Server power modeling for run-time energy optimization of cloud computing facilities

As advanced Cloud services are becoming mainstream, the contribution of data centers in the overall power consumption of modern cities is growing dramatically. The average consumption of a single data center is equivalent to the energy consumption of 25.000 households. Modeling the power consumption for these infrastructures is crucial to anticipate the effects of aggressive optimization policies, but accurate and fast power modeling is a complex challenge for high-end servers not yet satisfied by analytical approaches. This work proposes an automatic method, based on Multi-Objective Particle Swarm Optimization, for the identification of power models of enterprise servers in Cloud data centers. Our approach, as opposed to previous procedures, does not only consider the workload consolidation for deriving the power model, but also incorporates other non traditional factors like the static power consumption and its dependence with temperature. Our experimental results shows that we reach slightly better models than classical approaches, but simul- taneously simplifying the power model structure and thus the numbers of sensors needed, which is very promising for a short-term energy prediction. This work, validated with real Cloud applications, broadens the possibilities to derive efficient energy saving techniques for Cloud facilities.

Conditions for perfect focusing multiple point sources with the SMS design method

In this work, we demonstrate how it is possible to sharply image multiple object points. The Simultaneous Multiple Surface (SMS) design method has usually been presented as a method to couple N wave-front pairs with N surfaces, but recent findings show that when using N surfaces, we can obtain M image points when Nmethod, from its basics, to imaging two object points through one surface, the transition from two to three objet points obtained by increasing the parallelism, and getting to the designs of six surfaces imaging up to eight object points. These designs are limited with the condition that the surfaces cannot be placed at the aperture stop. In the process of maximizing the object points to sharp image, we try to exhaust the degrees of freedom of aspherics and free-forms. We conjecture that maximal SMS designs are very close to a good solution, hence using them as a starting point for the optimization will lead us faster to a final optical system. We suggest here different optimization strategies which combined with the SMS method are proven to give the best solution. Through the example of imaging with the high aspect ratio, we compare the results obtained optimizing the rotational lens and using a combination of SMS method and optimization, showing that the second approach is giving significantly smaller value of overall RMS spot diameter.

Análisis teórico de la variación aleatoria de los esfuerzos de montaje de los cables en los puentes atirantados

