Determination of the average ionization and thermodynamic regimes of xenon plasmas with an application to the characterization of blast waves launched in xenon clusters

Radiative shock waves play a pivotal role in the transport energy into the stellar medium. This fact has led to many efforts to scale the astrophysical phenomena to accessible laboratory conditions and their study has been highlighted as an area requiring further experimental investigations. Low density material with high atomic mass is suitable to achieve radiative regime, and, therefore, low density xenon gas is commonly used for the medium in which the radiative shock propagates. In this work the averageionization and the thermodynamicregimes of xenonplasmas are determined as functions of the matter density and temperature in a wide range of plasma conditions. The results obtained will be applied to characterize blastwaveslaunched in xenonclusters

Tropospheric scintillation with concurrent rain attenuation at 50 GHz in Madrid

Tropospheric scintillation can become a significant impairment in satellite communication systems, especially in those with low fade-margin. Moreover, fast amplitude fluctuations due to scintillation are even larger when rain is present on the propagation path. Few studies of scintillation during rain have been reported and the statistical characterization is still not totally clear. This paper presents experimental results on the relationship between scintillation and rain attenuation obtained from slant-path attenuation measurements at 50 GHz. The study is focused on the probability density function (PDF) of various scintillation parameters. It is shown that scintillation intensity, measured as the standard deviation of the amplitude fluctuations, increases with rain attenuation; in the range 1-10 dB this relationship can be expressed by power-law or linear equations. The PDFs of scintillation intensity conditioned to a given rain attenuation level are lognormal, while the overall long-term PDF is well fltted by a generalized extreme valué (GEV) distribution. The short-term PDFs of amplitude conditioned to a given intensity are normal, although skewness effects are observed for the strongest intensities. A procedure is given to derive numerically the overall PDF of scintillation amplitude using a combination of conditional PDFs and local statistics of rain attenuation.

Reconstructing the Timing and Dispersion Routes of HIV-1 Subtype B Epidemics in The Caribbean and Central America: A Phylogenetic Story.

The Caribbean and Central America are among the regions with highest HIV-1B prevalence worldwide. Despite of this high virus burden, little is known about the timing and the migration patterns of HIV-1B in these regions. Migration is one of the major processes shaping the genetic structure of virus populations. Thus, reconstruction of epidemiological network may contribute to understand HIV-1B evolution and reduce virus prevalence. We have investigated the spatio-temporal dynamics of the HIV-1B epidemic in The Caribbean and Central America using 1,610 HIV-1B partial pol sequences from 13 Caribbean and 5 Central American countries. Timing of HIV-1B introduction and virus evolutionary rates, as well as the spatial genetic structure of the HIV-1B populations and the virus migration patterns were inferred. Results revealed that in The Caribbean and Central America most of the HIV-1B variability was generated since the 80 s. At odds with previous data suggesting that Haiti was the origin of the epidemic in The Caribbean, our reconstruction indicated that the virus could have been disseminated from Puerto Rico and Antigua. These two countries connected two distinguishable migration areas corresponding to the (mainly Spanish-colonized) Easter and (mainly British-colonized) Western islands, which indicates that virus migration patterns are determined by geographical barriers and by the movement of human populations among culturally related countries. Similar factors shaped the migration of HIV-1B in Central America. The HIV-1B population was significantly structured according to the country of origin, and the genetic diversity in each country was associated with the virus prevalence in both regions, which suggests that virus populations evolve mainly through genetic drift. Thus, our work contributes to the understanding of HIV-1B evolution and dispersion pattern in the Americas, and its relationship with the geography of the area and the movements of human populations.

Contributions to trajectory prediction theory and its application to arrival management for air traffic control

