The fundamental components for processing all-optically represented data, namely optical switches and logic gates are investigated. Improved techniques for fabricating nonlinear Fabry-Perot etalons containing GaAs have brought a proliferation of GaAs optical bistable devices. These devices show significant improvements in speed, power requirements, operating temperature and thermal stability. Experiments verify predictions that one can operate a single nonlinear etalon as optical logic gates or two such etalons as a flip-flop. Optimization of the logic gates is then discussed from a systems approach.

<p>How organisms adapt and survive in continuously fluctuating environments is a central question of evolutionary biology. Additionally, organisms have to deal with the inherent stochasticity in all cellular processes. The purpose of this thesis is to gain insights into how organisms can use epigenetics and the stochasticity of gene expression to deal with a fluctuating environment. To accomplish this, two cases at different temporal and structural scales were explored: (1) the early transcriptional response to an environmental stimulus in single cells, and (2) the evolutionary dynamics of a population adapting to a recurring fluctuating environment. Mathematical models of stochastic gene expression, population dynamics, and evolution were developed to explore these systems.</p><p>First, the information available in sparse single cell measurements was analyzed to better characterize the intrinsic stochasticity of gene expression regulation. A mathematical and statistical model was developed to characterize the kinetics of a single cell, single gene behavior in response to a single environmental stimulus. Bayesian inference approach was used to deduce the contribution of multiple gene promoter states on the experimentally measured cell-to-cell variability. The developed algorithm robustly estimated the kinetic parameters describing the early gene expression dynamics in response a stimulus in single neurons, even when the experimental samples were small and sparse. Additionally, this algorithm allowed testing and comparing different biological hypotheses, and can potentially be applied to a variety of systems.</p><p>Second, the evolutionary adaptation dynamics of epigenetic switches in a recurrent fluctuating environment were studied by observing the evolution of gene regulatory circuit in a population under multiple environmental cycles. The evolutionary advantage of using epigenetics to exploit the natural noise in gene expression was tested by competing this strategy against the classical genetic adaptation through mutations in a variety of evolutionary conditions. A trade-off between minimizing the adaptation time after each environmental transition and increasing the robustness of the phenotype during the constant environment between transitions was observed. Surviving lineages evolved bistable, epigenetic switching to adapt quickly in fast fluctuating environments, whereas genetic adaptation with high robustness was favored in slowly fluctuating environments.</p> / Dissertation

Chez B. subtilis, le régulateur Mta régule l'expression de deux gènes codant pour des pompes d'efflux de drogues, bmr et blt. Ce régulateur joue un rôle physiologique beaucoup plus large que la régulation des gènes impliqués dans la résistance aux drogues puisqu'il régule l'expression d'au moins 18 autres gènes. Dans un mutant mta la quantité de protéine CpgA est très diminuée. Cette protéine est une GTPase impliquée dans l'assemblage du ribosome et dans la formation de la paroi. Cette diminution est supprimée par une mutation secondaire qui restaure un niveau intracellulaire de CpgA supérieur à celui de la souche sauvage. Cette mutation confère également un avantage de croissance, sur la souche sauvage et sur le mutant mta, au double mutant résultant. L'augmentation de la quantité de CpgA est corrélée avec l'augmentation du niveau d'expression du gène cpgA ainsi que de celui des gènes def et prpC avec lesquels cpgA est en opéron. Le gène def code pour une déformylase, une protéine impliquée dans la traduction, et prpC pour une Ser/Thr phosphatase capable de déphosphoryler CpgA. Dans le mutant supprimé, la surexpression de l'opéron def-cpgA est accompagnée d'un phénotype drastique de cellules enchaînées et immobiles en phase exponentielle de croissance (phénotype Mhp). Ces cellules contiennent le facteur alternatif de transcription SigD nécessaire à l'expression des gènes dont les produits sont impliqués dans la mobilité cellulaire et dans le clivage des septa lors de la division cellulaire, mais SigD est inactif dans ces cellules (SigD OFF). / In B. subtilis, the regulator Mta regulates the expression of two genes encoding drug efflux pumps, bmr and blt. This regulator has a physiological role far wider than the regulation of genes involved in resistance to drugs since it regulates the expression of at least 18 other genes. In a mta mutant, the amount of the CpgA protein is markedly reduced. This protein is a GTPase involved in ribosome assembly and in cell wall expansion. This decrease is suppressed by a secondary mutation that restores a higher level of intracellular CpgA than that of the wild type strain. This mutation also confers a growth advantage to the resulting double mutant over the wild type and the mta mutant strains. The increased amount of CpgA is correlated with increased level of cpgA gene expression and of the prpC and def genes with which cpgA is in operon. The def gene encodes a deformylase, a protein involved in translation, and prpC for a Ser / Thr phosphatase able to dephosphorylate CpgA. In the double mutant, overexpression of the def-cpgA operon is accompanied by a drastic phenotype of chained non-motile cells in the exponential phase of growth (Mhp phenotype). These cells contain SigD, an alternative sigma factor, necessary for the expression of genes whose products are involved in cell motility and in the cleavage of septa during cell division, but SigD is inactive in these cells (SigD OFF). In exponential growth phase, a wild type strain of B. subtilis shows a heterogeneous population consisting of cells SigD ON, motile and isolated, and cells SigD OFF, chained and non-motile. In the mta strain, the transition from one state to another is reversible as in the wild type strain.

