Uma perspectiva computacional sobre catálise enzimática

Enzymes are extremely efficient catalysts. Here, part of the mechanisms proposed to explain this catalytic power will be compared to quantitative experimental results and computer simulations. Influence of the enzymatic environment over species along the reaction coordinate will be analysed. Concepts of transition state stabilisation and reactant destabilisation will be confronted. Divided site model and near-attack conformation hypotheses will also be discussed. Molecular interactions such as covalent catalysis, general acid-base catalysis, electrostatics, entropic effects, steric hindrance, quantum and dynamical effects will also be analysed as sources of catalysis. Reaction mechanisms, in particular that catalysed by protein tyrosine phosphatases, illustrate the concepts.

Space–Time Block Codes and the Complexity of Sphere Decoding

In wireless communications the transmitted signals may be affected by noise. The receiver must decode the received message, which can be mathematically modelled as a search for the closest lattice point to a given vector. This problem is known to be NP-hard in general, but for communications applications there exist algorithms that, for a certain range of system parameters, offer polynomial expected complexity. The purpose of the thesis is to study the sphere decoding algorithm introduced in the article On Maximum-Likelihood Detection and the Search for the Closest Lattice Point, which was published by M.O. Damen, H. El Gamal and G. Caire in 2003. We concentrate especially on its computational complexity when used in space–time coding. Computer simulations are used to study how different system parameters affect the computational complexity of the algorithm. The aim is to find ways to improve the algorithm from the complexity point of view. The main contribution of the thesis is the construction of two new modifications to the sphere decoding algorithm, which are shown to perform faster than the original algorithm within a range of system parameters.

Flexible multibody approach in bone strain estimation during physical activity:

Bone strain plays a major role as the activation signal for the bone (re)modeling process, which is vital for keeping bones healthy. Maintaining high bone mineral density reduces the chances of fracture in the event of an accident. Numerous studies have shown that bones can be strengthened with physical exercise. Several hypotheses have asserted that a stronger osteogenic (bone producing) effect results from dynamic exercise than from static exercise. These previous studies are based on short-term empirical research, which provide the motivation for justifying the experimental results with a solid mathematical background. The computer simulation techniques utilized in this work allow for non-invasive bone strain estimation during physical activity at any bone site within the human skeleton. All models presented in the study are threedimensional and actuated by muscle models to replicate the real conditions accurately. The objective of this work is to determine and present loading-induced bone strain values resulting from physical activity. It includes a comparison of strain resulting from four different gym exercises (knee flexion, knee extension, leg press, and squat) and walking, with the results reported for walking and jogging obtained from in-vivo measurements described in the literature. The objective is realized primarily by carrying out flexible multibody dynamics computer simulations. The dissertation combines the knowledge of finite element analysis and multibody simulations with experimental data and information available from medical field literature. Measured subject-specific motion data was coupled with forward dynamics simulation to provide natural skeletal movement. Bone geometries were defined using a reverse engineering approach based on medical imaging techniques. Both computed tomography and magnetic resonance imaging were utilized to explore modeling differences. The predicted tibia bone strains during walking show good agreement with invivo studies found in the literature. Strain measurements were not available for gym exercises; therefore, the strain results could not be validated. However, the values seem reasonable when compared to available walking and running invivo strain measurements. The results can be used for exercise equipment design aimed at strengthening the bones as well as the muscles during workout. Clinical applications in post fracture recovery exercising programs could also be the target. In addition, the methodology introduced in this study, can be applied to investigate the effect of weightlessness on astronauts, who often suffer bone loss after long time spent in the outer space.

Do We Understand Hydrodynamic Dispersion in Sedimenting Suspensions?

Microstructural changes, that is an important feature for the understanding of the velocity variance in sedimentation is investigated with numerical simulations. The simulations are used to describe velocity fluctuations and hydrodynamic dispersion in a suspension of interacting point-particles sedimenting in a rectangular box with periodic sides and impenetrable bottom and top. It is observed how the positions of the particles evolve in a finite container. The suspension that was initially random in the gravity direction only, tends to be fully randomized as a result of the relative arrangements of the particles and the hydrodynamic interactions between them. The computer simulations, based on statistics over a significant number of particle configurations, suggest velocity variances and diffusivities dependent on the size of the simulated system but with anisotropy in velocity fluctuations and diffusion coefficients nearly independent of the box size.

