On the use of liquid bridges as accelerometers

The shape of the interface of a drop of liquid held by surface tension forces between two solid disks,a liquid bridge, depends on the geometry of the supporting disks, the volume of liquid and the external forces acting on the drop. Therefore, once the geometry of the supporting disks and the volume of liquid are fixed, and assuming that the value of the surface tension is known, a way to measure such external forces could be by measuring the deformation of the liquid bridge interface.

Nonlinear seismic behaviour of concrete arch bridges

Arch bridge structural solution has been known for centuries, in fact the simple nature of arch that require low tension and shear strength was an advantage as the simple materials like stone and brick were the only option back in ancient centuries. By the pass of time especially after industrial revolution, the new materials were adopted in construction of arch bridges to reach longer spans. Nowadays one long span arch bridge is made of steel, concrete or combination of these two as "CFST", as the result of using these high strength materials, very long spans can be achieved. The current record for longest arch belongs to Chaotianmen bridge over Yangtze river in China with 552 meters span made of steel and the longest reinforced concrete type is Wanxian bridge which also cross the Yangtze river through a 420 meters span. Today the designer is no longer limited by span length as long as arch bridge is the most applicable solution among other approaches, i.e. cable stayed and suspended bridges are more reasonable if very long span is desired. Like any super structure, the economical and architectural aspects in construction of a bridge is extremely important, in other words, as a narrower bridge has better appearance, it also require smaller volume of material which make the design more economical. Design of such bridge, beside the high strength materials, requires precise structural analysis approaches capable of integrating the combination of material behaviour and complex geometry of structure and various types of loads which may be applied to bridge during its service life. Depend on the design strategy, analysis may only evaluates the linear elastic behaviour of structure or consider the nonlinear properties as well. Although most of structures in the past were designed to act in their elastic range, the rapid increase in computational capacity allow us to consider different sources of nonlinearities in order to achieve a more realistic evaluations where the dynamic behaviour of bridge is important especially in seismic zones where large movements may occur or structure experience P - _ effect during the earthquake. The above mentioned type of analysis is computationally expensive and very time consuming. In recent years, several methods were proposed in order to resolve this problem. Discussion of recent developments on these methods and their application on long span concrete arch bridges is the main goal of this research. Accordingly available long span concrete arch bridges have been studied to gather the critical information about their geometrical aspects and properties of their materials. Based on concluded information, several concrete arch bridges were designed for further studies. The main span of these bridges range from 100 to 400 meters. The Structural analysis methods implemented in in this study are as following: Elastic Analysis: Direct Response History Analysis (DRHA): This method solves the direct equation of motion over time history of applied acceleration or imposed load in linear elastic range. Modal Response History Analysis (MRHA): Similar to DRHA, this method is also based on time history, but the equation of motion is simplified to single degree of freedom system and calculates the response of each mode independently. Performing this analysis require less time than DRHA. Modal Response Spectrum Analysis (MRSA): As it is obvious from its name, this method calculates the peak response of structure for each mode and combine them using modal combination rules based on the introduced spectra of ground motion. This method is expected to be fastest among Elastic analysis. Inelastic Analysis: Nonlinear Response History Analysis (NL-RHA): The most accurate strategy to address significant nonlinearities in structural dynamics is undoubtedly the nonlinear response history analysis which is similar to DRHA but extended to inelastic range by updating the stiffness matrix for every iteration. This onerous task, clearly increase the computational cost especially for unsymmetrical buildings that requires to be analyzed in a full 3D model for taking the torsional effects in to consideration. Modal Pushover Analysis (MPA): The Modal Pushover Analysis is basically the MRHA but extended to inelastic stage. After all, the MRHA cannot solve the system of dynamics because the resisting force fs(u; u_ ) is unknown for inelastic stage. The solution of MPA for this obstacle is using the previously recorded fs to evaluate system of dynamics. Extended Modal Pushover Analysis (EMPA): Expanded Modal pushover is a one of very recent proposed methods which evaluates response of structure under multi-directional excitation using the modal pushover analysis strategy. In one specific mode,the original pushover neglect the contribution of the directions different than characteristic one, this is reasonable in regular symmetric building but a structure with complex shape like long span arch bridges may go through strong modal coupling. This method intend to consider modal coupling while it take same time of computation as MPA. Coupled Nonlinear Static Pushover Analysis (CNSP): The EMPA includes the contribution of non-characteristic direction to the formal MPA procedure. However the static pushovers in EMPA are performed individually for every mode, accordingly the resulted values from different modes can be combined but this is only valid in elastic phase; as soon as any element in structure starts yielding the neutral axis of that section is no longer fixed for both response during the earthquake, meaning the longitudinal deflection unavoidably affect the transverse one or vice versa. To overcome this drawback, the CNSP suggests executing pushover analysis for governing modes of each direction at the same time. This strategy is estimated to be more accurate than MPA and EMPA, moreover the calculation time is reduced because only one pushover analysis is required. Regardless of the strategy, the accuracy of structural analysis is highly dependent on modelling and numerical integration approaches used in evaluation of each method. Therefore the widely used Finite Element Method is implemented in process of all analysis performed in this research. In order to address the study, chapter 2, starts with gathered information about constructed long span arch bridges, this chapter continuous with geometrical and material definition of new models. Chapter 3 provides the detailed information about structural analysis strategies; furthermore the step by step description of procedure of all methods is available in Appendix A. The document ends with the description of results and conclusion of chapter 4.