Este trabalho apresenta um estudo acerca dos principais parâmetros que caracterizam o fenômeno da biestabilidade em dois tubos dispostos lado a lado submetidos a escoamento cruzado turbulento. A técnica experimental da anemometria de fio quente em canal aerodinâmico é aplicada na medição das flutuações de velocidade do escoamento após os tubos. As séries temporais obtidas são utilizadas como dados de entrada para determinação das funções densidade de probabilidade (PDF) usando um modelo de mistura finita, de acordo com uma função t de Student assimétrica e com o auxílio do método de Monte Carlo. Transformadas de ondaletas discretas e contínuas são aplicadas na filtragem das séries temporais para determinadas bandas de frequências e na análise do conteúdo de energia destes sinais. Através de conceitos de sistemas caóticos, é realizada a reconstrução do atrator do problema pelo método dos atrasos temporais, a partir das séries experimentais de velocidade, permitindo a determinação da dimensão de imersão e o cálculo do maior expoente de Lyapunov. Os resultados mostram a existência de dois patamares distintos de velocidade média nas séries temporais, correspondentes aos dois modos do escoamento, cada qual com números de Strouhal e funções densidade de probabilidade distintas. Uma análise conjunta das componentes axial e transversal do escoamento e suas PDF indicam as regiões no plano de medições onde o fenômeno se manifesta, sendo que reconstruções da trajetória filtrada das séries temporais para determinadas bandas de frequências apresentam características caóticodeterminísticas. O maior expoente de Lyapunov das séries experimentais é positivo, o que é um indício de comportamento caótico. / This work presents a study of the main parameters that characterize the phenomenon of bistability in two tubes placed side by side submitted to turbulent crossflow. The experimental technique of hot wire anemometry in aerodynamic channel is applied in the measurement of velocity fluctuations of the flow after the tubes. The time series obtained are used as input data for determining the probability density functions (PDF) using a finite mixture model, according to an asymmetric Student t function and with the aid of a Monte Carlo method. Wavelet transforms are applied in discrete and continuous filtering of time series for certain frequency bands and in the analysis of the energy content of these signals. By means of chaotic systems concepts, the attractor reconstruction of the problem is performed using the method of time delays from the experimental series of velocity, allowing the determination of the embedding dimension and calculating the largest Lyapunov exponent. The results show the existence of two different levels of mean velocity in time series, corresponding to two flow modes, each one with different Strouhal numbers and probability density functions. A joint analysis of axial and transverse components of flow and its PDF indicate the regions in the measurement plan where the phenomenon is manifested, and reconstructions of the trajectory of the filtered time series for certain frequency bands have chaotic-deterministic characteristics. The largest Lyapunov exponent of experimental series is positive, which is an indication of chaotic behavior.

