Horizontal visibility graphs generated by type-I intermittency

The type-I intermittency route to (or out of) chaos is investigated within the horizontal visibility (HV) graph theory. For that purpose, we address the trajectories generated by unimodal maps close to an inverse tangent bifurcation and construct their associatedHVgraphs.We showhowthe alternation of laminar episodes and chaotic bursts imprints a fingerprint in the resulting graph structure. Accordingly, we derive a phenomenological theory that predicts quantitative values for several network parameters. In particular, we predict that the characteristic power-law scaling of the mean length of laminar trend sizes is fully inherited by the variance of the graph degree distribution, in good agreement with the numerics. We also report numerical evidence on how the characteristic power-law scaling of the Lyapunov exponent as a function of the distance to the tangent bifurcation is inherited in the graph by an analogous scaling of block entropy functionals defined on the graph. Furthermore, we are able to recast the full set of HV graphs generated by intermittent dynamics into a renormalization-group framework, where the fixed points of its graph-theoretical renormalization-group flow account for the different types of dynamics.We also establish that the nontrivial fixed point of this flow coincides with the tangency condition and that the corresponding invariant graph exhibits extremal entropic properties.

Limits of the frequency response for the analysis of ripple-based controllers

Advanced control techniques like V2, Vout hysteresis or V2Ic can strongly reduce the required output capacitance in PowerSoC converters. Techniques to analyze power converters based on the analysis of the frequency response are not suitable for ripple-based controllers that use fast-scale dynamics to control the power stage. This paper proves that the use of discrete modeling together with Floquet theory is a very powerful tool to model the system and derive stable region diagrams for sensitivity analysis. It is applied to V 2Ic control, validating experimentally that Floquet theory predicts accurately subharmonic oscillations. This method is applied to several ripplebased controllers, providing higher accuracy when it is compared with other techniques based on the frequency response. The paper experimentally validates the usefulness of the discrete modeling and the Floquet theory on a 5 MHz Buck converter with a V 2Ic control.

Generación de modelos físicos personalizados y segmentación de la pared arterial y el trombo intraluminal en imágenes de aneurismas aórticos abdominales