Analysis and design of reconfigurable multimode multiport microstrip antennas for mimo systems and diversity schemes

Las comunicaciones inalámbricas han transformado profundamente la forma en la que la gente se comunica en el día a día y es, sin lugar a dudas, una de las tecnologías de nuestro tiempo que más rápidamente evoluciona. Este rápido crecimiento implica retos enormes en la tecnología subyacente, debido y entre otros motivos, a la gran demanda de capacidad de los nuevos servicios inalámbricos. Los sistemas Multiple Input Multiple Output (MIMO) han despertado mucho interés como medio de mejorar el rendimiento global del sistema, satisfaciendo de este modo y en cierta medida los nuevo requisitos exigidos. De hecho, el papel relevante de esta tecnología en los actuales esfuerzos de estandarización internacionales pone de manifiesto esta utilidad. Los sistemas MIMO sacan provecho de los grados de libertad espaciales, disponibles a través del entorno multitrayecto, para mejorar el rendimiento de la comunicación con una destacable eficiencia espectral. Con el fin de alcanzar esta mejora en el rendimiento, la diversidad espacial y por diagrama han sido empleadas tradicionalmente para reducir la correlación entre los elementos radiantes, ya que una correlación baja es condición necesaria, si bien no suficiente, para dicha mejora. Tomando como referencia, o punto de partida, las técnicas empleadas para obtener diversidad por diagrama, esta tesis doctoral surge de la búsqueda de la obtención de diversidad por diagrama y/o multiplexación espacial a través del comportamiento multimodal de la antena microstrip, proponiendo para ello un modelo cuasi analítico original para el análisis y diseño de antenas microstrip multipuerto, multimodo y reconfigurables. Este novedoso enfoque en este campo, en vez de recurrir a simulaciones de onda completa por medio de herramientas comerciales tal y como se emplea en las publicaciones existentes, reduce significativamente el esfuerzo global de análisis y diseño, en este último caso por medio de guías de diseño generales. Con el fin de lograr el objetivo planteado y después de una revisión de los principales conceptos de los sistemas MIMO que se emplearán más adelante, se fija la atención en encontrar, implementar y verificar la corrección y exactitud de un modelo analítico que sirva de base sobre la cual añadir las mejoras necesarias para obtener las características buscadas del modelo cuasi analítico propuesto. Posteriormente y partiendo del modelo analítico base seleccionado, se exploran en profundidad y en diferentes entornos multitrayecto, las posibilidades en cuanto a rendimiento se refiere de diversidad por diagrama y multiplexación espacial, proporcionadas por el comportamiento multimodal de las antenas parche microstrip sin cargar. Puesto que cada modo de la cavidad tiene su propia frecuencia de resonancia, es necesario encontrar formas de desplazar la frecuencia de resonancia de cada modo empleado para ubicarlas en la misma banda de frecuencia, manteniendo cada modo al mismo tiempo tan independiente como sea posible. Este objetivo puede lograrse cargando adecuadamente la cavidad con cargas reactivas, o alterando la geometría del parche radiante. Por consiguiente, la atención en este punto se fija en el diseño, implementación y verificación de un modelo cuasi analítico para el análisis de antenas parche microstrip multipuerto, multimodo y cargadas que permita llevar a cabo la tarea indicada, el cuál es una de las contribuciones principales de esta tesis doctoral. Finalmente y basándose en el conocimiento adquirido a través del modelo cuasi analítico, se proporcionan y aplican guías generales para el diseño de antenas microstrip multipuerto, multimodo y reconfigurables para sistemas MIMO, con el fin de mejorar su diversidad por diagrama y/o su capacidad por medio del comportamiento multimodal de las antenas parche microstrip. Se debe destacar que el trabajo presentado en esta tesis doctoral