Este trabalho apresenta um estudo experimental acerca da influência da razão de espaçamento e da intensidade de turbulência no escoamento biestável. É estudado o escoamento sobre dois cilindros dispostos lado a lado, para o canal aerodinâmico com intensidade de turbulência inferior a 1%, para o canal aerodinâmico com grade promotora de turbulência com intensidade de turbulência de 8 a 7%, e para uma seção do canal aerodinâmico sem paredes laterais. A técnica experimental aplicada consiste na medição das flutuações de velocidade no canal aerodinâmico utilizando a técnica da anemometria de fio quente. As medições são realizadas com duas sondas, uma fixa e outra móvel que foi posicionada em seis pontos diferentes do escoamento. Os dados medidos são tratados através de ferramentas estatísticas, análise espectral e transformadas de ondaletas. Os resultados confirmam a existência do fenômeno da biestabilidade e mostram como o fenômeno sofre alterações quando exposto às condições de maior intensidade de turbulência e redução da razão de bloqueio pela retirada das paredes laterais em uma seção do canal. Para a condição de maior intensidade de turbulência, os resultados mostram que as trocas de modo se intensificam, e em alguns dos pontos de medição os sinais referentes à sonda móvel não apresentam características de biestabilidade. Para o caso sem paredes laterais, os sinais apresentam características de biestabilidade até o momento em que as paredes são removidas. / This work presents an experimental study, about the influence of the pitch to diameter ratio and the turbulence intensity on a bistable flow. The flow through two cylinders side-by-side is studied in an aerodynamic channel with turbulence intensity lower than 1%, in an aerodynamic channel with a turbulence grid, that increased the turbulence intensity to about 8 to 7%, and a section of the aerodynamic channel without lateral walls. The experimental technique consists in the measurements of the fluctuating velocities in the aerodynamic channel, using hot wire anemometry. The measurements are performed with two probes, one static, and one movable, positioned in six different points of the flow. The acquired data are analysed through statistical, spectral and wavelet tools. The results confirmed the occurrence of the bistable phenomenon and shows how it behaves when exposed to different conditions of turbulence intensity, and reduction of the blockage ratio aspect due to removal of the lateral walls of a channel section. The results for the higher turbulence intensity condition shows that the switches are intensified, some data resulting of the measurements of the second probe, do not show bistable characteristics. In the no-walls section case, the signals showed bistable features, until the moment the walls were removed.

Exciton-polaritons are the fundamental excitations arising from the strong coupling of quantum well excitons and cavity photons in semiconductor microcavities. They are compound bosons for which stimulated scattering and macroscopic occupation of single quantum states can occur at sufficiently high densities. One way of creating such polariton condensates is with nonresonant optical pumping. Doing so creates a large density of free- carriers and excitons that strongly interact and blueshift the polariton energy levels. Using spatially patterned nonresonant fields, the polariton potential landscape can be tailored and optically trapped condensates can be created. This thesis shows that the spin properties of polariton condensates are strongly modified by such trapping. Under linearly polarised pumping, helicity can spontaneously develop at a critical occupation, breaking the parity symmetry. This formation of spin-up/spin-down condensates is explained within a Gross-Pitaevskii model which accurately reproduces the influence of electric fields and condensate density. Under elliptically polarised pumping, two phenomena are observed: the formation of condensates with the opposite handedness to the pump and hysteresis of both occupation and spin with respect to pump power. The spatial dependence of these effects highlights the limitations of commonly used models of polariton condensation. Finally, the suitability of patterned optical fields for the creation of polariton lattices is explored. For small chains of condensates, controllable coupling between adjacent spins is demonstrated, with the formation of antiferromagnetic and ferromagnetic domains. The extent of these domains is strongly affected by sample nonuniformity, fundamentally limiting the scalability of these lattices.