Esta tesis doctoral está encuadrada dentro del marco general de la ingeniería biomédica aplicada al tratamiento de las enfermedades cardiovasculares, enfermedades que provocan alrededor de 1.9 millones (40%) de muertes al año en la Unión Europea. En este contexto surge el proyecto europeo SCATh-Smart Catheterization, cuyo objetivo principal es mejorar los procedimientos de cateterismo aórtico introduciendo nuevas tecnologías de planificación y navegación quirúrgica y minimizando el uso de fluoroscopía. En particular, esta tesis aborda el modelado y diagnóstico de aneurismas aórticos abdominales (AAA) y del trombo intraluminal (TIL), allí donde esté presente, así como la segmentación de estas estructuras en imágenes preoperatorias de RM. Los modelos físicos específicos del paciente, construidos a partir de imágenes médicas preoperatorias, tienen múltiples usos, que van desde la evaluación preoperatoria de estructuras anatómicas a la planificación quirúrgica para el guiado de catéteres. En el diagnóstico y tratamiento de AAA, los modelos físicos son útiles a la hora de evaluar diversas variables biomecánicas y fisiológicas de las estructuras vasculares. Existen múltiples técnicas que requieren de la generación de modelos físicos que representen la anatomía vascular. Una de las principales aplicaciones de los modelos físicos es el análisis de elementos finitos (FE). Las simulaciones de FE para AAA pueden ser específicas para el paciente y permiten modelar estados de estrés complejos, incluyendo los efectos provocados por el TIL. La aplicación de métodos numéricos de análisis tiene como requisito previo la generación de una malla computacional que representa la geometría de interés mediante un conjunto de elementos poliédricos, siendo los hexaédricos los que presentan mejores resultados. En las estructuras vasculares, generar mallas hexaédricas es un proceso especialmente exigente debido a la compleja anatomía 3D ramificada. La mayoría de los AAA se encuentran situados en la bifurcación de la arteria aorta en las arterias iliacas y es necesario modelar de manera fiel dicha bifurcación. En el caso de que la sangre se estanque en el aneurisma provocando un TIL, éste forma una estructura adyacente a la pared aórtica. De este modo, el contorno externo del TIL es el mismo que el contorno interno de la pared, por lo que las mallas resultantes deben reflejar esta particularidad, lo que se denomina como "mallas conformadas". El fin último de este trabajo es modelar las estructuras vasculares de modo que proporcionen nuevas herramientas para un mejor diagnóstico clínico, facilitando medidas de riesgo de rotura de la arteria, presión sistólica o diastólica, etc. Por tanto, el primer objetivo de esta tesis es diseñar un método novedoso y robusto para generar mallas hexaédricas tanto de la pared aórtica como del trombo. Para la identificación de estas estructuras se utilizan imágenes de resonancia magnética (RM). Deben mantenerse sus propiedades de adyacencia utilizando elementos de alta calidad, prestando especial atención al modelado de la bifurcación y a que sean adecuadas para el análisis de FE. El método tiene en cuenta la evolución de la línea central del vaso en el espacio tridimensional y genera la malla directamente a partir de las imágenes segmentadas, sin necesidad de reconstruir superficies triangulares. Con el fin de reducir la intervención del usuario en el proceso de generación de las mallas, es también objetivo de esta tesis desarrollar un método de segmentación semiautomática de las distintas estructuras de interés. Las principales contribuciones de esta tesis doctoral son: 1. El diseño, implementación y evaluación de un algoritmo de generación de mallas hexaédricas conformadas de la pared y el TIL a partir de los contornos segmentados en imágenes de RM. Se ha llevado a cabo una evaluación de calidad que determine su aplicabilidad a métodos de FE. Los resultados demuestran que el algoritmo desarrollado genera mallas conformadas de alta calidad incluso en la región de la bifurcación, que son adecuadas para su uso en métodos de análisis de FE. 2. El diseño, implementación y evaluación de un método de segmentación automático de las estructuras de interés. La luz arterial se segmenta de manera semiautomática utilizando un software disponible a partir de imágenes de RM con contraste. Los resultados de este proceso sirven de inicialización para la segmentación automática de las caras interna y externa de la pared aórtica utilizando métodos basado en modelos de textura y forma a partir de imágenes de RM sin contraste. Los resultados demuestran que el algoritmo desarrollado proporciona segmentaciones fieles de las distintas estructuras de interés. En conclusión, el trabajo realizado en esta tesis doctoral corrobora las hipótesis de investigación postuladas, y pretende servir como aportación para futuros avances en la generación de modelos físicos de geometrías biológicas. ABSTRACT The frame of this PhD Thesis is the biomedical engineering applied to the treatment of cardiovascular diseases, which cause around 1.9 million deaths per year in the European Union and suppose about 40% of deaths per year. In this context appears the European project SCATh-Smart Catheterization. The main objective of this project is creating a platform which improves the navigation of catheters in aortic catheterization minimizing the use of fluoroscopy. In the framework of this project, the specific field of this PhD Thesis is the diagnosis and modeling of abdominal aortic aneurysm (AAAs) and the intraluminal thrombus (ILT) whenever it is present. Patient-specific physical models built from preoperative imaging are becoming increasingly important in the area of minimally invasive surgery. These models can be employed for different purposes, such as the preoperatory evaluation of anatomic structures or the surgical planning for catheter guidance. In the specific case of AAA diagnosis and treatment, physical models are especially useful for evaluating pressures over vascular structures. There are multiple techniques that require the generation of physical models which represent the target anatomy. Finite element (FE) analysis is one the principal applications for physical models. FE simulations for AAA may be patient-specific and allow modeling biomechanical and physiological variables including those produced by ILT, and also the segmentation of those anatomical structures in preoperative MR images. Applying numeric methods requires the generation of a proper computational mesh. These meshes represent the patient anatomy using a set of polyhedral elements, with hexahedral elements providing better results. In the specific case of vascular structures, generating hexahedral meshes is a challenging task due to the complex 3D branching anatomy. Each patient’s aneurysm is unique, characterized by its location and shape, and must be accurately represented for subsequent analyses to be meaningful. Most AAAs are located in the region where the aorta bifurcates into the iliac arteries and it is necessary to model this bifurcation precisely and reliably. If blood stagnates in the aneurysm and forms an ILT, it exists as a conforming structure with the aortic wall, i.e. the ILT’s outer contour is the same as the wall’s inner contour. Therefore, resulting meshes must also be conforming. The main objective of this PhD Thesis is designing a novel and robust method for generating conforming hexahedral meshes for the aortic wall and the thrombus. These meshes are built using largely high-quality elements, especially at the bifurcation, that are suitable for FE analysis of tissue stresses. The method accounts for the evolution of the vessel’s centerline which may develop outside a single plane, and generates the mesh directly from segmented images without the requirement to reconstruct triangular surfaces. In order to reduce the user intervention in the mesh generation process is also a goal of this PhD. Thesis to develop a semiautomatic segmentation method for the structures of interest. The segmentation is performed from magnetic resonance image (MRI) sequences that have tuned to provide high contrast for the arterial tissue against the surrounding soft tissue, so that we determine the required information reliably. The main contributions of this PhD Thesis are: 1. The design, implementation and evaluation of an algorithm for generating hexahedral conforming meshes of the arterial wall and the ILT from the segmented contours. A quality inspection has been applied to the meshes in order to determine their suitability for FE methods. Results show that the developed algorithm generates high quality conforming hexahedral meshes even at the bifurcation region. Thus, these meshes are suitable for FE analysis. 2. The design, implementation and evaluation of a semiautomatic segmentation method for the structures of interest. The lumen is segmented in a semiautomatic way from contrast filled MRI using an available software. The results obtained from this process are used to initialize the automatic segmentation of the internal and external faces of the aortic wall. These segmentations are performed by methods based on texture and shape models from MRI with no contrast. The results show that the algorithm provides faithful segmentations of the structures of interest requiring minimal user intervention. In conclusion, the work undertaken in this PhD. Thesis verifies the investigation hypotheses. It intends to serve as basis for future physical model generation of proper biological anatomies used by numerical methods.

