Dynamic properties of Josephson junctions are interesting due to the emission of high frequency radiation (up to THz range) from Josephson junctions, closely related to fluxon dynamics. A better understanding of this dynamics can help to improve the Josephson devices used for applications. Josephson junctions can also be of great use as T-shaped multiple Josephson junctions in Josephson electronic circuits. In general, T-junctions consist of two attached Josephson transmission lines: a main Josephson transmission line (MJTL) along the -axis, and an additional Josephson transmission line (AJTL) along the -axis. These junctions can use to create fluxons (solitons) in junctions without applied magnetic field, (called flux cloning phenomenon). This work is devoted to contributing to a clarification of the dynamic behaviour of solitons (fluxons) in 2D extended conventional T-shaped Josephson junctions (extended means an AJTL is larger than MJTL). A conventional T-junction is a MJTL along the x-axis which divides into two Josephson transmission lines along the x- and y-axes. In addition, we also attempt to elucidate further the concept of flux cloning in rotated T-junctions, which are 90 degrees anticlockwise rotation of conventional T-junction. In rotated Tjunction, a MJTL along the x-axis divide into two Josephson transmission lines along the y-axis. We find the first evidence of moving semifluxon and observe for the first time new phenomena of semifluxons and anti-semifluxons in both extended conventional and rotated T-junctions. We numerically study the electrodynamics behaviour of solitons in the standard Tshaped Josephson junction (conventional T-junction) in a magnetic field. Therefore, we describe theoretically how flux cloning circuits exist and give an opportunity for use as flux flow oscillators operating without applied magnetic field. The results that emerge give further support to the flux cloning mechanism.

The surface (photosphere) of the Sun is threaded throughout by magnetic fields. Groups of magnetic fields form magnetic features (of a wide range of sizes in flux and area) on the surface where the fields are directed into or out of the Sun. The aim of this thesis is to examine in detail the four key processes, emergence, cancellation, fragmentation and coalescence, which determine the behaviour of small-scale magnetic features, in the Sun's photosphere. I identify features in both Hinode/NFI and SOHO/MDI full-disk to enable these processes to be examined at the currently smallest observable scales and over an entire solar cycle. The emerging event frequency versus flux distribution, for intranetwork emerging regions to active regions, is found to follow a power-law distribution with index -2.50, which spans nearly 7 orders of magnitude in flux (10¹⁶ - 10²³ Mx) and 18 orders of magnitude in frequency. The global rate of flux emergence is found to be 3.9 x 10²⁴ Mx day⁻¹. Since the slope of all emerged fluxes is less than -2 this implies that most of the new flux that is fed into the solar atmosphere is from small-scale emerging events. This single power-law distribution over all emerged fluxes suggest a scale-free dynamo, therefore indicating that in addition to dynamo actions in the tachocline producing sunspots, a turbulent dynamo may act throughout the convection zone. Similarly for cancellations I find a power-law relationship between the frequency of cancellation and the peak flux lost per cancelling event (for events detected in both Hinode/NFI and SOHO/MDI full-disk), with slope -2.10. Again, the process of cancellation appears to be scale free and the slope is less than -2 indicating that numerous small-scale features are cancelling the majority of flux on the Sun. I also estimate the frequency of all surface processes at solar maximum and find, 1.3 x 10⁸, 4.5 x 10⁷, 4.0 x 10⁷ and 3.6 x 10⁶ events per day over the whole surface for emergence, cancellation, fragmentation and coalescence events, respectively. All the surface processes are found to behave in a similar manner over all flux scales. The majority of events for all processes occur in features with flux below 10²º Mx, which highlights the dynamic nature of the magnetic carpet. Using SOHO/MDI full-disk data I investigate the cyclic variation of the 4 key processes throughout cycle 23. It is found that the rate of emerging events, cancellations, fragmentations and coalescences varied in anti-phase with the solar cycle by factors of 3.4, 3.1, 2.4 and 2.2, respectively over the cycle. Not surprisingly, therefore, the number of network features detected throughout the cycle also exhibits an anti-phase variation over the solar cycle by a factor of 1.9. The mean peak flux of tracked small-scale network, fragmenting, coalescing and cancelling features showed in-phase relationships with the solar cycle by factors of 1.4, 1.7, 2.4 and 1.2, respectively. The total flux which is emerged and cancelled by small-scale events, varied in anti-phase with the solar cycle, by factors of 1.9 and 3.2. This is clearly due to the variation in the number of emerging and cancelling events and the fact that the flux of individual emerging events showed no cyclic variation. The results in this thesis show that the large-scale solar cycle plays a complex role in the surface processes features undergo. The fact that the number of ephemeral regions emerging has an anti-phase variation to the solar cycle has a knock-on effect in the number of features which are available to undergo surface processes. Also decaying active regions, during more active periods, contribute more small-scale features, with high flux density, into the network which has an effect on the surface processes. This work has revealed the significant importance of small-scale features in the flux budget through continual emergence and cancellation, plus highlighted how through dynamic surface motions, small-scale features form the fundamental components with which the network is developed.

