NURBS-Based Geometry Parameterization for Aerodynamic Shape Optimization

La motivación de esta tesis es el desarrollo de una herramienta de optimización automática para la mejora del rendimiento de formas aerodinámicas enfocado en la industria aeronáutica. Este trabajo cubre varios aspectos esenciales, desde el empleo de Non-Uniform Rational B-Splines (NURBS), al cálculo de gradientes utilizando la metodología del adjunto continuo, el uso de b-splines volumétricas como parámetros de diseño, el tratamiento de la malla en las intersecciones, y no menos importante, la adaptación de los algoritmos de la dinámica de fluidos computacional (CFD) en arquitecturas hardware de alto paralelismo, como las tarjetas gráficas, para acelerar el proceso de optimización. La metodología adjunta ha posibilitado que los métodos de optimización basados en gradientes sean una alternativa prometedora para la mejora de la eficiencia aerodinámica de los aviones. La formulación del adjunto permite calcular los gradientes de una función de coste, como la resistencia aerodinámica o la sustentación, independientemente del número de variables de diseño, a un coste computacional equivalente a una simulación CFD. Sin embargo, existen problemas prácticos que han imposibilitado su aplicación en la industria, que se pueden resumir en: integrabilidad, rendimiento computacional y robustez de la solución adjunta. Este trabajo aborda estas contrariedades y las analiza en casos prácticos. Como resumen, las contribuciones de esta tesis son: • El uso de NURBS como variables de diseño en un bucle de automático de optimización, aplicado a la mejora del rendimiento aerodinámico de alas en régimen transónico. • El desarrollo de algoritmos de inversión de punto, para calcular las coordenadas paramétricas de las coordenadas espaciales, para ligar los vértices de malla a las NURBS. • El uso y validación de la formulación adjunta para el calculo de los gradientes, a partir de las sensibilidades de la solución adjunta, comparado con diferencias finitas. • Se ofrece una estrategia para utilizar la geometría CAD, en forma de parches NURBS, para tratar las intersecciones, como el ala-fuselaje. • No existen muchas alternativas de librerías NURBS viables. En este trabajo se ha desarrollado una librería, DOMINO NURBS, y se ofrece a la comunidad como código libre y abierto. • También se ha implementado un código CFD en tarjeta gráfica, para realizar una valoración de cómo se puede adaptar un código sobre malla no estructurada a arquitecturas paralelas. • Finalmente, se propone una metodología, basada en la función de Green, como una forma eficiente de paralelizar simulaciones numéricas. Esta tesis ha sido apoyada por las actividades realizadas por el Área de Dinámica da Fluidos del Instituto Nacional de Técnica Aeroespacial (INTA), a través de numerosos proyectos de financiación nacional: DOMINO, SIMUMAT, y CORESFMULAERO. También ha estado en consonancia con las actividades realizadas por el departamento de Métodos y Herramientas de Airbus España y con el grupo Investigación y Tecnología Aeronáutica Europeo (GARTEUR), AG/52. ABSTRACT The motivation of this work is the development of an automatic optimization strategy for large scale shape optimization problems that arise in the aeronautics industry to improve the aerodynamic performance; covering several aspects from the use of Non-Uniform Rational B-Splines (NURBS), the calculation of the gradients with the continuous adjoint formulation, the development of volumetric b-splines parameterization, mesh adaptation and intersection handling, to the adaptation of Computational Fluid Dynamics (CFD) algorithms to take advantage of highly parallel architectures in order to speed up the optimization process. With the development of the adjoint formulation, gradient-based methods for aerodynamic optimization become a promising approach to improve the aerodynamic performance of aircraft designs. The adjoint methodology allows the evaluation the gradients to all design variables of a cost function, such as drag or lift, at the equivalent cost of more or less one CFD simulation. However, some practical problems have been delaying its full implementation to the industry, which can be summarized as: integrability, computer performance, and adjoint robustness. This work tackles some of these issues and analyse them in well-known test cases. As summary, the contributions comprises: • The employment of NURBS as design variables in an automatic optimization loop for the improvement of the aerodynamic performance of aircraft wings in transonic regimen. • The development of point inversion algorithms to calculate the NURBS parametric coordinates from the space coordinates, to link with the computational grid vertex. • The use and validation of the adjoint formulation to calculate the gradients from the surface sensitivities in an automatic optimization loop and evaluate its reliability, compared with finite differences. • This work proposes some algorithms that take advantage of the underlying CAD geometry description, in the form of NURBS patches, to handle intersections and mesh adaptations. • There are not many usable libraries for NURBS available. In this work an open source library DOMINO NURBS has been developed and is offered to the community as free, open source code. • The implementation of a transonic CFD solver from scratch in a graphic card, for an assessment of the implementability of conventional CFD solvers for unstructured grids to highly parallel architectures. • Finally, this research proposes the use of the Green's function as an efficient paralellization scheme of numerical solvers. The presented work has been supported by the activities carried out at the Fluid Dynamics branch of the National Institute for Aerospace Technology (INTA) through national founding research projects: DOMINO, SIMUMAT, and CORESIMULAERO; in line with the activities carried out by the Methods and Tools and Flight Physics department at Airbus and the Group for Aeronautical Research and Technology in Europe (GARTEUR) action group AG/52.