High-quality conforming hexahedral meshes of patient-specific abdominal aortic aneurysms including their intraluminal thrombi

In order to perform finite element (FE) analyses of patient-specific abdominal aortic aneurysms, geometries derived from medical images must be meshed with suitable elements. We propose a semi-automatic method for generating conforming hexahedral meshes directly from contours segmented from medical images. Magnetic resonance images are generated using a protocol developed to give the abdominal aorta high contrast against the surrounding soft tissue. These data allow us to distinguish between the different structures of interest. We build novel quadrilateral meshes for each surface of the sectioned geometry and generate conforming hexahedral meshes by combining the quadrilateral meshes. The three-layered morphology of both the arterial wall and thrombus is incorporated using parameters determined from experiments. We demonstrate the quality of our patient-specific meshes using the element Scaled Jacobian. The method efficiently generates high-quality elements suitable for FE analysis, even in the bifurcation region of the aorta into the iliac arteries. For example, hexahedral meshes of up to 125,000 elements are generated in less than 130 s, with 94.8 % of elements well suited for FE analysis. We provide novel input for simulations by independently meshing both the arterial wall and intraluminal thrombus of the aneurysm, and their respective layered morphologies.

Limit load instabilities in structural elements

Este trabajo analiza distintas inestabilidades en estructuras formadas por distintos materiales. En particular, se capturan y se modelan las inestabilidades usando el método de Riks. Inicialmente, se analiza la bifurcación en depósitos cilíndricos formados por material anisótropo sometidos a carga axial y presión interna. El análisis de bifurcación y post-bifurcación asociados con cilindros de pared gruesa se formula para un material incompresible reforzado con dos fibras que son mecánicamente equivalentes y están dispuestas simétricamente. Consideramos dos casos en la naturaleza de la anisotropía: (i) Fibras refuerzo que tienen una influencia particular sobre la respuesta a cortante del material y (ii) Fibras refuerzo que influyen sólo si la fibra cambia de longitud con la deformación. Se analiza la propagación de las inestabilidades. En concreto, se diferencia en el abultamiento (bulging) entre la propagación axial y la propagación radial de la inestabilidad. Distintos modelos sufren una u otra propagación. Por último, distintas inestabilidades asociadas al mecanismo de ablandamiento del material (material softening) en contraposición al de endurecimiento (hardening) en una estructura (viga) de a: hormigón y b: hormigón reforzado son modeladas utilizando una metodología paralela a la desarrollada en el análisis de inestabilidades en tubos sometidos a presión interna. This present work deals with the instability of structures made of various materials. It captures and models different types of instabilities using numerical analysis. Firstly, we consider bifurcation for anisotropic cylindrical shells subject to axial loading and internal pressure. Analysis of bifurcation and post bifurcation of inflated hyperelastic thick-walled cylinder is formulated using a numerical procedure based on the modified Riks method for an incompressible material with two preferred directions which are mechanically equivalent and are symmetrically disposed. Secondly, bulging/necking motion in doubly fiber-reinforced incompressible nonlinearly elastic cylindrical shells is captured and we consider two cases for the nature of the anisotropy: (i) reinforcing models that have a particular influence on the shear response of the material and (ii) reinforcing models that depend only on the stretch in the fiber direction. The different instability motions are considered. Axial propagation of the bulging instability mode in thin-walled cylinders under inflation is analyzed. We present the analytical solution for this particular motion as well as for radial expansion during bulging evolution. For illustration, cylinders that are made of either isotropic incompressible non-linearly elastic materials or doubly fiber reinforced incompressible non-linearly elastic materials are considered. Finally, strain-softening constitutive models are considered to analyze two concrete structures: a reinforced concrete beam and an unreinforced notch beam. The bifurcation point is captured using the Riks method used previously to analyze bifurcation of a pressurized cylinder.

