The spatial and population dynamics of avian scavengers are poorly understood. This information is key for management and conservation interventions that guarantee long-term species conservation. My goal in this dissertation is to fill information gaps on the movement ecology of New World vultures using the Turkey Vulture (Cathartes aura) as a model species. I used a continental-wide satellite telemetry dataset to study the migration ecology, space-use, and demography of the three North American breeding populations of Turkey Vultures wintering in the Neotropics during a 17-year period. I found that primary productivity, but not weather, triggered Turkey Vulture migratory behavior, migration initiated when primary productivity dropped at the end of the breeding and non-breeding season. Migratory connectivity was high at the species level (0.85, 95% CI: 0.74–0.94). However, I found evidence of intrapopulation segregation during the non-breeding season demonstrated by lower values of migratory connectivity in each population. I investigated how seasonality interacted with human disturbance, landscape composition and configuration to mediate patterns of geographic and environmental space-use, and annual and seasonal survival probabilities. Environmental space-use was best explained by landscape configuration. Geographic space-use exhibited a quadratic response to landscape configuration metrics, suggesting that Turkey Vultures maximize space-use in landscape with intermediate disturbance. Human disturbance, but not but not landscape composition and configuration, influenced survival rates in space and time. Overall annual survival averaged 0.87 (95% CI = 0.74 – 0.98). Mortality risk was low in western and central populations but was 3.7 times greater for vultures in the eastern population. Risk of mortality for all vulture populations increased with road density, and this was greater during the non-breeding and return migration seasons. My results suggest that spatial and population dynamics are affected at a continental scale by the energy landscape, intermediate disturbance and human disturbance. My dissertation emphasizes the importance of an integrative empirical-modeling approach to address questions on effects of resources availability and search efficiency in the spatial and population dynamics of avian scavengers.

<p>Research in the last few decades has revealed the great capacity of the RNA molecule. RNA, which previously was assumed to play a main role only as an intermediate in the translation of genes to proteins, is today known to play many important roles in the cell in addition to that as a messenger RNA and transfer RNA, including the ability to catalyze reactions and gene regulations at various levels.</p><p>This thesis investigates several computational aspects of RNA. We will discuss identification of novel RNAs and RNAs that are known to exist in related species, RNA secondary structure prediction, as well as more general tools for analyzing, visualizing and classifying RNA sequences.</p><p>We present two benchmark studies concerning RNA identification, both de novo identification/characterization of single RNA sequences and homology search methods.</p><p>We develope a novel algorithm for analysis of the RNA folding landscape that is based on the nearest neighbor energy model adopted in many secondary structure prediction programs. We implement this algorithm, which computes structural neighbors of a given RNA secondary structure, in the program RNAbor, which is accessible on a web server.</p><p>Furthermore, we combine a mutual information based structure prediction algorithm with a sequence logo visualization to create a novel visualization tool for analyzing an RNA alignment and identifying covarying sites.</p><p>Finally, we present extensions to sequence logos for the purpose of tRNA identity analysis. We introduce function logos, which display features that distinguish functional subclasses within a large set of structurally related sequences, as well as the inverse logos, which display underrepresented features. For the purpose of comparing tRNA identity elements between different taxa we introduce two contrasting logos, the information difference and the Kullback-Leibler divergence difference logos.</p>

Research in the last few decades has revealed the great capacity of the RNA molecule. RNA, which previously was assumed to play a main role only as an intermediate in the translation of genes to proteins, is today known to play many important roles in the cell in addition to that as a messenger RNA and transfer RNA, including the ability to catalyze reactions and gene regulations at various levels. This thesis investigates several computational aspects of RNA. We will discuss identification of novel RNAs and RNAs that are known to exist in related species, RNA secondary structure prediction, as well as more general tools for analyzing, visualizing and classifying RNA sequences. We present two benchmark studies concerning RNA identification, both de novo identification/characterization of single RNA sequences and homology search methods. We develope a novel algorithm for analysis of the RNA folding landscape that is based on the nearest neighbor energy model adopted in many secondary structure prediction programs. We implement this algorithm, which computes structural neighbors of a given RNA secondary structure, in the program RNAbor, which is accessible on a web server. Furthermore, we combine a mutual information based structure prediction algorithm with a sequence logo visualization to create a novel visualization tool for analyzing an RNA alignment and identifying covarying sites. Finally, we present extensions to sequence logos for the purpose of tRNA identity analysis. We introduce function logos, which display features that distinguish functional subclasses within a large set of structurally related sequences, as well as the inverse logos, which display underrepresented features. For the purpose of comparing tRNA identity elements between different taxa we introduce two contrasting logos, the information difference and the Kullback-Leibler divergence difference logos.