Tridimensional simulation of the speed, pressure and turbulence fields of the air flow on the geometry of a freight truck inside a wind tunnel

This study shows the air flow behavior through the geometry of a freight truck inside a AF6109 wind tunnel with the purpose to predict the speed, pressure and turbulence fields made by the air flow, to decrease the aerodynamic resistance, to calculate the dragging coefficient, to evaluate the aerodynamics of the geometry of the prototype using the CFD technique and to compare the results of the simulation with the results obtained experimentally with the “PETER 739 HAULER” scaled freight truck model located on the floor of the test chamber. The Geometry went through a numerical simulation process using the CFX 5,7. The obtained results showed the behavior of the air flow through the test chamber, and also it showed the variations of speed and pressure at the exit of the chamber and the calculations of the coefficient and the dragging force on the geometry of the freight truck. The evaluation of the aerodynamics showed that the aerodynamic deflector is a device that helped the reduction the dragging produced in a significant way by the air. Furthermore, the dragging coefficient and force on the prototype freight truck could be estimated establishing an incomplete similarity.

Coherent structures in statistically-stationary homogeneous shear turbulence

La región cerca de la pared de flujos turbulentos de pared ya está bien conocido debido a su bajo número de Reynolds local y la separación escala estrecha. La región lejos de la pared (capa externa) no es tan interesante tampoco, ya que las estadísticas allí se escalan bien por las unidades exteriores. La región intermedia (capa logarítmica), sin embargo, ha estado recibiendo cada vez más atención debido a su propiedad auto-similares. Además, de acuerdo a Flores et al. (2007) y Flores & Jiménez (2010), la capa logarítmica es más o menos independiente de otras capas, lo que implica que podría ser inspeccionado mediante el aislamiento de otras dos capas, lo que reduciría significativamente los costes computacionales para la simulación de flujos turbulentos de pared. Algunos intentos se trataron después por Mizuno & Jiménez (2013), quien simulan la capa logarítmica sin la región cerca de la pared con estadísticas obtenidas de acuerdo razonablemente bien con los de las simulaciones completas. Lo que más, la capa logarítmica podría ser imitado por otra turbulencia sencillo de cizallamiento de motor. Por ejemplo, Pumir (1996) encontró que la turbulencia de cizallamiento homogéneo estadísticamente estacionario (SS-HST) también irrumpe, de una manera muy similar al proceso de auto-sostenible en flujos turbulentos de pared. Según los consideraciones arriba, esta tesis trata de desvelar en qué medida es la capa logarítmica de canales similares a la turbulencia de cizalla más sencillo, SS-HST, mediante la comparación de ambos cinemática y la dinámica de las estructuras coherentes en los dos flujos. Resultados sobre el canal se muestran mediante Lozano-Durán et al. (2012) y Lozano-Durán & Jiménez (2014b). La hoja de ruta de esta tarea se divide en tres etapas. En primer lugar, SS-HST es investigada por medio de un código nuevo de simulación numérica directa, espectral en las dos direcciones horizontales y compacto-diferencias finitas en la dirección de la cizalla. Sin utiliza remallado para imponer la condición de borde cortante periódica. La influencia de la geometría de la caja computacional se explora. Ya que el HST no tiene ninguna longitud característica externa y tiende a llenar el dominio computacional, las simulaciopnes a largo plazo del HST son ’mínimos’ en el sentido de que contiene sólo unas pocas estructuras media a gran escala. Se ha encontrado que el límite principal es el ancho de la caja de la envergadura, Lz, que establece las escalas de longitud y velocidad de la turbulencia, y que las otras dos dimensiones de la caja debe ser suficientemente grande (Lx > 2LZ, Ly > Lz) para evitar que otras direcciones estando limitado también. También se encontró que las cajas de gran longitud, Lx > 2Ly, par con el paso del tiempo la condición de borde cortante periódica, y desarrollar fuertes ráfagas linealizadas no físicos. Dentro de estos límites, el flujo muestra similitudes y diferencias