Assessment of Young Learners’ English Proficiency in Bilingual Content Instruction CLIL

This applied linguistic study in the field of second language acquisition investigated the assessment practices of class teachers as well as the challenges and visions of language assessment in bilingual content instruction (CLIL) at primary level in Finnish basic education. Furthermore, pupils’ and their parents’ perceptions of language assessment and LangPerform computer simulations as an alternative, modern assessment method in CLIL contexts were examined. The study was conducted for descriptive and developmental purposes in three phases: 1) a CLIL assessment survey; 2) simulation 1; and 3) simulation 2. All phases had a varying number of participants. The population of this mixed methods study were CLIL class teachers, their pupils and the pupils’ parents. The sampling was multi-staged and based on probability and random sampling. The data were triangulated. Altogether 42 CLIL class teachers nationwide, 109 pupils from the 3rd, 4th and 5th grade as well as 99 parents from two research schools in South-Western Finland participated in the CLIL assessment survey followed by an audio-recorded theme interview of volunteers (10 teachers, 20 pupils and 7 parents). The simulation experimentations 1 and 2 produced 146 pupil and 39 parental questionnaires as well as video interviews of volunteered pupils. The data were analysed both quantitatively using percentages and numerical frequencies and qualitatively employing thematic content analysis. Based on the data, language assessment in primary CLIL is not an established practice. It largely appears to be infrequent, incidental, implicit and based on impressions rather than evidence or the curriculum. The most used assessment methods were teacher observation, bilingual tests and dialogic interaction, and the least used were portfolios, simulations and peer assessment. Although language assessment was generally perceived as important by teachers, a fifth of them did not gather assessment information systematically, and 38% scarcely gave linguistic feedback to pupils. Both pupils and parents wished to receive more information on CLIL language issues; 91% of pupils claimed to receive feedback rarely or occasionally, and 63% of them wished to get more information on their linguistic coping in CLIL subjects. Of the parents, 76% wished to receive more information on the English proficiency of their children and their linguistic development. This may be a response to indirect feedback practices identified in this study. There are several challenges related to assessment; the most notable is the lack of a CLIL curriculum, language objectives and common ground principles of assessment. Three diverse approaches to language in CLIL that appear to affect teachers’ views on language assessment were identified: instrumental (language as a tool), dual (language as a tool and object of learning) and eclectic (miscellaneous views, e.g. affective factors prioritised). LangPerform computer simulations seem to be perceived as an appropriate alternative assessment method in CLIL. It is strongly recommended that the fundamentals for assessment (curricula and language objectives) and a mutual assessment scheme should be determined and stakeholders’ knowledge base of CLIL strengthened. The principles of adequate assessment in primary CLIL are identified as well as several appropriate assessment methods suggested.

Dynamical and Chemical Structure of Galactic Halos

This doctoral dissertation presents studies of the formation and evolution of galaxies, through observations and simulations of galactic halos. The halo is the component of galaxies which hosts some of the oldest objects we know of in the cosmos; it is where clues to the history of galaxies are found, for example, by how the chemical structure is related to the dynamics of objects in the halo. The dynamical and chemical structure of halos, both in the Milky Way’s own halo, and in two elliptical galaxies, is the underlying theme in the research. I focus on the density falloff and chemistry of the two external halos, and on the dynamics, density falloff, and chemistry of the Milky Way halo. I first study galactic halos via computer simulations, to test the long- term stability of an anomalous feature recently found in kinematics of the Milky Way’s metal-poor stellar halo. I find that the feature is transient, making its origin unclear. I use a second set of simulations to test if an initially strong relation between the dynamics and chemistry of halo glob-ular clusters in a Milky Way-type galaxy is affected by a merging satellite galaxy, and find that the relation remains strong despite a merger in which the satellite is a third of the mass of the host galaxy. From simulations, I move to observing halos in nearby galaxies, a challenging procedure as most of the light from galaxies comes from the disk and bulge components as opposed to the halo. I use Hubble Space Tele scope observations of the halo of the galaxy M87 and, comparing to similar observations of NGC 5128, find that the chemical structure of the inner halo is similar for both of these giant elliptical galaxies. I use Very Large Telescope observations of the outer halo of NGC 5128 (Centaurus A) and, because of the difficultly in resolving dim extragalac- tic stellar halo populations, I introduce a new technique to subtract the contaminating background galaxies. A transition from a metal-rich stellar halo to a metal-poor has previously been discovered in two different types of galaxies, the disk galaxy M31 and the classic elliptical NGC 3379. Unexpectedly, I discover in this third type of galaxy, the merger remnant NGC 5128, that the density of metal-rich and metal-poor halo stars falls at the same rate within the galactocentric radii of 8 − 65 kpc, the limit of our observations. This thesis presents new results which open opportunities for future investigations.