La gestión del tráfico aéreo (Air Traffic Management, ATM) está experimentando un cambio de paradigma hacia las denominadas operaciones basadas trayectoria. Bajo dicho paradigma se modifica el papel de los controladores de tráfico aéreo desde una operativa basada su intervención táctica continuada hacia una labor de supervisión a más largo plazo. Esto se apoya en la creciente confianza en las soluciones aportadas por las herramientas automatizadas de soporte a la decisión más modernas. Para dar soporte a este concepto, se precisa una importante inversión para el desarrollo, junto con la adquisición de nuevos equipos en tierra y embarcados, que permitan la sincronización precisa de la visión de la trayectoria, basada en el intercambio de información entre ambos actores. Durante los últimos 30 a 40 años las aerolíneas han generado uno de los menores retornos de la inversión de entre todas las industrias. Sin beneficios tangibles, la industria aérea tiene dificultades para atraer el capital requerido para su modernización, lo que retrasa la implantación de dichas mejoras. Esta tesis tiene como objetivo responder a la pregunta de si las capacidades actualmente instaladas en las aeronaves comerciales se pueden aplicar para lograr la sincronización de la trayectoria con el nivel de calidad requerido. Además, se analiza en ella si, conjuntamente con mejoras en las herramientas de predicción trayectorias instaladas en tierra en para facilitar la gestión de las arribadas, dichas capacidades permiten obtener los beneficios esperados en el marco de las operaciones basadas en trayectoria. Esto podría proporcionar un incentivo para futuras actualizaciones de la aviónica que podrían llevar a mejoras adicionales. El concepto operacional propuesto en esta tesis tiene como objetivo permitir que los aviones sean pilotados de una manera consistente con las técnicas actuales de vuelo optimizado. Se permite a las aeronaves que desciendan en el denominado “modo de ángulo de descenso gestionado” (path-managed mode), que es el preferido por la mayoría de las compañías aéreas, debido a que conlleva un reducido consumo de combustible. El problema de este modo es que en él no se controla de forma activa el tiempo de llegada al punto de interés. En nuestro concepto operacional, la incertidumbre temporal se gestiona en mediante de la medición del tiempo en puntos estratégicamente escogidos a lo largo de la trayectoria de la aeronave, y permitiendo la modificación por el control de tierra de la velocidad de la aeronave. Aunque la base del concepto es la gestión de las ordenes de velocidad que se proporcionan al piloto, para ser capaces de operar con los niveles de equipamiento típicos actualmente, dicho concepto también constituye un marco en el que la aviónica más avanzada (por ejemplo, que permita el control por el FMS del tiempo de llegada) puede integrarse de forma natural, una vez que esta tecnología este instalada. Además de gestionar la incertidumbre temporal a través de la medición en múltiples puntos, se intenta reducir dicha incertidumbre al mínimo mediante la mejora de las herramienta de predicción de la trayectoria en tierra. En esta tesis se presenta una novedosa descomposición del proceso de predicción de trayectorias en dos etapas. Dicha descomposición permite integrar adecuadamente los datos de la trayectoria de referencia calculada por el Flight Management System (FMS), disponibles usando Futuro Sistema de Navegación Aérea (FANS), en el sistema de predicción de trayectorias en tierra. FANS es un equipo presente en los aviones comerciales de fuselaje ancho actualmente en la producción, e incluso algunos aviones de fuselaje estrecho pueden tener instalada avionica FANS. Además de informar automáticamente de la posición de la aeronave, FANS permite proporcionar (parte de) la trayectoria de referencia en poder de los FMS, pero la explotación de esta capacidad para la mejora de la predicción de trayectorias no se ha estudiado en profundidad en el pasado. La predicción en dos etapas proporciona una solución adecuada al problema de sincronización de trayectorias aire-tierra dado que permite la sincronización de las dimensiones controladas por el sistema de guiado utilizando la información de la trayectoria de referencia proporcionada mediante FANS, y también facilita la mejora en la predicción de las dimensiones abiertas restantes usado un modelo del guiado que explota los modelos meteorológicos mejorados disponibles en tierra. Este proceso de predicción de la trayectoria de dos etapas se aplicó a una muestra de 438 vuelos reales que realizaron un descenso continuo (sin intervención del controlador) con destino Melbourne. Dichos vuelos son de aeronaves del modelo Boeing 737-800, si bien la metodología descrita es extrapolable a otros tipos de aeronave. El método propuesto de predicción de trayectorias permite una mejora en la desviación estándar del error de la estimación del tiempo de llegada al punto de interés, que es un 30% menor que la que obtiene el FMS. Dicha trayectoria prevista mejorada se puede utilizar para establecer la secuencia de arribadas y para la asignación de las franjas horarias para cada aterrizaje (slots). Sobre la base del slot asignado, se determina un perfil de velocidades que permita cumplir con dicho slot con un impacto mínimo en la eficiencia del vuelo. En la tesis se propone un nuevo algoritmo que determina las velocidades requeridas sin necesidad de un proceso iterativo de búsqueda sobre el sistema de predicción de trayectorias. El algoritmo se basa en una parametrización inteligente del proceso de predicción de la trayectoria, que permite relacionar el tiempo estimado de llegada con una función polinómica. Resolviendo dicho polinomio para el tiempo de llegada deseado, se obtiene de forma natural el perfil de velocidades optimo para cumplir con dicho tiempo de llegada sin comprometer la eficiencia. El diseño de los sistemas de gestión de arribadas propuesto en esta tesis aprovecha la aviónica y los sistemas de comunicación instalados de un modo mucho más eficiente, proporcionando valor añadido para la industria. Por tanto, la solución es compatible con la transición hacia los sistemas de aviónica avanzados que están desarrollándose actualmente. Los beneficios que se obtengan a lo largo de dicha transición son un incentivo para inversiones subsiguientes en la aviónica y en los sistemas de control de tráfico en tierra. ABSTRACT Air traffic management (ATM) is undergoing a paradigm shift towards trajectory based operations where the role of an air traffic controller evolves from that of continuous intervention towards supervision, as decision making is improved based on increased confidence in the solutions provided by advanced automation. To support this concept, significant investment for the development and acquisition of new equipment is required on the ground as well as in the air, to facilitate the high degree of trajectory synchronisation and information exchange required. Over the past 30-40 years the airline industry has generated one of the lowest returns on invested capital among all industries. Without tangible benefits realised, the airline industry may find it difficult to attract the required investment capital and delay acquiring equipment needed to realise the concept of trajectory based operations. In response to these challenges facing the modernisation of ATM, this thesis aims to answer the question whether existing aircraft capabilities can be applied to achieve sufficient trajectory synchronisation and improvements to ground-based trajectory prediction in support of the arrival management process, to realise some of the benefits envisioned under trajectory based operations, and to provide an incentive for further avionics upgrades. The proposed operational concept aims to permit aircraft to operate in a manner consistent with current optimal aircraft operating techniques. It allows aircraft to descend in the fuel efficient path managed mode as preferred by a majority of airlines, with arrival time not actively controlled by the airborne automation. The temporal uncertainty is managed through metering at strategically chosen points along the aircraft’s trajectory with primary use of speed advisories. While the focus is on speed advisories to support all aircraft and different levels of equipage, the concept also constitutes a framework in which advanced avionics as airborne time-of-arrival control can be integrated once this technology is widely available. In addition to managing temporal uncertainty through metering at multiple points, this temporal uncertainty is minimised by improving the supporting trajectory prediction capability. A novel two-stage trajectory prediction process is presented to adequately integrate aircraft trajectory data available through Future Air Navigation Systems (FANS) into the ground-based trajectory predictor. FANS is standard equipment on any wide-body aircraft in production today, and some single-aisle aircraft are easily capable of being fitted with FANS. In addition to automatic position reporting, FANS provides the ability to provide (part of) the reference trajectory held by the aircraft’s Flight Management System (FMS), but this capability has yet been widely overlooked. The two-stage process provides a ‘best of both world’s’ solution to the air-ground synchronisation problem by synchronising with the FMS reference trajectory those dimensions controlled by the guidance mode, and improving on the prediction of the remaining open dimensions by exploiting the high resolution meteorological forecast available to a ground-based system. The two-stage trajectory prediction process was applied to a sample of 438 FANS-equipped Boeing 737-800 flights into Melbourne conducting a continuous descent free from ATC intervention, and can be extrapolated to other types of aircraft. Trajectories predicted through the two-stage approach provided estimated time of arrivals with a 30% reduction in standard deviation of the error compared to estimated time of arrival calculated by the FMS. This improved predicted trajectory can subsequently be used to set the sequence and allocate landing slots. Based on the allocated landing slot, the proposed system calculates a speed schedule for the aircraft to meet this landing slot at minimal flight efficiency impact. A novel algorithm is presented that determines this speed schedule without requiring an iterative process in which multiple calls to a trajectory predictor need to be made. The algorithm is based on parameterisation of the trajectory prediction process, allowing the estimate time of arrival to be represented by a polynomial function of the speed schedule, providing an analytical solution to the speed schedule required to meet a set arrival time. The arrival management solution proposed in this thesis leverages the use of existing avionics and communications systems resulting in new value for industry for current investment. The solution therefore supports a transition concept from mixed equipage towards advanced avionics currently under development. Benefits realised under this transition may provide an incentive for ongoing investment in avionics.