ha dado lugar a una publicación en una revista técnica internacional de un alto factor de impacto. De igual manera, el trabajo también ha sido presentado en algunas de las más importantes conferencias internacionales en el ámbito de las antenas ABSTRACT Wireless communications have deeply transformed the way people communicate on daily basis and it is undoubtedly one of the most rapidly evolving technologies of our time. This fast growing behaviour involves huge challenges on the bearing technology, due to and among others reasons, the high demanding capacity of new wireless services. MIMO systems have given rise to considerable interest as a means to enhance the overall system performance, thus satisfying somehow the new demanding requirements. Indeed, the significant role of this technology on current international standardization efforts, highlights this usefulness. MIMO systems make profit from the spatial degrees of freedom available through the multipath scenario to improve the communication performance with a remarkable spectral efficiency. In order to achieve this performance improvement, spatial and pattern diversity have been traditionally used to decrease the correlation between antenna elements, as low correlation is a necessary but not sufficient condition. Taking as a reference, or starting point, the techniques used to achieve pattern diversity, this Philosophiae Doctor (Ph.D.) arises from the pursuit of obtaining pattern diversity and/or spatial multiplexing capabilities through the multimode microstrip behaviour, thus proposing a novel quasi analytical model for the analysis and design of reconfigurable multimode multiport microstrip antennas. This innovative approach on this field, instead of resorting to full-wave simulations through commercial tools as done in the available publications, significantly reduces the overall analysis and design effort, in this last case through comprehensive design guidelines. In order to achieve this goal and after a review of the main concepts of MIMO systems which will be followed used, the spotlight is fixed on finding, implementing and verifying the correctness and accuracy of a base quasi analytical model over which add the necessary enhancements to obtain the sought features of the quasi analytical model proposed. Afterwards and starting from the base quasi analytical model selected, the pattern diversity and spatial multiplexing performance capabilities provided by the multimode behaviour of unloaded microstrip patch antennas under different multipath environments are fully explored. As each cavity mode has its own resonant frequency, it is required to find ways to displace the resonant frequency of each used mode to place them at the same frequency band while keeping each mode as independent as possible. This objective can be accomplished with an appropriate loading of the cavity with reactive loads, or through the alteration of the geometry of the radiation patch. Thus, the focus is set at this point on the design, implementation and verification of a quasi analytical model for the analysis of loaded multimode multiport microstrip patch antennas to carry out the aforementioned task, which is one of the main contributions of this Ph.D. Finally and based on the knowledge acquired through the quasi analytical model, comprehensive guidelines to design reconfigurable multimode MIMO microstrip antennas to improve the spatial multiplexing and/or diversity system performance by means of the multimode microstrip patch antenna behaviour are given and applied. It shall be highlighted that the work presented in this Ph.D. has given rise to a publication in an international technical journal of high impact factor. Moreover, the work has also been presented at some of the most important international conferences in antenna area.

Pulsatile blood flow interaction with arterial walls of aorta : autoregulation and impedance pressure boundary condition and its biomedical applications

