Localization and Tracking in Energy-Constrained Networks with Dynamic Connectivity

Systems used for target localization, such as goods, individuals, or animals, commonly rely on operational means to meet the final application demands. However, what would happen if some means were powered up randomly by harvesting systems? And what if those devices not randomly powered had their duty cycles restricted? Under what conditions would such an operation be tolerable in localization services? What if the references provided by nodes in a tracking problem were distorted? Moreover, there is an underlying topic common to the previous questions regarding the transfer of conceptual models to reality in field tests: what challenges are faced upon deploying a localization network that integrates energy harvesting modules? The application scenario of the system studied is a traditional herding environment of semi domesticated reindeer (Rangifer tarandus tarandus) in northern Scandinavia. In these conditions, information on approximate locations of reindeer is as important as environmental preservation. Herders also need cost-effective devices capable of operating unattended in, sometimes, extreme weather conditions. The analyses developed are worthy not only for the specific application environment presented, but also because they may serve as an approach to performance of navigation systems in absence of reasonably accurate references like the ones of the Global Positioning System (GPS). A number of energy-harvesting solutions, like thermal and radio-frequency harvesting, do not commonly provide power beyond one milliwatt. When they do, battery buffers may be needed (as it happens with solar energy) which may raise costs and make systems more dependent on environmental temperatures. In general, given our problem, a harvesting system is needed that be capable of providing energy bursts of, at least, some milliwatts. Many works on localization problems assume that devices have certain capabilities to determine unknown locations based on range-based techniques or fingerprinting which cannot be assumed in the approach considered herein. The system presented is akin to range-free techniques, but goes to the extent of considering very low node densities: most range-free techniques are, therefore, not applicable. Animal localization, in particular, uses to be supported by accurate devices such as GPS collars which deplete batteries in, maximum, a few days. Such short-life solutions are not particularly desirable in the framework considered. In tracking, the challenge may times addressed aims at attaining high precision levels from complex reliable hardware and thorough processing techniques. One of the challenges in this Thesis is the use of equipment with just part of its facilities in permanent operation, which may yield high input noise levels in the form of distorted reference points. The solution presented integrates a kinetic harvesting module in some nodes which are expected to be a majority in the network. These modules are capable of providing power bursts of some milliwatts which suffice to meet node energy demands. The usage of harvesting modules in the aforementioned conditions makes the system less dependent on environmental temperatures as no batteries are used in nodes with harvesters--it may be also an advantage in economic terms. There is a second kind of nodes. They are battery powered (without kinetic energy harvesters), and are, therefore, dependent on temperature and battery replacements. In addition, their operation is constrained by duty cycles in order to extend node lifetime and, consequently, their autonomy. There is, in turn, a third type of nodes (hotspots) which can be static or mobile. They are also battery-powered, and are used to retrieve information from the network so that it is presented to users. The system operational chain starts at the kinetic-powered nodes broadcasting their own identifier. If an identifier is received at a battery-powered node, the latter stores it for its records. Later, as the recording node meets a hotspot, its full record of detections is transferred to the hotspot. Every detection registry comprises, at least, a node identifier and the position read from its GPS module by the battery-operated node previously to detection. The characteristics of the system presented make the aforementioned operation own certain particularities which are also studied. First, identifier transmissions are random as they depend on movements at kinetic modules--reindeer movements in our application. Not every movement suffices since it must overcome a certain energy threshold. Second, identifier transmissions may not be heard unless there is a battery-powered node in the surroundings. Third, battery-powered nodes do not poll continuously their GPS module, hence localization errors rise even more. Let's recall at this point that such behavior is tight to the aforementioned power saving policies to extend node lifetime. Last, some time is elapsed between the instant an identifier random transmission is detected and the moment the user is aware of such a detection: it takes some time to find a hotspot. Tracking is posed as a problem of a single kinetically-powered target and a population of battery-operated nodes with higher densities than before in localization. Since the latter provide their approximate positions as reference locations, the study is again focused on assessing the impact of such distorted references on performance. Unlike in localization, distance-estimation capabilities based on signal parameters are assumed in this problem. Three variants of the Kalman filter family are applied in this context: the regular Kalman filter, the alpha-beta filter, and the unscented Kalman filter. The study enclosed hereafter comprises both field tests and simulations. Field tests were used mainly to assess the challenges related to power supply and operation in extreme conditions as well as to model nodes and some aspects of their operation in the application scenario. These models are the basics of the simulations developed later. The overall system performance is analyzed according to three metrics: number of detections per kinetic node, accuracy, and latency. The links between these metrics and the operational conditions are also discussed and characterized statistically. Subsequently, such statistical characterization is used to forecast performance figures given specific operational parameters. In tracking, also studied via simulations, nonlinear relationships are found between accuracy and duty cycles and cluster sizes of battery-operated nodes. The solution presented may be more complex in terms of network structure than existing solutions based on GPS collars. However, its main gain lies on taking advantage of users' error tolerance to reduce costs and become more environmentally friendly by diminishing the potential amount of batteries that can be lost. Whether it is applicable or not depends ultimately on the conditions and requirements imposed by users' needs and operational environments, which is, as it has been explained, one of the topics of this Thesis.