Los puentes atirantados son una de las tipologías estructurales con mas desarrollo en los últimos años ya que cuentan con un ámbito de aplicación que se ha extendido en gran medida, llegando hasta el rango de luces de más de 1000 m. Por otra parte, para el caso de luces medias, este tipo de puentes aporta unas características resistentes y formales que los hacen muy adecuados en gran número de situaciones. Simultaneamente al importante número de realizaciones llevadas a cabo con esta tipología en los últimos años, se ha producido un gran desarrollo del conocimiento teórico de diferentes aspectos técnicos específicos de estos puentes, tanto a nivel de su comportamiento estructural como de la simulación y mejora de sus procesos constructivos. Estos desarrollos se han producido en gran parte gracias al avance en las capacidad de computación disponible hoy en día con los numerosos y cada vez más sofisticados programas comerciales de cálculo estructural, los cuales permiten la realización de análisis que hasta hace poco tiempo eran muy complicados de desarrollar. Una de las principales características de este tipo de estructuras, además de su elevado hiperestatismo, es la importancia del proceso constructivo, y en concreto del proceso de tesado de los cables, a la hora de conseguir alcanzar una situación final con la estructura en servicio que cumpla los requisitos establecidos a priori. Por este motivo se han llevado a cabo bastantes investigaciones orientadas a la optimización de los axiles a aplicar a los cables en el momento de su colocación y en su situación final. Parte de estos análisis se han centrado en particular en la posible influencia de ciertos parámetros geométricos y mecánicos aleatorios sobre los esfuerzos provocados sobre la estructura. Por otra parte, el propio comportamiento resistente de un tirante introduce ciertas incertidumbres en los formatos de seguridad asociados a los esfuerzos generados sobre ellos, en concreto en relación a la dependencia de estas fuerzas respecto de las cargas permanentes y a su consideración a nivel de coeficientes de seguridad asociados a dichas acciones. En vista de estos aspectos particulares se ha procedido a desarrollar la investigación que se expone a continuación, en la que se ha pretendido obtener un conocimiento adicional de algunos de estos aspectos para así poder contrastar la validez de las hipótesis que hoy en día son establecidas por la normativa vigente. De esta forma el planteamiento adoptado en esta tesis ha sido en primer lugar proponer un método novedoso de introducción de errores aleatorios sobre los esfuerzos o deformaciones de tesado de los cables, de tal manera que se pueda aplicar dicha técnica a distintas tipologías de puentes atirantados. Se pretende con ello conocer la influencia de dichos errores sobre el comportamiento de estas estructuras y valorar la magnitud de las desviaciones finalmente creadas respecto de la situación teórica. Una vez conocida la implicación que supone la aleatoriedad aplicada en la colocación de los tirantes, tanto cualitativa como cuantitativamente, se ha procedido a realizar un análisis de las consecuencias respecto de los formatos de seguridad que de estos datos se deducen. Señalar que esta tesis se ha centrado en el caso concreto de puentes atirantados construidos por voladizos sucesivos y con tableros de hormigón, dado el gran numero de puentes ejecutados con estas características, y con el objetivo de concentrar el estudio realizado en una tipología particular, pero de gran aplicación. Cable-stayed bridges represent one of the most developed structural typologies being used recently as it has a span range that can extend beyond 1000m. Furthermore, when it comes to bridges that span to a medium range we could say their shape and resistance are features that make this kind of bridge suitable for many different applications. Moreover, due to this type of bridge being used newly more extensively it has allowed for a better understanding of the theoretical knowledge of the various technical aspects both at a structural and simulation level in order to improve the constructions process of this type of bridge. Knowledge and development of these bridges can be attributed to the increasing apprehension of I.T. skills and the development of more advanced computer software with regards to structural calculations. The latter can aide more demanding analysis that was previously difficult to ascertain Defining features of this type of structure, besides its hyper static attributes, is the importance of the construction process, namely the cable tensioning process, which determines whether the requirements set out in the construction process will be met once the bridge is finished and traffic loads are applied. This is why much research has been conducted into the optimization of the axial forces to be applied to the cables. Focus, of part of this research, goes into the possible influences of random geometrical and mechanical parametres on the forces applied to the structure. We have therefore proceeded to develop research in which we have tried to gain more in depth knowledge which considers these aspects so that we can validate the hypothesis which are currently established in the regulations Firstly, the purpose of this thesis is to provide a new method to introduce random errors on the forces or deformations of cable tensioning so that this technique can be extended to various models of cable-staying bridges. It is important to highlight that this thesis has focused on cable-stayed bridges built through the balanced cantilever method and with concrete girders and considering there are many actual bridges with these characteristics the research has focused on a specific yet extensively applied method.

