprocal connections, or typological processes underlying. The final discussion extracts conclusions that help us to understand the effective nature of the types found in Soria’s vernacular construction, particularly those for domestic use. There is no doubt that these buildings share a common character with another ones belonging to different territories of larger dimensions, that could be concisely studied in other place. Thus, these studied constructive phenomena can be considered, beyond the specific local scope, as a sample for more complex architectures, both in conceptual and physical terms, which seem to be guided by similar principles.

Guidelines for the design of an environmental flow regime program at the regional scale: Application of the ELOHA framework in the Ebro River basin

La gestión de los recursos hídricos se convierte en un reto del presente y del futuro frente a un panorama de continuo incremento de la demanda de agua debido al crecimiento de la población, el crecimiento del desarrollo económico y los posibles efectos del calentamiento global. La política hidráulica desde los años 60 en España se ha centrado en la construcción de infraestructuras que han producido graves alteraciones en el régimen natural de los ríos. Estas alteraciones han provocado y acrecentado los impactos sobre los ecosistemas fluviales y ribereños. Desde los años 90, sin embargo, ha aumentado el interés de la sociedad para conservar estos ecosistemas. El concepto de caudales ambientales consiste en un régimen de caudales que simula las características principales del régimen natural. Los caudales ambientales están diseñados para conservar la estructura y funcionalidad de los ecosistemas asociados al régimen fluvial, bajo la hipótesis de que los elementos que conforman estos ecosistemas están profundamente adaptados al régimen natural de caudales, y que cualquier alteración del régimen natural puede provocar graves daños a todo el sistema. El método ELOHA (Ecological Limits of Hydrological Alteration) tiene como finalidad identificar las componentes del régimen natural de caudales que son clave para mantener el equilibrio de los ecosistemas asociados, y estimar los límites máximos de alteración de estas componentes para garantizar su buen estado. Esta tesis presenta la aplicación del método ELOHA en la cuenca del Ebro. La cuenca del Ebro está profundamente regulada e intervenida por el hombre, y sólo las cabeceras de los principales afluentes del Ebro gozan todavía de un régimen total o cuasi natural. La tesis se estructura en seis capítulos que desarrollan las diferentes partes del método. El primer capítulo explica cómo se originó el concepto “caudales ambientales” y en qué consiste el método ELOHA. El segundo capítulo describe el área de estudio. El tercer capítulo realiza una clasificación de los regímenes naturales de la cuenca (RNC) del Ebro, basada en series de datos de caudal mínimamente alterado y usando exclusivamente parámetros hidrológicos. Se identificaron seis tipos diferentes de régimen natural: pluvial mediterráneo, nivo-pluvial, pluvial mediterréaneo con una fuerte componente del caudal base, pluvial oceánico, pluvio-nival oceánico y Mediterráneo. En el cuarto capítulo se realiza una regionalización a toda la cuenca del Ebro de los seis RNC encontrados en la cueca. Mediante parámetros climáticos y fisiográficos se extrapola la información del tipo de RNC a puntos donde no existen datos de caudal inalterado. El patrón geográfico de los tipos de régimen fluvial obtenido con la regionalización resultó ser coincidente con el patrón obtenido a través de la clasificación hidrológica. El quinto capítulo presenta la validación biológica de los procesos de clasificación anteriores: clasificación hidrológica y regionalización. La validación biológica de los tipos de regímenes fluviales es imprescindible, puesto que los diferentes tipos de régimen fluvial van a servir de unidades de gestión para favorecer el mantenimiento de los ecosistemas fluviales. Se encontraron diferencias significativas entre comunidades biológicas en cinco de los seis tipos de RNC encontrados en la cuenca. Finalmente, en el sexto capítulo se estudian las relaciones hidro-ecológicas existentes en tres de los seis tipos de régimen fluvial encontrados en la cuenca del Ebro. Mediante la construcción de curvas hidro-ecológicas a lo largo de un gradiente de alteración hidrológica, se pueden sugerir los límites de alteración hidrológica (ELOHAs) para garantizar el buen estado ecológico en cada uno de los tipos fluviales estudiados. Se establecieron ELOHAs en tres de los seis tipos de