With the recent discoveries of phenomena such as plateau potentials, bistability, and synaptic amplification the focus of motoneuron research has been directed to the dendritic processes giving rise to these latent behaviors. The common consensus is that the mechanism behind bistability (an L-type calcium channel generating a persistent inward current, PIC; Schwindt and Crill 1980, Hounsgaard and Kiehn 1985, 1989) is also responsible for the amplification of synaptic input in motoneurons. However, modeling studies utilizing only calcium-based PICs (Powers 1993, Booth et al. 1997, Elbasinouy et al. 2005) have been unable to reproduce the high degree of synaptic amplification observed in experimental preparations (Prather et al. 2001, Lee et al. 2003, Hultborn et al. 2003). The present work examines a theoretical amplification mechanism (electrotonic compression), based on a sodium PIC of dendritic origin, which acts to supplement the synaptic amplification due to the calcium PIC. The current goal is to test the "goodness-of-fit" of electrotonic compression with established mechanisms and behaviors. The findings of this modeling study support the concept of a dendritic sodium PIC which acts to reduce the attenuation of synaptic currents enroute to the motoneuron soma. Furthermore, it is suggested that the ratiometric expression of ion channels giving rise to this mechanism takes the form of a distribution "rule" applied ubiquitously across the dendritic tree, while the plateau-producing L-type calcium channels undergo a more discretized or regional distribution. This study demonstrates the power inherent to the controlled expansion of morphological complexity in an already complex model. While modeling studies are suitable testbeds for the evaluation of theoretical and/or experimentally intractable facets of physiology, great care and consideration should be given to the specification of models with high dimensionality. With the continual progression of our knowledge-base and computational capabilities, we can expect that more and more empirical observations will find their way into models of increasing complexity wherein the layers of embedded hypotheses are frequently implicit. It is therefore imperative that the neural modeling discipline adopt more rigorous methodologies to both accommodate and rein-in this growing complexity.

The opportunistic pathogen P. aeruginosa is a leading cause of hospital-accquired infections, and is also the primary cause of morbidity and mortality in patients with cystic fibrosis (CF). In this thesis, I describe the identification and characterization of a novel LysR-type transcription regulator (LTTR) of P. aeruginosa named BexR. I show that BexR exhibits reversible ON/OFF bistable expression, which leads to the bistable expression of several genes including one encoding a virulence factor. I present results suggesting that this bistable expression depends on positive feedback of BexR. This work illuminates the simplicity with which a transcription regulatory network can exhibit a complex behavior and generate phenotypic diversity in a clonal population.