Analysis and optimization for a hexapod walking robot for planetary missions

La tecnología de las máquinas móviles autónomas ha sido objeto de una gran investigación y desarrollo en las últimas décadas. En muchas actividades y entornos, los robots pueden realizar operaciones que son duras, peligrosas o simplemente imposibles para los humanos. La exploración planetaria es un buen ejemplo de un entorno donde los robots son necesarios para realizar las tareas requeridas por los científicos. La reciente exploración de Marte con robots autónomos nos ha mostrado la capacidad de las nuevas tecnologías. Desde la invención de la rueda, que esta acertadamente considerado como el mayor invento en la historia del transporte humano, casi todos los vehículos para exploración planetaria han empleado las ruedas para su desplazamiento. Las nuevas misiones planetarias demandan maquinas cada vez mas complejas. En esta Tesis se propone un nuevo diseño de un robot con patas o maquina andante que ofrecerá claras ventajas en entornos extremos. Se demostrara que puede desplazarse en los terrenos donde los robots con ruedas son ineficientes, convirtiéndolo en una elección perfecta para misiones planetarias. Se presenta una reseña histórica de los principales misiones espaciales, en particular aquellos dirigidos a la exploración planetaria. A través de este estudio será posible analizar las desventajas de los robots con ruedas utilizados en misiones anteriores. El diseño propuesto de robot con patas será presentado como una alternativa para aquellas misiones donde los robots con ruedas puedan no ser la mejor opción. En esta tesis se presenta el diseño mecánico de un robot de seis patas capaz de soportar las grandes fuerzas y momentos derivadas del movimiento de avance. Una vez concluido el diseño mecánico es necesario realizar un análisis que permita entender el movimiento y comportamiento de una maquina de esta complejidad. Las ecuaciones de movimiento del robot serán validadas por dos métodos: cinemático y dinámico. Dos códigos Matlab® han sido desarrollados para resolver dichos sistemas de ecuaciones y han sido verificados por un tercer método, un modelo de elementos finitos, que también verifica el diseño mecánico. El robot con patas presentado, ha sido diseñado para la exploración planetaria en Marte. El comportamiento del robot durante sus desplazamientos será probado mediante un código de Matlab®, desarrollado para esta tesis, que permite modificar las trayectorias, el tipo de terreno, y el número y altura de los obstáculos. Estos terrenos y requisitos iniciales no han sido elegidos de forma aleatoria, si no que están basados en mi experiencia como miembro del equipo de MSL-NASA que opera un instrumento a bordo del rover Curiosity en Marte. El robot con patas desarrollado y fabricado por el Centro de Astrobiología (INTA-CSIC), esta basado en el diseño mecánico y análisis presentados en esta tesis. ABSTRACT The autonomous machines technology has undergone a major research and development during the last decades. In many activities and environments, robots can perform operations that are tought, dangerous or simply imposible to humans. Planetary exploration is a good example of such environment where robots are needed to perform the tasks required by the scientits. Recent Mars exploration based on autonomous vehicles has shown us the capacity of the new technologies. From the invention of the wheel, which is rightly regarded as the greatest invention in the history of human transportation, nearly all-planetary vehicles are based in wheeled locomotion, but new missions demand new types of machines due to the complex tasks needed to be performed. It will be proposed in this thesis a new design of a legged robot or walking machine, which may offer clear advantages in tough environments. This Thesis will show that the proposed walking machine can travel, were terrain difficulties make wheeled vehicles ineffective, making it a perfect choice for planetary mission. A historical background of the main space missions, in particular those aimed at planetary exploration will be presented. From this study the disadvantages found in the existing wheel rovers will be analysed. The legged robot designed will be introduced as an alternative were wheeled rovers could be no longer the best option for planetary exploration. This thesis introduces the mechanical design of a six-leg robot capable of withstanding high forces and moments due to the walking motion. Once the mechanical design is concluded, and in order to analyse a machine of this complexity an understanding of its movement and behaviour is mandatory. This movement equation will be validated by two methods: kinematics and dynamics. Two Matlab® codes have been developed to solve the systems of equations and validated by a third method, a finite element model, which also verifies the mechanical design. The legged robot presented has been designed for a Mars planetary exploration. The movement behaviour of the robot will be tested in a Matlab® code developed that allows to modify the trajectories, the type of terrain, number and height of obstacles. These terrains and initial requirements have not been chosen randomly, those are based on my experience as a member of the MSL NASA team, which operates an instrument on-board of the Curiosity rover in Mars. The walking robot developed and manufactured by the Center of Astrobiology (CAB) is based in the mechanical design and analysis that will be presented in this thesis.

A panel method free-wake code for aeroelastic rotor predictions

A panel method free-wake model to analyse the rotor flapping is presented. The aerodynamic model consists of a panel method, which takes into account the three-dimensional rotor geometry, and a free-wake model, to determine the wake shape. The main features of the model are the wake division into a near-wake sheet and a far wake represented by a single tip vortex, and the modification of the panel method formulation to take into account this particular wake description. The blades are considered rigid with a flap degree of freedom. The problem solution is approached using a relaxation method, which enforces periodic boundary conditions. Finally, several code validations against helicopter and wind turbine experimental data are performed, showing good agreement