Direct and adjoint global stability analysis of turbulent transonic flows over a NACA0012 profile

In this work, various turbulent solutions of the two-dimensional (2D) and three-dimensional compressible Reynolds averaged Navier?Stokes equations are analyzed using global stability theory. This analysis is motivated by the onset of flow unsteadiness (Hopf bifurcation) for transonic buffet conditions where moderately high Reynolds numbers and compressible effects must be considered. The buffet phenomenon involves a complex interaction between the separated flow and a shock wave. The efficient numerical methodology presented in this paper predicts the critical parameters, namely, the angle of attack and Mach and Reynolds numbers beyond which the onset of flow unsteadiness appears. The geometry, a NACA0012 profile, and flow parameters selected reproduce situations of practical interest for aeronautical applications. The numerical computation is performed in three steps. First, a steady baseflow solution is obtained; second, the Jacobian matrix for the RANS equations based on a finite volume discretization is computed; and finally, the generalized eigenvalue problem is derived when the baseflow is linearly perturbed. The methodology is validated predicting the 2D Hopf bifurcation for a circular cylinder under laminar flow condition. This benchmark shows good agreement with the previous published computations and experimental data. In the transonic buffet case, the baseflow is computed using the Spalart?Allmaras turbulence model and represents a mean flow where the high frequency content and length scales of the order of the shear-layer thickness have been averaged. The lower frequency content is assumed to be decoupled from the high frequencies, thus allowing a stability analysis to be performed on the low frequency range. In addition, results of the corresponding adjoint problem and the sensitivity map are provided for the first time for the buffet problem. Finally, an extruded three-dimensional geometry of the NACA0012 airfoil, where all velocity components are considered, was also analyzed as a Triglobal stability case, and the outcoming results were compared to the previous 2D limited model, confirming that the buffet onset is well detected.

Estudio del flujo sanguíneo para diferentes técnicas de implantación de stents en bifurcaciones coronarias