Space-time ocean wave measurement using variational stereo vision systems

Remote sensing imaging systems for the measurement of oceanic sea states have recently attracted renovated attention. Imaging technology is economical, non-invasive and enables a better understanding of the space-time dynamics of ocean waves over an area rather than at selected point locations of previous monitoring methods (buoys, wave gauges, etc.). We present recent progress in space-time measurement of ocean waves using stereo vision systems on offshore platforms. Both traditional disparity-based systems and modern elevation-based ones are presented in a variational optimization framework: the main idea is to pose the stereoscopic reconstruction problem of the surface of the ocean in a variational setting and design an energy functional whose minimizer is the desired temporal sequence of wave heights. The functional combines photometric observations as well as spatial and temporal smoothness priors. Disparity methods estimate the disparity between images as an intermediate step toward retrieving the depth of the waves with respect to the cameras, whereas elevation methods estimate the ocean surface displacements directly in 3-D space. Both techniques are used to measure ocean waves from real data collected at offshore platforms in the Black Sea (Crimean Peninsula, Ukraine) and the Northern Adriatic Sea (Venice coast, Italy). Then, the statistical and spectral properties of the resulting observed waves are analyzed. We show the advantages and disadvantages of the presented stereo vision systems and discuss the improvement of their performance in critical issues such as the robustness of the camera calibration in spite of undesired variations of the camera parameters.

Urban wind energy: empirical optimization of high-rise building roof shape for the wind energy exploitation

