Dynamical structure functions were developed as a partial structure representation of linear time-invariant systems to be used in the reconstruction of biological networks. Dynamical structure functions contain more information about structure than a system's transfer function, while requiring less a priori information for reconstruction than the complete computational structure associated with the state space realization. Early sufficient conditions for network reconstruction with dynamical structure functions severely restricted the possible applications of the reconstruction process to networks where each input independently controls a measured state. The first contribution of this thesis is to extend the previously established sufficient conditions to incorporate both necessary and sufficient conditions for reconstruction. These new conditions allow for the reconstruction of a larger number of networks, even networks where independent control of measured states is not possible. The second contribution of this thesis is to extend the robust reconstruction algorithm to all reconstructible networks. This extension is important because it allows for the reconstruction of networks from real data, where noise is present in the measurements of the system. The third contribution of this thesis is a Matlab toolbox that implements the robust reconstruction algorithm discussed above. The Matlab toolbox takes in input-output data from simulations or real-life perturbation experiments and returns the proposed Boolean structure of the network. The final contribution of this thesis is to increase the applicability of dynamical structure functions to more than just biological networks by applying our reconstruction method to wireless communication networks. The reconstruction of wireless networks produces a dynamic interference map that can be used to improve network performance or interpret changes of link rates in terms of changes in network structure, enabling novel anomaly detection and security schemes.

In this work, experimental and theoretical approaches are applied to the study of chemical reaction dynamics. In Chapter 2, two applications of transition state theory are presented: (1) Application of microcanonical transition state theory to determine the rate constant of dissociation of C2F3I after π∗ ← π excitation. It was found that this reaction has a very fast rate constant and thus is a promising system for testing the statistical assumption of molecular reaction dynamics. (2) A general rate constant expression for the reaction of atoms and molecules at surfaces was derived within the statistical framework of flexible transition state theory. In Chapter 4, a computationally efficient TDDFT approach was found to produce useful potential energy surface landscapes for application to non-adiabatic predissociative dynamics of the molecule CS2 after excitation from the ground state to the singlet C-state. In Chapter 5, ultrafast experimental results of excitation of CS2 to the predissociative neutral singlet C-state is presented. The bandwidth of the excitation laser was carefully tuned to span a two-component scattering resonance with each component differently evolving electronically with respect to excited state character during the quasi-bound oscillation. Scalar time-resolved photoelectron spectra (TRPES) and vector time-resolved photoelectron angular distribution (TRPAD) observables were recorded during the predissociation. The TRPES yield of photoelectrons was found to oscillate with a quantum beat pattern for the photoelectrons corresponding to ionization to the vibrationless cation ground state; this beat pattern was obscured for photoelectron energies corresponding to ionization from the vibrationally excited CS2 cation. The TRPAD data was recorded for two general molecular ensemble cases: with and without a pre-excitation alignment laser pulse. It was found that in the case of ensemble alignment (Chapter 6), the “molecular frame” TRPAD (i.e. TRMFPAD) was able to image the purely valence electronic dynamics of the evolving CS2 C-state. The unaligned ensemble TRPAD observable suffers from excessive orientational averaging and was unable to observe the quantum beat. Engineering efforts were also undertaken to eliminate scattered light background signal (Chapter 7, Appendix A) and improve laser stability as a function of ambient pressure (Appendix B) for TRMFPAD experiments. / Thesis (Ph.D, Chemistry) -- Queen's University, 2012-09-11 22:18:20.89

Motivated by the existence of complex behaviors arising from interactions between chemistry and fluid dynamics in numerous research problems and every-day life situations, we theoretically investigate the dynamics resulting from the interplay between chemistry, diffusion, and fluid motions in a reactive aqueous solution. As a chemical reaction induces changes in the temperature and in the composition of the reactive medium, such a reaction can modify the properties of the solution (density, viscosity, surface tension,…) and thereby trigger convective motions, which in turn affect the reaction. Two classes of convective flows are commonly occurring in solutions open to air, namely Marangoni flows arising from surface tension gradients and buoyancy flows driven by density gradients. As both flows can be induced by compositional changes as well as thermal changes and in turn modify them, the resulting experimental dynamics are often complex. The purpose of our thesis is to gain insight into these intricate dynamics thanks to the theoretical analysis of model systems where only one type of convective flow is present. In particular, we numerically study the spatio-temporal evolution of model chemical fronts resulting from the coupling between reactions, diffusion, and convection. Such fronts correspond to self-organized interfaces between the products and the reactants, which typically have different density and surface tension. Fluid motions are therefore spontaneously induced due to these differences across the front.