Análisis y simulación numérica de problemas electrohidrodinámicos relacionados con el electrospray

La presente tesis es un estudio analítico y numérico del electrospray. En la configuración más sencilla, un caudal constante del líquido a atomizar, que debe tener una cierta conductividad eléctrica, se inyecta en un medio dieléctrico (un gas u otro líquido inmiscible con el primero) a través de un tubo capilar metálico. Entre este tubo y un electrodo lejano se aplica un voltaje continuo que origina un campo eléctrico en el líquido conductor y en el espacio que lo rodea. El campo eléctrico induce una corriente eléctrica en el líquido, que acumula carga en su superficie, y da lugar a un esfuerzo eléctrico sobre la superficie, que tiende a alargarla en la dirección del campo eléctrico. El líquido forma un menisco en el extremo del tubo capilar cuando el campo eléctrico es suficientemente intenso y el caudal suficientemente pequeño. Las variaciones de presión y los esfuerzos viscosos asociados al movimiento del líquido son despreciables en la mayor parte de este menisco, siendo dominantes los esfuerzos eléctrico y de tensión superficial que actúan sobre la superficie del líquido. En el modo de funcionamiento llamado de conochorro, el balance de estos esfuerzos hace que el menisco adopte una forma cónica (el cono de Taylor) en una región intermedia entre el extremo del tubo y la punta del menisco. La velocidad del líquido aumenta al acercarse al vértice del cono, lo cual propicia que las variaciones de la presión en el líquido generadas por la inercia o por la viscosidad entren en juego, desequilibrando el balance de esfuerzos mencionado antes. Como consecuencia, del vértice del cono sale un delgado chorro de líquido, que transporta la carga eléctrica que se acumula en la superficie. La acción del campo eléctrico tangente a la superficie sobre esta carga origina una tracción eléctrica que tiende a alargar el chorro. Esta tracción no es relevante en el menisco, donde el campo eléctrico tangente a la superficie es muy pequeño, pero se hace importante en el chorro, donde es la causa del movimiento del líquido. Lejos del cono, el chorro puede o bien desarrollar una inestabilidad asimétrica que lo transforma en una espiral (whipping) o bien romperse en un spray de gotas prácticamente monodispersas cargadas eléctricamente. La corriente eléctrica transportada por el líquido es la suma de la corriente de conducción en el interior del líquido y la corriente debida a la convección de la carga acumulada en su superficie. La primera domina en el menisco y la segunda en el chorro lejano, mientras que las dos son comparables en una región intermedia de transferencia de corriente situada al comienzo del chorro aunque aguas abajo de la región de transición cono-chorro, en la que el menisco deja de ser un cono de Taylor. Para un campo exterior dado, la acumulación de carga eléctrica en la superficie del líquido reduce el campo eléctrico en el interior del mismo, que llega a anularse cuando la carga alcanza un estado final de equilibrio. El tiempo característico de este proceso es el tiempo de relajación dieléctrica, que es una propiedad del líquido. Cuando el tiempo de residencia del líquido en la región de transición cono-chorro (o en otra región del campo fluido) es grande frente al tiempo de relajación dieléctrica, la carga superficial sigue una sucesión de estados de equilibrio y apantalla al líquido del campo exterior. Cuando esta condición deja de cumplirse, aparecen efectos de relajación de carga, que se traducen en que el campo exterior penetra en el líquido, a no ser que su constante dieléctrica sea muy alta, en cuyo caso el campo inducido por la carga de polarización evita la entrada del campo exterior en el menisco y en una cierta región del chorro. La carga eléctrica en equilibrio en la superficie de un menisco cónico intensifica el campo eléctrico y determina su variación espacial hasta distancias aguas abajo del menisco del orden de su tamaño. Este campo, calculado por Taylor, es independiente del voltaje aplicado, por lo que las condiciones locales del flujo y el valor de la corriente eléctrica son también independientes del voltaje en tanto los tamaños de las regiones que determinan estas propiedades sean pequeños frente al tamaño del menisco. Los resultados experimentales publicados en la literatura muestran que existe un caudal mínimo para el que el modo cono-chorro que acabamos de describir deja de existir. El valor medio y la desviación típica de la distribución de tamaños de las gotas generadas por un electrospray son mínimos cuando se opera cerca del caudal mínimo. A pesar de que los mecanismos responsables del caudal mínimo han sido muy estudiados, no hay aún una teoría completa del mismo, si bien su existencia parece estar ligada a la aparición de efectos de relajación de carga en la región de transición cono-chorro. En esta tesis, se presentan estimaciones de orden de magnitud, algunas existentes y otras nuevas, que muestran los balances dominantes responsables de las distintas regiones de la estructura asintótica de la solución en varios casos de interés. Cuando la inercia del líquido juega un papel en la transición cono-chorro, los resultados muestran que la región de transferencia de corriente, donde la mayor parte de la corriente pasa a la superficie, está en el chorro aguas abajo de la región de transición cono-chorro. Los efectos de relajación de carga aparecen de forma simultánea en el chorro y la región de transición cuando el caudal se disminuye hasta valores de un cierto orden. Para caudales aún menores, los efectos de relajación de carga se notan en el menisco, en una región grande comparada con la de transición cono-chorro. Cuando el efecto de las fuerzas de viscosidad es dominante en la región de transición, la región de transferencia de corriente está en el chorro pero muy próxima a la región de transición cono-chorro. Al ir disminuyendo el caudal, los efectos de relajación de carga aparecen progresivamente en el chorro, en la región de transición y por último en el menisco. Cuando el caudal es mucho mayor que el mínimo del modo cono-chorro, el menisco deja de ser cónico. El campo eléctrico debido al voltaje aplicado domina en la región de transferencia de corriente, y tanto la corriente eléctrica como el tamaño de las