RNC de la cuenca del Ebro Esta tesis, además, pone en evidencia la falta de datos biológicos asociados a registros de caudal. Para llevar a cabo la implantación de un régimen de caudales ambientales en la cuenca, la ubicación de los puntos de muestreo biológico cercanos a estaciones de aforo es imprescindible para poder extraer relaciones causa-efecto de la gestión hidrológica sobre los ecosistemas dependientes. ABSTRACT In view of a growing freshwater demand because of population raising, improvement of economies and the potential effects of climate change, water resources management has become a challenge for present and future societies. Water policies in Spain have been focused from the 60’s on constructing hydraulic infrastructures, in order to dampen flow variability and granting water availability along the year. Consequently, natural flow regimes have been deeply altered and so the depending habitats and its ecosystems. However, an increasing acknowledgment of societies for preserving healthy freshwater ecosystems started in the 90’s and agreed that to maintain healthy freshwater ecosystems, it was necessary to set environmental flow regimes based on the natural flow variability. The Natural Flow Regime paradigm (Richter et al. 1996, Poff et al. 1997) bases on the hypothesis that freshwater ecosystems are made up by elements adapted to natural flow conditions, and any change on these conditions can provoke deep impacts on the whole system. Environmental flow regime concept consists in designing a flow regime that emulates natural flow characteristics, so that ecosystem structure, functions and services are maintained. ELOHA framework (Ecological Limits of Hydrological Alteration) aims to identify key features of the natural flow regime (NFR) that are needed to maintain and preserve healthy freshwater and riparian ecosystems. Moreover, ELOHA framework aims to quantify thresholds of alteration of these flow features according to ecological impacts. This thesis describes the application of the ELOHA framework in the Ebro River Basin. The Ebro River basin is the second largest basin in Spain and it is highly regulated for human demands. Only the Ebro headwaters tributaries still have completely unimpaired flow regime. The thesis has six chapters and the process is described step by step. The first chapter makes an introduction to the origin of the environmental flow concept and the necessity to come up. The second chapter shows a description of the study area. The third chapter develops a classification of NFRs in the basin based on natural flow data and using exclusively hydrological parameters. Six NFRs were found in the basin: continental Mediterranean-pluvial, nivo-pluvial, continental Mediterranean pluvial (with groundwater-dominated flow pattern), pluvio-oceanic, pluvio-nival-oceanic and Mediterranean. The fourth chapter develops a regionalization of the six NFR types across the basin by using climatic and physiographic variables. The geographical pattern obtained from the regionalization process was consistent with the pattern obtained with the hydrologic classification. The fifth chapter performs a biological validation of both classifications, obtained from the hydrologic classification and the posterior extrapolation. When the aim of flow classification is managing water resources according to ecosystem requirements, a validation based on biological data is compulsory. We found significant differences in reference macroinvertebrate communities between five over the six NFR types identified in the Ebro River basin. Finally, in the sixth chapter we explored the existence of significant and explicative flow alteration-ecological response relationships (FA-E curves) within NFR types in the Ebro River basin. The aim of these curves is to find out thresholds of hydrological alteration (ELOHAs), in order to preserve healthy freshwater ecosystem. We set ELOHA values in three NFR types identified in the Ebro River basin. During the development of this thesis, an inadequate biological monitoring in the Ebro River basin was identified. The design and establishment of appropriate monitoring arrangements is a critical final step in the assessment and implementation of environmental flows. Cause-effect relationships between hydrology and macroinvertebrate community condition are the principal data that sustain FA-E curves. Therefore, both data sites must be closely located, so that the effects of external factors are minimized. The scarce hydro-biological pairs of data available in the basin prevented us to apply the ELOHA method at all NFR types.