Optical tweezers are a technique in which microscopic-sized particles, including living cells and bacteria, can be non-intrusively trapped with high accuracy solely using focused light. The technique has therefore become a powerful tool in the field of biophysics. Optical tweezers thereby provide outstanding manipulation possibilities of cells as well as semi-transparent materials, both non-invasively and non-destructively, in biological systems. In addition, optical tweezers can measure minute forces (&lt; 10-12 N), probe molecular interactions and their energy landscapes, and apply both static and dynamic forces in biological systems in a controlled manner. The assessment of intermolecular forces with force measuring optical tweezers, and thereby the biomechanical structure of biological objects, has therefore considerably facilitated our understanding of interactions and structures of biological systems. Adhesive bacterial organelles, so called pili, mediate adhesion to host cells and are therefore crucial for the initial bacterial-cell contact. Thus, they serve as an important virulence factor. The investigation of pili, both their biogenesis and their expected in vivo properties, brings information that can be of importance for the design of new drugs to prevent bacterial infections, which is crucial in the era of increased bacterial resistance towards antibiotics. In this thesis, an experimental setup of a force measuring optical tweezers system and the results of a number of biomechanical investigations of adhesive bacterial organelles are presented. Force measuring optical tweezers have been used to characterize three different types of adhesive organelles under various conditions, P, type 1, and S pili, which all are expressed by uropathogenic Escherichia coli. A quantitative biophysical force-extension model, built upon the structure and force response, has been developed. It is found, that this model describes the biomechanical properties for all three pili in an excellent way. Various parameters in their energy landscape, e.g., bond lengths and transition barrier heights, are assessed and the difference in behavior is compared. The work has resulted in a method that in a swift way allows us to probe different types of pili with high force and high spatial resolution, which has provided an enhanced understanding of the biomechanical function of these pili. / Optisk pincett är en teknik i vilken mikrometerstora objekt, inkluderande levande celler och bakterier, beröringsfritt kan fångas och förflyttas med hög noggrannhet enbart med hjälp av ljus. Den optiska pincetten har därmed blivit ett kraftfullt verktyg inom biofysiken, som möjliggör enastående precisions-manipulering av celler och semi-transparenta objekt. Dessutom kan denna manipulation göras intracellulärt, dvs. utan att fysiskt öppna eller penetrera cellernas membran. Den optiska pincetten kan även mäta mycket små krafter och interaktioner (&lt; 10-12 N) samt applicera både statiska och dynamiska krafter i biologiska system med utmärkt precision. Optisk pincett är därför en utmärkt teknik för mätning av intermolekylära krafter och för bestämning av biomekaniska strukturer och dess funktioner. Vissa typer av bakterier har specifika vidhäftningsorganeller som kallas för pili. Dessa förmedlar vidhäftningen till värdceller och är därför viktiga vid bakteriens första kontakt. En djupare förståelse av pilis uppbyggnad och biomekanik kan därmed ge information, som kan vara vital i framtagandet av nya mediciner som förhindrar bakteriella infektioner. Detta är av stor vikt i skenet av den ökande antibiotikaresistensen i vårt samhälle. I denna avhandling presenteras konstruktionen av en experimentell uppställning av kraftmätande optiskt pincett tillsammans med resultat från biomekaniska undersökningar av vidhäftande bakteriella organeller. Kraftmätande optisk pincett har använts för att karakterisera tre olika typer av pili, P, typ 1, och S pili, vilka kan uttryckas av uropatogena Escherichia coli. En kvantitativ biofysikalisk modell som beskriver deras förlängningsegenskaper under pålagd kraft har konstruerats. Modellen bygger på pilis strukturella uppbyggnad samt på dess respons som uppmäts med den kraftmätande optiska pincetten. Modellen beskriver de biomekaniska egenskaperna väl för alla tre pili. Dessutom kan ett antal specifika bindnings- och subenhetsparametrar bestämmas, t.ex. interaktionsenergier och bindningslängder. Skillnaden mellan dessa parametrar hos de tre pilis samt deras olika kraftrespons har jämförts. Detta arbete har dels resulterat i en förbättrad förståelse av pilis biomekaniska funktion och dels i en metod som, med hög noggrannhet, tillåter oss att bestämma ett antal biomekaniska egenskaper hos olika organeller på ett effektivt sätt.

