The work here presents two main parts. In the first part, chapters 1 – 3 focus on dynamical systems modeling in plant immunity, whereas chapters 4 – 6 describe contributions to computational modeling and analysis of proteomics and genomics data. Chapter 1 investigates dynamical and biochemical patterns of reversibly oxidized cysteines (RevOxCys) during effector-triggered immunity (ETI) in Arabidopsis, examines the regulatory patterns associated with Arabidopsis thimet oligopeptidase 1 and 2’s (TOP1 and TOP2), roles in the RevOxCys events during ETI, and analyzes the redox phenotype of the top1top2 mutant. The second chapter investigates the peptidome dynamics during ETI in wild-type (WT) and top1top2 mutant, introduces a novel method to learn the cleavage motif for TOPs and predicts and validates bioactive peptides association with TOPs activity. The third chapter examines gene expression dynamics during Systemic Acquired Resistance (SAR). Time-series clustering identifies unique oscillatory patterns in gene transcription associated with the early onset of SAR. It then describes a mathematical model using ordinary differential equations to represent WT's transcriptional dynamics. The second part of this dissertation explores imputation and statistical modeling for proteomics data analysis and proposes a network inference methodology for polymorphic cysteines. The fourth chapter analyzes the performance of linear models (limma) and the effect of imputation in proteomics data. It shows the advantage of data imputation over filtering and the benefit of using limma over t-test for the statistical decision of differences in means between conditions for different peptides, PTMs, etc. The fifth chapter proposes a statistical model for proteomics data analysis using mean-variance (M-V) trend modeling. It describes a gamma regression to model the dependency of the variance on the mean of observations. Finally, a Bayesian decision model is proposed; the model shows an improvement over existing methods in statistical decision performance. The sixth and final chapter describes a network inference procedure that identifies genetic dependencies between polymorphic cysteines. It models the interactions between cysteines (nodes) as signed edges for positive or inhibitory relations. It utilizes local network structures for inferences about the relationship between the cysteines. The algorithm exhibits stability and efficiency, converging rapidly to inferred solutions.

Dans ce mémoire de maîtrise, nous étudions l'asymptotique spectrale pour les problèmes d'oscillation de deux fluides incompressibles idéaux remplissant un volume arbitraire avec une surface supérieure ouverte ou fermée. Dans le premier chapitre, nous introduisons les notions de base de la géométrie spectrale, illustrons le problème de Steklov pour un fluide dans un volume arbitraire ainsi que les principaux résultats qui seront nécessaires pour comprendre et démontrer les énoncés du manuscrit. Nous dérivons également les principales relations et équations des petites oscillations d'un fluide incompressible idéal. La deuxième partie présente les principaux résultats sur les petites oscillations de deux liquides à surface supérieure fermée, obtenus par Solomyak, Kopachevsky et leurs collaborateurs, qui justifient et vérifient la cohérence des résultats pour le problème considéré. Finalement, nous traitons le problème avec une surface ouverte. Une question similaire a été abordée par Kuznetsov. Un canal rectangulaire rempli de deux liquides est un exemple révélateur vérifiant tous les principaux résultats de la recherche. Entre autres, nous avons trouvé un cas particulier intéressant dans lequel la famille de solutions correspondant au paramètre spectral disparaît. En conclusion, nous trouvons sur les conditions d'existence et l'unicité des solutions. / In this M.Sc. thesis, we investigate the spectral asymptotics for a problem describing oscillations of two ideal incompressible fluids filling an arbitrary volume with either open or closed upper surface. In the first chapter, we introduce the basic notions of spectral geometry and illustrate the Steklov problem for fluid in an arbitrary volume, as well as the main results needed to understand and prove the statements in the manuscript. We also derive the equations of small oscillations of an ideal incompressible fluid. The second part presents the main results on small oscillations of two liquids with a closed upper surface, obtained by Solomyak, Kopachevsky, and their collaborators that justify and verify the consistency of the findings for the problem under consideration. In the third chapter, we treat the problem with an open surface. A similar question was previously addressed by Kuznetsov. A rectangular channel filled with two liquids is a telling example that confirms all the main research results. Interestingly enough, we found a particular case in which the family of solutions corresponding to the spectral parameter disappears. In conclusion, we describe the condition of existence and the uniqueness of such solutions.

No description available.