El programa Europeo HORIZON2020 en Futuras Ciudades Inteligentes establece como objetivo que el 20% de la energía eléctrica sea generada a partir de fuentes renovables. Este objetivo implica la necesidad de potenciar la generación de energía eólica en todos los ámbitos. La energía eólica reduce drásticamente las emisiones de gases de efecto invernadero y evita los riesgos geo-políticos asociados al suministro e infraestructuras energéticas, así como la dependencia energética de otras regiones. Además, la generación de energía distribuida (generación en el punto de consumo) presenta significativas ventajas en términos de elevada eficiencia energética y estimulación de la economía. El sector de la edificación representa el 40% del consumo energético total de la Unión Europea. La reducción del consumo energético en este área es, por tanto, una prioridad de acuerdo con los objetivos "20-20-20" en eficiencia energética. La Directiva 2010/31/EU del Parlamento Europeo y del Consejo de 19 de mayo de 2010 sobre el comportamiento energético de edificaciones contempla la instalación de sistemas de suministro energético a partir de fuentes renovables en las edificaciones de nuevo diseño. Actualmente existe una escasez de conocimiento científico y tecnológico acerca de la geometría óptima de las edificaciones para la explotación de la energía eólica en entornos urbanos. El campo tecnológico de estudio de la presente Tesis Doctoral es la generación de energía eólica en entornos urbanos. Específicamente, la optimization de la geometría de las cubiertas de edificaciones desde el punto de vista de la explotación del recurso energético eólico. Debido a que el flujo del viento alrededor de las edificaciones es exhaustivamente investigado en esta Tesis empleando herramientas de simulación numérica, la mecánica de fluidos computacional (CFD en inglés) y la aerodinámica de edificaciones son los campos científicos de estudio. El objetivo central de esta Tesis Doctoral es obtener una geometría de altas prestaciones (u óptima) para la explotación de la energía eólica en cubiertas de edificaciones de gran altura. Este objetivo es alcanzado mediante un análisis exhaustivo de la influencia de la forma de la cubierta del edificio en el flujo del viento desde el punto de vista de la explotación energética del recurso eólico empleando herramientas de simulación numérica (CFD). Adicionalmente, la geometría de la edificación convencional (edificio prismático) es estudiada, y el posicionamiento adecuado para los diferentes tipos de aerogeneradores es propuesto. La compatibilidad entre el aprovechamiento de las energías solar fotovoltaica y eólica también es analizado en este tipo de edificaciones. La investigación prosigue con la optimización de la geometría de la cubierta. La metodología con la que se obtiene la geometría óptima consta de las siguientes etapas: - Verificación de los resultados de las geometrías previamente estudiadas en la literatura. Las geometrías básicas que se someten a examen son: cubierta plana, a dos aguas, inclinada, abovedada y esférica. - Análisis de la influencia de la forma de las aristas de la cubierta sobre el flujo del viento. Esta tarea se lleva a cabo mediante la comparación de los resultados obtenidos para la arista convencional (esquina sencilla) con un parapeto, un voladizo y una esquina curva. - Análisis del acoplamiento entre la cubierta y los cerramientos verticales (paredes) mediante la comparación entre diferentes variaciones de una cubierta esférica en una edificación de gran altura: cubierta esférica estudiada en la literatura, cubierta esférica integrada geométricamente con las paredes (planta cuadrada en el suelo) y una cubierta esférica acoplada a una pared cilindrica. El comportamiento del flujo sobre la cubierta es estudiado también considerando la posibilidad de la variación en la dirección del viento incidente. - Análisis del efecto de las proporciones geométricas del edificio sobre el flujo en la cubierta. - Análisis del efecto de la presencia de edificaciones circundantes sobre el flujo del viento en la cubierta del edificio objetivo. Las contribuciones de la presente Tesis Doctoral pueden resumirse en: - Se demuestra que los modelos de turbulencia RANS obtienen mejores resultados para la simulación del viento alrededor de edificaciones empleando los coeficientes propuestos por Crespo y los propuestos por Bechmann y Sórensen que empleando los coeficientes estándar. - Se demuestra que la estimación de la energía cinética turbulenta del flujo empleando modelos de turbulencia RANS puede ser validada manteniendo el enfoque en la cubierta de la edificación. - Se presenta una nueva modificación del modelo de turbulencia Durbin k — e que reproduce mejor la distancia de recirculación del flujo de acuerdo con los resultados experimentales. - Se demuestra una relación lineal entre la distancia de recirculación en una cubierta plana y el factor constante involucrado en el cálculo de la escala de tiempo de la velocidad turbulenta. Este resultado puede ser empleado por la comunidad científica para la mejora del modelado de la turbulencia en diversas herramientas computacionales (OpenFOAM, Fluent, CFX, etc.). - La compatibilidad entre las energías solar fotovoltaica y eólica en cubiertas de edificaciones es analizada. Se demuestra que la presencia de los módulos solares provoca un descenso en la intensidad de turbulencia. - Se demuestran conflictos en el cambio de escala entre simulaciones de edificaciones a escala real y simulaciones de modelos a escala reducida (túnel de viento). Se demuestra que para respetar las limitaciones de similitud (número de Reynolds) son necesarias mediciones en edificaciones a escala real o experimentos en túneles de viento empleando agua como fluido, especialmente cuando se trata con geometrías complejas, como es el caso de los módulos solares. - Se determina el posicionamiento más adecuado para los diferentes tipos de aerogeneradores tomando en consideración la velocidad e intensidad de turbulencia del flujo. El posicionamiento de aerogeneradores es investigado en las geometrías de cubierta más habituales (plana, a dos aguas, inclinada, abovedada y esférica). - Las formas de aristas más habituales (esquina, parapeto, voladizo y curva) son analizadas, así como su efecto sobre el flujo del viento en la cubierta de un edificio de gran altura desde el punto de vista del aprovechamiento eólico. - Se propone una geometría óptima (o de altas prestaciones) para el aprovechamiento de la energía eólica urbana. Esta optimización incluye: verificación de las geometrías