interesantes con otros flujos de cizalla, y, en particular, con la capa logarítmica de flujos turbulentos de pared. Ellos son exploradas con cierto detalle. Incluyen un proceso autosostenido de rayas a gran escala y con una explosión cuasi-periódica. La escala de tiempo de ruptura es de aproximadamente universales, ~20S~l(S es la velocidad de cizallamiento media), y la disponibilidad de dos sistemas de ruptura diferentes permite el crecimiento de las ráfagas a estar relacionado con algo de confianza a la cizalladura de turbulencia inicialmente isotrópico. Se concluye que la SS-HST, llevado a cabo dentro de los parámetros de cílculo apropiados, es un sistema muy prometedor para estudiar la turbulencia de cizallamiento en general. En segundo lugar, las mismas estructuras coherentes como en los canales estudiados por Lozano-Durán et al. (2012), es decir, grupos de vórticidad (fuerte disipación) y Qs (fuerte tensión de Reynolds tangencial, -uv) tridimensionales, se estudia mediante simulación numérica directa de SS-HST con relaciones de aspecto de cuadro aceptables y número de Reynolds hasta Rex ~ 250 (basado en Taylor-microescala). Se discute la influencia de la intermitencia de umbral independiente del tiempo. Estas estructuras tienen alargamientos similares en la dirección sentido de la corriente a las familias separadas en los canales hasta que son de tamaño comparable a la caja. Sus dimensiones fractales, longitudes interior y exterior como una función del volumen concuerdan bien con sus homólogos de canales. El estudio sobre sus organizaciones espaciales encontró que Qs del mismo tipo están alineados aproximadamente en la dirección del vector de velocidad en el cuadrante al que pertenecen, mientras Qs de diferentes tipos están restringidos por el hecho de que no debe haber ningún choque de velocidad, lo que hace Q2s (eyecciones, u < 0,v > 0) y Q4s (sweeps, u > 0,v < 0) emparejado en la dirección de la envergadura. Esto se verifica mediante la inspección de estructuras de velocidad, otros cuadrantes como la uw y vw en SS-HST y las familias separadas en el canal. La alineación sentido de la corriente de Qs ligada a la pared con el mismo tipo en los canales se debe a la modulación de la pared. El campo de flujo medio condicionado a pares Q2-Q4 encontró que los grupos de vórticidad están en el medio de los dos, pero prefieren los dos cizalla capas alojamiento en la parte superior e inferior de Q2s y Q4s respectivamente, lo que hace que la vorticidad envergadura dentro de las grupos de vórticidad hace no cancele. La pared amplifica la diferencia entre los tamaños de baja- y alta-velocidad rayas asociados con parejas de Q2-Q4 se adjuntan como los pares alcanzan cerca de la pared, el cual es verificado por la correlación de la velocidad del sentido de la corriente condicionado a Q2s adjuntos y Q4s con diferentes alturas. Grupos de vórticidad en SS-HST asociados con Q2s o Q4s también están flanqueadas por un contador de rotación de los vórtices sentido de la corriente en la dirección de la envergadura como en el canal. La larga ’despertar’ cónica se origina a partir de los altos grupos de vórticidad ligada a la pared han encontrado los del Álamo et al. (2006) y Flores et al. (2007), que desaparece en SS-HST, sólo es cierto para altos grupos de vórticidad ligada a la pared asociados con Q2s pero no para aquellos asociados con Q4s, cuyo campo de flujo promedio es en realidad muy similar a la de SS-HST. En tercer lugar, las evoluciones temporales de Qs y grupos de vórticidad se estudian mediante el uso de la método inventado por Lozano-Durán & Jiménez (2014b). Las estructuras se clasifican en las ramas, que se organizan más en los gráficos. Ambas resoluciones espaciales y temporales se eligen para ser capaz de capturar el longitud y el tiempo de Kolmogorov puntual más probable en el momento más extrema. Debido al efecto caja mínima, sólo hay un gráfico principal consiste en casi todas las ramas, con su volumen y el número de estructuras instantáneo seguien la energía cinética y enstrofía intermitente. La vida de las ramas, lo que tiene más sentido para las ramas primarias, pierde su significado en el SS-HST debido a las aportaciones de ramas primarias al total de Reynolds estrés o enstrofía son casi insignificantes. Esto también es cierto en la capa exterior de los canales. En