diferentes regiones del problema pasan a depender del voltaje aplicado. Como resultado de esta dependencia, el plano caudal-voltaje se divide en diferentes regiones que se analizan separadamente. Para caudales suficientemente grandes, la inercia del líquido termina dominando frente a las fuerzas de la viscosidad. Estos resultados teóricos se han validado con simulaciones numéricas. Para ello se ha formulado un modelo simplificado del flujo, el campo eléctrico y el transporte de carga en el menisco y el chorro del electrospray. El movimiento del líquido se supone casi unidireccional y se describe usando la aproximación de Cosserat para un chorro esbelto. Esta aproximación, ampliamente usada en la literatura, permite simular con relativa facilidad múltiples casos y cubrir amplios rangos de valores de los parámetros reteniendo los efectos de la viscosidad y la inercia del líquido. Los campos eléctricos dentro y fuera del liquido están acoplados y se calculan sin simplificación alguna usando un método de elementos de contorno. La solución estacionaria del problema se calcula mediante un método iterativo. Para explorar el espacio de los parámetros, se comienza calculando una solución para valores fijos de las propiedades del líquido, el voltaje aplicado y el caudal. A continuación, se usa un método de continuación que permite delinear la frontera del dominio de existencia del modo cono-chorro, donde el método iterativo deja de converger. Cuando el efecto de la inercia del líquido domina en la región de transición cono-chorro, el caudal mínimo para el cual el método iterativo deja de converger es del orden del valor estimado del caudal para el que comienza a haber efectos de relajación de carga en el chorro y el cono. Aunque las simulaciones no convergen por debajo de dicho caudal, el valor de la corriente eléctrica para valores del caudal ligeramente mayores parece ajustarse a las estimaciones para caudales menores, reflejando un posible cambio en los balances aplicables. Por el contrario, cuando las fuerzas viscosas dominan en la región de transición, se pueden obtener soluciones estacionarias para caudales bastante menores que aquel para el que aparecen efectos de relajación de carga en la región de transición cono-chorro. Los resultados numéricos obtenidos para estos pequeños caudales se ajustan perfectamente a las estimaciones de orden de magnitud que se describen en la memoria. Por último, se incluyen como anexos dos estudios teóricos que han surgido de forma natural durante el desarrollo de la tesis. El primero hace referencia a la singularidad en el campo eléctrico que aparece en la línea de contacto entre el líquido y el tubo capilar en la mayoría de las simulaciones. Primero se estudia en qué situaciones el campo eléctrico tiende a infinito en la línea de contacto. Después, se comprueba que dicha singularidad no supone un fallo en la descripción del problema y que además no afecta a la solución lejos de la línea de contacto. También se analiza si los esfuerzos eléctricos infinitamente grandes a los que da lugar dicha singularidad pueden ser compensados por el resto de esfuerzos que actúan en la superficie del líquido. El segundo estudio busca determinar el tamaño de la región de apantallamiento en un chorro de líquido dieléctrico sin carga superficial. En esta región, el campo exterior es compensado parcialmente por el campo que induce la carga de polarización en la superficie del líquido, de forma que en el interior del líquido el campo eléctrico es mucho menor que en el exterior. Una región como ésta aparece en las estimaciones cuando los efectos de relajación de carga son importantes en la región de transferencia de corriente en el chorro. ABSTRACT This aim of this dissertation is a theoretical and numerical analysis of an electrospray. In its most simple configuration, a constant flow rate of the liquid to be atomized, which has to be an electrical conductor, is injected into a dielectric medium (a gas or another inmiscible fluid) through a metallic capillary tube. A constant voltage is applied between this tube and a distant electrode that produces an electric field in the liquid and the surrounding medium. This electric field induces an electric current in the liquid that accumulates charge at its surface and leads to electric stresses that stretch the surface in the direction of the electric field. A meniscus appears on the end of the capillary tube when the electric field is sufficiently high and the flow rate is small. Pressure variations and viscous stresses due to the motion of the liquid are negligible in most of the meniscus, where normal electric and surface tension stresses acting on the surface are dominant. In the so-called cone-jet mode, the balance of these stresses forces the surface to adopt a conical shape -Taylor cone- in a intermediate region between the end of the tube and the tip of the meniscus. When approaching the cone apex, the velocity of the liquid increases and leads to pressure variations that eventually disturb the balance of surfaces tension and electric stresses. A thin jet emerges then from the tip of the meniscus that transports the charge accumulated at its surface. The electric field tangent to the surface of the jet acts on this charge and continuously stretches the jet. This electric force is negligible in the meniscus, where the component of the electric field tangent to the surface is small, but becomes very important in the jet. Far from the cone, the jet can either develop an asymmetrical instability named “whipping”, whereby the jet winds into a spiral, or break into a spray of small, nearly monodisperse, charged droplets. The electric current transported by the liquid has two components, the conduction current in the bulk of the liquid and the convection current due to the transport of the surface charge by the flow. The first component dominates in the meniscus, the second one in the far jet, and both are comparable in a current transfer region located in the jet downstream of the cone-jet transition region where the meniscus ceases to be a Taylor cone. Given an external electric field, the charge that accumulates at the surface of the liquid reduces the electric field inside the liquid, until an equilibrium is reached in which the electric field induced by the surface charge counters