Development of an Elevated Temperature Loop Heat Pipe for Space Applications and Investigation of Non Condensable Gas Impact on its Performance

Un caloducto en bucle cerrado o Loop Heat Pipe (LHP) es un dispositivo de transferencia de calor cuyo principio de operación se basa en la evaporación/condensación de un fluido de trabajo, que es bombeado a través de un circuito cerrado gracias a fuerzas de capilaridad. Gracias a su flexibilidad, su baja masa y su mínimo (incluso nulo) consumo de potencia, su principal aplicación ha sido identificada como parte del subsistema de control térmico de vehículos espaciales. En el presente trabajo se ha desarrollado un LHP capaz de funcionar eficientemente a temperaturas de hasta 125 oC, siguiendo la actual tendencia de los equipos a bordo de satélites de incrementar su temperatura de operación. En la selección del diseño optimo para dicho LHP, la compatibilidad entre materiales y fluido de trabajo se identificó como uno de los puntos clave. Para seleccionar la mejor combinación, se llevó a cabo una exhaustiva revisión del estado del arte, además de un estudio especifico que incluía el desarrollo de un banco de ensayos de compatibilidad. Como conclusión, la combinación seleccionada como la candidata idónea para ser integrada en el LHP capaz de operar hasta 125 oC fue un evaporador de acero inoxidable, líneas de titanio y amoniaco como fluido de trabajo. En esa línea se diseñó y fabricó un prototipo para ensayos y se desarrolló un modelo de simulación con EcosimPro para evaluar sus prestaciones. Se concluyó que el diseño era adecuado para el rango de operación definido. La incompatibilidad entre el fluido de trabajo y los materiales del LHP está ligada a la generación de gases no condensables. Para un estudio más detallado de los efectos de dichos gases en el funcionamiento del LHP se analizó su comportamiento con diferentes cantidades de nitrógeno inyectadas en su cámara de compensación, simulando un gas no condensable formado en el interior del dispositivo. El estudio se basó en el análisis de las temperaturas medidas experimentalmente a distintos niveles de potencia y temperatura de sumidero o fuente fría. Adicionalmente, dichos resultados se compararon con las predicciones obtenidas por medio del modelo en EcosimPro. Las principales conclusiones obtenidas fueron dos. La primera indica que una cantidad de gas no condensable más de dos veces mayor que la cantidad generada al final de la vida de un satélite típico de telecomunicaciones (15 años) tiene efectos casi despreciables en el funcionamiento del LHP. La segunda es que el principal efecto del gas no condensable es una disminución de la conductancia térmica, especialmente a bajas potencias y temperaturas de sumidero. El efecto es más significativo cuanto mayor es la cantidad de gas añadida. Asimismo, durante la campaña de ensayos se observó un fenómeno no esperado para grandes cantidades de gas no condensable. Dicho fenómeno consiste en un comportamiento oscilatorio, detectado tanto en los ensayos como en la simulación. Este efecto es susceptible de una investigación más profunda y los resultados obtenidos pueden constituir la base para dicha tarea. ABSTRACT Loop Heat Pipes (LHPs) are heat transfer devices whose operating principle is based on the evaporation/condensation of a working fluid, and which use capillary pumping forces to ensure the fluid circulation. Thanks to their flexibility, low mass and minimum (even null) power consumption, their main application has been identified as part of the thermal control subsystem in spacecraft. In the present work, an LHP able to operate efficiently up to 125 oC has been developed, which is in line with the current tendency of satellite on-board equipment to increase their operating temperatures. In selecting the optimal LHP design for the elevated temperature application, the compatibility between the materials and working fluid has been identified as one of the main drivers. An extensive literature review and a dedicated trade-off were performed, in order to select the optimal combination of fluids and materials for the LHP. The trade-off included the development of a dedicated compatibility test stand. In conclusion, the combination of stainless steel evaporator, titanium piping and ammonia as working fluid was selected as the best candidate to operate up to 125 oC. An LHP prototype was designed and manufactured and a simulation model in EcosimPro was developed to evaluate its performance. The first conclusion was that the defined LHP was suitable for the defined operational range. Incompatibility between the working fluid and LHP materials is linked to Non Condensable Gas (NCG) generation. Therefore, the behaviour of the LHP developed with different amounts of nitrogen injected in its compensation chamber to simulate NCG generation, was analyzed. The LHP performance was studied by analysis of the test results at different temperatures and power levels. The test results were also compared to simulations in EcosimPro. Two additional conclusions can be drawn: (i) the effects of an amount of more than two times the expected NCG at the end of life of a typical telecommunications satellite (15 years) is almost negligible on the LHP operation, and (ii) the main effect of the NCG is a decrease in the LHP thermal conductance, especially at low temperatures and low power levels. This decrease is more significant with the progressive addition of NCG. An unexpected phenomenon was observed in the LHP operation with large NCG amounts. Namely, an oscillatory behaviour, which was observed both in the tests and the simulation. This effect provides the basis for further studies concerning oscillations in LHPs.