<p><p>In this context, we first address the propagation of a model autocatalytic front in a horizontal solution layer, in the presence of pure Marangoni convection on the one hand and of pure buoyancy convection on the other hand. We evidence that, in both cases, the system attains an asymptotic dynamics characterized by a steady fluid vortex traveling with the front at a constant speed. The presence of convection results in a deformation and acceleration of the chemical front compared to the reaction-diffusion situation. However we note important differences between the Marangoni and buoyancy cases that could help differentiate experimentally between the influence of each hydrodynamic effect arising in solutions open to the air. We also consider how the kinetics and the exothermicity of the reaction influence the dynamics of the system. The propagation of an isothermal front occurring when two diffusive reactants are initially separated and react according to a simple bimolecular reaction is next studied in the presence of chemically-induced buoyancy convection. We show that the reaction-diffusion predictions established for convection-free systems are modified in the presence of fluid motions and propose a new way to classify the various possible reaction-diffusion-convection dynamics./En induisant des changements de composition et de température, une réaction chimique peut modifier les propriétés physiques (densité, viscosité, tension superficielle,…) de la solution dans laquelle elle se déroule et ainsi générer des mouvements de convection qui, à leur tour, peuvent affecter la réaction. Les deux sources de convection les plus courantes en solution ouverte à l’air sont les gradients de tension superficielle, ou effets Marangoni, et les gradients de densité. Comme ces deux sources sont en compétition et peuvent toutes deux résulter de différences de concentration ou de température, les dynamiques observées expérimentalement sont souvent complexes. Le but de notre thèse est de contribuer à la compréhension de telles dynamiques par une étude théorique analysant des modèles réaction-diffusion-convection simples. En particulier, nous étudions numériquement l’évolution spatio-temporelle de fronts chimiques résultant du couplage entre chimie non-linéaire, diffusion et hydrodynamique. Ces fronts constituent l’interface auto-organisée entre les produits et les réactifs qui typiquement ont des densités et tensions superficielles différentes. Des mouvements du fluide peuvent dès lors être spontanément initiés dus à ces différences au travers du front.<p> <p>Dans ce contexte, nous étudions la propagation d’un front chimique autocatalytique se propageant dans une solution aqueuse horizontale, d’une part en la seule présence d’effets Marangoni, et d’autre part en présence uniquement d’effets de densité. Nous avons montré que dans les deux cas, le système atteint une dynamique asymptotique caractérisée par la présence d’un rouleau de convection stationnaire se propageant à vitesse constante avec le front. Ce front est à la fois déformé et accéléré par les mouvements convectifs par rapport à la situation réaction-diffusion. Nous avons mis en évidence d’importantes différences entre les deux régimes hydrodynamiques qui pourraient aider les expérimentateurs à différencier les effets de tension superficielle de ceux de densité générés par la propagation de fronts chimiques en solution. Nous avons également considéré l’influence de la cinétique de réaction ainsi que de l’exothermicité sur la dynamique de ces fronts. Enfin, nous avons étudié la propagation en présence de convection d’un front de réaction impliquant deux espèces de densités différentes, initialement séparées et réagissant selon une cinétique bimoléculaire. Nous avons montré que la convection modifie les propriétés réaction-diffusion du système et nous proposons de nouveaux critères pour classifier les dynamiques réaction-diffusion-convection.<p><p><p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Le procédé de coextrusion permet de combiner à l’état fondu plusieurs couches de polymères dans une même structure. La compatibilisation des différentes couches est généralement réalisée à l’aide de liants qui réagissent in-situ. Bien que la compatibilisation puisse permettre de réduire ou même supprimer les instabilités macroscopiques d’écoulement, un nouveau défaut qualifié de « granité » peut apparaitre. Très peu de travaux de la littérature traitent les mécanismes gouvernant ce type de défaut. Les phénomènes mis en jeu sont particulièrement complexes puisqu’ils impliquent de façon couplée des phénomènes hydrodynamiques via l’écoulement, la rhéologie des différentes couches et des phénomènes physico-chimiques via la diffusion et la réaction chimique aux interfaces polymère/polymère. Ce mémoire s’articule autour d’une étude multi-échelle du rôle des copolymères aux interfaces sur la stabilité des écoulements stratifiés. L’étude a été réalisée à la fois sur des systèmes non-réactifs et réactifs constitués d’une couche barrière, le polyamide 6 (PA6) ou le poly(éthylène-co-alcool vinylique) (EVOH), avec un polypropylène (PP) ou un polypropylène greffé anhydride maléique (PP-g-AM). Le défaut de « granité » a été mis en évidence en coextrusion. Les paramètres procédé et matériaux influençant son apparition ont été identifiés. Il a pu être différencié des défauts et des instabilités interfaciales généralement rencontrées en coextrusion. Le phénomène de compatibilisation a également été étudié via les caractérisations morphologiques (MET, MEB, AFM) et physico-chimiques (XPS) aux interfaces. Le comportement rhéologique en cisaillement et élongation en viscoélasticité linéaire et non linéaire s’est révélé très sensible à l’effet la présence de copolymères aux interfaces et à leur architecture moléculaire. Cette étude a permis de déterminer les propriétés intrinsèques de l’interface/interphase en fonction du copolymère formé entre le liant et le PA6 ou l’EVOH. Elles ont pu être