cambio, la vida de los gráficos en los canales se compara con el tiempo de ruptura en SS-HST. Grupos de vórticidad están asociados con casi el mismo cuadrante en términos de sus velocidades medias durante su tiempo de vida, especialmente para los relacionados con las eyecciones y sweeps. Al igual que en los canales, las eyecciones de SS-HST se mueven hacia arriba con una velocidad promedio vertical uT (velocidad de fricción) mientras que lo contrario es cierto para los barridos. Grupos de vórticidad, por otra parte, son casi inmóvil en la dirección vertical. En la dirección de sentido de la corriente, que están advección por la velocidad media local y por lo tanto deforman por la diferencia de velocidad media. Sweeps y eyecciones se mueven más rápido y más lento que la velocidad media, respectivamente, tanto por 1.5uT. Grupos de vórticidad se mueven con la misma velocidad que la velocidad media. Se verifica que las estructuras incoherentes cerca de la pared se debe a la pared en vez de pequeño tamaño. Los resultados sugieren fuertemente que las estructuras coherentes en canales no son especialmente asociado con la pared, o incluso con un perfil de cizalladura dado. ABSTRACT Since the wall-bounded turbulence was first recognized more than one century ago, its near wall region (buffer layer) has been studied extensively and becomes relatively well understood due to the low local Reynolds number and narrow scale separation. The region just above the buffer layer, i.e., the logarithmic layer, is receiving increasingly more attention nowadays due to its self-similar property. Flores et al. (20076) and Flores & Jim´enez (2010) show that the statistics of logarithmic layer is kind of independent of other layers, implying that it might be possible to study it separately, which would reduce significantly the computational costs for simulations of the logarithmic layer. Some attempts were tried later by Mizuno & Jimenez (2013), who simulated the logarithmic layer without the buffer layer with obtained statistics agree reasonably well with those of full simulations. Besides, the logarithmic layer might be mimicked by other simpler sheardriven turbulence. For example, Pumir (1996) found that the statistically-stationary homogeneous shear turbulence (SS-HST) also bursts, in a manner strikingly similar to the self-sustaining process in wall-bounded turbulence. Based on these considerations, this thesis tries to reveal to what extent is the logarithmic layer of channels similar to the simplest shear-driven turbulence, SS-HST, by comparing both kinematics and dynamics of coherent structures in the two flows. Results about the channel are shown by Lozano-Dur´an et al. (2012) and Lozano-Dur´an & Jim´enez (20146). The roadmap of this task is divided into three stages. First, SS-HST is investigated by means of a new direct numerical simulation code, spectral in the two horizontal directions and compact-finite-differences in the direction of the shear. No remeshing is used to impose the shear-periodic boundary condition. The influence of the geometry of the computational box is explored. Since HST has no characteristic outer length scale and tends to fill the computational domain, longterm simulations of HST are ‘minimal’ in the sense of containing on average only a few large-scale structures. It is found that the main limit is the spanwise box width, Lz, which sets the length and velocity scales of the turbulence, and that the two other box dimensions should be sufficiently large (Lx > 2LZ, Ly > Lz) to prevent other directions to be constrained as well. It is also found that very long boxes, Lx > 2Ly, couple with the passing period of the shear-periodic boundary condition, and develop strong unphysical linearized bursts. Within those limits, the flow shows interesting similarities and differences with other shear flows, and in particular with the logarithmic layer of wallbounded turbulence. They are explored in some detail. They include a self-sustaining process for large-scale streaks and quasi-periodic bursting. The bursting time scale is approximately universal, ~ 20S~l (S is the mean shear rate), and the availability of two different bursting systems allows the growth of the bursts to be related with some confidence to the shearing of initially isotropic turbulence. It is concluded