Direct Vlasov simulations of electron-attracting cylindrical Langmuir probes in flowing plasmas

Current collection by positively polarized cylindrical Langmuir probes immersed in flowing plasmas is analyzed using a non-stationary direct Vlasov-Poisson code. A detailed description of plasma density spatial structure as a function of the probe-to-plasma relative velocity U is presented. Within the considered parametric domain, the well-known electron density maximum close to the probe is weakly affected by U. However, in the probe wake side, the electron density minimum becomes deeper as U increases and a rarified plasma region appears. Sheath radius is larger at the wake than at the front side. Electron and ion distribution functions show specific features that are the signature of probe motion. In particular, the ion distribution function at the probe front side exhibits a filament with positive radial velocity. It corresponds to a population of rammed ions that were reflected by the electric field close to the positively biased probe. Numerical simulations reveal that two populations of trapped electrons exist: one orbiting around the probe and the other with trajectories confined at the probe front side. The latter helps to neutralize the reflected ions, thus explaining a paradox in past probe theory.

Modified Gutenberg-Richter coefficient for damage evaluation in reinforced concrete structures subjected to seismic simulations on a shaking table

This paper presents analysis and discussion of the b- and ib-values calculated from the acoustic emission (AE) signals recorded during dynamic shake-table tests conducted on a reinforced concrete (RC) frame subjected to several uniaxial seismic simulations of increasing intensity until collapse. The intensity of shaking was controlled by the peak acceleration applied to the shake-table in each seismic simulation, and it ranged from 0.08 to 0.47 times the acceleration of gravity. The numerous spurious signals not related to concrete damage that inevitably contaminate AE measurements obtained from complex dynamic shake-table tests were properly filtered with an RMS filter and the use of guard sensors. Comparing the b- and ib-values calculated through the tests with the actual level of macro-cracking and damage observed during testing, it was concluded that the limit value of 0.05 proposed in previous research to determine the onset of macro-cracks should be revised in the case of earthquake-type dynamic loading. Finally, the b- and ibvalues were compared with the damage endured by the RC frame evaluated both visually and quantitatively in terms of the inter-story drift index.

Multiscale modeling of the plastic behaviour in single crystal tungsten: from atomistic to crystal plasticity simulations