estudiadas en el estado del arte, análisis de la influencia de las aristas de la cubierta en el flujo del viento, estudio del acoplamiento entre la cubierta y las paredes, análisis de sensibilidad del grosor de la cubierta, exploración de la influencia de las proporciones geométricas de la cubierta y el edificio, e investigación del efecto de las edificaciones circundantes (considerando diferentes alturas de los alrededores) sobre el flujo del viento en la cubierta del edificio objetivo. Las investigaciones comprenden el análisis de la velocidad, la energía cinética turbulenta y la intensidad de turbulencia en todos los casos. ABSTRACT The HORIZON2020 European program in Future Smart Cities aims to have 20% of electricity produced by renewable sources. This goal implies the necessity to enhance the wind energy generation, both with large and small wind turbines. Wind energy drastically reduces carbon emissions and avoids geo-political risks associated with supply and infrastructure constraints, as well as energy dependence from other regions. Additionally, distributed energy generation (generation at the consumption site) offers significant benefits in terms of high energy efficiency and stimulation of the economy. The buildings sector represents 40% of the European Union total energy consumption. Reducing energy consumption in this area is therefore a priority under the "20-20-20" objectives on energy efficiency. The Directive 2010/31/EU of the European Parliament and of the Council of 19 May 2010 on the energy performance of buildings aims to consider the installation of renewable energy supply systems in new designed buildings. Nowadays, there is a lack of knowledge about the optimum building shape for urban wind energy exploitation. The technological field of study of the present Thesis is the wind energy generation in urban environments. Specifically, the improvement of the building-roof shape with a focus on the wind energy resource exploitation. Since the wind flow around buildings is exhaustively investigated in this Thesis using numerical simulation tools, both computational fluid dynamics (CFD) and building aerodynamics are the scientific fields of study. The main objective of this Thesis is to obtain an improved (or optimum) shape of a high-rise building for the wind energy exploitation on the roof. To achieve this objective, an analysis of the influence of the building shape on the behaviour of the wind flow on the roof from the point of view of the wind energy exploitation is carried out using numerical simulation tools (CFD). Additionally, the conventional building shape (prismatic) is analysed, and the adequate positions for different kinds of wind turbines are proposed. The compatibility of both photovoltaic-solar and wind energies is also analysed for this kind of buildings. The investigation continues with the buildingroof optimization. The methodology for obtaining the optimum high-rise building roof shape involves the following stages: - Verification of the results of previous building-roof shapes studied in the literature. The basic shapes that are compared are: flat, pitched, shed, vaulted and spheric. - Analysis of the influence of the roof-edge shape on the wind flow. This task is carried out by comparing the results obtained for the conventional edge shape (simple corner) with a railing, a cantilever and a curved edge. - Analysis of the roof-wall coupling by testing different variations of a spherical roof on a high-rise building: spherical roof studied in the litera ture, spherical roof geometrically integrated with the walls (squared-plant) and spherical roof with a cylindrical wall. The flow behaviour on the roof according to the variation of the incident wind direction is commented. - Analysis of the effect of the building aspect ratio on the flow. - Analysis of the surrounding buildings effect on the wind flow on the target building roof. The contributions of the present Thesis can be summarized as follows: - It is demonstrated that RANS turbulence models obtain better results for the wind flow around buildings using the coefficients proposed by Crespo and those proposed by Bechmann and S0rensen than by using the standard ones. - It is demonstrated that RANS turbulence models can be validated for turbulent kinetic energy focusing on building roofs. - A new modification of the Durbin k — e turbulence model is proposed in order to obtain a better agreement of the recirculation distance between CFD simulations and experimental results. - A linear relationship between the recirculation distance on a flat roof and the constant factor involved in the calculation of the turbulence velocity time scale is demonstrated. This discovery can be used by the research community in order to improve the turbulence modeling in different solvers (OpenFOAM, Fluent, CFX, etc.). - The compatibility of both photovoltaic-solar and wind energies on building roofs is demonstrated. A decrease of turbulence intensity due to the presence of the solar panels is demonstrated. - Scaling issues are demonstrated between full-scale buildings and windtunnel reduced-scale models. The necessity of respecting the similitude constraints is demonstrated. Either full-scale measurements or wind-tunnel experiments using water as a medium are needed in order to accurately reproduce the wind flow around buildings, specially when dealing with complex shapes (as solar panels, etc.). - The most adequate position (most adequate roof region) for the different kinds of wind turbines is highlighted attending to both velocity and turbulence intensity. The wind turbine positioning was investigated for the most habitual kind of building-roof shapes (flat, pitched, shed, vaulted and spherical). - The most habitual roof-edge shapes (simple edge, railing, cantilever and curved) were investigated, and their effect on the wind flow on a highrise building roof were analysed from the point of view of the wind energy exploitation. - An optimum building-roof shape is proposed for the urban wind energy exploitation. Such optimization includes: state-of-the-art roof shapes test, analysis of the influence of the roof-edge shape on the wind flow, study of the roof-wall coupling, sensitivity analysis of the roof width, exploration of the aspect ratio of the building-roof shape and investigation of the effect of the neighbouring buildings (considering different surrounding heights) on the wind now on the target building roof. The investigations comprise analysis of velocity, turbulent kinetic energy and turbulence intensity for all the cases.