corrélées aux défauts macroscopiques observés dans les films multicouches coextrudés. La stabilité de ces écoulements stratifiés résulte d’un couplage de phénomènes qui se produisent à différentes échelles : nano (réaction de copolymérisation), micro (interphase) et macro (écoulement dans le procédé). / Several polymers can be combined in one multilayer structure by reactive coextrusion. Tie-layers are often used to compatibilize the adjacent layers and may reduce or suppress the interfacial instabilities and the defects in the multilayer coextrusion flow. However, an additional defect defined as the “grainy” defect can be observed. In the best of our knowledge, no study in literature has been devoted to understand its origin. The phenomena are quite complex due to the coupling of the effects of flow and the physico-chemical mechanisms at the interface. The aim of this work is to understand the relations between the instabilities and the defects encountered in multilayer coextruded films and the role of the copolymer formed in-situ between tie and barrier layers. Polyamide 6 (PA6) and ethylene-vinyl alcohol copolymer (EVOH) were used as the barrier layers sandwiched in a polypropylene (PP) with or without a polypropylene grafted maleic anhydride (PP-g-MA) as a tie-layer. The effect of the process parameters and the structure of the polymers on the generation of the “grainy” defect was assessed in correlation with the rheological and the physicochemical properties of the layers. These experiments have shown that this defect appeared mainly in the compatibilized EVOH system and could be distinguished from the usual coextrusion instabilities. The interfacial properties between tie and barrier layers were investigated. The characterization of the interfacial morphology by TEM and AFM highlighted an irregular and rough interface between PP-g-MA and EVOH while a flat interface was observed with PA6 and PP-g-MA. Step shear and startup elongation rheology was shown to be sensitive to the copolymer at the polymer/polymer interface. The study of the interfacial properties highlighted that the copolymer architecture significantly impacts the interfacial roughness and the rheology of the multilayer stuctures. Hence, relations between the relaxation process, the interfacial morphology and the copolymer architecture were established in correlation with the generation of the macroscopic grainy defect in coextrusion.

In this thesis extensions to the formalism of endoreversible thermodynamics for multi-extensity fluxes and chemical reactions are introduced. These extensions make it possible to model a great variety of systems which could not be investigated with standard endoreversible thermodynamics. Multi-extensity fluxes are important when studying processes with matter fluxes or processes in which volume and entropy are exchanged between subsystems. For including reversible as well as irreversible chemical reaction processes a new type of subsystems is introduced - the so called reactor. It is similar to endoreversible engines, because the fluxes connected to it are balanced. The difference appears in the balance equations for particle numbers, which contain production or destruction terms, and in the possible entropy production in the reactor. Both extensions are then applied to an endoreversible fuel cell model. The chemical reactions in the anode and cathode of the fuel cell are included with the newly introduced subsystem -- the reactor. For the transport of the reactants and products as well as the proton transport through the electrolyte membrane, the multi-extensity fluxes are used. This fuel cell model is then used to calculate power output, efficiency and cell voltage of a fuel cell with irreversibilities in the proton and electron transport. It directly connects the pressure and temperature dependencies of the cell voltage with the dissipation due to membrane resistance. Additionally, beside the listed performance measures it is possible to quantify and localize the entropy production and dissipated heat with only this one model. / In dieser Arbeit erweitere ich den Formalismus der endoreversiblen Thermodynamik, um Flüsse mit mehr als einer extensiven Größe sowie chemische Reaktionsprozesse modellieren zu können. Mit Hilfe dieser Erweiterungen eröffnen sich zahlreiche neue Anwendungsmöglichkeiten für endoreversible Modelle. Flüsse mit mehreren extensiven Größen sind für die Betrachtung von Masseströmen ebenso nötig wie für Prozesse, bei denen sowohl Volumen als auch Entropie zwischen zwei Teilsystem ausgetauscht werden. Für sowohl reversibel wie auch irreversibel geführte chemische Reaktionsprozesse wird ein neues Teilsystem - der "Reaktor" - vorgestellt, welches sich ähnlich wie endoreversible Maschinen durch Bilanzgleichungen auszeichnet. Der Unterschied zu den Maschinen besteht in den Produktions- bzw. Vernichtungstermen in den Teilchenzahlbilanzen sowie der möglichen Entropieproduktion innerhalb des Reaktors. Beide Erweiterungen finden dann in einem endoreversiblen Modell einer Brennstoffzelle Anwendung. Dabei werden Flüsse mehrerer gekoppelter Extensitäten für den Zustrom von Wasserstoff und Sauerstoff sowie für den Protonentransport durch die Elektrolytmembran benötigt. Chemische Reaktionen treten in der Anode und Kathode der Brennstoffzelle auf. Diese werden mit dem neu eingeführten Teilsystem, dem Reaktor, eingebunden. Mit Hilfe des Modells werden dann Wirkungsgrad, Zellspannung und Leistung einer Brennstoffzelle unter Berücksichtigung der Partialdrücke der Substanzen, der Temperatur sowie der Dissipation beim Protonentransport berechnet. Dabei zeigt sich, dass experimentelle Daten für die Zellspannung sowohl qualitativ als auch näherungsweise quantitativ durch das Modell abgebildet werden können. Der Vorteil des endoreversiblen Modells liegt dabei in der Möglichkeit, mit nur einem Modell neben den genannten Kenngrößen auch die abgegebene Wärme sowie die Entropieproduktion zu quantifizieren und den einzelnen Teilprozessen zuzuordnen.