Viability interactions between the left and right arms of the second chromosome of Drosophila melanogaster

Inter and intrachromosomal viability interactions have been detected in a few experimental studies. Computer simulations and analytical models have led to postulation of nonadditivity of gene action. This study reports evidence of strong nonadditive interactions between the arms of the metacentric second chromosome of Drosophila melanogaster. Mean viability for 40 homozygous lines of the second chromosomes was 0.720+0.265 • Mean viability for 40 half homozygous second chromosomes was 0.928!O.)10 • Significant heterogeneity among and within lines was found in both groups of chromosomes, as well as a highly significant viability difference between the two groups. Comparison of observed viabilities with the expected values, according to the theories of additive and multi - plicative gene action. was made for both groups. Highly significant departures from the expected values were found for over 90% of the lines in both groups of chromosomes, for both additive and multiplicative models of gene action.

Assessing the Reproducibility of Clustering of Molecular Dynamics Conformations on Self-Organizing Maps

The goal of most clustering algorithms is to find the optimal number of clusters (i.e. fewest number of clusters). However, analysis of molecular conformations of biological macromolecules obtained from computer simulations may benefit from a larger array of clusters. The Self-Organizing Map (SOM) clustering method has the advantage of generating large numbers of clusters, but often gives ambiguous results. In this work, SOMs have been shown to be reproducible when the same conformational dataset is independently clustered multiple times (~100), with the help of the Cramérs V-index (C_v). The ability of C_v to determine which SOMs are reproduced is generalizable across different SOM source codes. The conformational ensembles produced from MD (molecular dynamics) and REMD (replica exchange molecular dynamics) simulations of the penta peptide Met-enkephalin (MET) and the 34 amino acid protein human Parathyroid Hormone (hPTH) were used to evaluate SOM reproducibility. The training length for the SOM has a huge impact on the reproducibility. Analysis of MET conformational data definitively determined that toroidal SOMs cluster data better than bordered maps due to the fact that toroidal maps do not have an edge effect. For the source code from MATLAB, it was determined that the learning rate function should be LINEAR with an initial learning rate factor of 0.05 and the SOM should be trained by a sequential algorithm. The trained SOMs can be used as a supervised classification for another dataset. The toroidal 10×10 hexagonal SOMs produced from the MATLAB program for hPTH conformational data produced three sets of reproducible clusters (27%, 15%, and 13% of 100 independent runs) which find similar partitionings to those of smaller 6×6 SOMs. The χ^2 values produced as part of the C_v calculation were used to locate clusters with identical conformational memberships on independently trained SOMs, even those with different dimensions. The χ^2 values could relate the different SOM partitionings to each other.