the external electric field and shields the liquid from this field. The characteristic time of this process is the electric relaxation time, which is a property of the liquid. When the residence time of the liquid in the cone-jet transition region (or in other region of the flow) is greater than the electric relaxation time, the surface charge follows a succession of equilibrium states and continuously shield the liquid from the external field. When this condition is not satisfied, charge relaxation effects appear and the external field penetrates into the liquid unless the liquid permittivity is large. For very polar liquids, the field due to the polarization charge at the surface prevents the external field from entering the liquid in the cone and in certain region of the jet. The charge at the surface of a conical meniscus intensifies the electric field around the cone, determining its spatial variation up to distances downstream of the apex of the order of the size of the meniscus. This electric field, first computed by Taylor, is independent of the applied voltage. Therefore local flow characteristics and the electric current carried by the jet are also independent of the applied voltage provided the size of the regions that determine these magnitudes are small compared with the size of the meniscus. Many experiments in the literature show the existence of a minimum flow rate below which the cone-jet mode cannot be established. The mean value and the standard deviation of the electrospray droplet size distribution are minimum when the device is operated near the minimum flow rate. There is no complete explanation of the minimum flow rate, even though possible mechanisms have been extensively studied. The existence of a minimum flow rate seems to be connected with the appearance of charge relaxation effects in the transition region. In this dissertation, order of magnitude estimations are worked out that show the dominant balances in the different regions of the asymptotic structure of the solution for different conditions of interest. When the inertia of the liquid plays a role in the cone-jet transition region, the region where most of the electric current is transfered to the surface lies in the jet downstream the cone-jet transition region. When the flow rate decreases to a certain value, charge relaxation effects appear simultaneously in the jet and in the transition region. For smaller values of the flow rate, charge relaxation effects are important in a region of the meniscus larger than the transition region. When viscous forces dominate in the flow in the cone-jet transition region, the current transfer region is located in the jet immediately after the transition region. When flow rate is decreased, charge relaxation effects appears gradually, first in the jet, then in the transition region, and finally in the meniscus. When flow rate is much larger than the cone-jet mode minimum, the meniscus ceases to be a cone. The electric current and the structure of the solution begin to depend on the applied voltage. The flow rate-voltage plane splits into different regions that are analyzed separately. For sufficiently large flow rates, the effect of the inertia of the liquid always becomes greater than the effect of the viscous forces. A set of numerical simulations have been carried out in order to validate the theoretical results. A simplified model of the problem has been devised to compute the flow, the electric field and the surface charge in the meniscus and the jet of an electrospray. The motion of the liquid is assumed to be quasi-unidirectional and described by Cosserat’s approximation for a slender jet. This widely used approximation allows to easily compute multiple configurations and to explore wide ranges of values of the governing parameters, retaining the effects of the viscosity and the inertia of the liquid. Electric fields inside and outside the liquid are coupled and are computed without any simplification using a boundary elements method. The stationary solution of the problem is obtained by means of an iterative method. To explore the parameter space, a solution is first computed for a set of values of the liquid properties, the flow rate and the applied voltage, an then a continuation method is used to find the boundaries of the cone-jet mode domain of existence, where the iterative method ceases to converge. When the inertia of the liquid dominates in the cone-jet transition region, the iterative method ceases to converge for values of the flow rate for which order-of-magnitude estimates first predict charge relaxation effects to be important in the cone and the jet. The electric current computed for values of the flow rate slightly above the minimum for which convergence is obtained seems to agree with estimates worked out for lower flow rates. When viscous forces dominate in the transition region, stationary solutions can be obtained for flow rates significantly smaller than the one for which charge relaxation effects first appear in the transition region. Numerical results obtained for those small values of the flow rate agree with our order of magnitude estimates. Theoretical analyses of two issues that have arisen naturally during the thesis are summarized in two appendices. The first appendix contains a study of the singularity of the electric field that most of the simulations show at the contact line between the liquid and the capillary tube. The electric field near the contact line is analyzed to determine the ranges of geometrical configurations and liquid permittivity where a singularity appears. Further estimates show that this singularity does not entail a failure in the description of the problem and does not affect the solution far from the contact line. The infinite electric stresses that appear at the contact line can be effectively balanced by surface tension. The second appendix contains an analysis of the size and slenderness of the shielded region of a dielectric liquid in the absence of free surface charge. In this region, the external electric field is partially offset by the polarization charge so that the inner electric field is much lower than the outer one. A similar region appears in the estimates when charge relaxation effects are important in the current transfer region.