Para las decisiones urgentes sobre intervenciones quirúrgicas en el sistema cardiovascular se necesitan simulaciones computacionales con resultados fiables y que consuman un tiempo de cálculo razonable. Durante años los investigadores han trabajado en diversos métodos numéricos de cálculo que resulten atractivos para los cirujanos. Estos métodos, precisos pero costosos desde el punto de vista del coste computacional, crean un desajuste entre la oferta de los ingenieros que realizan las simulaciones y los médicos que operan en el quirófano. Por otra parte, los métodos de cálculo más simplificados reducen el tiempo de cálculo pero pueden proporcionar resultados no realistas. El objetivo de esta tesis es combinar los conceptos de autorregulación e impedancia del sistema circulatorio, la interacción flujo sanguíneo-pared arterial y modelos geométricos idealizados tridimensionales de las arterias pero sin pérdida de realismo, con objeto de proponer una metodología de simulación que proporcione resultados correctos y completos, con tiempos de cálculo moderados. En las simulaciones numéricas, las condiciones de contorno basadas en historias de presión presentan inconvenientes por ser difícil conocerlas con detalle, y porque los resultados son muy sensibles ante pequeñas variaciones de dichas historias. La metodología propuesta se basa en los conceptos de autorregulación, para imponer la demanda de flujo aguas abajo del modelo en el ciclo cardiaco, y la impedancia, para representar el efecto que ejerce el flujo en el resto del sistema circulatorio sobre las arterias modeladas. De este modo las historias de presión en el contorno son resultados del cálculo, que se obtienen de manera iterativa. El método propuesto se aplica en una geometría idealizada del arco aórtico sin patologías y en otra geometría correspondiente a una disección Stanford de tipo A, considerando la interacción del flujo pulsátil con las paredes arteriales. El efecto de los tejidos circundantes también se incorpora en los modelos. También se hacen aplicaciones considerando la interacción en una geometría especifica de un paciente anciano que proviene de una tomografía computarizada. Finalmente se analiza una disección Stanford tipo B con tres modelos que incluyen la fenestración del saco. Clinicians demand fast and reliable numerical results of cardiovascular biomechanic simulations for their urgent pre-surgery decissions. Researchers during many years have work on different numerical methods in order to attract the clinicians' confidence to their colorful contours. Though precise but expensive and time-consuming methodologies create a gap between numerical biomechanics and hospital personnel. On the other hand, simulation simplifications with the aim of reduction in computational time may cause in production of unrealistic outcomes. The main objective of the current investigation is to combine ideas such as autoregulation, impedance, fluid-solid interaction and idealized geometries in order to propose a computationally cheap methodology without excessive or unrealistic simplifications. The pressure boundary conditions are critical and polemic in numerical simulations of cardiovascular system, in which a specific arterial site is of interest and the rest of the netwrok is neglected but represented by a boundary condition. The proposed methodology is a pressure boundary condition which takes advantage of numerical simplicity of application of an imposed pressure boundary condition on outlets, while it includes more sophisticated concepts such as autoregulation and impedance to gain more realistic results. Incorporation of autoregulation and impedance converts the pressure boundary conditions to an active and dynamic boundary conditions, receiving feedback from the results during the numerical calculations and comparing them with the physiological requirements. On the other hand, the impedance boundary condition defines the shapes of the pressure history curves applied at outlets. The applications of the proposed method are seen on idealized geometry of the healthy arotic arch as well as idealized Stanford type A dissection, considering the interaction of the arterial walls with the pulsatile blood flow. The effect of surrounding tissues is incorporated and studied in the models. The simulations continue with FSI analysis of a patient-specific CT scanned geometry of an old individual. Finally, inspiring of the statistic results of mortality rates in Stanford type B dissection, three models of fenestrated dissection sac is studied and discussed. Applying the developed boundary condition, an alternative hypothesis is proposed by the author with respect to the decrease in mortality rates in patients with fenestrations.