En una planta de fusión, los materiales en contacto con el plasma así como los materiales de primera pared experimentan condiciones particularmente hostiles al estar expuestos a altos flujos de partículas, neutrones y grandes cargas térmicas. Como consecuencia de estas diferentes y complejas condiciones de trabajo, el estudio, desarrollo y diseño de estos materiales es uno de los más importantes retos que ha surgido en los últimos años para la comunidad científica en el campo de los materiales y la energía. Debido a su baja tasa de erosión, alta resistencia al sputtering, alta conductividad térmica, muy alto punto de fusión y baja retención de tritio, el tungsteno (wolframio) es un importante candidato como material de primera pared y como posible material estructural avanzado en fusión por confinamiento magnético e inercial. Sin embargo, el tiempo de vida del tungsteno viene controlado por diversos factores como son su respuesta termo-mecánica en la superficie, la posibilidad de fusión y el fallo por acumulación de helio. Es por ello que el tiempo de vida limitado por la respuesta mecánica del tungsteno (W), y en particular su fragilidad, sean dos importantes aspectos que tienes que ser investigados. El comportamiento plástico en materiales refractarios con estructura cristalina cúbica centrada en las caras (bcc) como el tungsteno está gobernado por las dislocaciones de tipo tornillo a escala atómica y por conjuntos e interacciones de dislocaciones a escalas más grandes. El modelado de este complejo comportamiento requiere la aplicación de métodos capaces de resolver de forma rigurosa cada una de las escalas. El trabajo que se presenta en esta tesis propone un modelado multiescala que es capaz de dar respuestas ingenieriles a las solicitudes técnicas del tungsteno, y que a su vez está apoyado por la rigurosa física subyacente a extensas simulaciones atomísticas. En primer lugar, las propiedades estáticas y dinámicas de las dislocaciones de tipo tornillo en cinco potenciales interatómicos de tungsteno son comparadas, determinando cuáles de ellos garantizan una mayor fidelidad física y eficiencia computacional. Las grandes tasas de deformación asociadas a las técnicas de dinámica molecular hacen que las funciones de movilidad de las dislocaciones obtenidas no puedan ser utilizadas en los siguientes pasos del modelado multiescala. En este trabajo, proponemos dos métodos alternativos para obtener las funciones de movilidad de las dislocaciones: un modelo Monte Cario cinético y expresiones analíticas. El conjunto de parámetros necesarios para formular el modelo de Monte Cario cinético y la ley de movilidad analítica son calculados atomísticamente. Estos parámetros incluyen, pero no se limitan a: la determinación de las entalpias y energías de formación de las parejas de escalones que forman las dislocaciones, la parametrización de los efectos de no Schmid característicos en materiales bcc,etc. Conociendo la ley de movilidad de las dislocaciones en función del esfuerzo aplicado y la temperatura, se introduce esta relación como ecuación de flujo dentro de un modelo de plasticidad cristalina. La predicción del modelo sobre la dependencia del límite de fluencia con la temperatura es validada experimentalmente con ensayos uniaxiales en tungsteno monocristalino. A continuación, se calcula el límite de fluencia al aplicar ensayos uniaxiales de tensión para un conjunto de orientaciones cristalográticas dentro del triángulo estándar variando la tasa de deformación y la temperatura de los ensayos. Finalmente, y con el objetivo de ser capaces de predecir una respuesta más dúctil del tungsteno para una variedad de estados de carga, se realizan ensayos biaxiales de tensión sobre algunas de las orientaciones cristalográficas ya estudiadas en función de la temperatura.-------------------------------------------------------------------------ABSTRACT ----------------------------------------------------------Tungsten and tungsten alloys are being considered as leading candidates for structural and functional materials in future fusion energy devices. The most attractive properties of tungsten for the design of magnetic and inertial fusion energy reactors are its high melting point, high thermal conductivity, low sputtering yield and low longterm disposal radioactive footprint. However, tungsten also presents a very low fracture toughness, mostly associated with inter-granular failure and bulk plasticity, that limits its applications. As a result of these various and complex conditions of work, the study, development and design of these materials is one of the most important challenges that have emerged in recent years to the scientific community in the field of materials for energy applications. The plastic behavior of body-centered cubic (bcc) refractory metals like tungsten is governed by the kink-pair mediated thermally activated motion of h¿ (\1 11)i screw dislocations on the atomistic scale and by ensembles and interactions of dislocations at larger scales. Modeling this complex behavior requires the application of methods capable of resolving rigorously each relevant scale. The work presented in this thesis proposes a multiscale model approach that gives engineering-level responses to the technical specifications required for the use of tungsten in fusion energy reactors, and it is also supported by the rigorous underlying physics of extensive atomistic simulations. First, the static and dynamic properties of screw dislocations in five interatomic potentials for tungsten are compared, determining which of these ensure greater physical fidelity and computational efficiency. The large strain rates associated with molecular dynamics techniques make the dislocation mobility functions obtained not suitable to be used in the next steps of the multiscale model. Therefore, it is necessary to employ mobility laws obtained from a different method. In this work, we suggest two alternative methods to get the dislocation mobility functions: a kinetic Monte Carlo model and analytical expressions. The set of parameters needed to formulate the kinetic Monte Carlo model and the analytical mobility law are calculated atomistically. These parameters include, but are not limited to: enthalpy and energy barriers of kink-pairs as a function of the stress, width of the kink-pairs, non-Schmid effects ( both twinning-antitwinning asymmetry and non-glide stresses), etc. The function relating dislocation velocity with applied stress and temperature is used as the main source of constitutive information into a dislocation-based crystal plasticity framework. We validate the dependence of the yield strength with the temperature predicted by the model against existing experimental data of tensile tests in singlecrystal tungsten, with excellent agreement between the simulations and the measured data. We then extend the model to a number of crystallographic orientations uniformly distributed in the standard triangle and study the effects of temperature and strain rate. Finally, we perform biaxial tensile tests and provide the yield surface as a function of the temperature for some of the crystallographic orientations explored in the uniaxial tensile tests.

