Monte-Carlo dosimetry on a realistic cell monolayer geometry exposed to alpha particles

The energy and specific energy absorbed in the main cell compartments (nucleus and cytoplasm) in typical radiobiology experiments are usually estimated by calculations as they are not accessible for a direct measurement. In most of the work, the cell geometry is modelled using the combination of simple mathematical volumes. We propose a method based on high resolution confocal imaging and ion beam analysis (IBA) in order to import realistic cell nuclei geometries in Monte-Carlo simulations and thus take into account the variety of different geometries encountered in a typical cell population. Seventy-six cell nuclei have been imaged using confocal microscopy and their chemical composition has been measured using IBA. A cellular phantom was created from these data using the ImageJ image analysis software and imported in the Geant4 Monte-Carlo simulation toolkit. Total energy and specific energy distributions in the 76 cell nuclei have been calculated for two types of irradiation protocols: a 3 MeV alpha particle microbeam used for targeted irradiation and a 239Pu alpha source used for large angle random irradiation. Qualitative images of the energy deposited along the particle tracks have been produced and show good agreement with images of DNA double strand break signalling proteins obtained experimentally. The methodology presented in this paper provides microdosimetric quantities calculated from realistic cellular volumes. It is based on open-source oriented software that is publicly available.

Análisis y diseño de un patrón de ruido térmico de 10 MHz a 26,5 GHz en tecnología coaxial