Global Stability Analysis of Turbulent Transonic Flows on Airfoil geometries

La aparición de inestabilidades en un flujo es un problema importante que puede afectar a algunas aplicaciones aerodinámicas. De hecho existen diferentes tipos de fenómenos no-estacionarios que actualmente son tema de investigación; casos como la separación a altos ángulos de ataque o el buffet transónico son dos ejemplos de cierta relevancia. El análisis de estabilidad global permite identificar la aparición de dichas condiciones inestables, proporcionando información importante sobre la región donde la inestabilidad es dominante y sobre la frecuencia del fenómeno inestable. La metodología empleada es capaz de calcular un flujo base promediado mediante una discretización con volúmenes finitos y posteriormente la solución de un problema de autovalores asociado a la linealización que aparece al perturbar el flujo base. El cálculo numérico se puede dividir en tres pasos: primero se calcula una solución estacionaria para las ecuaciones RANS, luego se extrae la matriz del Jacobiano que representa el problema linealizado y finalmente se deriva y se resuelve el problema de autovalores generalizado mediante el método iterativo de Arnoldi. Como primer caso de validación, la técnica descrita ha sido aplicada a un cilindro circular en condiciones laminares para detectar el principio de las oscilaciones de los vórtices de von Karman, y se han comparado los resultados con experimentos y cálculos anteriores. La parte más importante del estudio se centra en el análisis de flujos compresibles en régimen turbulento. La predicción de la aparición y la progresión de flujo separado a altos ángulos de ataque se han estudiado en el perfil NACA0012 en condiciones tanto subsónicas como supersónicas y en una sección del ala del A310 en condiciones de despegue. Para todas las geometrías analizadas, se ha podido observar que la separación gradual genera la aparición de un modo inestable específico para altos ángulos de ataque siempre mayores que el ángulo asociado al máximo coeficiente de sustentación. Además, se ha estudiado el problema adjunto para obtener información sobre la zona donde una fuerza externa provoca el máximo cambio en el campo fluido. El estudio se ha completado calculando el mapa de sensibilidad estructural y localizando el centro de la inestabilidad. En el presente trabajo de tesis se ha analizado otro importante fenómeno: el buffet transónico. En condiciones transónicas, la interacción entre la onda de choque y la capa límite genera una oscilación de la posición de la onda de choque y, por consiguiente, de las fuerzas aerodinámicas. El conocimiento de las condiciones críticas y su origen puede ayudar a evitar la oscilación causada por estas fuerzas. Las condiciones para las cuales comienza la inestabilidad han sido calculadas y comparadas con trabajos anteriores. Por otra parte, los resultados del correspondiente problema adjunto y el mapa de sensibilidad se han obtenido por primera vez para el buffet, indicando la región del dominio que sera necesario modificar para crear el mayor cambio en las propiedades del campo fluido. Dado el gran consumo de memoria requerido para los casos 3D, se ha realizado un estudio sobre la reducción del domino con la finalidad de reducirlo a la región donde está localizada la inestabilidad. La eficacia de dicha reducción de dominio ha sido evaluada investigando el cambio en la dimensión de la matriz del Jacobiano, no resultando muy eficiente en términos del consumo de memoria. Dado que el buffet es un problema en general tridimensional, el análisis TriGlobal de una geometría 3D podría considerarse el auténtico reto futuro. Como aproximación al problema, un primer estudio se ha realizado empleando una geometría tridimensional extruida del NACA00f2. El cálculo del flujo 3D y, por primera vez en casos tridimensionales compresibles y turbulentos, el análisis de estabilidad TriGlobal, se han llevado a cabo. La comparación de los resultados obtenidos con los resultados del anterior modelo 2D, ha permitido, primero, verificar la exactitud del cálculo 2D realizado anteriormente y también ha proporcionado una estimación del consumo de memoria requerido para el caso 3D. ABSTRACT Flow unsteadiness is an important problem in aerodynamic applications. In fact, there are several types of unsteady phenomena that are still at the cutting edge of research in the field; separation at high angles of attack and transonic buffet are two important examples. Global Stability Analysis can identify the unstable onset conditions, providing important information about the instability location in the domain and the frequency of the unstable phenomenon. The methodology computes a base flow averaged state based on a finite volume discretization and a solution for a generalized eigenvalue problem corresponding to the perturbed linearized equations. The numerical computation is then performed in three steps: first, a steady solution for the RANS equation is computed; second, the Jacobian matrix that represents the linearized problem is obtained; and finally, the generalized eigenvalue problem is derived and solved with an Arnoldi iterative method. As a first validation test, the technique has been applied on a laminar circular cylinder in order to detect the von Karman vortex shedding onset, comparing the results with experiments and with previous calculations. The main part of the study focusses on turbulent and compressible cases. The prediction of the origin and progression of separated flows at high angles of attack has been studied on the NACA0012 airfoil at subsonic and transonic conditions and for the A310 airfoil in take-off configuration. For all the analyzed geometries, it has been found that gradual separation generates the appearance of one specific unstable mode for angles of attack always greater than the ones related to the maximum lift coefficient. In addition, the adjoint problem has been studied to suggest the location of an external force that results in the largest change to the flow field. From the direct and the adjoint analysis the structural sensitivity map has been computed and the core of the instability has been located. The other important phenomenon analyzed in this work is the transonic buffet. In transonic conditions, the interaction between the shock wave and the boundary layer leads to an oscillation of the shock location and, consequently, of the aerodynamic forces. Knowing the critical operational conditions and its origin can be helpful in preventing such fluctuating forces. The instability onset has then been computed and compared with the literature. Moreover, results of the corresponding adjoint problem and a sensitivity map have been provided for the first time for the buffet problem, indicating the region that must be modified to create the biggest change in flow field properties. Because of the large memory consumption required when a 3D case is approached, a domain reduction study has been carried out with the aim of limiting the domain size to the region where the instability is located. The effectiveness of the domain reduction has been evaluated by investigating the change in the Jacobian matrix size, not being very efficient in terms of memory consumption. Since buffet is a three-dimensional problem, TriGlobal stability analysis can be seen as a future challenge. To approximate the problem, a first study has been carried out on an extruded three-dimensional geometry of the NACA0012 airfoil. The 3D flow computation and the TriGlobal stability analysis have been performed for the first time on a compressible and turbulent 3D case. The results have been compared with a 2D model, confirming that the buffet onset evaluated in the 2D case is well detected. Moreover, the computation has given an indication about the memory consumption for a 3D case.