Los espacios mineros abandonados. El caso de la Comunidad de Madrid

La Comunidad de Madrid ha tenido un pasado minero importante que ha dejado su vestigio en el territorio. Actualmente la explotación de minerales no metálicos y de rocas industriales y ornamentales continúa, pero no así la de la minería metálica que en el pasado fue abundante. Hoy en día todas estas minas están abandonadas, dando lugar a zonas degradadas con un elevado riesgo para la seguridad de las personas y de los animales terrestres que habitan por sus inmediaciones, y necesitan ser intervenidas atendiendo, además, a su integración o recuperación ecológica y paisajística en el territorio. El principal propósito de esta tesis es conocer la situación actual que presentan las minas abandonadas de metales y proponer unos modelos de actuación para la rehabilitación e integración de los espacios mineros abandonados de la Comunidad de Madrid, cuya ventaja también estriba en su posible extrapolación a otras aéreas de gestión con una problemática similar. Partiendo de una selección de cincuenta y siete minas de interior metálicas abandonadas, se ha hecho un diagnostico en función de su seguridad (riesgo), interés cultural, arqueológico e histórico y por su afección a espacios protegidos, resultando que en todas, excepto en tres de ellas, es preciso llevar a cabo medidas protectoras y de restauración e integración en el medio ambiente. El conjunto de minas catalogadas de alto riesgo para la seguridad son veintitrés, y sobre ellas se ha realizado un Análisis Clúster, en el que además de los criterios de gestión formulados: seguridad, protección del patrimonio minero-industrial e integración ecológico-paisajística, se han incorporado otros modificadores como distancia a poblaciones, caminos, pistas y vías pecuarias, y accesibilidad. Con los resultados de este análisis se obtienen una clasificación por grupos de las minas en relación con las características intrínsecas de las explotaciones preseleccionadas y la tipología de problemas que presentan, y a partir de ella se plantean soluciones viables que se concretan en la redacción de una serie de anteproyectos tipo. Una de las principales aportaciones es que se trata de un modelo de inventariocaracterización- actuación extrapolable a otros entornos similares con problemáticas parecidas. Las propuestas de actuación que figuran en los anteproyectos tipo se proponen como medidas aplicables en situaciones similares. La tesis además también incorpora una base de datos georreferenciada que permite la localización de las explotaciones mineras abandonadas, el acceso rápido a sus características y a la propuesta de restauración correspondiente. ABSTRACT The Community of Madrid had an important mining past that left its traces in the territory. Currently the explotation of non-metallic minerals and industrial and ornamental rocks continues, but not so much with the metal deposits that were abundant in the past. Today these mines are abandoned, resulting in degraded areas with a high risk to the safety of nearby people and animals that inhabit its vicinity, and they need to be intervened, by tending to their environment integration or ecological and landscape recovery. The main objective of this thesis is to know the current situation of abandoned metal mines and propose an action model for the rehabilitation and integration of abandoned mining areas of the Community of Madrid, whose advantage also is its possible extrapolation to other management areas with similar problems. From a selection of fifty-seven abandoned metal mines, a diagnosis has been made, based on safety (risk), cultural, archaeological and historical interests and how it can be related to protected areas, resulting that all but three of them need measures of protection, restoration and integration to the environment. The set of mines that are classified as a high security risk are twenty-three, and it has been made on them an Cluster Analysis, as in addition to the management formulated criteria, such as safety, protection of mining and industrial heritage and eco-landscape integration, it has been incorporated other modifying variables, such as distance to populations, roads, tracks and livestock paths, and accessibility. With the results of this analysis, a classification of similar groups of mines in relation with the intrinsic characteristics of the preselected mines and typology problems, and from it a set of viable solutions will be specified, being then drafted on a series of proposals. One of the main contributions of this research is that it consists of an inventorycharacterization- action model, which can be extrapolated to other similar environments with similar problems. The action measures that are contained in the proposals are defined as applicable to similar situations. The thesis also incorporates a geo-referenced database that allows finding the location of abandoned mines, thus giving quick access to its features and its corresponding restoration proposal.

Adaptation Strategies for Discontinuous Galerkin Spectral Element Methods by means of Truncation Error Estimations