Numerical experiments assuming land-use distributions of different heterogeneity of wet and dry surfaces were performed on a cloudy day in spring with a calm wind to examine their influences on the domain-averaged fluxes as well as on the distribution of the fluxes within the domain. The results substantiate that, for ]arge heterogeneity, i.e., small patches, the distribution of the patches plays no role in the magnitude of the atmospheric fluxes. For !arger patches, however, the domain-averaged latent heat-fluxes depend appreciably on both the heterogeneity as well as on the fractional coverage by the land-use types. On the average, for heterogeneous conditions, the prevailing land-use type governs the fluxes. Nevertheless, no exact linearity between the fractionally coverage of the two land-use types and the resulting fluxes exists. Discontinuities in the fluxes which lead to the non-linear behaviour of the domain-averaged fluxes occur at the border between two !arger areas of extremely different characteristics, namely, grass (wet, cool) and sand (dry, warm). Three different patterns of behaviour are found for the temporal development of the differences in the domain-averaged fluxes which depend on both the heterogeneity and the pattern of the land use. / Numerische Experimente, bei denen unterschiedlich heterogene Landnutzungsverteilungen trockener und feuchte Flächen angenommen werden, wurden für einen wolkigen Schwachwindtag im Frühjahr durchgeführt. Die Ergebnisse belegen, daß bei großer Heterogenität, d.h. kleinen Flächen, deren Anordnung keine Rolle spielt. Bei großen Flächen jedoch hängen die Gebietsmittelwerte der latenten Wärmeflüsse merklich sowohl von der Heterogenität als auch von dem Flächenanteil der Landnutzung ab. Im Mittel beherrscht der vorherrschende Landnutzungstyp die Flüsse. Dennoch ist kein exaktes lineares Verhalten zwischen dem Flächenanteil der Landnutzung und den resultierenden Flüssen vorhanden. Diskontinuitäten in der Verteilung der Flüsse, die letztendlich zu der Nichtlinearität der Gebietsmittelwerte der Flüsse führen, treten an den Grenzen der größeren Flächen unterschiedlicher Oberflächencharakteristika auf, in dieser Studie Gras (feucht, kühl) und Sand (trocken, warm). Drei unterschiedliche Verhaltensweisen im zeitlichen Verlauf der Differenzen der Gebietsmittelwerte der Flüsse wurden gefunden, die vom Muster und der Heterogenität der Landnutzung abhängen.

Le rôle central du phytoplancton à la base de la chaîne trophique aquatique motive une compréhension étayée des facteurs pouvant faire varier les populations et la composition des populations de phytoplancton. Cette compréhension est d'autant plus importante dans le contexte actuel, puisque nous savons que l'humain influence le climat et les milieux aquatiques par sa présence et ses activités. Nous tentons donc, dans notre étude, de déterminer les variables environnementales importantes qui dictent les changements de taille et de composition de la communauté de phytoplancton à l'échelle d'un lac et d'en déduire les niches réalisées des différentes espèces du lac. L'utilisation d'une station mobile de manière verticale dans le lac Montjoie (Saint-Denis-de-Brompton) a permis de collecter des données in situ à haute fréquence et résolution temporelle caractérisant la colonne d'eau. Combinée à ces mesures, une banque de données sur l'abondance de différentes catégories de phytoplancton a été créée à l'aide d'un cytomètre en flux imageur (IFCB) et d'un programme de reconnaissance d'images qui lui est associé. En combinant ces données nous avons déterminé que la température moyenne au-dessus de la thermocline et que la profondeur limite de chlorophylle (2 écarts-types sous le maximum de chlorophylle) étaient les 2 variables (parmi les variables mesurées) les plus appropriées pour déterminer les niches réalisées de nos catégories de phytoplancton. À l'aide de ces 2 variables, nous avons pu déterminer les niches réalisées d'une trentaine de catégories présentes dans notre lac. Les niches ont été déterminées à la fois sur les données d'abondance et sur les données de taux de croissance nette à l'aide de deux méthodes différentes, soit l'analyse canonique des correspondances (CCA) et la maximisation de l'entropie d'information (MaxEnt). Ce sont finalement les niches déterminées avec les taux de croissance nette qui sont les plus pertinentes. Les deux méthodes ont donné des résultats semblables, mais c'est MaxEnt qui est la plus versatile pour l'ajout de nouvelles variables explicatives et c'est donc celle-ci que nous privilégierons dans le futur.