Global instability analysis and control of three-dimensional long open cavity flow

The three-dimensional wall-bounded open cavity may be considered as a simplified geometry found in industrial applications such as leading gear or slotted flats on the airplane. Understanding the three-dimensional complex flow structure that surrounds this particular geometry is therefore of major industrial interest. At the light of the remarkable former investigations in this kind of flows, enough evidences suggest that the lateral walls have a great influence on the flow features and hence on their instability modes. Nevertheless, even though there is a large body of literature on cavity flows, most of them are based on the assumption that the flow is two-dimensional and spanwise-periodic. The flow over realistic open cavity should be considered. This thesis presents an investigation of three-dimensional wall-bounded open cavity with geometric ratio 6:2:1. To this aim, three-dimensional Direct Numerical Simulation (DNS) and global linear instability have been performed. Linear instability analysis reveals that the onset of the first instability in this open cavity is around Recr 1080. The three-dimensional shear layer mode with a complex structure is shown to be the most unstable mode. I t is noteworthy that the flow pattern of this high-frequency shear layer mode is similar to the observed unstable oscillations in supercritical unstable case. DNS of the cavity flow carried out at different Reynolds number from steady state until a nonlinear saturated state is obtained. The comparison of time histories of kinetic energy presents a clearly dominant energetic mode which shifts between low-frequency and highfrequency oscillation. A complete flow patterns from subcritical cases to supercritical case has been put in evidence. The flow structure at the supercritical case Re=1100 resembles typical wake-shedding instability oscillations with a lateral motion existed in the subcritical cases. Also, This flow pattern is similar to the observations in experiments. In order to validate the linear instability analysis results, the topology of the composite flow fields reconstructed by linear superposition of a three-dimensional base flow and its leading three-dimensional global eigenmodes has been studied. The instantaneous wall streamlines of those composited flows display distinguish influence region of each eigenmode. Attention has been focused on the leading high-frequency shear layer mode; the composite flow fields have been fully recognized with respect to the downstream wave shedding. The three-dimensional shear layer mode is shown to give rise to a typical wake-shedding instability with a lateral motions occurring downstream which is in good agreement with the experiment results. Moreover, the spanwise-periodic, open cavity with the same length to depth ratio has been also studied. The most unstable linear mode is different from the real three-dimensional cavity flow, because of the existence of the side walls. Structure sensitivity of the unstable global mode is analyzed in the flow control context. The adjoint-based sensitivity analysis has been employed to localized the receptivity region, where the flow is more sensible to momentum forcing and mass injection. Because of the non-normality of the linearized Navier-Stokes equations, the direct and adjoint field has a large spatial separation. The strongest sensitivity region is locate in the upstream lip of the three-dimensional cavity. This numerical finding is in agreement with experimental observations. Finally, a prototype of passive flow control strategy is applied.

Optimization of energy extraction in transverse galloping

A numerical method to analyse the stability of transverse galloping based on experimental measurements, as an alternative method to polynomial fitting of the transverse force coefficient Cz, is proposed in this paper. The Glauert–Den Hartog criterion is used to determine the region of angles of attack (pitch angles) prone to present galloping. An analytic solution (based on a polynomial curve of Cz) is used to validate the method and to evaluate the discretization errors. Several bodies (of biconvex, D-shape and rhomboidal cross sections) have been tested in a wind tunnel and the stability of the galloping region has been analysed with the new method. An algorithm to determine the pitch angle of the body that allows the maximum value of the kinetic energy of the flow to be extracted is presented.