In this work a p-adaptation (modification of the polynomial order) strategy based on the minimization of the truncation error is developed for high order discontinuous Galerkin methods. The truncation error is approximated by means of a truncation error estimation procedure and enables the identification of mesh regions that require adaptation. Three truncation error estimation approaches are developed and termed a posteriori, quasi-a priori and quasi-a priori corrected. Fine solutions, which are obtained by enriching the polynomial order, are required to solve the numerical problem with adequate accuracy. For the three truncation error estimation methods the former needs time converged solutions, while the last two rely on non-converged solutions, which lead to faster computations. Based on these truncation error estimation methods, algorithms for mesh adaptation were designed and tested. Firstly, an isotropic adaptation approach is presented, which leads to equally distributed polynomial orders in different coordinate directions. This first implementation is improved by incorporating a method to extrapolate the truncation error. This results in a significant reduction of computational cost. Secondly, the employed high order method permits the spatial decoupling of the estimated errors and enables anisotropic p-adaptation. The incorporation of anisotropic features leads to meshes with different polynomial orders in the different coordinate directions such that flow-features related to the geometry are resolved in a better manner. These adaptations result in a significant reduction of degrees of freedom and computational cost, while the amount of improvement depends on the test-case. Finally, this anisotropic approach is extended by using error extrapolation which leads to an even higher reduction in computational cost. These strategies are verified and compared in terms of accuracy and computational cost for the Euler and the compressible Navier-Stokes equations. The main result is that the two quasi-a priori methods achieve a significant reduction in computational cost when compared to a uniform polynomial enrichment. Namely, for a viscous boundary layer flow, we obtain a speedup of a factor of 6.6 and 7.6 for the quasi-a priori and quasi-a priori corrected approaches, respectively. RESUMEN En este trabajo se ha desarrollado una estrategia de adaptación-p (modificación del orden polinómico) para métodos Galerkin discontinuo de alto orden basada en la minimización del error de truncación. El error de truncación se estima utilizando el método tau-estimation. El estimador permite la identificación de zonas de la malla que requieren adaptación. Se distinguen tres técnicas de estimación: a posteriori, quasi a priori y quasi a priori con correción. Todas las estrategias requieren una solución obtenida en una malla fina, la cual es obtenida aumentando de manera uniforme el orden polinómico. Sin embargo, mientras que el primero requiere que esta solución esté convergida temporalmente, el resto utiliza soluciones no convergidas, lo que se traduce en un menor coste computacional. En este trabajo se han diseñado y probado algoritmos de adaptación de malla basados en métodos tau-estimation. En primer lugar, se presenta un algoritmo de adaptacin isótropo, que conduce a discretizaciones con el mismo orden polinómico en todas las direcciones espaciales. Esta primera implementación se mejora incluyendo un método para extrapolar el error de truncación. Esto resulta en una reducción significativa del coste computacional. En segundo lugar, el método de alto orden permite el desacoplamiento espacial de los errores estimados, permitiendo la adaptación anisotropica. Las mallas obtenidas mediante esta técnica tienen distintos órdenes polinómicos en cada una de las direcciones espaciales. La malla final tiene una distribución óptima de órdenes polinómicos, los cuales guardan relación con las características del flujo que, a su vez, depenen de la geometría. Estas técnicas de adaptación reducen de manera significativa los grados de libertad y el coste computacional. Por último, esta aproximación anisotropica se extiende usando extrapolación del error de truncación, lo que conlleva un coste computational aún menor. Las estrategias se verifican y se comparan en téminors de precisión y coste computacional utilizando las ecuaciones de Euler y Navier Stokes. Los dos métodos quasi a priori consiguen una reducción significativa del coste computacional en comparación con aumento uniforme del orden polinómico. En concreto, para una capa límite viscosa, obtenemos una mejora en tiempo de computación de 6.6 y 7.6 respectivamente, para las aproximaciones quasi-a priori y quasi-a priori con corrección.

Calcium block of Na+ channels and its effect on closing rate

Calcium ion transiently blocks Na+ channels, and it shortens the time course for closing of their activation gates. We examined the relation between block and closing kinetics by using the Na+ channels natively expressed in GH3 cells, a clonal line of rat pituitary cells. To simplify analysis, inactivation of the Na+ channels was destroyed by including papain in the internal medium. All divalent cations tested, and trivalent La3+, blocked a progressively larger fraction of the channels as their concentration increased, and they accelerated the closing of the Na+ channel activation gate. For calcium, the most extensively studied cation, there is an approximately linear relation between the fraction of the channels that are calcium-blocked and the closing rate. Extrapolation of the data to very low calcium suggests that closing rate is near zero when there is no block. Analysis shows that, almost with certainty, the channels can close when occupied by calcium. The analysis further suggests that the channels close preferentially or exclusively from the calcium-blocked state.

Simultaneous determination of helical unwinding angles and intrinsic association constants in ligand–DNA complexes: The interaction between DNA and calichearubicin B