On the role of global flow instability analysis in closed loop flow control

Control of linear flow instabilities has been demonstrated to be an effective theoretical flow control methodology, capable of modifying transitional flows on canonical geometries such as the plane channel and the flat-plate boundary layer. Extending the well-developed theoretical flow control techniques to flows over or through complex geometries requires addressing the issue of efficient capturing of the leading members of the global eigenspectrum pertinent to such flows. The present contribution describes state-of-the-art modal global instability analysis methodologies recently developed in our group, based on matrix formation and time-stepping, respectively. The relative performance of these algorithms is assessed on the recovery of BiGlobal and TriGlobal eigenspectra in the spanwise periodic and the cubic lid-driven cavity, respectively; the adjoint eigenspectrum in the latter flow is recovered for the first time. For three-dimensional flows without any homogeneous spatial direction, the time-stepping methodology was found to outperform the matrix-forming approach and permit recovering the leading TriGlobal eigenmodes in an three-dimensional open cavity of aspect ratio L : D : W = 5 : 1 : 1; theoretical flow control of this configuration is underway.

Contributions to the Resilience Management in the Internet of Things

El auge del "Internet de las Cosas" (IoT, "Internet of Things") y sus tecnologías asociadas han permitido su aplicación en diversos dominios de la aplicación, entre los que se encuentran la monitorización de ecosistemas forestales, la gestión de catástrofes y emergencias, la domótica, la automatización industrial, los servicios para ciudades inteligentes, la eficiencia energética de edificios, la detección de intrusos, la gestión de desastres y emergencias o la monitorización de señales corporales, entre muchas otras. La desventaja de una red IoT es que una vez desplegada, ésta queda desatendida, es decir queda sujeta, entre otras cosas, a condiciones climáticas cambiantes y expuestas a catástrofes naturales, fallos de software o hardware, o ataques maliciosos de terceros, por lo que se puede considerar que dichas redes son propensas a fallos. El principal requisito de los nodos constituyentes de una red IoT es que estos deben ser capaces de seguir funcionando a pesar de sufrir errores en el propio sistema. La capacidad de la red para recuperarse ante fallos internos y externos inesperados es lo que se conoce actualmente como "Resiliencia" de la red. Por tanto, a la hora de diseñar y desplegar aplicaciones o servicios para IoT, se espera que la red sea tolerante a fallos, que sea auto-configurable, auto-adaptable, auto-optimizable con respecto a nuevas condiciones que puedan aparecer durante su ejecución. Esto lleva al análisis de un problema fundamental en el estudio de las redes IoT, el problema de la "Conectividad". Se dice que una red está conectada si todo par de nodos en la red son capaces de encontrar al menos un camino de comunicación entre ambos. Sin embargo, la red puede desconectarse debido a varias razones, como que se agote la batería, que un nodo sea destruido, etc. Por tanto, se hace necesario gestionar la resiliencia de la red con el objeto de mantener la conectividad entre sus nodos, de tal manera que cada nodo IoT sea capaz de proveer servicios continuos, a otros nodos, a otras redes o, a otros servicios y aplicaciones. En este contexto, el objetivo principal de esta tesis doctoral se centra en el estudio del problema de conectividad IoT, más concretamente en el desarrollo de modelos para el análisis y gestión de la Resiliencia, llevado a la práctica a través de las redes WSN, con el fin de mejorar la capacidad la tolerancia a fallos de los nodos que componen la red. Este reto se aborda teniendo en cuenta dos enfoques distintos, por una parte, a diferencia de otro tipo de redes de dispositivos convencionales, los nodos en una red IoT son propensos a perder la conexión, debido a que se despliegan en entornos aislados, o en entornos con condiciones extremas; por otra parte, los nodos suelen ser recursos con bajas capacidades en términos de procesamiento, almacenamiento y batería, entre otros, por lo que requiere que el diseño de la gestión de su resiliencia sea ligero, distribuido y energéticamente eficiente. En este sentido, esta tesis desarrolla técnicas auto-adaptativas que permiten a una red IoT, desde la perspectiva del control de su topología, ser resiliente ante fallos en sus nodos. Para ello, se utilizan técnicas basadas en lógica difusa y técnicas de control proporcional, integral y derivativa (PID - "proportional-integral-derivative"), con el objeto de mejorar la conectividad de la red, teniendo en cuenta que el consumo de energía debe preservarse tanto como sea posible. De igual manera, se ha tenido en cuenta que el algoritmo de control debe ser distribuido debido a que, en general, los enfoques centralizados no suelen ser factibles a despliegues a gran escala. El presente trabajo de tesis implica varios retos que conciernen a la conectividad de red, entre los que se incluyen: la creación y el análisis de modelos matemáticos que describan la red, una propuesta de sistema de control auto-adaptativo en respuesta a fallos en los nodos, la optimización de los parámetros del sistema de control, la validación mediante una implementación siguiendo un enfoque de ingeniería del software y finalmente la evaluación en una aplicación real. Atendiendo a los retos anteriormente mencionados, el presente trabajo justifica, mediante una análisis matemático, la relación existente entre el "grado de un nodo" (definido como el número de nodos en la vecindad del nodo en cuestión) y la conectividad de la red, y prueba la eficacia de varios tipos de controladores que permiten ajustar la potencia de trasmisión de los nodos de red en respuesta a eventuales fallos, teniendo en cuenta el consumo de energía como parte de los objetivos de control. Así mismo, este trabajo realiza una evaluación y comparación con otros algoritmos representativos; en donde se demuestra que el enfoque desarrollado es más tolerante a fallos aleatorios en los nodos de la red, así como en su eficiencia energética. Adicionalmente, el uso de algoritmos bioinspirados ha permitido la optimización de los parámetros de control de redes dinámicas de gran tamaño. Con respecto a la implementación en un sistema real, se han integrado las propuestas de esta tesis en un modelo de programación OSGi ("Open Services Gateway Initiative") con el objeto de crear un middleware auto-adaptativo que mejore la gestión de la resiliencia, especialmente la reconfiguración en tiempo de ejecución de componentes software cuando se ha producido un fallo. Como conclusión, los resultados de esta tesis doctoral contribuyen a la investigación teórica y, a la aplicación práctica del control resiliente de la topología en redes distribuidas de gran tamaño. Los diseños y algoritmos presentados pueden ser vistos como una prueba novedosa de algunas técnicas para la próxima era de IoT. A continuación, se enuncian de forma resumida las principales contribuciones de esta tesis: (1) Se han analizado matemáticamente propiedades relacionadas con la conectividad de la red. Se estudia, por ejemplo, cómo varía la probabilidad de conexión de la red al modificar el alcance de comunicación de los nodos, así como cuál es el mínimo número de nodos que hay que añadir al sistema desconectado para su re-conexión. (2) Se han propuesto sistemas de control basados en lógica difusa para alcanzar el grado de los nodos deseado, manteniendo la conectividad completa de la red. Se han evaluado diferentes tipos de controladores basados en lógica difusa mediante simulaciones, y los resultados se han comparado con otros algoritmos representativos. (3) Se ha investigado más a fondo, dando un enfoque más simple y aplicable, el sistema de control de doble bucle, y sus parámetros de control se han optimizado empleando algoritmos heurísticos como el método de la entropía cruzada (CE, "Cross Entropy"), la optimización por enjambre de partículas (PSO, "Particle Swarm Optimization"), y la evolución diferencial (DE, "Differential Evolution"). (4) Se han evaluado mediante simulación, la mayoría de los diseños aquí presentados; además, parte de los trabajos se han implementado y validado en una aplicación real combinando técnicas de software auto-adaptativo, como por ejemplo las de una arquitectura orientada a servicios (SOA, "Service-Oriented Architecture"). ABSTRACT The advent of the Internet of Things (IoT) enables a tremendous number of applications, such as forest monitoring, disaster management, home automation, factory automation, smart city, etc. However, various kinds of unexpected disturbances may cause node failure in the IoT, for example battery depletion, software/hardware malfunction issues and malicious attacks. So, it can be considered that the IoT is prone to failure. The ability of the network to recover from unexpected internal and external failures is known as "resilience" of the network. Resilience usually serves as an important non-functional requirement when designing IoT, which can further be broken down into "self-*" properties, such as self-adaptive, self-healing, self-configuring, self-optimization, etc. One of the