A variety of factors such as increasing electrical energy demand, slow expansion of transmission infrastructures, and electric energy market deregulation, are forcing utilities and system operators to operate power systems closer to their design limits. Operating under stressed regimes can have a detrimental effect on the rotor-angle stability of the system. This stability reduction is often reflected by the emergence or worsening of poorly damped low-frequency electromechanical oscillations. Without appropriate measures these can lead to costly blackouts. To guarantee system security, operators are sometimes forced to limit power transfers that are economically beneficial but that can result in poorly damped oscillations. Controllers that damp these oscillations can improve system reliability by preventing blackouts and provide long term economic gains by enabling more extensive utilization of the transmission infrastructure. Previous research in the use of artificial neural network-based intelligent controllers for power system damping control has shown promise when tested in small power system models. However, these controllers do not scale-up well enough to be deployed in realistically-sized power systems. The work in this dissertation focuses on improving the scalability of intelligent power system stabilizing controls so that they can significantly improve the rotor-angle stability of large-scale power systems. A framework for designing effective and robust intelligent controllers capable of scaling-up to large scale power systems is proposed. Extensive simulation results on a large-scale power system simulation model demonstrate the rotor-angle stability improvements attained by controllers designed using this framework.

In this thesis we examine intra-seasonal oscillations (ISO) in the aqua-planet setup of the Community Atmospheric Model (CAM) version 5.1, mainly based on July and January climatological sea surface temperature (SST). We investigate mainly two questions -what should be the SST distribution for the existence of (a) northward moving ISO in summer, and (b) eastward moving MJO-like modes in winter. In the first part of the thesis we discuss the northward propagation. A series of experiments were performed with zonally symmetric and asymmetric SST distributions. The basic lower boundary condition is specified from zonally averaged observed July and January SST. The zonally symmetric July SST experiment produced an inter tropical convergence zone (ITCZ) on both sides of the equator. Poleward movement is not clear, and it is confined to the region between the double ITCZ. In July, the Bay of Bengal (BOB) and West Pacific SST is high compared to the rest of the northern tropics. When we impose a zonally asymmetric SST structure with warm SST spanning about 80 of longitude, the model shows a monsoon-like circulation, and some northward propagating convective events. Analysis of these events shows that two adjacent cells with cyclonic and anticyclonic vorticity are created over the warm SST anomaly and to the west. The propagation occurs due to the convective region drawn north in the convergence zone between these vortices. Zonally propagating Madden-Julian oscillations (MJO) are discussed in the second part of the thesis. All the experiments in this part are based on the zonally symmetric SST. The zonally symmetric January SST configuration gives an MJO-like mode, with zonal wave number 1 and a period of 40-90 days. The SST structure has a nearly meridionally symmetric structure, with local SST maxima on either side of the equator, and a small dip in the equatorial region. If we replace this dip with an SST maximum, the time-scale of MJO becomes significantly smaller (20-40 days). The implication is that an SST maximum in the equatorial region reduces the strength of MJO, and a flat SST profile in the equatorial region is required for more energetic of MJO. This result was tested and found to be valid in a series of further experiments.

This thesis deals with mathematical modeling of multiphysics FSI (fluid-structure interaction) problem, describing mutual interaction of pressure pulsations and vibrations of indirect pipe in a 2D region. Firstly, physical partial differential equations are derived separately for both media, which are in turn coupled and solved analytically. Results of mentioned models include natural frequency values, amplitude-frequency characteristics and both natural and driven damped oscillations of pipe and liquid.

Previous studies have demonstrated the sensitivity of the amplitude of the microwave radiation-induced magnetoresistance oscillations to the microwave polarization. These studies have also shown that there exists a phase shift in the linear polarization angle dependence. But the physical origin of this phase shift is still unclear. Therefore, the first part of this dissertation analyzes the phase shift by averaging over other small contributions, when those contributions are smaller than experimental uncertainties. The analysis indicates nontrivial frequency dependence of the phase shift. The second part of the dissertation continues the study of the phase shift and the results suggest that the specimen exhibits only one preferred radiation orientation for different Hall-bar sections. The third part of the dissertation summarizes our study of the Hall and longitudinal resistance oscillations induced by microwave frequency and dc bias at low filling factors. Here, the phase of these resistance oscillations depends on the contact pair on the device, and the period of oscillations appears to be inversely proportional to radiation frequency.