Esta Tesis Doctoral presenta las investigaciones y los trabajos desarrollados durante los años 2008 a 2012 para el análisis y diseño de un patrón primario de ruido térmico de banda ancha en tecnología coaxial. Para ubicar esta Tesis en su campo científico es necesario tomar conciencia de que la realización de mediciones fiables y trazables forma parte del sostenimiento del bienestar de una sociedad moderna y juega un papel crítico en apoyo de la competitividad económica, la fabricación y el comercio, así como de la calidad de vida. En el mundo moderno actual, una infraestructura de medición bien desarrollada genera confianza en muchas facetas de nuestra vida diaria, porque nos permite el desarrollo y fabricación de productos fiables, innovadores y de alta calidad; porque sustenta la competitividad de las industrias y su producción sostenible; además de contribuir a la eliminación de barreras técnicas y de dar soporte a un comercio justo, garantizar la seguridad y eficacia de la asistencia sanitaria, y por supuesto, dar respuesta a los grandes retos de la sociedad moderna en temas tan complicados como la energía y el medio ambiente. Con todo esto en mente se ha desarrollado un patrón primario de ruido térmico con el fin de aportar al sistema metrológico español un nuevo patrón primario de referencia capaz de ser usado para desarrollar mediciones fiables y trazables en el campo de la medida y calibración de dispositivos de ruido electromagnético de radiofrecuencia y microondas. Este patrón se ha planteado para que cumpla en el rango de 10 MHz a 26,5 GHz con las siguientes especificaciones: Salida nominal de temperatura de ruido aproximada de ~ 83 K. Incertidumbre de temperatura de ruido menor que ± 1 K en todo su rango de frecuencias. Coeficiente de reflexión en todo su ancho de banda de 0,01 a 26,5 GHz lo más bajo posible. Se ha divido esta Tesis Doctoral en tres partes claramente diferenciadas. La primera de ellas, que comprende los capítulos 1, 2, 3, 4 y 5, presenta todo el proceso de simulaciones y ajustes de los parámetros principales del dispositivo con el fin de dejar definidos los que resultan críticos en su construcción. A continuación viene una segunda parte compuesta por el capítulo 6 en donde se desarrollan los cálculos necesarios para obtener la temperatura de ruido a la salida del dispositivo. La tercera y última parte, capítulo 7, se dedica a la estimación de la incertidumbre de la temperatura de ruido del nuevo patrón primario de ruido obtenida en el capítulo anterior. Más concretamente tenemos que en el capítulo 1 se hace una exhaustiva introducción del entorno científico en donde se desarrolla este trabajo de investigación. Además se detallan los objetivos que se persiguen y se presenta la metodología utilizada para conseguirlos. El capítulo 2 describe la caracterización y selección del material dieléctrico para el anillo del interior de la línea de transmisión del patrón que ponga en contacto térmico los dos conductores del coaxial para igualar las temperaturas entre ambos y mantener la impedancia característica de todo el patrón primario de ruido. Además se estudian las propiedades dieléctricas del nitrógeno líquido para evaluar su influencia en la impedancia final de la línea de transmisión. En el capítulo 3 se analiza el comportamiento de dos cargas y una línea de aire comerciales trabajando en condiciones criogénicas. Se pretende con este estudio obtener la variación que se produce en el coeficiente de reflexión al pasar de temperatura ambiente a criogénica y comprobar si estos dispositivos resultan dañados por trabajar a temperaturas criogénicas; además se estudia si se modifica su comportamiento tras sucesivos ciclos de enfriamiento – calentamiento, obteniendo una cota de la variación para poder así seleccionar la carga que proporcione un menor coeficiente de reflexión y una menor variabilidad. En el capítulo 4 se parte del análisis de la estructura del anillo de material dieléctrico utilizada en la nota técnica NBS 1074 del NIST con el fin de obtener sus parámetros de dispersión que nos servirán para calcular el efecto que produce sobre el coeficiente de reflexión de la estructura coaxial completa. Además se realiza un estudio posterior con el fin de mejorar el diseño de la nota técnica NBS 1074 del NIST, donde se analiza el anillo de material dieléctrico, para posteriormente realizar modificaciones en la geometría de la zona donde se encuentra éste con el fin de reducir la reflexión que produce. Concretamente se estudia el ajuste del radio del conductor interior en la zona del anillo para que presente la misma impedancia característica que la línea. Y para finalizar se obtiene analíticamente la relación entre el radio del conductor interior y el radio de la transición de anillo térmico para garantizar en todo punto de esa transición la misma impedancia característica, manteniendo además criterios de robustez del dispositivo y de fabricación realistas. En el capítulo 5 se analiza el comportamiento térmico del patrón de ruido y su influencia en la conductividad de los materiales metálicos. Se plantean las posibilidades de que el nitrógeno líquido sea exterior a la línea o que éste penetre en su interior. En ambos casos, dada la simetría rotacional del problema, se ha simulado térmicamente una sección de la línea coaxial, es decir, se ha resuelto un problema bidimensional, aunque los resultados son aplicables a la estructura real tridimensional. Para la simulación térmica se ha empleado la herramienta PDE Toolbox de Matlab®. En el capítulo 6 se calcula la temperatura de ruido a la salida del dispositivo. Se parte del estudio de la aportación a la temperatura de ruido final de cada sección que compone el patrón. Además se estudia la influencia de las variaciones de determinados parámetros de los elementos que conforman el patrón de ruido sobre las características fundamentales de éste, esto es, el coeficiente de reflexión a lo largo de todo el dispositivo. Una vez descrito el patrón de ruido electromagnético se procede, en el capítulo 7, a describir los pasos seguidos para estimar la incertidumbre de la temperatura de ruido electromagnético a su salida. Para ello se utilizan dos métodos, el clásico de la guía para la estimación de la incertidumbre [GUM95] y el método de simulación de Monte Carlo. En el capítulo 8 se describen las conclusiones y lo logros conseguidos. Durante el desarrollo de esta Tesis Doctoral se ha obtenido un dispositivo novedoso susceptible de ser patentado, que ha sido registrado en la Oficina Española de Patentes y Marcas (O.E.P.M.) en Madrid, de conformidad con lo establecido en el artículo 20 de la Ley 11/1986, de 20 de Marzo, de Patentes, con el título Patrón Primario de Ruido Térmico de Banda Ancha (Referencia P-101061) con fecha 7 de febrero de 2011. ABSTRACT This Ph. D. work describes a number of investigations that were performed along the years 2008 to 2011, as a preparation for the study and design of a coaxial cryogenic reference noise standard. Reliable and traceable measurement underpins the welfare of a modern society and plays a critical role in supporting economic competitiveness, manufacturing and trade as well as quality of life. In our modern world, a well developed measurement infrastructure gives confidence in many aspects of our daily life, for example by enabling the development and manufacturing of reliable, high quality and innovative products; by supporting industry to be competitive and sustainable in its production; by removing technical barriers to trade and supporting fair trade; by ensuring safety and effectiveness of healthcare; by giving response to the major challenges in key sectors such energy and environment, etc. With all this in mind we have developed a primary standard thermal noise with the aim of providing the Spanish metrology system with a new primary standard for noise reference. This standard will allow development of reliable and traceable measurements in the field of calibration and measurement of electromagnetic noise RF and microwave devices. This standard has been designed to work in the frequency range from 10 MHz to 26.5 GHz, meeting the following specifications: 1. Noise temperature output is to be nominally ~ 83 K. 2. Noise temperature uncertainty less than ± 1 K in the frequency range from 0.01 to 26.5 GHz. 3. Broadband performance requires as low a reflection coefficient as possible from 0.01 to 26.5 GHz. The present Ph. D. work is divided into three clearly differentiated parts. The first one, which comprises Chapters 1 to 5, presents the whole process of simulation and adjustment of the main parameters of the device in order to define those of them which are critical for the manufacturing of the device. Next, the second part consists of Chapter 6 where the necessary computations to obtain the output noise temperature of the device are carried out. The third and last part, Chapter 7, is devoted to the estimation of the uncertainty related to the noise temperature of the noise primary standard as obtained in the preceding chapter. More specifically, Chapter 1 provides a thorough introduction to the scientific and technological environment where this research takes place. It also details the objectives to be achieved and presents the methodology used to achieve them. Chapter 2 describes the characterization and selection of the bead dielectric material inside the transmission line, intended to connect the two coaxial conductors equalizing the temperature between the two of them and thus keeping the characteristic impedance constant for the whole standard. In addition the dielectric properties of liquid nitrogen are analyzed in order to assess their influence on the impedance of the transmission line. Chapter 3 analyzes the behavior of two different loads and of a commercial airline when subjected to cryogenic working conditions. This study is intended to obtain the variation in the reflection coefficient when the temperature changes from room to cryogenic temperature, and to check whether these devices can be damaged as a result of working at cryogenic temperatures. Also we try to see whether the load changes its behavior after successive cycles of cooling / heating, in order to obtain a bound for the allowed variation of the reflection coefficient of the load. Chapter 4 analyzes the ring structure of the dielectric material used in the NBS technical note 1074 of NIST, in order to obtain its scattering parameters that will be used for computation of its effect upon the reflection coefficient of the whole coaxial structure. Subsequently, we perform a further investigation with the aim of improving the design of NBS technical note 1074 of NIST, and modifications are introduced in the geometry of the transition area in order to reduce the reflection it produces. We first analyze the ring, specifically the influence of the radius of inner conductor of the bead, and then make changes in its geometry so that it presents the same characteristic impedance as that of the line. Finally we analytically obtain the relationship between the inner conductor radius and the radius of the transition from ring, in order to ensure the heat flow through the transition thus keeping the same reflection coefficient, and at the same time meeting the robustness requirements and the feasibility of manufacturing. Chapter 5 analyzes the thermal behavior of the noise standard and its influence on the conductivity of metallic materials. Both possibilities are raised that the liquid nitrogen is kept outside the line or that it penetrates inside. In both cases, given the rotational symmetry of the structure, we have simulated a section of coaxial line, i.e. the equivalent two-dimensional problem has been resolved, although the results are applicable to the actual three-dimensional structure. For thermal simulation Matlab™ PDE Toolbox has been used. In Chapter 6 we compute the output noise temperature of the device. The starting point is the analysis of the contribution to the overall noise temperature of each section making up the standard. Moreover the influence of the variations in the parameters of all elements of the standard is analyzed, specifically the variation of the reflection coefficient along the entire device. Once the electromagnetic noise standard has been described and analyzed, in Chapter 7 we describe the steps followed to estimate the uncertainty of the output electromagnetic noise temperature. This is done using two methods, the classic analytical approach following the Guide to the Estimation of Uncertainty [GUM95] and numerical simulations made with the Monte Carlo method. Chapter 8 discusses the conclusions and achievements. During the development of this thesis, a novel device was obtained which was potentially patentable, and which was finally registered through the Spanish Patent and Trademark Office (SPTO) in Madrid, in accordance with the provisions of Article 20 of Law 11/1986 about Patents, dated March 20th, 1986. It was registered under the denomination Broadband Thermal Noise Primary Standard (Reference P-101061) dated February 7th, 2011.