A time-domain finite element method for seakeeping and wave resistance problems

El objetivo de la tesis es la investigación de algoritmos numéricos para el desarrollo de herramientas numéricas para la simulación de problemas tanto de comportamiento en la mar como de resistencia al avance de buques y estructuras flotantes. La primera herramienta desarrollada resuelve el problema de difracción y radiación de olas. Se basan en el método de los elementos finitos (MEF) para la resolución de la ecuación de Laplace, así como en esquemas basados en MEF, integración a lo largo de líneas de corriente, y en diferencias finitas desarrollados para la condición de superficie libre. Se han desarrollado herramientas numéricas para la resolución de la dinámica de sólido rígido en sistemas multicuerpos con ligaduras. Estas herramientas han sido integradas junto con la herramienta de resolución de olas difractadas y radiadas para la resolución de problemas de interacción de cuerpos con olas. También se han diseñado algoritmos de acoplamientos con otras herramientas numéricas para la resolución de problemas multifísica. En particular, se han realizado acoplamientos con una herramienta numérica basada de cálculo de estructuras con MEF para problemas de interacción fluido-estructura, otra de cálculo de líneas de fondeo, y con una herramienta numérica de cálculo de flujos en tanques internos para problemas acoplados de comportamiento en la mar con “sloshing”. Se han realizado simulaciones numéricas para la validación y verificación de los algoritmos desarrollados, así como para el análisis de diferentes casos de estudio con aplicaciones diversas en los campos de la ingeniería naval, oceánica, y energías renovables marinas. ABSTRACT The objective of this thesis is the research on numerical algorithms to develop numerical tools to simulate seakeeping problems as well as wave resistance problems of ships and floating structures. The first tool developed is a wave diffraction-radiation solver. It is based on the finite element method (FEM) in order to solve the Laplace equation, as well as numerical schemes based on FEM, streamline integration, and finite difference method tailored for solving the free surface boundary condition. It has been developed numerical tools to solve solid body dynamics of multibody systems with body links across them. This tool has been integrated with the wave diffraction-radiation solver to solve wave-body interaction problems. Also it has been tailored coupling algorithms with other numerical tools in order to solve multi-physics problems. In particular, it has been performed coupling with a MEF structural solver to solve fluid-structure interaction problems, with a mooring solver, and with a solver capable of simulating internal flows in tanks to solve couple seakeeping-sloshing problems. Numerical simulations have been carried out to validate and verify the developed algorithms, as well as to analyze case studies in the areas of marine engineering, offshore engineering, and offshore renewable energy.

Spectral bifurcations in dispersive wave turbulence

Dispersive wave turbulence is studied numerically for a class of one-dimensional nonlinear wave equations. Both deterministic and random (white noise in time) forcings are studied. Four distinct stable spectra are observed—the direct and inverse cascades of weak turbulence (WT) theory, thermal equilibrium, and a fourth spectrum (MMT; Majda, McLaughlin, Tabak). Each spectrum can describe long-time behavior, and each can be only metastable (with quite diverse lifetimes)—depending on details of nonlinearity, forcing, and dissipation. Cases of a long-live MMT transient state dcaying to a state with WT spectra, and vice-versa, are displayed. In the case of freely decaying turbulence, without forcing, both cascades of weak turbulence are observed. These WT states constitute the clearest and most striking numerical observations of WT spectra to date—over four decades of energy, and three decades of spatial, scales. Numerical experiments that study details of the composition, coexistence, and transition between spectra are then discussed, including: (i) for deterministic forcing, sharp distinctions between focusing and defocusing nonlinearities, including the role of long wavelength instabilities, localized coherent structures, and chaotic behavior; (ii) the role of energy growth in time to monitor the selection of MMT or WT spectra; (iii) a second manifestation of the MMT spectrum as it describes a self-similar evolution of the wave, without temporal averaging; (iv) coherent structures and the evolution of the direct and inverse cascades; and (v) nonlocality (in k-space) in the transferral process.