Les mécanismes cellulaires et moléculaires qui sous-tendent la mémoire et l’apprentissage chez les mammifères sont incomplètement compris. Le rythme thêta de l’hippocampe constitue l’état « en ligne » de cette structure qui est cruciale pour la mémoire déclarative. Dans la région CA1 de l’hippocampe, les interneurones inhibiteurs LM/RAD démontrent des oscillations de potentiel membranaire (OPM) intrinsèques qui pourraient se révéler importantes pour la génération du rythme thêta. Des travaux préliminaires ont suggéré que le courant K+ I(A) pourrait être impliqué dans la génération de ces oscillations. Néanmoins, peu de choses sont connues au sujet de l’identité des sous-unités protéiques principales et auxiliaires qui soutiennent le courant I(A) ainsi que l’ampleur de la contribution fonctionnelle de ce courant K+ dans les interneurones. Ainsi, cette thèse de doctorat démontre que le courant I(A) soutient la génération des OPM dans les interneurones LM/RAD et que des protéines Kv4.3 forment des canaux qui contribuent à ce courant. De plus, elle approfondit les connaissances sur les mécanismes qui régissent les interactions entre les sous-unités principales de canaux Kv4.3 et les protéines accessoires KChIP1. Finalement, elle révèle que la protéine KChIP1 module le courant I(A)-Kv4.3 natif et la fréquence de décharge des potentiels d’action dans les interneurones. Nos travaux contribuent à l’avancement des connaissances dans le domaine de la modulation de l’excitabilité des interneurones inhibiteurs de l’hippocampe et permettent ainsi de mieux saisir les mécanismes qui soutiennent la fonction de l’hippocampe et possiblement la mémoire chez les mammifères. / Cellular and molecular mechanisms underlying learning and memory in mammals are incompletely understood. The theta rhythm in the hippocampus constitutes the « on-line » state of this structure which is crucial for declarative memory. In the CA1 hippocampal area, LM/RAD inhibitory interneurons exhibit intrinsic membrane potential oscillations (MPOs) that could be important for the generation of theta rhythm. Preliminary work suggested that K+ current I(A) could be involved in the generation of these oscillations. Nevertheless, little is known about the identity of the principal and auxiliary protein subunits underlying I(A) current and the extent of the functional contribution of this K+ current in hippocampal interneurons. Thus, this Ph.D. thesis shows that I(A) current underlies MPO generation in LM/RAD interneurons and that Kv4.3 proteins form channels that contribute to this current. Also, it deepens the knowledge on the mechanism controlling the interactions between Kv4.3 channel-forming principal subunits and KChIP1 auxiliary proteins. Finally, it reveals that KChIP1 modulates native I(A)-Kv4.3 current and the action potential discharge frequency in interneurons. Our work takes part in advancing the knowledge on the field of modulation of excitability in hippocampal inhibitory interneurons and allows a better understanding of the mechanisms underlying the function of the hippocampus and possibly memory in mammals.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Le somnambulisme est une parasomnie commune, caractérisée par des éveils incomplets lors des stades de sommeil lent, au cours desquels les individus atteints présentent des comportements moteurs d’une complexité variable accompagnés de confusion et d’un jugement altéré. La littérature actuelle suggère que ce trouble serait associé à des particularités de l’activité en ondes lentes et des oscillations lentes, deux indices de l’intégrité du processus homéostatique et de la profondeur du sommeil. Toutefois, en raison de certaines lacunes méthodologiques dans les études existantes, le rôle de ces marqueurs électroencéphalographiques dans la pathophysiologie du somnambulisme reste à éclaircir. Notre premier article a donc investigué d’éventuelles anomalies de l’activité en ondes lentes et des oscillations lentes chez les somnambules, en comparant leur sommeil au cours de la nuit entière à celui de participants contrôles. De plus, comme les somnambules semblent réagir différemment (en termes de fragmentation du sommeil notamment) des dormeurs normaux à une pression homéostatique accrue, nous avons comparé l’activité en ondes lentes et les oscillations lentes en nuit de base et suite à une privation de sommeil de 38 heures. Les résultats de nos enregistrements électroencéphalographiques chez 10 somnambules adultes et neuf participants contrôles montrent une élévation de la puissance spectrale de l’activité en ondes lentes et de la densité des oscillations lentes en nuit de récupération par rapport à la nuit de base pour nos deux groupes. Toutefois, contrairement à plusieurs études précédentes, nous ne