that SS-HST, conducted within the proper computational parameters, is a very promising system to study shear turbulence in general. Second, the same coherent structures as in channels studied by Lozano-Dur´an et al. (2012), namely three-dimensional vortex clusters (strong dissipation) and Qs (strong tangential Reynolds stress, -uv), are studied by direct numerical simulation of SS-HST with acceptable box aspect ratios and Reynolds number up to Rex ~ 250 (based on Taylor-microscale). The influence of the intermittency to time-independent threshold is discussed. These structures have similar elongations in the streamwise direction to detached families in channels until they are of comparable size to the box. Their fractal dimensions, inner and outer lengths as a function of volume agree well with their counterparts in channels. The study about their spatial organizations found that Qs of the same type are aligned roughly in the direction of the velocity vector in the quadrant they belong to, while Qs of different types are restricted by the fact that there should be no velocity clash, which makes Q2s (ejections, u < 0, v > 0) and Q4s (sweeps, u > 0, v < 0) paired in the spanwise direction. This is verified by inspecting velocity structures, other quadrants such as u-w and v-w in SS-HST and also detached families in the channel. The streamwise alignment of attached Qs with the same type in channels is due to the modulation of the wall. The average flow field conditioned to Q2-Q4 pairs found that vortex clusters are in the middle of the pair, but prefer to the two shear layers lodging at the top and bottom of Q2s and Q4s respectively, which makes the spanwise vorticity inside vortex clusters does not cancel. The wall amplifies the difference between the sizes of low- and high-speed streaks associated with attached Q2-Q4 pairs as the pairs reach closer to the wall, which is verified by the correlation of streamwise velocity conditioned to attached Q2s and Q4s with different heights. Vortex clusters in SS-HST associated with Q2s or Q4s are also flanked by a counter rotating streamwise vortices in the spanwise direction as in the channel. The long conical ‘wake’ originates from tall attached vortex clusters found by del A´ lamo et al. (2006) and Flores et al. (2007b), which disappears in SS-HST, is only true for tall attached vortices associated with Q2s but not for those associated with Q4s, whose averaged flow field is actually quite similar to that in SS-HST. Third, the temporal evolutions of Qs and vortex clusters are studied by using the method invented by Lozano-Dur´an & Jim´enez (2014b). Structures are sorted into branches, which are further organized into graphs. Both spatial and temporal resolutions are chosen to be able to capture the most probable pointwise Kolmogorov length and time at the most extreme moment. Due to the minimal box effect, there is only one main graph consist by almost all the branches, with its instantaneous volume and number of structures follow the intermittent kinetic energy and enstrophy. The lifetime of branches, which makes more sense for primary branches, loses its meaning in SS-HST because the contributions of primary branches to total Reynolds stress or enstrophy are almost negligible. This is also true in the outer layer of channels. Instead, the lifetime of graphs in channels are compared with the bursting time in SS-HST. Vortex clusters are associated with almost the same quadrant in terms of their mean velocities during their life time, especially for those related with ejections and sweeps. As in channels, ejections in SS-HST move upwards with an average vertical velocity uτ (friction velocity) while the opposite is true for sweeps. Vortex clusters, on the other hand, are almost still in the vertical direction. In the streamwise direction, they are advected by the local mean velocity and thus deformed by the mean velocity difference. Sweeps and ejections move faster and slower than the mean velocity respectively, both by 1.5uτ . Vortex clusters move with the same speed as the mean velocity. It is verified that the incoherent structures near the wall is due to the wall instead of small size. The results suggest that coherent structures in channels are not particularly associated with the wall, or even with a given shear profile.