Design, implementation and evaluation of an unconstrained and contactless biometric system based on hand geometry and stress detection

Esta tesis propone un sistema biométrico de geometría de mano orientado a entornos sin contacto junto con un sistema de detección de estrés capaz de decir qué grado de estrés tiene una determinada persona en base a señales fisiológicas Con respecto al sistema biométrico, esta tesis contribuye con el diseño y la implementación de un sistema biométrico de geometría de mano, donde la adquisición se realiza sin ningún tipo de contacto, y el patrón del usuario se crea considerando únicamente datos del propio individuo. Además, esta tesis propone un algoritmo de segmentación multiescala para solucionar los problemas que conlleva la adquisición de manos en entornos reales. Por otro lado, respecto a la extracción de características y su posterior comparación esta tesis tiene una contribución específica, proponiendo esquemas adecuados para llevar a cabo tales tareas con un coste computacional bajo pero con una alta precisión en el reconocimiento de personas. Por último, este sistema es evaluado acorde a la norma estándar ISO/IEC 19795 considerando seis bases de datos públicas. En relación al método de detección de estrés, esta tesis propone un sistema basado en dos señales fisiológicas, concretamente la tasa cardiaca y la conductancia de la piel, así como la creación de un innovador patrón de estrés que recoge el comportamiento de ambas señales bajo las situaciones de estrés y no-estrés. Además, este sistema está basado en lógica difusa para decidir el grado de estrés de un individuo. En general, este sistema es capaz de detectar estrés de forma precisa y en tiempo real, proporcionando una solución adecuada para sistemas biométricos actuales, donde la aplicación del sistema de detección de estrés es directa para evitar situaciónes donde los individuos sean forzados a proporcionar sus datos biométricos. Finalmente, esta tesis incluye un estudio de aceptabilidad del usuario, donde se evalúa cuál es la aceptación del usuario con respecto a la técnica biométrica propuesta por un total de 250 usuarios. Además se incluye un prototipo implementado en un dispositivo móvil y su evaluación. ABSTRACT: This thesis proposes a hand biometric system oriented to unconstrained and contactless scenarios together with a stress detection method able to elucidate to what extent an individual is under stress based on physiological signals. Concerning the biometric system, this thesis contributes with the design and implementation of a hand-based biometric system, where the acquisition is carried out without contact and the template is created only requiring information from a single individual. In addition, this thesis proposes an algorithm based on multiscale aggregation in order to tackle with the problem of segmentation in real unconstrained environments. Furthermore, feature extraction and matching are also a specific contributions of this thesis, providing adequate schemes to carry out both actions with low computational cost but with certain recognition accuracy. Finally, this system is evaluated according to international standard ISO/IEC 19795 considering six public databases. In relation to the stress detection method, this thesis proposes a system based on two physiological signals, namely heart rate and galvanic skin response, with the creation of an innovative stress detection template which gathers the behaviour of both physiological signals under both stressing and non-stressing situations. Besides, this system is based on fuzzy logic to elucidate the level of stress of an individual. As an overview, this system is able to detect stress accurately and in real-time, providing an adequate solution for current biometric systems, where the application of a stress detection system is direct to avoid situations where individuals are forced to provide the biometric data. Finally, this thesis includes a user acceptability evaluation, where the acceptance of the proposed biometric technique is assessed by a total of 250 individuals. In addition, this thesis includes a mobile implementation prototype and its evaluation.