n’observons pas de différence entre somnambules et dormeurs normaux quant à l’activité en ondes lentes et aux oscillations lentes pour aucune des deux nuits. Au-delà ce certaines considérations méthodologiques ayant pu contribuer à ce résultat inattendu, nous croyons qu’il justifie un questionnement sur l’hétérogénéité des somnambules comme population. Notre deuxième article s’est penché sur les facteurs électroencéphalographiques transitoires susceptibles d’être associés au déclenchement des épisodes de somnambulisme. Nous avons comparé les fluctuations d’activité en ondes lentes et des oscillations lentes dans les minutes avant des épisodes de somnambulisme spontanés (c.a.d.: non associés à un stimulus identifiable) à celles survenant avant des éveils normaux comparables chez 12 somnambules adultes. Nous montrons que, comparativement aux éveils normaux, les épisodes de somnambulisme sont précédés d’un sommeil plus profond, tel qu’indiqué par une plus grande densité spectrale de l’activité en ondes lentes et une plus grande densité des oscillations lentes. Cet approfondissement du sommeil, spécifique aux épisodes de somnambulisme, semble survenir sur un laps de temps relativement long (>3 minutes), et non abruptement au cours des secondes précédant l’épisode. Ces données ouvrent un questionnement quant aux mécanismes en jeu dans la survenue des épisodes de somnambulisme spontanés. Globalement, cette thèse suggère que des phénomènes liés à l’activité en ondes lentes et aux oscillations lentes seraient liés au déclenchement des épisodes de somnambulisme, mais que des études supplémentaires devront être menées afin de délimiter le rôle précis que ces marqueurs jouent dans la pathophysiologie du somnambulisme. / Sleepwalking is a common parasomnia characterized by sudden but incomplete arousals out of non-rapid eye movement sleep during which predisposed individuals display motor behaviours of various complexity, accompanied by mental confusion and altered judgement. A growing body of evidence suggests that this condition could be associated with atypical patterns in slow wave activity and slow oscillations, both markers of the integrity of the homeostasis process and of sleep intensity. However, due to methodological limitations in past studies, the role of these electroencephalographic markers in the pathophysiology of sleepwalking remains unclear. Our first article aimed at describing slow wave activity and slow oscillations abnormalities in sleepwalkers by comparing whole night sleep in 10 adult sleepwalkers and 9 control participants. In addition, since past studies have shown that increased homeostatic pressure has differential effects on sleepwalkers versus normal controls (e.g., in terms of sleep fragmentation), we compared slow wave activity and slow oscillations during baseline sleep and recovery sleep after 38 hours of sleep deprivation in patients and controls. Results show that sleep deprivation increases slow wave activity power density and slow oscillations density in both groups. However, contrary to our predictions, no group differences were noted on any of the two nights on slow wave activity or slow oscillations. Beyond methodological considerations which may partially account for this unexpected result, this study opens questions as to the homogeneity of sleepwalkers as a clinical population. Our second study focused on transient electroencephalographic fluctuations that may be associated with the onset of sleepwalking episodes. We compared slow wave activity and slow oscillations fluctuations in the moments leading up to spontaneous (that is, occurring without an identifiable internal or external stimuli) somnambulistic episodes recorded in the sleep laboratory in 12 adult sleepwalkers and comparing these patterns to those observed prior to non-behavioural awakenings observed in the same patients. We showed that when compared to non-behavioural awakenings from the same sleep stage and sleep period, somnambulistic episodes were preceded by deeper sleep, as indicated by higher slow wave activity power density and slow oscillations density. This deepening of sleepwalkers’ sleep occurs over a relatively long period of time (>3 minutes) before the episode, rather than abruptly in the seconds preceding episode onset. These findings raise key questions about fundamental mechanisms involved in the occurrence of spontaneously recorded somnambulistic episodes. Taken as a whole, the results from the work presented in this thesis show that electrophysiological processes related to slow wave activity and slow oscillations play a role in the occurrence of somnambulistic episodes. However, the functional significance of these electroencephalographic markers in the pathophysiology of sleepwalking remains to be clarified.