Musiquer : plaidoyer évolutionniste transdisciplinaire

Le sujet prend appui sur une hypothèse : à l’origine, la musique est un phénomène culturel et biologique, social (et donc pas privé) et communautaire (et donc pas individuel). Les travaux de plusieurs théoriciens évolutionnistes du langage et/ou de la musique étayent l’hypothèse selon laquelle l’objet de la musique dépasse l’opposition nature-culture. Quelle est alors l’influence de ces caractéristiques sur l’apparition de la musicalité ou d’une faculté de musique ? Pour avancer dans notre réflexion, nous mesurons la contribution des recherches sur les amusies quant à la question des origines de la musique. Par la suite, nous étudions le rapport entre l’intentionnalité et l’évolution de la musique. Nous nous concentrons sur la nature sociale du phénomène musical, puis proposons l'intégration de la caractérisation biologique et sociale de la musique dans une conception institutionnelle et communautaire. Ainsi fondée philosophiquement, notre hypothèse de départ devient le véhicule du dépassement disciplinaire convoité. Enfin, certaines options proposées par différents auteurs décrivant la contribution de la musique au développement de réseaux neuronaux à la propriété miroir sont évoquées. Et nous tentons de répondre à cette question, inévitable : la musique peut-elle, étant donné son caractère irréductiblement culturel, social et communautaire, entretenir des connexions neuronales? Nous examinons notamment à cette fin les implications de la théorie du chaos et des résultats des simulations informatiques multi-agents.

Méthode numérique d'estimation du mouvement des masses molles

L’analyse biomécanique du mouvement humain en utilisant des systèmes optoélectroniques et des marqueurs cutanés considère les segments du corps comme des corps rigides. Cependant, le mouvement des tissus mous par rapport à l'os, c’est à dire les muscles et le tissu adipeux, provoque le déplacement des marqueurs. Ce déplacement est le fait de deux composantes, une composante propre correspondant au mouvement aléatoire de chaque marqueur et une composante à l’unisson provoquant le déplacement commun des marqueurs cutanés lié au mouvement des masses sous-jacentes. Si nombre d’études visent à minimiser ces déplacements, des simulations ont montré que le mouvement des masses molles réduit la dynamique articulaire. Cette observation est faite uniquement par la simulation, car il n'existe pas de méthodes capables de dissocier la cinématique des masses molles de celle de l’os. L’objectif principal de cette thèse consiste à développer une méthode numérique capable de distinguer ces deux cinématiques. Le premier objectif était d'évaluer une méthode d'optimisation locale pour estimer le mouvement des masses molles par rapport à l’humérus obtenu avec une tige intra-corticale vissée chez trois sujets. Les résultats montrent que l'optimisation locale sous-estime de 50% le déplacement des marqueurs et qu’elle conduit à un classement de marqueurs différents en fonction de leur déplacement. La limite de cette méthode vient du fait qu'elle ne tient pas compte de l’ensemble des composantes du mouvement des tissus mous, notamment la composante en unisson. Le second objectif était de développer une méthode numérique qui considère toutes les composantes du mouvement des tissus mous. Plus précisément, cette méthode devait fournir une cinématique similaire et une plus grande estimation du déplacement des marqueurs par rapport aux méthodes classiques et dissocier ces composantes. Le membre inférieur est modélisé avec une chaine cinématique de 10 degrés de liberté reconstruite par optimisation globale en utilisant seulement les marqueurs placés sur le pelvis et la face médiale du tibia. L’estimation de la cinématique sans considérer les marqueurs placés sur la cuisse et le mollet permet d'éviter l’influence de leur déplacement sur la reconstruction du modèle cinématique. Cette méthode testée sur 13 sujets lors de sauts a obtenu jusqu’à 2,1 fois plus de déplacement des marqueurs en fonction de la méthode considérée en assurant des cinématiques similaires. Une approche vectorielle a montré que le déplacement des marqueurs est surtout dû à la composante à l’unisson. Une approche matricielle associant l’optimisation locale à la chaine cinématique a montré que les masses molles se déplacent principalement autour de l'axe longitudinal et le long de l'axe antéro-postérieur de l'os. L'originalité de cette thèse est de dissocier numériquement la cinématique os de celle des masses molles et les composantes de ce mouvement. Les méthodes développées dans cette thèse augmentent les connaissances sur le mouvement des masses molles et permettent d’envisager l’étude de leur effet sur la dynamique articulaire.