Kinetic equilibrium of forces and molecular events in muscle contraction

In biomolecular systems, the mechanical transfer of free energy occurs with both high efficiency and high speed. It is shown here that such a transfer can be achieved only if the participating free-energy-storing elements exhibit opposing relationships between their content of free energy and the force they exert in the transfer direction. A kinetic equilibrium of forces (KEF) results, in which the transfer of free energy is mediated essentially by thermal molecular motion. On the basis of present evidence, KEF is used as a guiding principle in developing a mechanical model of the crossbridge cycle in muscle contraction. The model allows the basic features of molecular events to be visualized in terms of plausible structures. Real understanding of the process will require identification of the elements that perform the functions described here. Besides chemomechanical energy transduction, KEF may have a role in other biomolecular processes in which free energy is transferred mechanically over large distances.

Brain-wave representation of words by superposition of a few sine waves

Data from three previous experiments were analyzed to test the hypothesis that brain waves of spoken or written words can be represented by the superposition of a few sine waves. First, we averaged the data over trials and a set of subjects, and, in one case, over experimental conditions as well. Next we applied a Fourier transform to the averaged data and selected those frequencies with high energy, in no case more than nine in number. The superpositions of these selected sine waves were taken as prototypes. The averaged unfiltered data were the test samples. The prototypes were used to classify the test samples according to a least-squares criterion of fit. The results were seven of seven correct classifications for the first experiment using only three frequencies, six of eight for the second experiment using nine frequencies, and eight of eight for the third experiment using five frequencies.

The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin

The grail of protein science is the connection between structure and function. For myoglobin (Mb) this goal is close. Described as only a passive dioxygen storage protein in texts, we argue here that Mb is actually an allosteric enzyme that can catalyze reactions among small molecules. Studies of the structural, spectroscopic, and kinetic properties of Mb lead to a model that relates structure, energy landscape, dynamics, and function. Mb functions as a miniature chemical reactor, concentrating and orienting diatomic molecules such as NO, CO, O2, and H2O2 in highly conserved internal cavities. Reactions can be controlled because Mb exists in distinct taxonomic substates with different catalytic properties and connectivities of internal cavities.

Top-down free-energy minimization on protein potential energy landscapes

The hierarchical properties of potential energy landscapes have been used to gain insight into thermodynamic and kinetic properties of protein ensembles. It also may be possible to use them to direct computational searches for thermodynamically stable macroscopic states, i.e., computational protein folding. To this end, we have developed a top-down search procedure in which conformation space is recursively dissected according to the intrinsic hierarchical structure of a landscape's effective-energy barriers. This procedure generates an inverted tree similar to the disconnectivity graphs generated by local minima-clustering methods, but it fundamentally differs in the manner in which the portion of the tree that is to be computationally explored is selected. A key ingredient is a branch-selection algorithm that takes advantage of statistically predictive properties of the landscape to guide searches down the tree branches that are most likely to lead to the physically relevant macroscopic states. Using the computational folding of a β-hairpin-forming peptide as an example, we show that such predictive properties indeed exist and can be used for structure prediction by free-energy global minimization.

Kinetic coupling between electron and proton transfer in cytochrome c oxidase: simultaneous measurements of conductance and absorbance changes.

Bovine heart cytochrome c oxidase is an electron-current driven proton pump. To investigate the mechanism by which this pump operates it is important to study individual electron- and proton-transfer reactions in the enzyme, and key reactions in which they are kinetically and thermodynamically coupled. In this work, we have simultaneously measured absorbance changes associated with electron-transfer reactions and conductance changes associated with protonation reactions following pulsed illumination of the photolabile complex of partly reduced bovine cytochrome c oxidase and carbon monoxide. Following CO dissociation, several kinetic phases in the absorbance changes were observed with time constants ranging from approximately 3 microseconds to several milliseconds, reflecting internal electron-transfer reactions within the enzyme. The data show that the rate of one of these electron-transfer reactions, from cytochrome a3 to a on a millisecond time scale, is controlled by a proton-transfer reaction. These results are discussed in terms of a model in which cytochrome a3 interacts electrostatically with a protonatable group, L, in the vicinity of the binuclear center, in equilibrium with the bulk through a proton-conducting pathway, which determines the rate of proton transfer (and indirectly also of electron transfer). The interaction energy of cytochrome a3 with L was determined independently from the pH dependence of the extent of the millisecond-electron transfer and the number of protons released, as determined from the conductance measurements. The magnitude of the interaction energy, 70 meV (1 eV = 1.602 x 10(-19) J), is consistent with a distance of 5-10 A between cytochrome a3 and L. Based on the recently determined high-resolution x-ray structures of bovine and a bacterial cytochrome c oxidase, possible candidates for L and a physiological role for L are discussed.

Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

The search for novel leads is a critical step in the drug discovery process. Computational approaches to identify new lead molecules have focused on discovering complete ligands by evaluating the binding affinity of a large number of candidates, a task of considerable complexity. A new computational method is introduced in this work based on the premise that the primary molecular recognition event in the protein binding site may be accomplished by small core fragments that serve as molecular anchors, providing a structurally stable platform that can be subsequently tailored into complete ligands. To fulfill its role, we show that an effective molecular anchor must meet both the thermodynamic requirement of relative energetic stability of a single binding mode and its consistent kinetic accessibility, which may be measured by the structural consensus of multiple docking simulations. From a large number of candidates, this technique is able to identify known core fragments responsible for primary recognition by the FK506 binding protein (FKBP-12), along with a diverse repertoire of novel molecular cores. By contrast, absolute energetic criteria for selecting molecular anchors are found to be promiscuous. A relationship between a minimum frustration principle of binding energy landscapes and receptor-specific molecular anchors in their role as "recognition nuclei" is established, thereby unraveling a mechanism of lead discovery and providing a practical route to receptor-biased computational combinatorial chemistry.

Kinetic traps in lysozyme folding.

Folding of lysozyme from hen egg white was investigated by using interrupted refolding experiments. This method makes use of a high energy barrier between the native state and transient folding intermediates, and, in contrast to conventional optical techniques, it enables one to specifically monitor the amount of native molecules during protein folding. The results show that under strongly native conditions lysozyme can refold on parallel pathways. The major part of the lysozyme molecules (86%) refold on a slow kinetic pathway with well-populated partially folded states. Additionally, 14% of the molecules fold faster. The rate constant of formation of native molecules on the fast pathway corresponds well to the rate constant expected for folding to occur by a two-state process without any detectable intermediates. The results suggest that formation of the native state for the major fraction of lysozyme molecules is retarded compared with the direct folding process. Partially structured intermediates that transiently populate seem to be kinetically trapped in a conformation that can only slowly reach the native structure.

Excitations in Bose-Einstein condensates: collective modes, quantum turbulence and matter wave statistics

In this thesis, we present the generation and studies of a 87Rb Bose-Einstein condensate (BEC) perturbed by an oscillatory excitation. The atoms are trapped in a harmonic magnetic trap where, after an evaporative cooling process, we produce the BEC. In order to study the effect caused by oscillatory excitations, a quadrupole magnetic field time oscillatory is superimposed to the trapping potential. Through this perturbation, collective modes were observed. The dipole mode is excited even for low excitation amplitudes. However, a minimum excitation energy is needed to excite the condensate quadrupole mode. Observing the excited cloud in TOF expansion, we note that for excitation amplitude in which the quadrupole mode is excited, the cloud expands without invert its aspect ratio. By looking these clouds, after long time-of-flight, it was possible to see vortices and, sometimes, a turbulent state in the condensed cloud. We calculated the momentum distribution of the perturbed BECs and a power law behavior, like the law to Kolmogorov turbulence, was observed. Furthermore, we show that using the method that we have developed to calculate the momentum distribution, the distribution curve (including the power law exponent) exhibits a dependence on the quadrupole mode oscillation of the cloud. The randomness distribution of peaks and depletions in density distribution image of an expanded turbulent BEC, remind us to the intensity profile of a speckle light beam. The analogy between matter-wave speckle and light speckle is justified by showing the similarities in the spatial propagation (or time expansion) of the waves. In addition, the second order correlation function is evaluated and the same dependence with distance was observed for the both waves. This creates the possibility to understand the properties of quantum matter in a disordered state. The propagation of a three-dimensional speckle field (as the matter-wave speckle described here) creates an opportunity to investigate the speckle phenomenon existing in dimensions higher than 2D (the case of light speckle).