Funicularity and equilibrium for high-performance conceptual structural design

Las estructuras que trabajan por forma se caracterizan por la íntima e indisociable relación entre geometría y comportamiento estructural. Por consiguiente, la elección de una apropiada geometría es el paso previo indispensable en el diseño conceptual de dichas estructuras. En esa tarea, la selección de las posibles geometrías antifuniculares para las distribuciones de cargas permanentes más habituales son más bien limitadas y, muchas veces, son criterios no estructurales (adaptabilidad funcional, estética, proceso constructivo, etc.) los que no permiten la utilización de dichas geometrías que garantizarían el máximo aprovechamiento del material. En este contexto, esta tesis estudia la posibilidad de obtener una estructura sin momentos flectores incluso si la geometría no es antifunicular para sus cargas permanentes. En efecto, esta tesis presenta un procedimiento, basado en la estática gráfica, que demuestra cómo un conjunto de cargas adicionales, introducidas a través de un sistema de pretensado exterior con elementos post-tesos, puede eliminar los momentos flectores debidos a cargas permanentes en cualquier geometría plana. Esto se traduce en una estructura antifunicular que proporciona respuestas innovadoras a demandas conjuntas de versatilidad arquitectónica y optimización del material. Dicha metodología gráfica ha sido implementada en un software distribuido libremente (EXOEQUILIBRIUM), donde el análisis estructural y la variación geométrica están incluidos en el mismo entorno interactivo y paramétrico. La utilización de estas herramientas permite más versatilidad en la búsqueda de nuevas formas eficientes, lo cual tiene gran importancia en el diseño conceptual de estructuras, liberando al ingeniero de la limitación del propio cálculo y de la incomprensión del comportamiento estructural, facilitando extraordinariamente el hecho creativo a la luz de una metodología de este estilo. Esta tesis incluye la aplicación de estos procedimientos a estructuras de cualquier geometría y distribución inicial de cargas, así como el estudio de diferentes posibles criterios de diseño para optimizar la posición del sistema de post-tesado. Además, la metodología ha sido empleada en el proyecto de maquetas a escala reducida y en la construcción de un pabellón hecho enteramente de cartón, lo que ha permitido obtener una validación física del procedimiento desarrollado. En definitiva, esta tesis expande de manera relevante el rango de posibles geometrías antifuniculares y abre enormes posibilidades para el diseño de estructuras que combinan eficiencia estructural y flexibilidad arquitectónica.Curved structures are characterized by the critical relationship between their geometry and structural behaviour, and selecting an appropriate shape in the conceptual design of such structures is important for achieving materialefficiency. However, the set of bending-free geometries are limited and, often, non-structural design criteria (e.g., usability, architectural needs, aesthetics) prohibit the selection of purely funicular or antifunicular shapes. In response to this issue, this thesis studies the possibility of achieving an axial-only behaviour even if the geometry departs from the ideally bending-free shape. This dissertation presents a new design approach, based on graphic statics that shows how bending moments in a two-dimensional geometry can be eliminated by adding forces through an external post-tensioning system. This results in bending-free structures that provide innovative answers to combined demands on versatility and material optimization. The graphical procedure has been implemented in a free-downloadable design-driven software (EXOEQUILIBRIUM) where structural performance evaluations and geometric variation are embedded within an interactive and parametric working environment. This provides greater versatility in finding new efficient structural configurations during the first design stages, bridging the gap between architectural shaping and structural analysis. The thesis includes the application of the developed graphical procedure to shapes with random curvature and distribution of loads. Furthermore, the effect of different design criteria on the internal force distribution has been analyzed. Finally, the construction of reduced- and large-scale models provides further physical validation of the method and insights about the structural behaviour of these structures. In summary, this work strongly expands the range of possible forms that exhibit a bending-free behaviour and, de facto, opens up new possibilities for designs that combine high-performing solutions with architectural freedom.

Automated wordlength optimization framework for multi-source statistical interval-based analysis of nonlinear systems with control-flow structures