The C-terminal SET domains of ALL-1 and TRITHORAX interact with the INI1 and SNR1 proteins, components of the SWI/SNF complex

The ALL-1 gene was discovered by virtue of its involvement in human acute leukemia. Its Drosophila homolog trithorax (trx) is a member of the trx-Polycomb gene family, which maintains correct spatial expression of the Antennapedia and bithorax complexes during embryogenesis. The C-terminal SET domain of ALL-1 and TRITHORAX (TRX) is a 150-aa motif, highly conserved during evolution. We performed yeast two hybrid screening of Drosophila cDNA library and detected interaction between a TRX polypeptide spanning SET and the SNR1 protein. SNR1 is a product of snr1, which is classified as a trx group gene. We found parallel interaction in yeast between the SET domain of ALL-1 and the human homolog of SNR1, INI1 (hSNF5). These results were confirmed by in vitro binding studies and by demonstrating coimmunoprecipitation of the proteins from cultured cells and/or transgenic flies. Epitope-tagged SNR1 was detected at discrete sites on larval salivary gland polytene chromosomes, and these sites colocalized with around one-half of TRX binding sites. Because SNR1 and INI1 are constituents of the SWI/SNF complex, which acts to remodel chromatin and consequently to activate transcription, the interactions we observed suggest a mechanism by which the SWI/SNF complex is recruited to ALL-1/trx targets through physical interactions between the C-terminal domains of ALL-1 and TRX and INI1/SNR1.