Soil aggregate geometry: Measurements and morphology

Aggregates provide physical microenvironments for microorganisms, the vital actors of soil systems, and thus play a major role as both, an arena and a product of soil carbon stabilization and dynamics. The surface of an aggregate is what enables exchange of the materials and air and water fluxes between aggregate exterior and interior regions. We made use of 3D images from X-ray CT of aggregates and mathematical morphology to provide an exhaustive quantitative description of soil aggregate morphology that includes both intra-aggregate pore space structure and aggregate surface features. First, the evolution of Minkowski functionals (i.e. volume, boundary surface, curvature and connectivity) for successive dilations of the solid part of aggregates was investigated to quantify its 3D geometrical features. Second, the inner pore space was considered as the object of interest. We devised procedures (a) to define the ends of the accessible pores that are connected to the aggregate surface and (b) to separate accessible and inaccessible porosity. Geometrical Minkowski functionals of the intra-aggregate pore space provide the exhaustive characterization of the inner structure of the aggregates. Aggregates collected from two different soil treatments were analyzed to explore the utility of these morphological tools in capturing the impact on their morphology of two different soil managements, i.e. conventional tillage management, and native succession vegetation treatment. The quantitative tools of mathematical morphology distinguished differences in patterns of aggregate structure associated to the different soil managements.

Quantifying the relationship between drainage networks at hillslope scale and particle size distribution at pedon scale

Nowadays, translating information about hydrologic and soil properties and processes across scales has emerged as a major theme in soil science and hydrology, and suitable theories for upscaling or downscaling hydrologic and soil information are being looked forward. The recognition of low-order catchments as self-organized systems suggests the existence of a great amount of links at different scales between their elements. The objective of this work was to research in areas of homogeneous bedrock material, the relationship between the hierarchical structure of the drainage networks at hillslope scale and the heterogeneity of the particle-size distribution at pedon scale. One of the most innovative elements in this work is the choice of the parameters to quantify the organization level of the studied features. The fractal dimension has been selected to measure the hierarchical structure of the drainage networks, while the Balanced Entropy Index (BEI) has been the chosen parameter to quantify the heterogeneity of the particle-size distribution from textural data. These parameters have made it possible to establish quantifiable relationships between two features attached to different steps in the scale range. Results suggest that the bedrock lithology of the landscape constrains the architecture of the drainage networks developed on it and the particle soil distribution resulting in the fragmentation processes.