Speech sample estimation from composite zerocrossings and encoding via adaptive switching of transforms

This thesis investigates the potential use of zerocrossing information for speech sample estimation. It provides 21 new method tn) estimate speech samples using composite zerocrossings. A simple linear interpolation technique is developed for this purpose. By using this method the A/D converter can be avoided in a speech coder. The newly proposed zerocrossing sampling theory is supported with results of computer simulations using real speech data. The thesis also presents two methods for voiced/ unvoiced classification. One of these methods is based on a distance measure which is a function of short time zerocrossing rate and short time energy of the signal. The other one is based on the attractor dimension and entropy of the signal. Among these two methods the first one is simple and reguires only very few computations compared to the other. This method is used imtea later chapter to design an enhanced Adaptive Transform Coder. The later part of the thesis addresses a few problems in Adaptive Transform Coding and presents an improved ATC. Transform coefficient with maximum amplitude is considered as ‘side information’. This. enables more accurate tfiiz assignment enui step—size computation. A new bit reassignment scheme is also introduced in this work. Finally, sum ATC which applies switching between luiscrete Cosine Transform and Discrete Walsh-Hadamard Transform for voiced and unvoiced speech segments respectively is presented. Simulation results are provided to show the improved performance of the coder

Entwicklung und experimentelle Regelung eines servopneumatischen räumlichen Mehrachsenprüfstands

In dieser Arbeit wurde ein räumlich bewegter pneumatischer Mehrachsenprüfstand als spezielle mechanische Variante eines Parallelroboters entwickelt, im Labor aufgebaut und in Rechnersimulationen sowie in Laborexperimenten regelungstechnisch untersucht. Für diesen speziellen Parallelroboter MAP-RTS-6 wurden Regelalgorithmen, die mittels moderner Verfahren der linearen und nichtlinearen Regelungstheorie abgeleitet wurden, hinsichtlich ihrer praktischen Anwendbarkeit, Echtzeitfähigkeit und Qualität entwickelt, implementiert und überprüft. Mit diesen Regelalgorithmen ist der MAP-RTS-6 in der Lage, große räumliche Transienten schnell und präzise nachzufahren. Der MAP-RTS-6 wird in erster Linie als räumlicher Bewegungsmanipulator für große nichtlineare Transienten (Translationen und Rotationen), als räumlicher Vibrationsprüfstand für starre und flexible Prüfkörper unterschiedlicher Konfigurationen und als Mechanismus für die Implementierung und experimentelle Überprüfung unterschiedlicher Regelungs- und Identifikationsalgorithmen und Sicherheitskonzepte verwendet. Die Voraussetzung zum Betrieb des Mehrachsenprüfstands für unterschiedliche redundante Antriebskonfigurationen mit sieben und acht Antrieben MAP-RTS-7 und MAP-RTS-8 wurde in dieser Arbeit geschaffen. Dazu zählen die konstruktive Vorbereitung der Prüfstandsmechanik und Pneumatik zum Anschluss weiterer Antriebe, die Vorbereitung zusätzlicher I/O-Schnittstellen zur Prüfstandselektronik und zum Regelungssystem und die Ableitung von Algorithmen zur analytischen Arbeitsraumüberwachung für redundante Antriebskonfigurationen mit sieben und acht Antrieben.

Structural Dynamics Model of a Cartesian Robot

Methods are developed for predicting vibration response characteristics of systems which change configuration during operation. A cartesian robot, an example of such a position-dependent system, served as a test case for these methods and was studied in detail. The chosen system model was formulated using the technique of Component Mode Synthesis (CMS). The model assumes that he system is slowly varying, and connects the carriages to each other and to the robot structure at the slowly varying connection points. The modal data required for each component is obtained experimentally in order to get a realistic model. The analysis results in prediction of vibrations that are produced by the inertia forces as well as gravity and friction forces which arise when the robot carriages move with some prescribed motion. Computer simulations and experimental determinations are conducted in order to calculate the vibrations at the robot end-effector. Comparisons are shown to validate the model in two ways: for fixed configuration the mode shapes and natural frequencies are examined, and then for changing configuration the residual vibration at the end of the mode is evaluated. A preliminary study was done on a geometrically nonlinear system which also has position-dependency. The system consisted of a flexible four-bar linkage with elastic input and output shafts. The behavior of the rocker-beam is analyzed for different boundary conditions to show how some limiting cases are obtained. A dimensional analysis leads to an evaluation of the consequences of dynamic similarity on the resulting vibration.