The central concern of this thesis is the study of non-equilibrium behaviour in magnetic materials and its interpretation within the framework of the Preisach model of hysteresis. Comprehensive experimental characterizations of the field and temperature and time dependence of a suite of standard magnetic response functions have been performed on a variety of magnetic materials, including a naturally occurring mineral of nanodimensional titanomagnetite particles embedded in volcanic glass, a compressed powder of nanodimensional magnetite particles immobilized in an organic binder, a thin film of nanodimensional Fe particles embedded in alumina, and a series of sintered, bond-disordered CaxSr1-xRuO3 ferromagnets. The measurements were compared with numerical simulations based on a model Preisach ensemble of thermally activated two-level subsystems, characterized individually by a double well free energy profile in a two-dimensional configuration space, an elementary moment reversal, a dissipation field and a bias field, and characterized collectively by a distribution of these characteristic fields. Our efforts were concentrated on two principal spheres of investigation. (1) By performing detailed numerical simulations of the relaxation response of model Preisach collections of two-level subsystems under the same field and temperature protocols used to probe experimentally the relaxation dynamics of spin glasses, we have been able to show that aging, memory and rejuvenation effects are ubiquitous features of all materials which possess a broad distribution of free energy barriers which block the approach to thermal equilibrium. (2) We propose a general strategy for isolating and quantifying the two principal mechanisms, thermal fluctuations and barrier growth, which are jointly responsible for shaping the measured temperature dependence of the magnetic properties of all magnetic materials which exhibit a history dependent response to an external field excitation, and is based on the analysis of viscosity isotherms and, in particular, on a plot of T ln(tr/0) versus Ha , where tr is the time at which a viscosity isotherm measured in a field Ha at temperature T reverses sign. When thermal activation dominates barrier growth, this plot will yield a universal curve while, in the opposite limit the plot fractures into a family of isothermal curves. The strategy is applied to the analysis of each magnetic material listed above. / February 2009

Chemically and physically patterned surfaces can be used as templates to guide nano- and micro- scale particle assembly, but the design is often limited by an inability to sufficiently characterize how pattern features influence local particle-surface interactions on the order of thermal energy, kT. The research outlined in this dissertation describes comprehensive optical microscopy (i.e. evanescent wave, video) measurements and analyses of many-body and multi-dimensional interactions, dynamics and structure in inhomogeneous colloidal fluid systems. In particular, I demonstrate how non-intrusive observation of an ensemble of particles diffusing past each other and over a physically patterned surface topography can be used to obtain sensitive images of energy landscape features. I also link diffusing colloidal probe dynamics to energy landscape features, which is important for understanding the temporal imaging process and self-assembly kinetics. A complementary effort in this dissertation investigated the use of external AC electric fields to reversibly tune colloidal interactions to produce metastable ordered configurations. In addition, the electrical impedance spectra associated with colloidal assemblies formed between interfacial microelectrode gaps was measured and consistently modelled using representative equivalent circuits. Significant results from this dissertation include the synergistic use of the very same colloids as both imaging probes and building blocks in feedback controlled selfassembly on patterns. Cycling the AC field frequencies was found to be an effective way to anneal equilibrium colloidal configurations. Quantitative predictions of dominant transport mechanisms as a function of AC electric field amplitude and frequency were able to consistently explain the steady-state colloidal microstructures formed within electrode gaps observed using video microscopy. A functional electrical switch using gold nanoparticles was realized by reversibly forming and breaking colloidal wires between electrode gaps. Extension of the concepts developed in this dissertation suggest a general strategy to engineer the assembly of colloidal particles into ordered materials and controllable devices that provide the basis for numerous emerging technologies (e.g. photonic crystals, nanowires, reconfigurable antennas, biomimetic materials).