Die Surface Renewal Analysis wurde zur Bestimmung sensibler Wärmeflußdichten im bodennahen Bereich der atmosphärischen Grenzschicht genutzt und mit der Eddy - Korrelations - Methode verglichen. Dazu wurden beide Berechnungsmethoden auf Temperatur - und Vertikalwinddaten angewandt, die unter Verwendung von Strukturfunktionen simuliert wurden. Zur Überprüfung der Resultate wurden über zwei verschiedenen Unterlagen (Wiese und Düne) hochfrequente Zeitreihen von Temperatur und Vertikalwind gemessen und mit der Surface Renewal Analysis und der Eddy - Korrelations - Methode analysiert. / The Surface Renewal Analysis was used to estimate the sensible heat flux density in the ground near area of the boundary layer. The results were compared with eddy correlation method. For it both methods were used to analyse temperature- and vertical velocity-data, which were simulated by the application of structure functions. Time series of high frequency temperature- and vertical velocity-data over two different canopies (meadow and dune) were measured to examine the results. The data were analysed with surface renewal analysis and eddy correlation.

Due to the relatively small amount of work concerning radiation, it was thought feasible to use ionizing radiation as a tool to study the relationship between water and salt flux in isolated root systems. Moreover, the more quantitative potometric method lends itself well to such a study, since the two processes can be followed simultaneously. the aims of this study, therefore, were 1) to determine effects of X-irradiation on water, calcium and potassium flux in excised onion roots; 2) to determine the dose levels required for producing permeability changes; 3) to investigate the nature of radiation damage to root systems; and 4) to attempt to shed light on the relation between water transport and ion movement in root systems.

Inductively Coupled Plasma (ICP) facilities create high enthalpy ows to recreate atmospheric entry conditions. Although no condition has been duplicated exactly in a ground test facility, it is important to characterize the condition to understand how close a facility can come to doing so. An ICP facility was constructed at the University of Vermont for aerospace material testing in 2010. The current setup can operate using air, carbon dioxide, nitrogen, and argon to test samples in a chamber. In this work we investigate di erent ways to increase measured heat ux and expand our facility to operate supersonically. To do so, a water cooled injection system was designed to overcome failure points of the prior system. An investigation of heat ux methods that provide a baseline for the facility were also examined and tested. A nozzle con guration was also developed with an overall goal of increasing the plasma ow to reach sonic and supersonic velocities, allowing it to be compared with the existing subsonic system. An iterative approach was taken to develop a nozzle design that is robust enough to handle the harsh environment, yet adaptable to the pre-existing facility components. The current design uses interchangeable sonic and supersonic nozzles which also allow for appropriate plasma gas expansion. Data are taken through retractable and goose-neck probe sample holders during testing. Heat ux can be determined by use of a Gardon gage, slug calorimeter, and water cooled calorimeter. Total and static pressure are determined from a pitot tube and pressure tap, which are then manipulated into a velocity measurement. A comparison between subsonic and supersonic operation is then made with these data. Existing literature uses correlations between jet diameter and velocity gradients to determine the e ective heat ux. This investigation found that the experimental and theoretical heat ux results scale correctly according to the correlations.