Singularities and undefinitions in the calibration functions of sonic anemometers

A mathematical model of the process employed by a sonic anemometer to build up the measured wind vector in a steady flow is presented to illustrate the way the geometry of these sensors as well as the characteristics of aerodynamic disturbance on the acoustic path can lead to singularities in the transformation function that relates the measured (disturbed) wind vector with the real (corrected) wind vector, impeding the application of correction/calibration functions for some wind conditions. An implicit function theorem allows for the identification of those combinations of real wind conditions and design parameters that lead to undefined correction/ calibration functions. In general, orthogonal path sensors do not show problematic combination of parameters. However, some geometric sonic sensor designs, available in the market, with paths forming smaller angles could lead to undefined correction functions for some levels of aerodynamic disturbances and for certain wind directions. The parameters studied have a strong influence on the existence and number of singularities in the correction/ calibration function as well as on the number of singularities for some combination of parameters. Some conclusions concerning good design practices are included.

On multiple-path sonic anemometer measurement theory

In this paper, a model of the measuring process of sonic anemometers with more than one measuring path is presented. The main hypothesis of the work is that the time variation of the turbulent speed field during the sequence of pulses that produces a measure of the wind speed vector affects the measurement. Therefore, the previously considered frozen flow, or instantaneous averaging, condition is relaxed. This time variation, quantified by the mean Mach number of the flow and the time delay between consecutive pulses firings, in combination with both the full geometry of sensors (acoustic path location and orientation) and the incidence angles of the mean with speed vector, give rise to significant errors in the measurement of turbulence which are not considered by models based on the hypothesis of instantaneous line averaging. The additional corrections (relative to the ones proposed by instantaneous line-averaging models) are strongly dependent on the wave number component parallel to the mean wind speed, the time delay between consecutive pulses, the Mach number of the flow, the geometry of the sensor and the incidence angles of mean wind speed vector. Kaimal´s limit k W1=1/l (where k W1 is the wave number component parallel to mean wind speed and l is the path length) for the maximum wave numbers from which the sonic process affects the measurement of turbulence is here generalized as k W1=C l /l, where C l is usually lesser than unity and depends on all the new parameters taken into account by the present model.

A single point mutation in the pore region of the epithelial Na+ channel changes ion selectivity by modifying molecular sieving

The epithelial Na+ channel (ENaC) belongs to a new class of channel proteins called the ENaC/DEG superfamily involved in epithelial Na+ transport, mechanotransduction, and neurotransmission. The role of ENaC in Na+ homeostasis and in the control of blood pressure has been demonstrated recently by the identification of mutations in ENaC β and γ subunits causing hypertension. The function of ENaC in Na+ reabsorption depends critically on its ability to discriminate between Na+ and other ions like K+ or Ca2+. ENaC is virtually impermeant to K+ ions, and the molecular basis for its high ionic selectivity is largely unknown. We have identified a conserved Ser residue in the second transmembrane domain of the ENaC α subunit (αS589), which when mutated allows larger ions such as K+, Rb+, Cs+, and divalent cations to pass through the channel. The relative ion permeability of each of the αS589 mutants is related inversely to the ionic radius of the permeant ion, indicating that αS589 mutations increase the molecular cutoff of the channel by modifying the pore geometry at the selectivity filter. Proper geometry of the pore is required to tightly accommodate Na+ and Li+ ions and to exclude larger cations. We provide evidence that ENaC discriminates between cations mainly on the basis of their size and the energy of dehydration.