El uso de aritmética de punto fijo es una opción de diseño muy extendida en sistemas con fuertes restricciones de área, consumo o rendimiento. Para producir implementaciones donde los costes se minimicen sin impactar negativamente en la precisión de los resultados debemos llevar a cabo una asignación cuidadosa de anchuras de palabra. Encontrar la combinación óptima de anchuras de palabra en coma fija para un sistema dado es un problema combinatorio NP-hard al que los diseñadores dedican entre el 25 y el 50 % del ciclo de diseño. Las plataformas hardware reconfigurables, como son las FPGAs, también se benefician de las ventajas que ofrece la aritmética de coma fija, ya que éstas compensan las frecuencias de reloj más bajas y el uso más ineficiente del hardware que hacen estas plataformas respecto a los ASICs. A medida que las FPGAs se popularizan para su uso en computación científica los diseños aumentan de tamaño y complejidad hasta llegar al punto en que no pueden ser manejados eficientemente por las técnicas actuales de modelado de señal y ruido de cuantificación y de optimización de anchura de palabra. En esta Tesis Doctoral exploramos distintos aspectos del problema de la cuantificación y presentamos nuevas metodologías para cada uno de ellos: Las técnicas basadas en extensiones de intervalos han permitido obtener modelos de propagación de señal y ruido de cuantificación muy precisos en sistemas con operaciones no lineales. Nosotros llevamos esta aproximación un paso más allá introduciendo elementos de Multi-Element Generalized Polynomial Chaos (ME-gPC) y combinándolos con una técnica moderna basada en Modified Affine Arithmetic (MAA) estadístico para así modelar sistemas que contienen estructuras de control de flujo. Nuestra metodología genera los distintos caminos de ejecución automáticamente, determina las regiones del dominio de entrada que ejercitarán cada uno de ellos y extrae los momentos estadísticos del sistema a partir de dichas soluciones parciales. Utilizamos esta técnica para estimar tanto el rango dinámico como el ruido de redondeo en sistemas con las ya mencionadas estructuras de control de flujo y mostramos la precisión de nuestra aproximación, que en determinados casos de uso con operadores no lineales llega a tener tan solo una desviación del 0.04% con respecto a los valores de referencia obtenidos mediante simulación. Un inconveniente conocido de las técnicas basadas en extensiones de intervalos es la explosión combinacional de términos a medida que el tamaño de los sistemas a estudiar crece, lo cual conlleva problemas de escalabilidad. Para afrontar este problema presen tamos una técnica de inyección de ruidos agrupados que hace grupos con las señales del sistema, introduce las fuentes de ruido para cada uno de los grupos por separado y finalmente combina los resultados de cada uno de ellos. De esta forma, el número de fuentes de ruido queda controlado en cada momento y, debido a ello, la explosión combinatoria se minimiza. También presentamos un algoritmo de particionado multi-vía destinado a minimizar la desviación de los resultados a causa de la pérdida de correlación entre términos de ruido con el objetivo de mantener los resultados tan precisos como sea posible. La presente Tesis Doctoral también aborda el desarrollo de metodologías de optimización de anchura de palabra basadas en simulaciones de Monte-Cario que se ejecuten en tiempos razonables. Para ello presentamos dos nuevas técnicas que exploran la reducción del tiempo de ejecución desde distintos ángulos: En primer lugar, el método interpolativo aplica un interpolador sencillo pero preciso para estimar la sensibilidad de cada señal, y que es usado después durante la etapa de optimización. En segundo lugar, el método incremental gira en torno al hecho de que, aunque es estrictamente necesario mantener un intervalo de confianza dado para los resultados finales de nuestra búsqueda, podemos emplear niveles de confianza más relajados, lo cual deriva en un menor número de pruebas por simulación, en las etapas iniciales de la búsqueda, cuando todavía estamos lejos de las soluciones optimizadas. Mediante estas dos aproximaciones demostramos que podemos acelerar el tiempo de ejecución de los algoritmos clásicos de búsqueda voraz en factores de hasta x240 para problemas de tamaño pequeño/mediano. Finalmente, este libro presenta HOPLITE, una infraestructura de cuantificación automatizada, flexible y modular que incluye la implementación de las técnicas anteriores y se proporciona de forma pública. Su objetivo es ofrecer a desabolladores e investigadores un entorno común para prototipar y verificar nuevas metodologías de cuantificación de forma sencilla. Describimos el flujo de trabajo, justificamos las decisiones de diseño tomadas, explicamos su API pública y hacemos una demostración paso a paso de su funcionamiento. Además mostramos, a través de un ejemplo sencillo, la forma en que conectar nuevas extensiones a la herramienta con las interfaces ya existentes para poder así expandir y mejorar las capacidades de HOPLITE. ABSTRACT Using fixed-point arithmetic is one of the most common design choices for systems where area, power or throughput are heavily constrained. In order to produce implementations where the cost is minimized without negatively impacting the accuracy of the results, a careful assignment of word-lengths is required. The problem of finding the optimal combination of fixed-point word-lengths for a given system is a combinatorial NP-hard problem to which developers devote between 25 and 50% of the design-cycle time. Reconfigurable hardware platforms such as FPGAs also benefit of the advantages of fixed-point arithmetic, as it compensates for the slower clock frequencies and less efficient area utilization of the hardware platform with respect to ASICs. As FPGAs become commonly used for scientific computation, designs constantly grow larger and more complex, up to the point where they cannot be handled efficiently by current signal and quantization noise modelling and word-length optimization methodologies. In this Ph.D. Thesis we explore different aspects of the quantization problem and we present new methodologies for each of them: The techniques based on extensions of intervals have allowed to obtain accurate models of the signal and quantization noise propagation in systems with non-linear operations. We take this approach a step further by introducing elements of MultiElement Generalized Polynomial Chaos (ME-gPC) and combining them with an stateof- the-art Statistical Modified Affine Arithmetic (MAA) based methodology in order to model systems that contain control-flow structures. Our methodology produces the different execution paths automatically, determines the regions of the input domain that will exercise them, and extracts the system statistical moments from the partial results. We use this technique to estimate both the dynamic range and the round-off noise in systems with the aforementioned control-flow structures. We show the good accuracy of our approach, which in some case studies with non-linear operators shows a 0.04 % deviation respect to the simulation-based reference values. A known drawback of the techniques based on extensions of intervals is the combinatorial explosion of terms as the size of the targeted systems grows, which leads to scalability problems. To address this issue we present a clustered noise injection technique that groups the signals in the system, introduces the noise terms in each group independently and then combines the results at the end. In this way, the number of noise sources in the system at a given time is controlled and, because of this, the combinato rial explosion is minimized. We also present a multi-way partitioning algorithm aimed at minimizing the deviation of the results due to the loss of correlation between noise terms, in order to keep the results as accurate as possible. This Ph.D. Thesis also covers the development of methodologies for word-length optimization based on Monte-Carlo simulations in reasonable times. We do so by presenting two novel techniques that explore the reduction of the execution times approaching the problem in two different ways: First, the interpolative method applies a simple but precise interpolator to estimate the sensitivity of each signal, which is later used to guide the optimization effort. Second, the incremental method revolves on the fact that, although we strictly need to guarantee a certain confidence level in the simulations for the final results of the optimization process, we can do it with more relaxed levels, which in turn implies using a considerably smaller amount of samples, in the initial stages of the process, when we are still far from the optimized solution. Through these two approaches we demonstrate that the execution time of classical greedy techniques can be accelerated by factors of up to ×240 for small/medium sized problems. Finally, this book introduces HOPLITE, an automated, flexible and modular framework for quantization that includes the implementation of the previous techniques and is provided for public access. The aim is to offer a common ground for developers and researches for prototyping and verifying new techniques for system modelling and word-length optimization easily. We describe its work flow, justifying the taken design decisions, explain its public API and we do a step-by-step demonstration of its execution. We also show, through an example, the way new extensions to the flow should be connected to the existing interfaces in order to expand and improve the capabilities of HOPLITE.