In this thesis, a set of some prevailing rate-based models for bistable perception have been considered in order to find the implications of the novel results reported in Pastukhov & Braun (2011). These authors have quantified not only salient aspects of bistable perception (mean and dispersion of dominance distributions), but also some hidden hysteresis effects ignored up to now. Extensive computational simulations of different prevailing models rigorously demonstrate that the history-dependence of the perceptual process shown by Pastukhov & Braun (2011), effectively constrains the region of the parameter space able to replicate the empirical data. Concretely, that just small regions residing inside a bistable or two-attractor region of the whole parameter space are actually adequate to reproduce the experimental results, both for BR and KDE displays. Remarkably, the results remain valid across all the different classes of models considered, regardless the details of the neuronal implementation. The biological plausibility of the parameter region found for each of the models considered, is further stressed with respect to the widely known Levelt’s propositions. To that end, we make use of weighted sums across the parameter regions computed for each subject in the first part of this Thesis, an algorithm that constitutes an important improvement to the methodology proposed by Shpiro et al. (2007) to fit behavioral data by rate-based models. It is shown how different neuronal mechanisms clearly differ in their suitability to replicate Levelt’s propositions. For instance, models with a slow fatiguing process given by spike-frequency adaptation Wilson (2003); Shpiro et al. (2007), no matter if they are being described by linear Shpiro et al. (2007) or nonlinear Curtu et al. (2008)) functions of the activity, replicate quite well Levelt’s second law. Oppositely, a notable discrepancy between model and empirical results is found when such negative feedback is described as a long-term depression affecting the synapses between the competing neurons representing the two alternative interpretations Laing & Chow (2002); Shpiro et al. (2007). The present work finishes with a study about the capability of the mentioned models to reproduce the resonance effects happening when varying external frequencies, as shown by Kim et al. (2006). Importantly, a resonance respect to the noise dispersion (i.e., a true stochastic resonance ) is clearly demonstrated here for the first time. Previous estimations of noise dispersion (20 − 30% of the input) and its locus (adaptation variables) are questioned, by demonstrating that increased sensitivity to even weak signals of the order of less than 10% can be obtained with the models considered, with the noise variable simply entering as part of the net input feeding the neuron. / En este trabajo, son considerados una serie de modelos para frecuencia neuronal ampliamente aceptados en percepción bi-estable, con el objetivo de evaluar las implicaciones de los resultados recientemente reportados en Pastukhov & Braun (2011). Estos autores han cuantificado no solamente aspectos más conocidos sobre el fenómeno (media y dispersión de las distribuciones de dominancia), sino también efectos de historia que habían sido ignorados hasta el presente. Por medio de simulaciones computacionales, se demuestra rigurosamente que la dependencia de la historia del proceso perceptual encontrada por Pastukhov & Braun (2011) efectivamente restringe la región válida de parámetros que es adecuada para reproducir los datos empíricos. Concretamente, que solamente pequeñas regiones del espacio de parámetros disponible, y que se encuentran dentro de una región dinámica bi-estable caracterizada por dos atractores, son realmente adecuadas, tanto para rivalidad binocular (BR) como para estímulos de estructura por movimiento (KDE). Resulta importante destacar que los resultados permanecen válidos de un modelo a otro, independientemente de los detalles de implementación neuronal. La plausibilidad biológica de la región de parámetros encontrada para cada modelo es entonces considerada, en el contexto de las ampliamente conocidas proposiciones de Levelt. Con tal objetivo, hacemos uso de un algoritmo de suma pesada para extraer valores medios de la regiones de parámetros correspondientes a cada sujeto. Este algoritmo constituye una importante mejora a la metodología propuesta por Shpiro et al. (2007) para ajustar modelos de frecuencia neuronal a datos comportamentales de percepción bi-estable. Es entonces mostrado como cada mecanismo neuronal considerado es clara- mente diferente en su capacidad para reproducir las proposiciones de Levelt. Por ejemplo, modelos conteniendo procesos lentos de retroalimentación negativa da- dos por adaptación de frecuencia de disparo Wilson (2003); Shpiro et al. (2007), sin importar si están descritos por funciones lineales Shpiro et al. (2007) or no lineales Curtu et al. (2008)) de la actividad, consiguen reproducir de modo razonable la segunda proposición de Levelt. Por el contrario, una notable discrepancia entre modelo y resultados empíricos es encontrada cuando tales procesos están dados por la presencia de depresión sináptica de larga duración. El presente trabajo culmina con un estudio sobre la capacidad de los mencionados modelos para reproducir los efectos de resonancia que ocurren al variar la frecuencia externa de modulación Kim et al. (2006). Es de destacar que en nuestro caso, un efecto de resonancia es encontrado respecto a la dispersión del ruido, lo cual indica la presencia de una verdadera resonancia del tipo estocástico. Este efecto es claramente demostrado para estos modelos, por primera vez, en el presente trabajo. Previas estimaciones de la dispersión del ruido (20 − 30 % de la señal de entrada) y su localización (variables de adaptación) son analizadas. Se demuestra que un incremento de la sensibilidad a incluso muy pequeñas señales de menos del 10% puede ser encontrada en estos modelos, con sólo incluir la variable de ruido como parte de la corriente neta que alimenta la neurona.

Thesis (Ph.D.)--Ohio University, June, 2007. / Includes bibliographical references (leaves 186-191)