The central concern of this thesis is the study of non-equilibrium behaviour in magnetic materials and its interpretation within the framework of the Preisach model of hysteresis. Comprehensive experimental characterizations of the field and temperature and time dependence of a suite of standard magnetic response functions have been performed on a variety of magnetic materials, including a naturally occurring mineral of nanodimensional titanomagnetite particles embedded in volcanic glass, a compressed powder of nanodimensional magnetite particles immobilized in an organic binder, a thin film of nanodimensional Fe particles embedded in alumina, and a series of sintered, bond-disordered CaxSr1-xRuO3 ferromagnets. The measurements were compared with numerical simulations based on a model Preisach ensemble of thermally activated two-level subsystems, characterized individually by a double well free energy profile in a two-dimensional configuration space, an elementary moment reversal, a dissipation field and a bias field, and characterized collectively by a distribution of these characteristic fields. Our efforts were concentrated on two principal spheres of investigation. (1) By performing detailed numerical simulations of the relaxation response of model Preisach collections of two-level subsystems under the same field and temperature protocols used to probe experimentally the relaxation dynamics of spin glasses, we have been able to show that aging, memory and rejuvenation effects are ubiquitous features of all materials which possess a broad distribution of free energy barriers which block the approach to thermal equilibrium. (2) We propose a general strategy for isolating and quantifying the two principal mechanisms, thermal fluctuations and barrier growth, which are jointly responsible for shaping the measured temperature dependence of the magnetic properties of all magnetic materials which exhibit a history dependent response to an external field excitation, and is based on the analysis of viscosity isotherms and, in particular, on a plot of T ln(tr/0) versus Ha , where tr is the time at which a viscosity isotherm measured in a field Ha at temperature T reverses sign. When thermal activation dominates barrier growth, this plot will yield a universal curve while, in the opposite limit the plot fractures into a family of isothermal curves. The strategy is applied to the analysis of each magnetic material listed above.

The central concern of this thesis is the study of non-equilibrium behaviour in magnetic materials and its interpretation within the framework of the Preisach model of hysteresis. Comprehensive experimental characterizations of the field and temperature and time dependence of a suite of standard magnetic response functions have been performed on a variety of magnetic materials, including a naturally occurring mineral of nanodimensional titanomagnetite particles embedded in volcanic glass, a compressed powder of nanodimensional magnetite particles immobilized in an organic binder, a thin film of nanodimensional Fe particles embedded in alumina, and a series of sintered, bond-disordered CaxSr1-xRuO3 ferromagnets. The measurements were compared with numerical simulations based on a model Preisach ensemble of thermally activated two-level subsystems, characterized individually by a double well free energy profile in a two-dimensional configuration space, an elementary moment reversal, a dissipation field and a bias field, and characterized collectively by a distribution of these characteristic fields. Our efforts were concentrated on two principal spheres of investigation. (1) By performing detailed numerical simulations of the relaxation response of model Preisach collections of two-level subsystems under the same field and temperature protocols used to probe experimentally the relaxation dynamics of spin glasses, we have been able to show that aging, memory and rejuvenation effects are ubiquitous features of all materials which possess a broad distribution of free energy barriers which block the approach to thermal equilibrium. (2) We propose a general strategy for isolating and quantifying the two principal mechanisms, thermal fluctuations and barrier growth, which are jointly responsible for shaping the measured temperature dependence of the magnetic properties of all magnetic materials which exhibit a history dependent response to an external field excitation, and is based on the analysis of viscosity isotherms and, in particular, on a plot of T ln(tr/0) versus Ha , where tr is the time at which a viscosity isotherm measured in a field Ha at temperature T reverses sign. When thermal activation dominates barrier growth, this plot will yield a universal curve while, in the opposite limit the plot fractures into a family of isothermal curves. The strategy is applied to the analysis of each magnetic material listed above.