consequences that node failure brings to the IoT is that some nodes may be disconnected from others, such that they are not capable of providing continuous services for other nodes, networks, and applications. In this sense, the main objective of this dissertation focuses on the IoT connectivity problem. A network is regarded as connected if any pair of different nodes can communicate with each other either directly or via a limited number of intermediate nodes. More specifically, this thesis focuses on the development of models for analysis and management of resilience, implemented through the Wireless Sensor Networks (WSNs), which is a challenging task. On the one hand, unlike other conventional network devices, nodes in the IoT are more likely to be disconnected from each other due to their deployment in a hostile or isolated environment. On the other hand, nodes are resource-constrained in terms of limited processing capability, storage and battery capacity, which requires that the design of the resilience management for IoT has to be lightweight, distributed and energy-efficient. In this context, the thesis presents self-adaptive techniques for IoT, with the aim of making the IoT resilient against node failures from the network topology control point of view. The fuzzy-logic and proportional-integral-derivative (PID) control techniques are leveraged to improve the network connectivity of the IoT in response to node failures, meanwhile taking into consideration that energy consumption must be preserved as much as possible. The control algorithm itself is designed to be distributed, because the centralized approaches are usually not feasible in large scale IoT deployments. The thesis involves various aspects concerning network connectivity, including: creation and analysis of mathematical models describing the network, proposing self-adaptive control systems in response to node failures, control system parameter optimization, implementation using the software engineering approach, and evaluation in a real application. This thesis also justifies the relations between the "node degree" (the number of neighbor(s) of a node) and network connectivity through mathematic analysis, and proves the effectiveness of various types of controllers that can adjust power transmission of the IoT nodes in response to node failures. The controllers also take into consideration the energy consumption as part of the control goals. The evaluation is performed and comparison is made with other representative algorithms. The simulation results show that the proposals in this thesis can tolerate more random node failures and save more energy when compared with those representative algorithms. Additionally, the simulations demonstrate that the use of the bio-inspired algorithms allows optimizing the parameters of the controller. With respect to the implementation in a real system, the programming model called OSGi (Open Service Gateway Initiative) is integrated with the proposals in order to create a self-adaptive middleware, especially reconfiguring the software components at runtime when failures occur. The outcomes of this thesis contribute to theoretic research and practical applications of resilient topology control for large and distributed networks. The presented controller designs and optimization algorithms can be viewed as novel trials of the control and optimization techniques for the coming era of the IoT. The contributions of this thesis can be summarized as follows: (1) Mathematically, the fault-tolerant probability of a large-scale stochastic network is analyzed. It is studied how the probability of network connectivity depends on the communication range of the nodes, and what is the minimum number of neighbors to be added for network re-connection. (2) A fuzzy-logic control system is proposed, which obtains the desired node degree and in turn maintains the network connectivity when it is subject to node failures. There are different types of fuzzy-logic controllers evaluated by simulations, and the results demonstrate the improvement of fault-tolerant capability as compared to some other representative algorithms. (3) A simpler but more applicable approach, the two-loop control system is further investigated, and its control parameters are optimized by using some heuristic algorithms such as Cross Entropy (CE), Particle Swarm Optimization (PSO), and Differential Evolution (DE). (4) Most of the designs are evaluated by means of simulations, but part of the proposals are implemented and tested in a real-world application by combining the self-adaptive software technique and the control algorithms which are presented in this thesis.