Las enfermedades arteriales vienen presididas por la aterosclerosis, que es un proceso crónico de degeneración, que evoluciona hacia la obstrucción de la luz arterial. La pared de la arteria se engrosa debido al depósito de elementos grasos tales como el colesterol. Los stents intraluminales son diminutas estructuras tubulares autoexpandibles de malla de metal, que se colocan dentro de la arteria coronaria después de una angioplastia con balón para prevenir el cierre de dicha arteria. A pesar de estar diseñados para ser compatibles con el tejido humano, a menudo se da una reacción en cadena de consecuencias indeseables. La reestenosis intra-stent es un problema creciente debido al importante incremento que se ha producido en la utilización del stent intracoronario como forma de revascularización percutánea. Se habla de una incidencia global del 28%, siendo la causa principal de su aparición la proliferación neointimal a través de una compleja cascada de sucesos que pueden tardar meses en desarrollarse. Una de las reacciones más importantes es la trombosis o la formación de una fina capa de coágulo como respuesta a la presencia de un material extraño. Este proceso es multifactorial, y en él intervienen la regresión de la pared como consecuencia del estiramiento previo, la denudación endotelial, lo que permite la agregación plaquetaria, la proliferación neointimal, lo que facilita a los receptores de membrana desencadenar un proceso de agregación posterior y, por último, el remodelado negativo inadecuado de la pared, lo que produce pérdida de luz arterial. Se ha observado frecuentemente que el depósito de ateroma en la pared arterial está relacionado con el valor de los esfuerzos cortantes en la misma. Hay mayores probabilidades de engrosamiento de la pared en las zonas donde son bajos los esfuerzos cortantes, quizá por el mayor tiempo de residencia de las partículas circulantes por el torrente sanguíneo. Si nos centramos en la afirmación anterior, el siguiente paso sería buscar las zonas susceptibles de presentar un valor bajo de dichos esfuerzos. Las zonas potencialmente peligrosas son los codos y bifurcaciones, entre otras. Nos hemos centrado en una bifurcación coronaria, ya que los patrones de flujo que se suelen presentar, tales como recirculación y desprendimiento de vórtices están íntimamente relacionados con las técnicas de implantación de stents en esta zona. Proyectamos nuestros esfuerzos en el estudio de dos técnicas de implante, utilizando un único stent y una tercera a través de una configuración de culotte con el uso de dos stents. El primer caso trata de una bifurcación con un único stent en la rama principal cuyos struts cierran el orificio lateral que da salida a la rama secundaria de la bifurcación, es decir sería un stent sin orificio. El segundo consiste en un único stent también, pero con la diferencia de que éste presenta un orificio de comunicación con la rama lateral. Todas estas técnicas se aplicaron a bifurcaciones de 45º y de 90º. Introdujimos las geometrías -una vez confeccionadas con el código comercial Gambit- en el programa Ansys-Fluent contemplando régimen estacionario. Los resultados obtenidos fueron cotejados con los experimentales, que se realizaron paralelamente, con el fin de corroborarlos. Una vez validados, el estudio computacional ya contó con la fiabilidad suficiente como para abordar el régimen no estacionario, tanto en la versión de reposo como en la de ejercicio –hiperemia- El comportamiento reológico de la sangre para régimen no estacionario en estado de reposo es otra de las tareas abordadas, realizando una comparativa de los modelos Newtoniano, Carreau y Ley de Potencias. Finalmente, en una última etapa, debido a la reciente incursión de los stents diseñados específicamente frente a los convencionales, se aborda el comportamiento hemodinámico de los mismos. Concretamente, se comparó el patrón de flujo en un modelo de bifurcación coronaria con los nuevos stents (Stentys) y los convencionales. Se estudiaron cuatro modelos, a saber, stent simple en la rama principal, stent simple en la rama secundaria, culotte desplegando el primer stent en la rama principal y culotte desplegando el primer stent en la rama secundaria. La bifurcación estudiada presenta un ángulo de apertura de 45º y la relación de diámetros de las ramas hija se ajustaron de acuerdo a la ley de Finet. Se recogieron resultados experimentales en el laboratorio y se corrieron simulaciones numéricas con Ansys Fluent paralelamente. Las magnitudes que se tuvieron en cuenta con el fin de ubicar las regiones potencialmente ateroscleróticas fueron los esfuerzos cortantes, vorticidad y caída de presión. ABSTRACT Nowadays, restenosis after percutaneous dilation is the major drawback of coronary angioplasty. It represents a special form of atherosclerosis due to the healing process secondary to extensive vessel trauma induced after intracoronary balloon inflation. The use of coronary stents may decrease the incidence of this phenomenon. Unfortunately, intra-stent restenosis still occurs in 20-30% of the cases following the stent implantation. Most experiments suggest a correlation between low wall shear stress and wall thickness. The preferential locations for the atherosclerotic plaque are bifurcations. The objective of this work is to analyze the local hemodynamic changes caused in a coronary bifurcation by three different stenting techniques: simple stenting of the main vessel, simple stenting of the main vessel with kissing balloon in the side branch and culotte. To carry out this study an idealized geometry of a coronary bifurcation is used, and two bifurcation angles, 45º and 90º, are chosen as representative of the wide variety of real configurations. Both numerical simulations and experimental measurements are performed. First, steady simulations are carried out with the commercial code Ansys-Fluent, then, experimental measurements with PIV (Particle Image Velocimetry), obtained in the laboratory, are used to validate the numerical simulations. The steady computational simulations show a good overall agreement with the experimental data. Then, pulsatile flow is considered to take into account the transient effects. The time averaged wall shear stress, oscillatory shear index and pressure drop obtained numerically are used to compare the behavior of the stenting techniques. In a second step, the rheologic behavior of blood was considered comparing Newtonian, Carreau and Power Law models. Finally, as a result of previous investigations with conventional stents and after the recent emergence of several devices specifically designed for coronary bifurcations angioplasty, the hemodynamic performance of these new devices (Stentys) was compared to conventional ones and techniques in a coronary bifurcation model. Four different stenting techniques: simple stenting of the main vessel, simple stenting of the side vessel, culotte deploying the first stent in the main vessel and culotte deploying the first stent in the side vessel have been considered. To carry out this study an idealized geometry of a coronary bifurcation is used. A 45 degrees bifurcation angle is considered and the daughter branches diameters are obtained according to the Finet law. Both experiments in the laboratory and numerical simulations were used , focusing on important factors for the atherosclerosis development, like the wall shear stress, the oscillation shear index, the pressure loss and the vorticity.