De récentes études expérimentales de la dynamique de colloïdes illuminés par une figure d'interférence optique aléatoire (tavelures ou speckle) ont montré l'existence de phénomènes de sous-diffusion, de piégeage, ou de ségrégation dans le cas de mélanges, sous l'effet de cet environnement désordonné. L'objet de ce travail de doctorat est d'approfondir la compréhension de ces phénomènes par une étude théorique. Dans ce but, une version de la théorie de couplage de modes (MCT), initialement développée pour les fluides confinés dans des solides poreux désordonnés, a été appliquée au cas d'un fluide plongé dans un potentiel aléatoire gaussien de covariance gaussienne. La résolution numérique des équations asymptotiques de cette théorie a permis la construction de diagrammes d'état, lesquels reproduisent, par exemple, le comportement réentrant non trivial de la diffusivité observé dans les expériences, dont une interprétation physique simple est proposée.Les résultats suggèrent en outre une forte dépendance de la dynamique du système par rapport à la longueur de corrélation du désordre. Une étude détaillée de la relaxation du fluide a été effectuée, dans le but d'apporter une compréhension de la dynamique à toutes les échelles de temps. En parallèle, il a été montré que de nombreuses approximations classiques utilisées dans le calcul des propriétés structurales des fluides conduisent à des résultats non physiques dans le cas présent.Finalement, un programme de simulation Monte Carlo a été développé, et les premiers résultats sont comparés à la théorie et aux expériences. / Recent experimental studies of the dynamics of colloids beamed by a random light pattern (speckle) showed the existence of subdiffusion, trapping, or mixture separation phenomena, under the action of that disordered environment.To this end, a version of the Mode Coupling Theory (MCT), initially developed for fluids in confinement in sol id porous matrices has been applied to the case of a fluid plunged in a random Gaussian potential with a Gaussian correlation function.The aim of this PhD work is to further improve the understanding of these phenomena by the addition of a theoretical study.The numerical resolution of the asymptotic equations of this theory leads to the construction o phase diagrams, which reproduce for example the non trivial reentrent behaviour of the diffusivity, observed in related experiments, for which a physical interpretation is proposed. Furthermore, results suggest a strong depend ence of the dynamics on the disorder correlation length. A detailed study of the relaxation of the fluid has been made, in order to bring an understandin( of the dynamics at ali timescales. Simultaneously, it has been showed that a number of common approximations used in the calculation of the structural properties of fluids lead in the present case to non-physical results. Finally, a Monte-Carlo simulation program has been developed, and the first results are compared to theory and experiments.

In calculating the time evolution of an atomic system on diffusive timescales, off-lattice kinetic Monte Carlo (OLKMC) can sometimes be used to overcome the limitations of Molecular Dynamics. OLKMC relies on the harmonic approximation to Transition State Theory, in which the rate of rare transitions from one energy minimum to a neighboring minimum scales exponentially with an energy barrier on the potential energy surface. This requires locating the index-1 saddle point, commonly referred to as a transition state, that separates two neighboring energy minima. In modeling the evolution of an atomic system, it is desirable to find all the relevant transitions surrounding the current minimum. Due to the large number of minima on the potential energy surface, exhaustively searching the landscape for these saddle points is a challenging task. In examining the particular case of isolated Lennard-Jones clusters of around 50 particles, we observe very slow convergence of the total number of saddle points found as a function of successful searches. We seek to understand this behavior by modeling the distribution of successful searches and sampling this distribution to create a stochastic process that mimics this behavior. Finally, we will discuss an improvement to a rejection scheme for OLKMC where we terminate searches that appear to be failing early in the search process.