Conversion of agonist site to metal-ion chelator site in the β2-adrenergic receptor

Previously metal-ion sites have been used as structural and functional probes in seven transmembrane receptors (7TM), but as yet all the engineered sites have been inactivating. Based on presumed agonist interaction points in transmembrane III (TM-III) and -VII of the β2-adrenergic receptor, in this paper we construct an activating metal-ion site between the amine-binding Asp-113 in TM-III—or a His residue introduced at this position—and a Cys residue substituted for Asn-312 in TM-VII. No increase in constitutive activity was observed in the mutant receptors. Signal transduction was activated in the mutant receptors not by normal catecholamine ligands but instead either by free zinc ions or by zinc or copper ions in complex with small hydrophobic metal-ion chelators. Chelation of the metal ions by small hydrophobic chelators such as phenanthroline or bipyridine protected the cells from the toxic effect of, for example Cu2+, and in several cases increased the affinity of the ions for the agonistic site. Wash-out experiments and structure–activity analysis indicated, that the high-affinity chelators and the metal ions bind and activate the mutant receptor as metal ion guided ligand complexes. Because of the well-understood binding geometry of the small metal ions, an important distance constraint has here been imposed between TM-III and -VII in the active, signaling conformation of 7TM receptors. It is suggested that atoxic metal-ion chelator complexes could possibly in the future be used as generic, pharmacologic tools to switch 7TM receptors with engineered metal-ion sites on or off at will.

Localization of the C terminus of the assembly domain of hepatitis B virus capsid protein: Implications for morphogenesis and organization of encapsidated RNA

The capsid protein of hepatitis B virus, consisting of an “assembly” domain (residues 1–149) and an RNA-binding “protamine” domain (residues 150–183), assembles from dimers into icosahedral capsids of two different sizes. The C terminus of the assembly domain (residues 140–149) functions as a morphogenetic switch, longer C termini favoring a higher proportion of the larger capsids, it also connects the protamine domain to the capsid shell. We now have defined the location of this peptide in capsids assembled in vitro by engineering a mutant assembly domain with a single cysteine at its C terminus (residue 150), labeling it with a gold cluster and visualizing the cluster by cryo-electron microscopy. The labeled protein is unimpaired in its ability to form capsids. Our density map reveals a single undecagold cluster under each fivefold and quasi-sixfold vertex, connected to sites at either end of the undersides of the dimers. Considering the geometry of the vertices, the C termini must be more crowded at the fivefolds. Thus, a bulky C terminus would be expected to favor formation of the larger (T = 4) capsids, which have a greater proportion of quasi-sixfolds. Capsids assembled by expressing the full-length protein in Escherichia coli package bacterial RNAs in amounts equivalent to the viral pregenome. Our density map of these capsids reveals a distinct inner shell of density—the RNA. The RNA is connected to the protein shell via the C-terminal linkers and also makes contact around the dimer axes.

The importance of reactant positioning in enzyme catalysis: A hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase

Hybrid quantum mechanics/molecular mechanics calculations using Austin Model 1 system-specific parameters were performed to study the SN2 displacement reaction of chloride from 1,2-dichloroethane (DCE) by nucleophilic attack of the carboxylate of acetate in the gas phase and by Asp-124 in the active site of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. The activation barrier for nucleophilic attack of acetate on DCE depends greatly on the reactants having a geometry resembling that in the enzyme or an optimized gas-phase structure. It was found in the gas-phase calculations that the activation barrier is 9 kcal/mol lower when dihedral constraints are used to restrict the carboxylate nucleophile geometry to that in the enzyme relative to the geometries for the reactants without dihedral constraints. The calculated quantum mechanics/molecular mechanics activation barriers for the enzymatic reaction are 16.2 and 19.4 kcal/mol when the geometry of the reactants is in a near attack conformer from molecular dynamics and in a conformer similar to the crystal structure (DCE is gauche), respectively. This haloalkane dehalogenase lowers the activation barrier for dehalogenation of DCE by 2–4 kcal/mol relative to the single point energies of the enzyme's quantum mechanics atoms in the gas phase. SN2 displacements of this sort in water are infinitely slower than in the gas phase. The modest lowering of the activation barrier by the enzyme relative to the reaction in the gas phase is consistent with mutation experiments.