On the role of global flow instability analysis in closed loop flow control

Control of linear flow instabilities has been demonstrated to be an effective theoretical flow control methodology, capable of modifying transitional flow on canonical geometries such as the plane channel and the flat-plate boundary layer.

Monte Carlo simulations of densely-packed athermal polymers in the bulk and under confinement

We review the main results from extensive Monte Carlo (MC) simulations on athermal polymer packings in the bulk and under confinement. By employing the simplest possible model of excluded volume, macromolecules are represented as freely-jointed chains of hard spheres of uniform size. Simulations are carried out in a wide concentration range: from very dilute up to very high volume fractions, reaching the maximally random jammed (MRJ) state. We study how factors like chain length, volume fraction and flexibility of bond lengths affect the structure, shape and size of polymers, their packing efficiency and their phase behaviour (disorder–order transition). In addition, we observe how these properties are affected by confinement realized by flat, impenetrable walls in one dimension. Finally, by mapping the parent polymer chains to primitive paths through direct geometrical algorithms, we analyse the characteristics of the entanglement network as a function of packing density.

Implementation of road dust resuspension in air quality simulations of particulate matter in Madrid (Spain)

An evaluation of the concentration levels of Particulate Matter (PM) was carried out in Madrid (Spain) by introducing the emissions from road dust resuspension. Road dust resuspension emission factors (EF) for different types of vehicles were calculated from EPA-AP42, a global resuspension factor of 0.097 g veh−1km−1 as described in Amato et al. (2010) and a rain-dependent correction factor. With these resuspension EFs, a simulation at street canyon level was performed with the OSPM model without rainfall. Subsequently, a simulation using the CMAQ model was implemented adding resuspension emissions affected by the rain. These data were compared with monitored data obtained from air quality stations. OSPM model simulations with resuspension EFs but without the effect of rainfall improve the PM estimates in about 20gm−3μ compared to the simulation with default EFs. Total emissions were calculated by adding the emissions estimated with resuspension EFs to the default PM emissions to be used by CMAQ. For the study in the Madrid Area, resuspension emissions are approximately of the same order of magnitude as inventoried emissions. On a monthly scale, rain effects are negligible for resuspension emissions due to the dry weather conditions of Spain. With the exception of April and May, the decrease in resuspension emissions is not >3%. The predicted PM10 concentration increases up to 9μ gm−3 on annual average for each station compared to the same scenario without resuspension. However, in both cases, PM 10 estimates with resuspension are still underestimating observations. It should be noted that although that accounting for resuspension improves the quality of model predictions, other PM sources (e.g., Saharan dust) were not considered in this study.

The role of enzyme distortion in the single displacement mechanism of family 19 chitinases

By using molecular dynamics simulations, we have examined the binding of a hexaNAG substrate and two potential hydrolysis intermediates (an oxazoline ion and an oxocarbenium ion) to a family 19 barley chitinase. We find the hexaNAG substrate binds with all sugars in a chair conformation, unlike the family 18 chitinase which causes substrate distortion. Glu 67 is in a position to protonate the anomeric oxygen linking sugar residues D and E whereas Asn 199 serves to hydrogen bond with the C2′ N-acetyl group of sugar D, thus preventing the formation of an oxazoline ion intermediate. In addition, Glu 89 is part of a flexible loop region allowing a conformational change to occur within the active site to bring the oxocarbenium ion intermediate and Glu 89 closer by 4–5 Å. A hydrolysis product with inversion of the anomeric configuration occurs because of nucleophilic attack by a water molecule that is coordinated by Glu 89 and Ser 120. Issues important for the design of inhibitors specific to family 19 chitinases over family 18 chitinases also are discussed.

The ability of HIV type 1 to use CCR-3 as a coreceptor is controlled by envelope V1/V2 sequences acting in conjunction with a CCR-5 tropic V3 loop

Although infection by primary HIV type 1 (HIV-1) isolates normally requires the functional interaction of the viral envelope protein with both CD4 and the CCR-5 coreceptor, a subset of such isolates also are able to use the distinct CCR-3 receptor. By analyzing the ability of a series of wild-type and chimeric HIV-1 envelope proteins to mediate CCR-3-dependent infection, we have determined that CCR-3 tropism maps to the V1 and V2 variable region of envelope. Although substitution of the V1/V2 region of a CCR-3 tropic envelope into the context of a CCR-5 tropic envelope is both necessary and sufficient to confer CCR-3 tropism, this same substitution has no phenotypic effect when inserted into a CXCR-4 tropic HIV-1 envelope context. However, this latter chimera acquires both CCR-3 and CCR-5 tropism when a CCR-5 tropic V3 loop sequence also is introduced. These data demonstrate that the V1/2 region of envelope can, like the V3 loop region, encode a particular coreceptor requirement and suggest that a functional envelope:CCR-3 interaction may depend on the cooperative interaction of CCR-3 with both the V1/V2 and the V3 region of envelope.

AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana

The endogenous clock that drives circadian rhythms is thought to communicate temporal information within the cell via cycling downstream transcripts. A transcript encoding a glycine-rich RNA-binding protein, Atgrp7, in Arabidopsis thaliana undergoes circadian oscillations with peak levels in the evening. The AtGRP7 protein also cycles with a time delay so that Atgrp7 transcript levels decline when the AtGRP7 protein accumulates to high levels. After AtGRP7 protein concentration has fallen to trough levels, Atgrp7 transcript starts to reaccumulate. Overexpression of AtGRP7 in transgenic Arabidopsis plants severely depresses cycling of the endogenous Atgrp7 transcript. These data establish both transcript and protein as components of a negative feedback circuit capable of generating a stable oscillation. AtGRP7 overexpression also depresses the oscillation of the circadian-regulated transcript encoding the related RNA-binding protein AtGRP8 but does not affect the oscillation of transcripts such as cab or catalase mRNAs. We propose that the AtGRP7 autoregulatory loop represents a “slave” oscillator in Arabidopsis that receives temporal information from a central “master” oscillator, conserves the rhythmicity by negative feedback, and transduces it to the output pathway by regulating a subset of clock-controlled transcripts.