Pattern formation of parametrically driven surface waves induced by vibration

Esta tesis se centra en la generación de ondas superficiales subarmónicas en fluidos sometidos a vibración forzada en el régimen gravitatorio capilar con líquidos de baja viscosidad. Tres problemas diferentes han sido estudiados: un contenedor rectangular con vibración horizontal, la misma geometría pero con una combinación de vibración vertical y horizontal y un obstáculo completamente sumergido vibrado verticalmente en un contenedor grande. Se deriva una ecuación de amplitud desde primeros principios para describir las ondas subarmónicas con forzamiento parámetrico inducido por la vibración. La ecuación es bidimensional mientras que el problema original es tridimensional y admite un forzamiento espacial no uniforme. Usando esta ecuación los tres sistemas han sido analizados, centrándose en calcular la amplitud crítica, la orientación de los patrones y el carácter temporal de los patrones espaciotemporales, que pueden ser estrictamente subarmónicos o cuasiperiodicos con una frecuencia de modulación temporal. La dependencia con los parámetros adimensionales también se considera. La teoría será comparada con los experimentos disponibles en la literatura. Abstract This thesis focus on the generation of subharmonic surface waves on fluids subject to forced vibration in the gravity-capillary regime with liquids of small viscosity. Three different problems have been considered: a rectangular container under horizontal vibration; the same geometry but under a combination of horizontal and vertical vibration; and a fully submerged vertically vibrated obstacle in a large container. An amplitude equation is derived from first principles that fairly precisely describes the subharmonic surfaces waves parametrically driven by vibration. That equation is two dimensional while the underlying problem is three-dimensional and permits spatially nonuniform forcing. Using this equation, the three systems have been analyzed, focusing on the calculation of the threshold amplitude, the pattern orientation, and the temporal character of the spatio-temporal patterns, which can be either strictly subharmonic or quasi-periodic, showing an additional modulation frequency. Dependence on the non-dimensional parameters is also considered. The theory is compared with the experiments available in the literature.

Discrete linear stability and sensitivity analysis of fluid flows

Este trabajo presenta un método discreto para el cálculo de estabilidad hidrodinámica y análisis de sensibilidad a perturbaciones externas para ecuaciones diferenciales y en particular para las ecuaciones de Navier-Stokes compressible. Se utiliza una aproximación con variable compleja para obtener una precisión analítica en la evaluación de la matriz Jacobiana. Además, mapas de sensibilidad para la sensibilidad a las modificaciones del flujo de base y a una fuerza constante permiten identificar las regiones del campo fluido donde una modificacin (ej. fuerza puntual) tiene un efecto estabilizador del flujo. Se presentan cuatro casos de prueba: (1) un caso analítico para comprobar la derivación discreta, (2) una cavidad cerrada a bajo Reynolds para mostrar la mayor precisión en el cálculo de los valores propios con la aproximación de paso complejo, (3) flujo 2D en un cilindro circular para validar la metodología, y (4) flujo en un cavidad abierta, presentado para validar el método en casos de inestabilidades convectivamente inestables. Los tres últimos casos mencionados (2-4) se resolvieron con las ecuaciones de Navier-Stokes compresibles, utilizando un método Discontinuous Galerkin Spectral Element Method. Se obtuvo una buena concordancia para el caso de validación (3), cuando se comparó el nuevo método con resultados de la literatura. Además, este trabajo muestra que para el cálculo de los modos propios directos y adjuntos, así como para los mapas de sensibilidad, el uso de variables complejas es de suprema importancia para obtener una predicción precisa. El método descrito es aplicado al análisis para la estabilización de la estela generada por un disco actuador, que representa un modelo sencillo para hélices, rotores de helicópteros o turbinas eólicas. Se explora la primera bifurcación del flujo para un disco actuador, y se sugiere que está asociada a una inestabilidad de tipo Kelvin-Helmholtz, cuya estabilidad se controla con en el número de Reynolds y en la resistencia del disco actuador (o fuerza resistente). En primer lugar, se verifica que la disminución de la resistencia del disco tiene un efecto estabilizador parecido a una disminución del Reynolds. En segundo lugar, el análisis hidrodinmico discreto identifica dos regiones para la colocación de una fuerza puntual que controle las inestabilidades, una cerca del disco y otra en una zona aguas abajo. En tercer lugar, se muestra que la inclusión de un forzamiento localizado cerca del actuador produce una estabilización más eficiente que al forzar aguas abajo. El análisis de los campos de flujo controlados confirma que modificando el gradiente de velocidad cerca del actuador es más eficiente para estabilizar la estela. Estos resultados podrían proporcionar nuevas directrices para la estabilización de la estela de turbinas de viento o de marea cuando estén instaladas en un parque eólico y minimizar las interacciones no estacionarias entre turbinas. ABSTRACT A discrete framework for computing the global stability and sensitivity analysis to external perturbations for any set of partial differential equations is presented. In particular, a complex-step approximation is used to achieve near analytical accuracy for the evaluation of the Jacobian matrix. Sensitivity maps for the sensitivity to base flow modifications and to a steady force are computed to identify regions of the flow field where an input could have a stabilising effect. Four test cases are presented: (1) an analytical test case to prove the theory of the discrete framework, (2) a lid-driven cavity at low Reynolds case to show the improved accuracy in the calculation of the eigenvalues when using the complex-step approximation, (3) the 2D flow past a circular cylinder at just below the critical Reynolds number is used to validate the methodology, and finally, (4) the flow past an open cavity is presented to give an example of the discrete method applied to a convectively unstable case. The latter three (2–4) of the aforementioned cases were solved with the 2D compressible Navier–Stokes equations using a Discontinuous Galerkin Spectral Element Method. Good agreement was obtained for the validation test case, (3), with appropriate results in the literature. Furthermore, it is shown that for the calculation of the direct and adjoint eigenmodes and their sensitivity maps to external perturbations, the use of complex variables is paramount for obtaining an accurate prediction. An analysis for stabilising the wake past an actuator disc, which represents a simple model for propellers, helicopter rotors or wind turbines is also presented. We explore the first flow bifurcation for an actuator disc and it suggests that it is associated to a Kelvin- Helmholtz type instability whose stability relies on the Reynolds number and the flow resistance applied through the disc (or actuator forcing). First, we report that decreasing the disc resistance has a similar stabilising effect to an decrease in the Reynolds number. Second, a discrete sensitivity analysis identifies two regions for suitable placement of flow control forcing, one close to the disc and one far downstream where the instability originates. Third, we show that adding a localised forcing close to the actuator provides more stabilisation that forcing far downstream. The analysis of the controlled flow fields, confirms that modifying the velocity gradient close to the actuator is more efficient to stabilise the wake than controlling the sheared flow far downstream. An interesting application of these results is to provide guidelines for stabilising the wake of wind or tidal turbines when placed in an energy farm to minimise unsteady interactions.