Crystal structure of chemically synthesized [N33A] stromal cell-derived factor 1α, a potent ligand for the HIV-1 “fusin” coreceptor

Stromal cell-derived factor-1α (SDF-1α ) is a member of the chemokine superfamily and functions as a growth factor and chemoattractant through activation of CXCR4/LESTR/Fusin, a G protein-coupled receptor. This receptor also functions as a coreceptor for T-tropic syncytium-inducing strains of HIV-1. SDF-1α antagonizes infectivity of these strains by competing with gp120 for binding to the receptor. The crystal structure of a variant SDF-1α ([N33A]SDF-1α ) prepared by total chemical synthesis has been refined to 2.2-Å resolution. Although SDF-1α adopts a typical chemokine β-β-β-α topology, the packing of the α-helix against the β-sheet is strikingly different. Comparison of SDF-1α with other chemokine structures confirms the hypothesis that SDF-1α may be either an ancestral protein from which all other chemokines evolved or the chemokine that is the least divergent from a primordial chemokine. The structure of SDF-1α reveals a positively charged surface ideal for binding to the negatively charged extracellular loops of the CXCR4 HIV-1 coreceptor. This ionic complementarity is likely to promote the interaction of the mobile N-terminal segment of SDF-1α with interhelical sites of the receptor, resulting in a biological response.

Iron regulatory protein 1 is not required for the modulation of ferritin and transferrin receptor expression by iron in a murine pro-B lymphocyte cell line

Iron regulatory proteins (IRPs) are cytoplasmic RNA binding proteins that are central components of a sensory and regulatory network that modulates vertebrate iron homeostasis. IRPs regulate iron metabolism by binding to iron responsive element(s) (IREs) in the 5′ or 3′ untranslated region of ferritin or transferrin receptor (TfR) mRNAs. Two IRPs, IRP1 and IRP2, have been identified previously. IRP1 exhibits two mutually exclusive functions as an RNA binding protein or as the cytosolic isoform of aconitase. We demonstrate that the Ba/F3 family of murine pro-B lymphocytes represents the first example of a mammalian cell line that fails to express IRP1 protein or mRNA. First, all of the IRE binding activity in Ba/F3-gp55 cells is attributable to IRP2. Second, synthesis of IRP2, but not of IRP1, is detectable in Ba/F3-gp55 cells. Third, the Ba/F3 family of cells express IRP2 mRNA at a level similar to other murine cell lines, but IRP1 mRNA is not detectable. In the Ba/F3 family of cells, alterations in iron status modulated ferritin biosynthesis and TfR mRNA level over as much as a 20- and 14-fold range, respectively. We conclude that IRP1 is not essential for regulation of ferritin or TfR expression by iron and that IRP2 can act as the sole IRE-dependent mediator of cellular iron homeostasis.

Copolymer 1 induces T cells of the T helper type 2 that crossreact with myelin basic protein and suppress experimental autoimmune encephalomyelitis

The synthetic amino acid copolymer copolymer 1 (Cop 1) suppresses experimental autoimmune encephalomyelitis (EAE) and is beneficial in multiple sclerosis. To further understand Cop 1 suppressive activity, we studied the cytokine secretion profile of various Cop 1-induced T cell lines and clones. Unlike T cell lines induced by myelin basic protein (MBP), which secreted either T cell helper type 1 (Th1) or both Th1 and Th2 cytokines, the T cell lines/clones induced by Cop 1 showed a progressively polarized development toward the Th2 pathway, until they completely lost the ability to secrete Th1 cytokines. Our findings indicate that the polarization of the Cop 1-induced lines did not result from the immunization vehicle or the in vitro growing conditions, but rather from the tendency of Cop 1 to preferentially induce a Th2 response. The response of all of the Cop 1 specific lines/clones, which were originated in the (SJL/J×BALB/c)F1 hybrids, was restricted to the BALB/c parental haplotype. Even though the Cop 1-induced T cells had not been exposed to the autoantigen MBP, they crossreacted with MBP by secretion of interleukin (IL)-4, IL-6, and IL-10. Administration of these T cells in vivo resulted in suppression of EAE induced by whole mouse spinal cord homogenate, in which several autoantigens may be involved. Secretion of anti-inflammatory cytokines by Cop 1-induced suppressor cells, in response to either Cop 1 or MBP, may explain the therapeutic effect of Cop 1 in EAE and in multiple sclerosis.