The interspecific mass–density relationship and plant geometry

We present an a priori theoretical framework for the interspecific allometric relationship between stand mass and plant population density. Our model predicts a slope of −\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}\frac{1}{3}\end{equation*}\end{document} between the logarithm of stand mass and the logarithm of stand density, thus conflicting with a previously assumed slope of −½. Our model rests on a heuristic separation of resource-limited living mass and structural mass in the plant body. We point out that because of similar resource requirements among plants of different sizes, a nonzero plant mass–density slope is primarily defined by structural mass. Specifically, the slope is a result of (i) the physical size-dependent relationship between stem width and height, (ii) foliage-dependent demands of conductance, and (iii) the cumulative nature of structural mass. The data support our model, both when the potential sampling bias of taxonomic relatedness is accounted for and when it is not. Independent contrasts analyses show that observed relationships among variables are not significantly different from the assumptions made to build the model or from its a priori predictions. We note that the dependence of the plant mass–density slope on the functions of structural mass provides a cause for the difference from the zero slope found in the animal population mass–density relationship; for the most part, animals do not have a comparable cumulative tissue type.

The making of the architecture of the plant cell wall: How cells exploit geometry

Cell wall deposition is a key process in the formation, growth, and differentiation of plant cells. The most important structural components of the wall are long cellulose microfibrils, which are synthesized by synthases embedded in the plasma membrane. A fundamental question is how the microfibrils become oriented during deposition at the plasma membrane. The current textbook explanation for the orientation mechanism is a guidance system mediated by cortical microtubules. However, too many contraindications are known in secondary cell walls for this to be a universal mechanism, particularly in the case of helicoidal arrangements, which occur in many situations. An additional construction mechanism involves liquid crystalline self-assembly [A. C. Neville (1993) Biology of Fibrous Composites: Development Beyond the Cell Membrane (Cambridge Univ. Press, Cambridge, U.K.)], but the required amount of bulk material that is able to equilibrate thermally is not normally present at any stage of the wall deposition process. Therefore, we have asked whether the complex ordered texture of helicoidal cell walls can be formed in the absence of direct cellular guidance mechanisms. We propose that they can be formed by a mechanism that is based on geometrical considerations. It explains the genesis of the complicated helicoidal texture and shows that the cell has intrinsic, versatile tools for creating a variety of textures. A compelling feature of the model is that local rules generate global order, a typical phenomenon of life.

Kinematic geometry of mass-triangles and reduction of Schrödinger’s equation of three-body systems to partial differential equations solely defined on triangular parameters

Schrödinger’s equation of a three-body system is a linear partial differential equation (PDE) defined on the 9-dimensional configuration space, ℝ9, naturally equipped with Jacobi’s kinematic metric and with translational and rotational symmetries. The natural invariance of Schrödinger’s equation with respect to the translational symmetry enables us to reduce the configuration space to that of a 6-dimensional one, while that of the rotational symmetry provides the quantum mechanical version of angular momentum conservation. However, the problem of maximizing the use of rotational invariance so as to enable us to reduce Schrödinger’s equation to corresponding PDEs solely defined on triangular parameters—i.e., at the level of ℝ6/SO(3)—has never been adequately treated. This article describes the results on the orbital geometry and the harmonic analysis of (SO(3),ℝ6) which enable us to obtain such a reduction of Schrödinger’s equation of three-body systems to PDEs solely defined on triangular parameters.

Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase

Oligonucleotides that recapitulate the acceptor stems of tRNAs are substrates for aminoacylation by many tRNA synthetases in vitro, even though these substrates are missing the anticodon trinucleotides of the genetic code. In the case of tRNAAla a single acceptor stem G⋅U base pair at position 3·70 is essential, based on experiments where the wobble pair has been replaced by alternatives such as I⋅U, G⋅C, and A⋅U, among others. These experiments led to the conclusion that the minor-groove free 2-amino group (of guanosine) of the G⋅U wobble pair is essential for charging. Moreover, alanine-inserting tRNAs (amber suppressors) that replace G⋅U with mismatches such as G⋅A and C⋅A are partially active in vivo and can support growth of an Escherichia coli tRNAAla knockout strain, leading to the hypothesis that a helix irregularity and nucleotide functionalities are important for recognition. Herein we investigate the charging in vitro of oligonucleotide and full-length tRNA substrates that contain mismatches at the position of the G⋅U pair. Although most of these substrates have undetectable activity, G⋅A and C⋅A variants retain some activity, which is, nevertheless, reduced by at least 100-fold. Thus, the in vivo assays are much less sensitive to large changes in aminoacylation kinetic efficiency of 3·70 variants than is the in vitro assay system. Although these functional data do not clarify all of the details, it is now clear that specific atomic groups are substantially more important in determining kinetic efficiency than is a helical distortion. By implication, the activity of mutant tRNAs measured in the in vivo assays appears to be more dependent on factors other than aminoacylation kinetic efficiency.

Geometry of circular vectors and pattern recognition of shape of a boundary

This paper deals with pattern recognition of the shape of the boundary of closed figures on the basis of a circular sequence of measurements taken on the boundary at equal intervals of a suitably chosen argument with an arbitrary starting point. A distance measure between two boundaries is defined in such a way that it has zero value when the associated sequences of measurements coincide by shifting the starting point of one of the sequences. Such a distance measure, which is invariant to the starting point of the sequence of measurements, is used in identification or discrimination by the shape of the boundary of a closed figure. The mean shape of a given set of closed figures is defined, and tests of significance of differences in mean shape between populations are proposed.

On the geometry of solutions of the quasi-geostrophic and Euler equations

We study solutions of the two-dimensional quasi-geostrophic thermal active scalar equation involving simple hyperbolic saddles. There is a naturally associated notion of simple hyperbolic saddle breakdown. It is proved that such breakdown cannot occur in finite time. At large time, these solutions may grow at most at a quadruple-exponential rate. Analogous results hold for the incompressible three-dimensional Euler equation.

Fos and Jun bend the AP-1 site: effects of probe geometry on the detection of protein-induced DNA bending.

The effect of Fos and Jun binding on the structure of the AP-1 recognition site is controversial. Results from phasing analysis and phase-sensitive detection studies of DNA bending by Fos and Jun have led to opposite conclusions. The differences between these assays, the length of the spacer between two bends and the length of the sequences flanking the bends, are investigated here using intrinsic DNA bend standards. Both an increase in the spacer length as well as a decrease in the length of flanking sequences resulted in a reduction in the phase-dependent variation in electrophoretic mobilities. Probes with a wide separation between the bends and short flanking sequences, such as those used in the phase-sensitive detection studies, displayed no phase-dependent mobility variation. This shape-dependent variation in electrophoretic mobilities was reproduced by complexes formed by truncated Fos and Jun. Results from ligase-catalyzed cyclization experiments have been interpreted to indicate the absence of DNA bending in the Fos-Jun-AP-1 complex. However, truncated Fos and Jun can alter the relative rates of inter- and intramolecular ligation through mechanisms unrelated to DNA bending, confounding the interpretation of cyclization data. The analogous phase- and shape-dependence of the electrophoretic mobilities of the Fos-Jun-AP-1 complex and an intrinsic DNA bend confirm that Fos and Jun bend DNA, which may contribute to their functions in transcription regulation.

Geometry of the SL(3,ℂ)-character variety of torus knots.

Let G be the fundamental group of the complement of the torus knot of type (m, n). It has a presentation G = . We find a geometric description of the character variety X(G) of characters of representations of G into SL(3,ℂ), GL(3,ℂ) and PGL(3,ℂ).