Crystal structures of the vitamin D receptor complexed to superagonist 20-epi ligands

The crystal structures of the ligand-binding domain (LBD) of the vitamin D receptor complexed to 1α,25(OH)2D3 and the 20-epi analogs, MC1288 and KH1060, show that the protein conformation is identical, conferring a general character to the observation first made for retinoic acid receptor (RAR) that, for a given LBD, the agonist conformation is unique, the ligands adapting to the binding pocket. In all complexes, the A- to D-ring moieties of the ligands adopt the same conformation and form identical contacts with the protein. Differences are observed only for the 17β-aliphatic chains that adapt their conformation to anchor the 25-hydroxyl group to His-305 and His-397. The inverted geometry of the C20 methyl group induces different paths of the aliphatic chains. The ligands exhibit a low-energy conformation for MC1288 and a more strained conformation for the two others. KH1060 compensates this energy cost by additional contacts. Based on the present data, the explanation of the superagonist effect is to be found in higher stability and longer half-life of the active complex, thereby excluding different conformations of the ligand binding domain.

Measuring the topology of the universe

Observations of microwave background fluctuations can yield information not only about the geometry of the universe but potentially about the topology of the universe. If the universe is negatively curved, then the characteristic scale for the topology of the universe is the curvature radius. Thus, if we are seeing the effects of the geometry of the universe, we can hope to soon see signatures of the topology of the universe. The cleanest signature of the topology of the universe is written on the microwave sky: There should be thousands of pairs of matched circles. These circles can be used to determine the precise topology and volume of the universe. Because we see hundreds of slices through the fundamental domain of the universe, we can use the microwave observations to reconstruct the initial conditions of the entire universe on the scale of a few megaparsecs.

BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} acts as a phosphate analog in proteins phosphorylated on aspartate: Structure of a BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} complex with phosphoserine phosphatase

Protein phosphoaspartate bonds play a variety of roles. In response regulator proteins of two-component signal transduction systems, phosphorylation of an aspartate residue is coupled to a change from an inactive to an active conformation. In phosphatases and mutases of the haloacid dehalogenase (HAD) superfamily, phosphoaspartate serves as an intermediate in phosphotransfer reactions, and in P-type ATPases, also members of the HAD family, it serves in the conversion of chemical energy to ion gradients. In each case, lability of the phosphoaspartate linkage has hampered a detailed study of the phosphorylated form. For response regulators, this difficulty was recently overcome with a phosphate analog, BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document}, which yields persistent complexes with the active site aspartate of their receiver domains. We now extend the application of this analog to a HAD superfamily member by solving at 1.5-Å resolution the x-ray crystal structure of the complex of BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} with phosphoserine phosphatase (PSP) from Methanococcus jannaschii. The structure is comparable to that of a phosphoenzyme intermediate: BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} is bound to Asp-11 with the tetrahedral geometry of a phosphoryl group, is coordinated to Mg2+, and is bound to residues surrounding the active site that are conserved in the HAD superfamily. Comparison of the active sites of BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document}⋅PSP and BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document}⋅CeY, a receiver domain/response regulator, reveals striking similarities that provide insights into the function not only of PSP but also of P-type ATPases. Our results indicate that use of BeF\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} for structural studies of proteins that form phosphoaspartate linkages will extend well beyond response regulators.

Faithful representation of similarities among three-dimensional shapes in human vision.

Efficient and reliable classification of visual stimuli requires that their representations reside a low-dimensional and, therefore, computationally manageable feature space. We investigated the ability of the human visual system to derive such representations from the sensory input-a highly nontrivial task, given the million or so dimensions of the visual signal at its entry point to the cortex. In a series of experiments, subjects were presented with sets of parametrically defined shapes; the points in the common high-dimensional parameter space corresponding to the individual shapes formed regular planar (two-dimensional) patterns such as a triangle, a square, etc. We then used multidimensional scaling to arrange the shapes in planar configurations, dictated by their experimentally determined perceived similarities. The resulting configurations closely resembled the original arrangements of the stimuli in the parameter space. This achievement of the human visual system was replicated by a computational model derived from a theory of object representation in the brain, according to which similarities between objects, and not the geometry of each object, need to be faithfully represented.