We present a helical unwinding assay for reversibly binding DNA ligands that uses closed circular DNA, topoisomerase I (Topo I), and two-dimensional agarose gel electrophoresis. Serially diluted Topo I relaxation reactions at constant DNA/ligand ratio are performed, and the resulting apparent unwinding of the closed circular DNA is used to calculate both ligand unwinding angle (φ) and intrinsic association constant (Ka). Mathematical treatment of apparent unwinding is formally analogous to that of apparent extinction coefficient data for optical binding titrations. Extrapolation to infinite DNA concentration yields the true unwinding angle of a given ligand and its association constant under Topo I relaxation conditions. Thus this assay delivers simultaneous structural and thermodynamic information describing the ligand–DNA complex. The utility of this assay has been demonstrated by using calichearubicin B (CRB), a synthetic hybrid molecule containing the anthraquinone chromophore of (DA) and the carbohydrate domain of calicheamicin γ1I. The unwinding angle for CRB calculated by this method is −5.3 ± 0.5°. Its Ka value is 0.20 × 106 M−1. For comparison, the unwinding angles of ethidium bromide and DA have been independently calculated, and the results are in agreement with canonical values for these compounds. Although a stronger binder to selected sites, CRB is a less potent unwinder than its parent compound DA. The assay requires only small amounts of ligand and offers an attractive option for analysis of DNA binding by synthetic and natural compounds.

Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium

A crucial step in exploiting the information inherent in genome sequences is to assign to each protein sequence its three-dimensional fold and biological function. Here we describe fold assignment for the proteins encoded by the small genome of Mycoplasma genitalium. The assignment was carried out by our computer server (http://www.doe-mbi.ucla.edu/people/frsvr/frsvr.html), which assigns folds to amino acid sequences by comparing sequence-derived predictions with known structures. Of the total of 468 protein ORFs, 103 (22%) can be assigned a known protein fold with high confidence, as cross-validated with tests on known structures. Of these sequences, 75 (16%) show enough sequence similarity to proteins of known structure that they can also be detected by traditional sequence–sequence comparison methods. That is, the difference of 28 sequences (6%) are assignable by the sequence–structure method of the server but not by current sequence–sequence methods. Of the remaining 78% of sequences in the genome, 18% belong to membrane proteins and the remaining 60% cannot be assigned either because these sequences correspond to no presently known fold or because of insensitivity of the method. At the current rate of determination of new folds by x-ray and NMR methods, extrapolation suggests that folds will be assigned to most soluble proteins in the next decade.

A selective phenomenology of the seismicity of Southern California.

Predictions of earthquakes that are based on observations of precursory seismicity cannot depend on the average properties of the seismicity, such as the Gutenberg-Richter (G-R) distribution. Instead it must depend on the fluctuations in seismicity. We summarize the observational data of the fluctuations of seismicity in space, in time, and in a coupled space-time regime over the past 60 yr in Southern California, to provide a basis for determining whether these fluctuations are correlated with the times and locations of future strong earthquakes in an appropriate time- and space-scale. The simple extrapolation of the G-R distribution must lead to an overestimate of the risk due to large earthquakes. There may be two classes of earthquakes: the small earthquakes that satisfy the G-R law and the larger and large ones. Most observations of fluctuations of seismicity are of the rate of occurrence of smaller earthquakes. Large earthquakes are observed to be preceded by significant quiescence on the faults on which they occur and by an intensification of activity at distance. It is likely that the fluctuations are due to the nature of fractures on individual faults of the network of faults. There are significant inhomogeneities on these faults, which we assume will have an important influence on the nature of self-organization of seismicity. The principal source of the inhomogeneity on the large scale is the influence of geometry--i.e., of the nonplanarity of faults and the system of faults.

The neck region of the myosin motor domain acts as a lever arm to generate movement.

The myosin head consists of a globular catalytic domain that binds actin and hydrolyzes ATP and a neck domain that consists of essential and regulatory light chains bound to a long alpha-helical portion of the heavy chain. The swinging neck-level model assumes that a swinging motion of the neck relative to the catalytic domain is the origin of movement. This model predicts that the step size, and consequently the sliding velocity, are linearly related to the length of the neck. We have tested this point by characterizing a series of mutant Dictyostelium myosins that have different neck lengths. The 2xELCBS mutant has an extra binding site for essential light chain. The delta RLCBS mutant myosin has an internal deletion that removes the regulatory light chain binding site. The delta BLCBS mutant lacks both light chain binding sites. Wild-type myosin and these mutant myosins were subjected to the sliding filament in vitro motility assay. As expected, mutants with shorter necks move slower than wild-type myosin in vitro. Most significantly, a mutant with a longer neck moves faster than the wild type, and the sliding velocities of these myosins are linearly related to the neck length, as predicted by the swinging neck-lever model. A simple extrapolation to zero speed predicts that the fulcrum point is in the vicinity of the SH1-SH2 region in the catalytic domain.