We numerically investigate the long-time behavior of the density-density auto-correlation function in driven lattice gases, with particle exclusion and periodic boundary conditions in one, two, and three dimensions using precise Monte Carlo simulations of larger system sizes than previous studies. In the one-dimensional asymmetric exclusion process on a ring with half the lattice sites occupied, we find that correlations induce extremely slow relaxation to the asymptotic power law decay We compare the crossover functions obtained from our simulations with various analytic results in the literature, and analyze the characteristic oscillations that occur in finite systems away from half-filling. As expected, correlations are weak in three dimensions and consequently the mean-field description is adequate. We also investigate the relaxation towards the non-equilibrium steady state in the two-time density-density auto-correlations, starting from strongly correlated initial conditions. We obtain simple aging scaling behavior in one, two, and three dimensions, with the expected power laws. We numerically investigate the behavior of driven lattice gases with nearest neighbor interactions at half-filling with periodic boundary conditions below and at the critical temperature using Monte Carlo simulations of very large lattices in two dimensions. This work is one of few that explores the relaxation to a non-equilibrium steady state. We obtain data collapse for the finite-size scaling form of density-density auto-correlation function at the critical point. We achieve data collapse using finite-size scaling of the time-dependent order parameter during the transient regime starting from strongly correlated initial conditions. We present simple aging scaling of the density-density auto-correlation function at the critical point starting from strongly correlated initial conditions using Monte Carlo simulations of two different lattice anisotropies. We thus unambiguously confirm the critical exponents determined by renormalization group methods using measurement of dynamic quantities in the transient regime. Measuring these dynamic quantities in the transient regime provides more conclusive measurements of the critical exponents than previous studies measuring static quantities in the stationary state. We provide qualitative arguments that the lattice anisotropy determines the steady-state for sub-critical quenches. / Ph. D.

We investigate the relaxation properties of two distinct systems: magnetic vortex lines in disordered type-II superconductors and charge carriers in the Coulomb glass in disordered semiconductors. We utilize an elastic line model to simulate magnetic flux lines in disordered type-II superconductors by performing Langevin molecular dynamics simulations. We study the non-equilibrium relaxation properties of flux lines in the presence of uncorrelated point-like disorder or extended linear defects analyzing the effects of rapid changes in the system's temperature or magnetic field on these properties. In a previously-equilibrated system, either the temperature is suddenly changed or the magnetic field is abruptly altered by adding or removing random flux lines to or from the system. One-time observables such as the radius of gyration are measured to characterize steady-state properties, and two-time correlation functions such as the vortex line height autocorrelations are computed to investigate the relaxation dynamics in the aging regime and therefore distinguish the complex relaxation features that result from the different types of disorder in the system. This study allows us to test the sensitivity of the system's non-equilibrium aging kinetics to the selection of initial states and to make closer contact to experimental setups. Furthermore, we employ Monte Carlo simulations to study the relaxation properties of the two-dimensional Coulomb glass in disordered semiconductors and the two-dimensional Bose glass in type-II superconductors in the presence of extended linear defects. We investigate the effects of adding non-zero random on-site energies from different distributions on the properties of the correlation-induced Coulomb gap in the density of states and on the non-equilibrium aging kinetics highlighted by the autocorrelation functions. We also probe the sensitivity of the system's equilibrium and non-equilibrium relaxation properties to instantaneous changes in the density of charge carriers in the Coulomb glass or flux lines in the Bose glass. / Ph. D.