PV-1 is a component of the fenestral and stomatal diaphragms in fenestrated endothelia

PV-1 is a novel endothelial protein shown by immunocytochemical tests to be specifically associated with the stomatal diaphragms of caveolae in lung endothelium. Although the highest expression levels of both mRNA and protein are in the lung, PV-1 also has been found to be expressed in other organs. Using a specific antibody to the extracellular domain of PV-1, we have extended the survey on the presence of this protein at light and electron microscope level in several rat organs. Here we show that by immunofluorescence the antibody recognizes with high specificity the endothelium of the fenestrated peritubular capillaries of the kidney and those of the intestinal villi, pancreas, and adrenals. By immunolocalization at electron microscope level, the antibody recognizes specifically the diaphragms of the fenestrae and the stomatal diaphragms of caveolae and transendothelial channels in the endothelia of these vascular beds. No signal was detected in the continuous endothelium of the heart, skeletal muscle, intestinal muscularis, or brain capillaries or the nondiaphragmed fenestrated endothelium of kidney glomeruli. Taken together, our findings define the only antigen to be localized thus far in fenestral diaphragms. They also show that the stomatal diaphragms of caveolae and transendothelial channels and the fenestral diaphragms might be biochemically related, in addition to being morphologically similar structures.

The amphiphysin-like protein 1 (ALP1) interacts functionally with the cABL tyrosine kinase and may play a role in cytoskeletal regulation

cABL is a protooncogene, activated in a subset of human leukemias, whose protein product is a nonreceptor tyrosine kinase of unknown function. cABL has a complex structure that includes several domains and motifs found in proteins implicated in signal transduction pathways. An approach to elucidate cABL function is to identify proteins that interact directly with cABL and that may serve as regulators or effectors of its activity. To this end, a protein-interaction screen of a phage expression library was undertaken to identify proteins that interact with specific domains of cABL. An SH3-domain-containing protein has been identified that interacts with sequences in the cABL carboxyl terminus. The cDNA encoding ALP1 (amphiphysin-like protein 1) was isolated from a 16-day mouse embryo. ALP1 has high homology to BIN1, a recently cloned myc-interacting protein, and also shows significant homology to amphiphysin, a neuronal protein cloned from human and chicken. The amino terminus has homology to two yeast proteins, Rvs167 and Rvs161, which are involved in cell entry into stationary phase and cytoskeletal organization. ALP1 binds cABL in vitro and in vivo. Expression of ALP1 results in morphological transformation of NIH 3T3 fibroblasts in a cABL-dependent manner. The properties of ALP1 suggest that it may be involved in possible cytoskeletal functions of the cABL kinase. Additionally, these results provide further evidence for the importance of the cABL carboxyl terminus and its binding proteins in the regulation of cABL function.

Phosphorylation of protein kinase N by phosphoinositide-dependent protein kinase-1 mediates insulin signals to the actin cytoskeleton

Growth factors such as insulin regulate phosphatidylinositol 3-kinase-dependent actin cytoskeleton rearrangement in many types of cells. However, the mechanism by which the insulin signal is transmitted to the actin cytoskeleton remains largely unknown. Yeast two-hybrid screening revealed that the phosphatidylinositol 3-kinase downstream effector phosphoinositide-dependent protein kinase-1 (PDK1) interacted with protein kinase N (PKN), a Rho-binding Ser/Thr protein kinase potentially implicated in a variety of cellular events, including phosphorylation of cytoskeletal components. PDK1 and PKN interacted in vitro and in intact cells, and this interaction was mediated by the kinase domain of PDK1 and the carboxyl terminus of PKN. In addition to a direct interaction, PDK1 also phosphorylated Thr774 in the activation loop and activated PKN. Insulin treatment or ectopic expression of the wild-type PDK1 or PKN, but not protein kinase Cζ, induced actin cytoskeleton reorganization and membrane ruffling in 3T3-L1 fibroblasts and Rat1 cells that stably express the insulin receptor (Rat1-IR). However, the insulin-stimulated actin cytoskeleton reorganization in Rat1-IR cells was prevented by expression of kinase-defective PDK1 or PDK1-phosphorylation site-mutated PKN. Thus, phosphorylation by PDK1 appears to be necessary for PKN to transduce signals from the insulin receptor to the actin cytoskeleton.

Measuring the thickness of the human cerebral cortex from magnetic resonance images

Accurate and automated methods for measuring the thickness of human cerebral cortex could provide powerful tools for diagnosing and studying a variety of neurodegenerative and psychiatric disorders. Manual methods for estimating cortical thickness from neuroimaging data are labor intensive, requiring several days of effort by a trained anatomist. Furthermore, the highly folded nature of the cortex is problematic for manual techniques, frequently resulting in measurement errors in regions in which the cortical surface is not perpendicular to any of the cardinal axes. As a consequence, it has been impractical to obtain accurate thickness estimates for the entire cortex in individual subjects, or group statistics for patient or control populations. Here, we present an automated method for accurately measuring the thickness of the cerebral cortex across the entire brain and for generating cross-subject statistics in a coordinate system based on cortical anatomy. The intersubject standard deviation of the thickness measures is shown to be less than 0.5 mm, implying the ability to detect focal atrophy in small populations or even individual subjects. The reliability and accuracy of this new method are assessed by within-subject test–retest studies, as well as by comparison of cross-subject regional thickness measures with published values.