Optimization of multijunction solar cells through indoor energy yield measurements

The variability of the solar spectra in the field may reduce the annual energy yield of multijunction solar cells. It would, therefore, be desirable to implement a cell design procedure based on the maximization of the annual energy yield. In this study, we present a measurement technique to generate maps of the real performance of the solar cell for a range of light spectrum contents using a solar simulator with a computer-controllable spectral content. These performance maps are demonstrated to be a powerful tool for analyzing the characteristics of any given set of annual spectra representative of a site and their influence on the energy yield of any solar cell. The effect of luminescence coupling on buffering against variations of the spectrum and improving the annual energy yield is demonstrated using this method.

Analysis, reliability and optimization of reinforced concrete 2-D structures

In this paper a consistent analysis of reinforced concrete (RC) two-dimensional (2-D) structures,namely slab structures subjected to in-plane and out-plane forces, is presented. By using this method of analysis the well established methodology for dimensioning and verifying RC sections of beam structures is extended to 2-D structures. The validity of the proposed analysis results is checked by comparing them with some published experimental test results. Several examples show some of these proposed analysis features, such as the influence of the reinforcement layout on the service and ultimate behavior of a slab structure and the non straightforward problem of the optimal dimension at a slab point subjected to several loading cases. Also, in these examples, the method applications to design situations as multiple steel families and non orthogonal reinforcement layout are commented.

The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small

In the maximum parsimony (MP) and minimum evolution (ME) methods of phylogenetic inference, evolutionary trees are constructed by searching for the topology that shows the minimum number of mutational changes required (M) and the smallest sum of branch lengths (S), respectively, whereas in the maximum likelihood (ML) method the topology showing the highest maximum likelihood (A) of observing a given data set is chosen. However, the theoretical basis of the optimization principle remains unclear. We therefore examined the relationships of M, S, and A for the MP, ME, and ML trees with those for the true tree by using computer simulation. The results show that M and S are generally greater for the true tree than for the MP and ME trees when the number of nucleotides examined (n) is relatively small, whereas A is generally lower for the true tree than for the ML tree. This finding indicates that the optimization principle tends to give incorrect topologies when n is small. To deal with this disturbing property of the optimization principle, we suggest that more attention should be given to testing the statistical reliability of an estimated tree rather than to finding the optimal tree with excessive efforts. When a reliability test is conducted, simplified MP, ME, and ML algorithms such as the neighbor-joining method generally give conclusions about phylogenetic inference very similar to those obtained by the more extensive tree search algorithms.