Influence of loudspeaker directivity and measurement geometry on direct acoustic levels over façades for acoustic insulation tests with the International Standard ISO 140-5

The International Standard ISO 140-5 on field measurements of airborne sound insulation of façades establishes that the directivity of the measurement loudspeaker should be such that the variation in the local direct sound pressure level (ΔSPL) on the sample is ΔSPL < 5 dB (or ΔSPL < 10 dB for large façades). This condition is usually not very easy to accomplish nor is it easy to verify whether the loudspeaker produces such a uniform level. Direct sound pressure levels on the ISO standard façade essentially depend on the distance and directivity of the loudspeaker used. This paper presents a comprehensive analysis of the test geometry for measuring sound insulation and explains how the loudspeaker directivity, combined with distance, affects the acoustic level distribution on the façade. The first sections of the paper are focused on analysing the measurement geometry and its influence on the direct acoustic level variations on the façade. The most favourable and least favourable positions to minimise these direct acoustic level differences are found, and the angles covered by the façade in the reference system of the loudspeaker are also determined. Then, the maximum dimensions of the façade that meet the conditions of the ISO 140-5 standard are obtained for the ideal omnidirectional sound source and the piston radiating in an infinite baffle, which is chosen as the typical radiation pattern for loudspeakers. Finally, a complete study of the behaviour of different loudspeaker radiation models (such as those usually utilised in the ISO 140-5 measurements) is performed, comparing their radiation maps on the façade for searching their maximum dimensions and the most appropriate radiation configurations.

Analysis of the performance of caissons with a yard and cylindrical geometry as a breakwater. Apollonius caisson

En el presente trabajo se analiza el cajón Apolonio como diseño conceptual para controlar la reflexión en monolitos de gravedad sometidos a esfuerzos dinámicos de oleaje.

Mathematical Analysis of the Effect of Rotor Geometry on Cup Anemometer Response

The calibration coefficients of two commercial anemometers equipped with different rotors were studied. The rotor cups had the same conical shape, while the size and distance to the rotation axis varied.The analysis was based on the 2-cup positions analytical model, derived using perturbation methods to include second-order effects such as pressure distribution along the rotating cups and friction.Thecomparison with the experimental data indicates a nonuniformdistribution of aerodynamic forces on the rotating cups, with higher forces closer to the rotating axis. The 2-cup analytical model is proven to be accurate enough to study the effect of complex forces on cup anemometer performance.

Optimal boundary geometry in an elasticity problem: a systematic adjoint approach

In different problems of Elasticity the definition of the optimal gcometry of the boundary, according to a given objective function, is an issue of great interest. Finding the shape of a hole in the middle of a plate subjected to an arbitrary loading such that the stresses along the hole minimizes some functional or the optimal middle curved concrete vault for a tunnel along which a uniform minimum compression are two typical examples. In these two examples the objective functional depends on the geometry of the boundary that can be either a curve (in case of 2D problems) or a surface boundary (in 3D problems). Typically, optimization is achieved by means of an iterative process which requires the computation of gradients of the objective function with respect to design variables. Gradients can by computed in a variety of ways, although adjoint methods either continuous or discrete ones are the more efficient ones when they are applied in different technical branches. In this paper the adjoint continuous method is introduced in a systematic way to this type of problems and an illustrative simple example, namely the finding of an optimal shape tunnel vault immersed in a linearly elastic terrain, is presented.

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.

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.

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.