Medidas de intervención para promoción de conductas saludables y prevención de riesgos laborales relacionados con accidentalidad y enfermedad laboral en trabajadores de minas de Carbón

Colombia en su legislación normatiza el sector de la minería de carbón, sin embargo se considera que las estrategias no han sido suficientes para la identificación, prevención y control de la accidentalidad y enfermedad laboral. Durante el año 2013 el índice de fatalidad fue de 1,59. Estadísticas del año 2004 evidencian que las neumoconiosis fueron las mayores causas de invalidez de origen profesional. Objetivo: Categorizar actividades de intervención en promoción y prevención de accidentalidad y enfermedad laboral en trabajadores de la minería de carbón. Metodología: Se realizó una revisión de literatura sobre minería de carbón y salud la cual fue obtenida de las bases de datos PUBMED, Sciendirect, VHL, SINAB por literatura publicada sin límites de año, en idioma inglés, español o portugués. Para la búsqueda se utilizaron términos en lenguaje controlado (términos MESH), revisión por pares de títulos y resúmenes. Las publicaciones fueron seleccionadas para revisión de texto completo bajo criterios de inclusión y exclusión. Los códigos contemplados para esta revisión fueron: a) país donde la intervención se llevó a cabo, b) salud ocupacional, c) prevención de accidentalidad, d) programas de promoción, e) tecnologías, f) resultados obtenidos. Resultados: Del total de 2500 artículos seleccionados por los autores principales se realizó la revisión de los primeros 300 artículos, 32 hacen referencia al tema de salud ocupacional y minería de carbón, 10 contienen intervenciones consideradas de relevancia para esta revisión bibliográfica. Se presentan intervenciones estadísticamente significativas (p<0.05) y que han demostrado ser de impacto positivo en la minería de carbón en promoción y prevención de accidentalidad y enfermedad ocupacional. Conclusiones: Se identificaron las siguientes cuatro tipos de intervención: 1) las de carácter educativo que hacen referencia a las capacitaciones participativas, el entrenamiento por medio de “degraded image”, la realización de gestión de autocontrol y retroalimentación para el uso de elementos de protección personal (EPP), la aplicación del Modelo de Proceso Paralelo Extendido; 2) intervenciones preventivas como la medición de alcoholimetría antes del turno, la presencia de personal de enfermería en minas de carbón y el reconocimiento de los predictores de la enfermedad para optimizar la prevención primaria; 3)intervenciones de vigilancia como la promovida en la metodología Estadísticas Europeas de Accidentes de Trabajo (EEAT) para la investigación de los accidentes de trabajo, la aplicación de las recomendaciones de la Organización Mundial de la Salud (OMS) para la detección de la neumoconiosis y 4) De carácter tecnológico consistente en la intervención de tareas a partir de los resultados de la aplicación del software desarrollado por el Instituto Nacional para la Seguridad y Salud Ocupacional (NIOSH). Estas intervenciones han demostrado ser eficaces en la promoción y prevención de accidentalidad y enfermedad ocupacional por lo cual se recomienda su aplicación en Colombia posterior al análisis de costo-efectividad.

Fronts from complex two-dimensional dispersal kernels: theory and application to Reid's paradox

Bimodal dispersal probability distributions with characteristic distances differing by several orders of magnitude have been derived and favorably compared to observations by Nathan [Nature (London) 418, 409 (2002)]. For such bimodal kernels, we show that two-dimensional molecular dynamics computer simulations are unable to yield accurate front speeds. Analytically, the usual continuous-space random walks (CSRWs) are applied to two dimensions. We also introduce discrete-space random walks and use them to check the CSRW results (because of the inefficiency of the numerical simulations). The physical results reported are shown to predict front speeds high enough to possibly explain Reid's paradox of rapid tree migration. We also show that, for a time-ordered evolution equation, fronts are always slower in two dimensions than in one dimension and that this difference is important both for unimodal and for bimodal kernels