Self-organized defensive behavior in honeybees

We investigated the defensive behavior of honeybees under controlled experimental conditions. During an attack on two identical targets, the spatial distribution of stings varied as a function of the total number of stings, evincing the classic “pitchfork bifurcation” phenomenon of nonlinear dynamics. The experimental results support a model of defensive behavior based on a self-organizing mechanism. The model helps to explain several of the characteristic features of the honeybee defensive response: (i) the ability of the colony to localize and focus its attack, (ii) the strong variability between different hives in the intensity of attack, as well as (iii) the variability observed within the same hive, and (iv) the ability of the colony to amplify small differences between the targets.

Comparison of the 5′ nuclease activities of Taq DNA polymerase and its isolated nuclease domain

Many eubacterial DNA polymerases are bifunctional molecules having both polymerization (P) and 5′ nuclease (N) activities, which are contained in separable domains. We previously showed that the DNA polymerase I of Thermus aquaticus (TaqNP) endonucleolytically cleaves DNA substrates, releasing unpaired 5′ arms of bifurcated duplexes. Here, we compare the substrate specificities of TaqNP and the isolated 5′ nuclease domain of this enzyme, TaqN. Both enzymes are significantly activated by primer oligonucleotides that are hybridized to the 3′ arm of the bifurcation; optimal stimulation requires overlap of the 3′ terminal nucleotide of the primer with the terminal base pair of the duplex, but the terminal nucleotide need not hybridize to the complementary strand in the substrate. In the presence of Mn2+ ions, TaqN can cleave both RNA and circular DNA at structural bifurcations. Certain anti-TaqNP mAbs block cleavage by one or both enzymes, whereas others can stimulate cleavage of nonoptimal substrates.

A model for amplification of hair-bundle motion by cyclical binding of Ca2+ to mechanoelectrical-transduction channels

Amplification of auditory stimuli by hair cells augments the sensitivity of the vertebrate inner ear. Cell-body contractions of outer hair cells are thought to mediate amplification in the mammalian cochlea. In vertebrates that lack these cells, and perhaps in mammals as well, active movements of hair bundles may underlie amplification. We have evaluated a mathematical model in which amplification stems from the activity of mechanoelectrical-transduction channels. The intracellular binding of Ca2+ to channels is posited to promote their closure, which increases the tension in gating springs and exerts a negative force on the hair bundle. By enhancing bundle motion, this force partially compensates for viscous damping by cochlear fluids. Linear stability analysis of a six-state kinetic model reveals Hopf bifurcations for parameter values in the physiological range. These bifurcations signal conditions under which the system’s behavior changes from a damped oscillatory response to spontaneous limit-cycle oscillation. By varying the number of stereocilia in a bundle and the rate constant for Ca2+ binding, we calculate bifurcation frequencies spanning the observed range of auditory sensitivity for a representative receptor organ, the chicken’s cochlea. Simulations using prebifurcation parameter values demonstrate frequency-selective amplification with a striking compressive nonlinearity. Because transduction channels occur universally in hair cells, this active-channel model describes a mechanism of auditory amplification potentially applicable across species and hair-cell types.