Extracellular neuroelectronic interfacing has important applications in the fields of neural prosthetics, biological computation and whole-cell biosensing for drug screening and toxin detection. While the field of neuroelectronic interfacing holds great promise, the recording of high-fidelity signals from extracellular devices has long suffered from the problem of low signal-to-noise ratios and changes in signal shapes due to the presence of highly dispersive dielectric medium in the neuron-microelectrode cleft. This has made it difficult to correlate the extracellularly recorded signals with the intracellular signals recorded using conventional patch-clamp electrophysiology. For bringing about an improvement in the signalto-noise ratio of the signals recorded on the extracellular microelectrodes and to explore strategies for engineering the neuron-electrode interface there exists a need to model, simulate and characterize the cell-sensor interface to better understand the mechanism of signal transduction across the interface. Efforts to date for modeling the neuron-electrode interface have primarily focused on the use of point or area contact linear equivalent circuit models for a description of the interface with an assumption of passive linearity for the dynamics of the interfacial medium in the cell-electrode cleft. In this dissertation, results are presented from a nonlinear dynamic characterization of the neuroelectronic junction based on Volterra-Wiener modeling which showed that the process of signal transduction at the interface may have nonlinear contributions from the interfacial medium. An optimization based study of linear equivalent circuit models for representing signals recorded at the neuron-electrode interface subsequently iv proved conclusively that the process of signal transduction across the interface is indeed nonlinear. Following this a theoretical framework for the extraction of the complex nonlinear material parameters of the interfacial medium like the dielectric permittivity, conductivity and diffusivity tensors based on dynamic nonlinear Volterra-Wiener modeling was developed. Within this framework, the use of Gaussian bandlimited white noise for nonlinear impedance spectroscopy was shown to offer considerable advantages over the use of sinusoidal inputs for nonlinear harmonic analysis currently employed in impedance characterization of nonlinear electrochemical systems. Signal transduction at the neuron-microelectrode interface is mediated by the interfacial medium confined to a thin cleft with thickness on the scale of 20-110 nm giving rise to Knudsen numbers (ratio of mean free path to characteristic system length) in the range of 0.015 and 0.003 for ionic electrodiffusion. At these Knudsen numbers, the continuum assumptions made in the use of Poisson-Nernst-Planck system of equations for modeling ionic electrodiffusion are not valid. Therefore, a lattice Boltzmann method (LBM) based multiphysics solver suitable for modeling ionic electrodiffusion at the mesoscale neuron-microelectrode interface was developed. Additionally, a molecular speed dependent relaxation time was proposed for use in the lattice Boltzmann equation. Such a relaxation time holds promise for enhancing the numerical stability of lattice Boltzmann algorithms as it helped recover a physically correct description of microscopic phenomena related to particle collisions governed by their local density on the lattice. Next, using this multiphysics solver simulations were carried out for the charge relaxation dynamics of an electrolytic nanocapacitor with the intention of ultimately employing it for a simulation of the capacitive coupling between the neuron and the v planar microelectrode on a microelectrode array (MEA). Simulations of the charge relaxation dynamics for a step potential applied at t = 0 to the capacitor electrodes were carried out for varying conditions of electric double layer (EDL) overlap, solvent viscosity, electrode spacing and ratio of cation to anion diffusivity. For a large EDL overlap, an anomalous plasma-like collective behavior of oscillating ions at a frequency much lower than the plasma frequency of the electrolyte was observed and as such it appears to be purely an effect of nanoscale confinement. Results from these simulations are then discussed in the context of the dynamics of the interfacial medium in the neuron-microelectrode cleft. In conclusion, a synergistic approach to engineering the neuron-microelectrode interface is outlined through a use of the nonlinear dynamic modeling, simulation and characterization tools developed as part of this dissertation research.