Dynamic weighting in Monte Carlo and optimization

Dynamic importance weighting is proposed as a Monte Carlo method that has the capability to sample relevant parts of the configuration space even in the presence of many steep energy minima. The method relies on an additional dynamic variable (the importance weight) to help the system overcome steep barriers. A non-Metropolis theory is developed for the construction of such weighted samplers. Algorithms based on this method are designed for simulation and global optimization tasks arising from multimodal sampling, neural network training, and the traveling salesman problem. Numerical tests on these problems confirm the effectiveness of the method.

Recent improvements in prediction of protein structure by global optimization of a potential energy function

Recent improvements of a hierarchical ab initio or de novo approach for predicting both α and β structures of proteins are described. The united-residue energy function used in this procedure includes multibody interactions from a cumulant expansion of the free energy of polypeptide chains, with their relative weights determined by Z-score optimization. The critical initial stage of the hierarchical procedure involves a search of conformational space by the conformational space annealing (CSA) method, followed by optimization of an all-atom model. The procedure was assessed in a recent blind test of protein structure prediction (CASP4). The resulting lowest-energy structures of the target proteins (ranging in size from 70 to 244 residues) agreed with the experimental structures in many respects. The entire experimental structure of a cyclic α-helical protein of 70 residues was predicted to within 4.3 Å α-carbon (Cα) rms deviation (rmsd) whereas, for other α-helical proteins, fragments of roughly 60 residues were predicted to within 6.0 Å Cα rmsd. Whereas β structures can now be predicted with the new procedure, the success rate for α/β- and β-proteins is lower than that for α-proteins at present. For the β portions of α/β structures, the Cα rmsd's are less than 6.0 Å for contiguous fragments of 30–40 residues; for one target, three fragments (of length 10, 23, and 28 residues, respectively) formed a compact part of the tertiary structure with a Cα rmsd less than 6.0 Å. Overall, these results constitute an important step toward the ab initio prediction of protein structure solely from the amino acid sequence.

An O(N log N) algorithm for shape modeling.

We present a shape-recovery technique in two dimensions and three dimensions with specific applications in modeling anatomical shapes from medical images. This algorithm models extremely corrugated structures like the brain, is topologically adaptable, and runs in O(N log N) time, where N is the total number of points in the domain. Our technique is based on a level set shape-recovery scheme recently introduced by the authors and the fast marching method for computing solutions to static Hamilton-Jacobi equations.

A fast marching level set method for monotonically advancing fronts.

A fast marching level set method is presented for monotonically advancing fronts, which leads to an extremely fast scheme for solving the Eikonal equation. Level set methods are numerical techniques for computing the position of propagating fronts. They rely on an initial value partial differential equation for a propagating level set function and use techniques borrowed from hyperbolic conservation laws. Topological changes, corner and cusp development, and accurate determination of geometric properties such as curvature and normal direction are naturally obtained in this setting. This paper describes a particular case of such methods for interfaces whose speed depends only on local position. The technique works by coupling work on entropy conditions for interface motion, the theory of viscosity solutions for Hamilton-Jacobi equations, and fast adaptive narrow band level set methods. The technique is applicable to a variety of problems, including shape-from-shading problems, lithographic development calculations in microchip manufacturing, and arrival time problems in control theory.

Robust fitting of Zernike polynomials to noisy point clouds defined over connected domains of arbitrary shape

A new method for fitting a series of Zernike polynomials to point clouds defined over connected domains of arbitrary shape defined within the unit circle is presented in this work. The method is based on the application of machine learning fitting techniques by constructing an extended training set in order to ensure the smooth variation of local curvature over the whole domain. Therefore this technique is best suited for fitting points corresponding to ophthalmic lenses surfaces, particularly progressive power ones, in non-regular domains. We have tested our method by fitting numerical and real surfaces reaching an accuracy of 1 micron in elevation and 0.1 D in local curvature in agreement with the customary tolerances in the ophthalmic manufacturing industry.