Multiple loop structures critical for ligand binding of the integrin α4 subunit in the upper face of the β-propeller mode 1

A non-I-domain integrin, α4β1, recognizes vascular cell adhesion molecule 1 (VCAM-1) and the IIICS portion of fibronectin. To localize regions of α4 critical for ligand binding, we swapped several predicted loops within or near the putative ligand-binding site of α4 (which spans repeats 2–5 of the seven N-terminal repeats) with the corresponding regions of α5. Swapping residues 112–131 in repeat 2, or residues 237–247 in repeat 4, completely blocked adhesion to immobilized VCAM-1 and connecting segment 1 (CS-1) peptide. However, swapping residues 40–52 in repeat 1, residues 151–164 in repeat 3, or residues 282–288 (which contain a putative cation binding motif) in repeat 5 did not affect or only slightly reduced adhesion to these ligands. The binding of several function-blocking antibodies is blocked by swapping residues 112–131, 151–164, and 186–191 (which contain previously identified residues critical for ligand binding, Tyr-187 and Gly-190). These results are consistent with the recently published β-propeller folding model of the integrin α4 subunit [Springer, T. A. (1997) Proc. Natl. Acad. Sci. USA 94, 65–72], in which seven four-stranded β-sheets are arranged in a torus around a pseudosymmetric axis. The regions of α4 critical for ligand binding are adjacent to each other and are located in the upper face, the predicted ligand-binding site, of the β-propeller model, although they are not adjacent in the primary structure.

Identification of specific Rp-phosphate oxygens in the tRNA anticodon loop required for ribosomal P-site binding

tRNA binding to the ribosomal P site is dependent not only on correct codon–anticodon interaction but also involves identification of structural elements of tRNA by the ribosome. By using a phosphorothioate substitution–interference approach, we identified specific nonbridging Rp-phosphate oxygens in the anticodon loop of tRNAPhe from Escherichia coli which are required for P-site binding. Stereo-specific involvement of phosphate oxygens at these positions was confirmed by using synthetic anticodon arm analogues at which single Rp- or Sp-phosphorothioates were incorporated. Identical interference results with yeast tRNAPhe and E. coli tRNAfMet indicate a common backbone conformation or common recognition elements in the anticodon loop of tRNAs. N-ethyl-N-nitrosourea modification–interference experiments with natural tRNAs point to the importance of the same phosphates in the loop. Guided by the crystal structure of tRNAPhe, we propose that specific Rp-phosphate oxygens are required for anticodon loop (“U-turn”) stabilization or are involved in interactions with the ribosome on correct tRNA–mRNA complex formation.

A conserved serine-rich stretch in the glutamate transporter family forms a substrate-sensitive reentrant loop

Neuronal and glial glutamate transporters remove the excitatory neurotransmitter glutamate from the synaptic cleft. The proteins belong to a large family of secondary transporters, which includes bacterial glutamate transporters. The C-terminal half of the glutamate transporters is well conserved and thought to contain the translocation path and the binding sites for substrate and coupling ions. A serine-rich sequence motif in this part of the proteins is located in a putative intracellular loop. Cysteine-scanning mutagenesis was applied to this loop in the glutamate transporter GltT of Bacillus stearothermophilus. The loop was found to be largely intracellular, but three consecutive positions in the conserved serine-rich motif (S269, S270, and E271) are accessible from both sides of the membrane. Single-cysteine mutants in the serine-rich motif were still capable of glutamate transport, but modification with N-ethylmaleimide blocked the transport activity in six mutants (T267C, A268C, S269C, S270C, E271C, and T272C). Two milimolars l-glutamate effectively protected against the modification of the cysteines at position 269–271 from the periplasmic side of the membrane but was unable to protect cysteine modification from the cytoplasmic side of the membrane. The results indicate that the conserved serine-rich motif in the glutamate transporter forms a reentrant loop, a structure that is found in several ion channels but is unusual for transporter proteins. The reentrant loop is of crucial importance for the function of the glutamate transporter.