Titration of chaos with added noise

Deterministic chaos has been implicated in numerous natural and man-made complex phenomena ranging from quantum to astronomical scales and in disciplines as diverse as meteorology, physiology, ecology, and economics. However, the lack of a definitive test of chaos vs. random noise in experimental time series has led to considerable controversy in many fields. Here we propose a numerical titration procedure as a simple “litmus test” for highly sensitive, specific, and robust detection of chaos in short noisy data without the need for intensive surrogate data testing. We show that the controlled addition of white or colored noise to a signal with a preexisting noise floor results in a titration index that: (i) faithfully tracks the onset of deterministic chaos in all standard bifurcation routes to chaos; and (ii) gives a relative measure of chaos intensity. Such reliable detection and quantification of chaos under severe conditions of relatively low signal-to-noise ratio is of great interest, as it may open potential practical ways of identifying, forecasting, and controlling complex behaviors in a wide variety of physical, biomedical, and socioeconomic systems.

Activation of NF-κB by nontypeable Hemophilus influenzae is mediated by toll-like receptor 2-TAK1-dependent NIK–IKKα/β–IκBα and MKK3/6–p38 MAP kinase signaling pathways in epithelial cells

Nontypeable Hemophilus influenzae (NTHi) is an important human pathogen in both children and adults. In children, it causes otitis media, the most common childhood infection and the leading cause of conductive hearing loss in the United States. In adults, it causes lower respiratory tract infections in the setting of chronic obstructive pulmonary disease, the fourth leading cause of death in the United States. The molecular mechanisms underlying the pathogenesis of NTHi-induced infections remain undefined, but they may involve activation of NF-κB, a transcriptional activator of multiple host defense genes involved in immune and inflammatory responses. Here, we show that NTHi strongly activates NF-κB in human epithelial cells via two distinct signaling pathways, NF-κB translocation-dependent and -independent pathways. The NF-κB translocation-dependent pathway involves activation of NF-κB inducing kinase (NIK)–IKKα/β complex leading to IκBα phosphorylation and degradation, whereas the NF-κB translocation-independent pathway involves activation of MKK3/6–p38 mitogen-activated protein (MAP) kinase pathway. Bifurcation of NTHi-induced NIK–IKKα/β-IκBα and MKK3/6–p38 MAP kinase pathways may occur at transforming growth factor-β activated kinase 1 (TAK1). Furthermore, we show that toll-like receptor 2 (TLR2) is required for NTHi-induced NF-κB activation. In addition, several key inflammatory mediators including IL-1β, IL-8, and tumor necrosis factor-α are up-regulated by NTHi. Finally, P6, a 16-kDa lipoprotein highly conserved in the outer membrane of all NTHi and H. influenzae type b strains, appears to also activate NF-κB via similar signaling pathways. Taken together, our results demonstrate that NTHi activates NF-κB via TLR2–TAK1-dependent NIK–IKKα/β-IκBα and MKK3/6–p38 MAP kinase signaling pathways. These studies may bring new insights into molecular pathogenesis of NTHi-induced infections and open up new therapeutic targets for these diseases.

Molecular characterization of the mosquito vitellogenin receptor reveals unexpected high homology to the Drosophila yolk protein receptor.

The mosquito (Aedes aegypti) vitellogenin receptor (AaVgR) is a large membrane-bound protein (214 kDa when linearized) that mediates internalization of vitellogenin, the major yolk-protein precursor, by oocytes during egg development. We have cloned and sequenced two cDNA fragments encompassing the entire coding region of AaVgR mRNA, to our knowledge the first insect VgR sequence to be reported. The 7.3-kb AaVgR mRNA is present only in female germ-line cells and is abundant in previtellogenic oocytes, suggesting that the AaVgR gene is expressed early in oocyte differentiation. The deduced amino acid sequence predicts a 202.7-kDa protein before posttranslational processing. The AaVgR is a member of the low density lipoprotein receptor superfamily, sharing significant homology with the chicken (Gallus gallus) VgR and particularly the Drosophila melanogaster yolk protein receptor, in spite of a very different ligand for the latter. Distance-based phylogenetic analyses suggest that the insect VgR/yolk protein receptor lineage and the vertebrate VgR/low density lipoprotein receptor lineage diverged before the bifurcation of nematode and deuterostome lines.