Gravitational lensing studies the distortions of a distant galaxy’s observed size, shape or flux due to the tidal bending of photons by matter between the source and observer. Such distortions can be used to infer knowledge on the mass distribution of the intervening matter, such as the dark matter halos in which clusters of individual galaxies may reside, or on cosmology through the statistics of the matter density of large scale structure and geometrical factors. In particular, gravitational lensing has the advantage that it is insensitive to the nature of the lensing matter. However, contamination of the signal by correlations between galaxy shape or size and local environment complicate a lensing analysis. Further, measurement of traditional lensing estimators is made more difficult by limitations on observations, in the form of atmospheric distortions or optical limits of the telescope itself. As a result, there has been a large effort within the lensing community to develop methods to either reduce or remove these contaminants, motivated largely by stringent science requirements for current and forthcoming surveys such as CFHTLenS, DES, LSST, HSC, Euclid and others. With the wealth of data from these wide-field surveys, it is more important than ever to understand the full range of independent probes of cosmology at our disposal. In particular, it is desirable to understand how each probe may be used, individually and in conjunction, to maximise the information of a lensing analysis and minimise or mitigate the systematics of each. With this in mind, I investigate the use of galaxy clustering measurements using photometric redshift information, including a contribution from flux magnification, as a probe of cosmology. I present cosmological forecasts when clustering data alone are used, and when clustering is combined with a cosmic shear analysis. I consider two types of clustering analysis: firstly, clustering with only redshift auto-correlations in tomographic redshift bins; secondly, clustering using all available redshift bin correlations. Finally, I consider how inferred cosmological parameters may be biased using each analysis when flux magnification is neglected. Results are presented for a Stage–III ground-based survey, and a Stage–IV space-based survey modelled with photometric redshift errors, and values for the slope of the luminosity function inferred from CFHTLenS catalogues. I find that combining clustering information with shear gives significant improvement on cosmological parameter constraints, with the largest improvement found when all redshift bins are included in the analysis. The addition of galaxy-galaxy lensing gives further improvement, with a full combined analysis improving constraints on dark energy parameters by a factor of > 3. The presence of flux magnification in a clustering analysis does not significantly affect the precision of cosmological constraints when combined with cosmic shear and galaxy-galaxy lensing. However if magnification is neglected, inferred cosmological parameter values are biased, with biases in some cosmological parameters found to be larger than statistical errors. We find that a combination of clustering, cosmic shear and galaxy-galaxy lensing can provide a significant reduction in statistical errors from each analysis individually, however care must be taken to measure and model flux magnification. Finally, I consider how measurements of galaxy size and flux may be used to constrain the dark matter profile of a foreground lens, such as galaxy- or galaxy-cluster-dark matter halos. I present a method of constructing probability distributions for halo profile free parameters using Bayes’ Theorem, provided the intrinsic size-magnitude distribution may be measured from data. I investigate the use of this method on mock clusters, with an aim of investigating the precision and accuracy of returned parameter constraints under certain conditions. As part of this analysis, I quantify the size and significance of inaccuracies in the dark matter reconstruction as a result of limitations in the data from which the sample and size-magnitude distribution is obtained. This method is applied to public data from the Space Telescope A901/902 Galaxy Evolution Survey (STAGES), and results are presented for the four STAGES clusters using measurements of source galaxy size and magnitude, and a combination of both. I find consistent results with existing shear measurements using measurements of galaxy magnitudes, but interesting inconsistent results when galaxy size measurements are used. The simplifying assumptions and limitations of the analysis are discussed, and extensions to the method presented.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Metabolites consumed and produced by microorganisms for mass and energy conservation may cause changes in a microorganism’s environment. The microorganisms are unable to tolerate a particular environment for a long period. They may leave their old existence to find a new environment to sustain life. Essentially, organisms need to maintain their metabolic processes to survive in the new environment. Limitations of experimental studies to explore cell functions and regulations in detail result in insufficient information to explain processes of metabolic expressions under environments of organisms. Consequently, mathematical modeling and computer simulations have been conducted to combine all possible cellular metabolic fluxes into single or multiple connected networks. Metabolic modeling based on linear programming (LP) subjected to constraints with an optimization approach is often applied metabolic reconstruction. The LP objective function is maximized to obtain an optimal value of biomass flux. Optimal solutions in LP problems can be used to explain how metabolites function in metabolic reactions. As an LP problem may have many optimal solutions, this study proposes a method for enumerating all alternate optimal solutions to evaluate important reactions of metabolic pathways in microorganisms. The algorithm for generating alternate optimal solutions is implemented in MetModelGUI, a Java-based software for creating and analyzing metabolic reconstructions. The algorithm is applied to models of five microorganisms: Trypanosoma cruzi, Thermobifida fusca, Helicobacter pylori, Cryptococcus neoformans and Clostridium thermocellum. The results are analyzed using principal component analysis, and insight into the essential and non-essential pathways for each organism is derived