Mesoporous materials are being widely used in the chemical industry in various environmentally friendly separation processes and as catalysts. Our research can be broadly described as an effort to understand the behavior of fluids confined in such materials. More specifically we try to understand the influence of state variables like temperature and pore variables like size, shape, connectivity and structural heterogeneity on both the dynamic and equilibrium behavior of confined fluids. The dynamic processes associated with the approach to equilibrium are largely unexplored. It is important to look into the dynamic behavior for two reasons. First, confined fluids experience enhanced metastabilities and large equilibration times in certain classes of mesoporous materials, and the approach to the metastable/stable equilibrium is of tremendous interest. Secondly, understanding the transport resistances in a microscopic scale will help better engineer heterogeneous catalysts and separation processes. Here we present some of our preliminary studies on dynamics of fluids in ideal pore geometries. The tool that we have used extensively to investigate the relaxation dynamics of fluids in pores is the dynamic mean field theory (DMFT) as developed by Monson[P. A. Monson, J. Chem. Phys., 128, 084701 (2008) ]. The theory is based on a lattice gas model of the system and can be viewed as a highly computationally efficient approximation to the dynamics averaged over an ensemble of Kawasaki dynamics Monte Carlo trajectories of the system. It provides a theory of the dynamics of the system consistent with the thermodynamics in mean field theory. The nucleation mechanisms associated with confined fluid phase transitions are emergent features in the calculations. We begin by describing the details of the theory and then present several applications of DMFT. First we present applications to three model pore networks (a) a network of slit pores with a single pore width; (b) a network of slit pores with two pore widths arranged in intersecting channels with a single pore width in each channel; (c) a network of slit pores with two pore widths forming an array of ink-bottles. The results illustrate the effects of pore connectivity upon the dynamics of vapor liquid phase transformations as well as on the mass transfer resistances to equilibration. We then present an application to a case where the solid-fluid interactions lead to partial wetting on a planar surface. The pore filling process in such systems features an asymmetric density distribution where a liquid droplet appears on one of the walls. We also present studies on systems where there is partial drying or drying associated with weakly attractive or repulsive interactions between the fluid and the pore walls. We describe the symmetries exhibited by the lattice model between pore filling for wetting states and pore emptying for drying states, for both the thermodynamics and dynamics. We then present an extension of DMFT to mixtures and present some examples that illustrate the utility of the approach. Finally we present an assessment the accuracy of the DMFT through comparisons with a higher order approximation based on the path probability method as well as Kawasaki dynamics.

No description available.

In general, this dissertation is concerned with modeling of mechanical behavior of protein molecules. In particular, we focus on coarse-grained models, which bridge the gap in time and length scale between the atomistic simulation and biological processes. The dissertation presents three independent studies involving such models. The first study is concerned with a rigorous coarse-graining method for dynamics of linear systems. In this method, as usual, the conformational space of the original atomistic system is divided into master and slave degrees of freedom. Under the assumption that the characteristic timescales of the masters are slower than those of the slaves, the method results in Langevin-type equations of motion governed by an effective potential of mean force. In addition, coarse-graining introduces hydrodynamic-like coupling among the masters as well as non-trivial inertial effects. Application of our method to the long-timescale part of the relaxation spectra of proteins shows that such dynamic coupling is essential for reproducing their relaxation rates and modes. The second study is concerned with calibration of elastic network models based on the so-called B-factors, obtained from x-ray crystallographic measurements. We show that a proper calibration procedure must account for rigid-body motion and constraints imposed by the crystalline environment on the protein. These fundamental aspects of protein dynamics in crystals are often ignored in currently used elastic network models, leading to potentially erroneous network parameters. We develop an elastic network model that properly takes rigid-body motion and crystalline constraints into account. This model reveals that B-factors are dominated by rigid-body motion rather than deformation, and therefore B-factors are poorly suited for identifying elastic properties of protein molecules. Furthermore, it turns out that B-factors for a benchmark set of three hundred and thirty protein molecules can be well approximated by assuming that the protein molecules are rigid. The third study is concerned with the polymer mediated interaction between two planar surfaces. In particular, we consider the case where a thin polymer layer bridges two parallel plates. We consider two models of monodisperse and polydisperse for the polymer layer and obtain an analytical expression for the force-distance relationship of the two plates. / text

The thermal and dynamical properties of free-standing films are strongly dependent on the boundary conditions and the presence of an external field. Using distinct theoretical models and the dynamic light scattering experimental setup, we study the surface and external field effects on the relaxation dynamics, fluctuation-induced interaction energy, and phase transitions of smectic films. Using an extended McMillan model, we study as a homeotropic anchoring stabilizes the smetic order above the bulk transition temperature of the system. In particular, we determine as the transition temperature depends on the surface ordering and film thickness. We identify a characteristic anchoring for which the transition temperature does not depend on the film thickness. For strong surface ordering, we observe that the transition temperature presents a power law scaling behavior with the film thickness, in agreement with a series of existing experimental results in the literature. Within a Gaussian functional approximation, we also investigate how the fluctuationinduced interaction force depends on the nematic and smectic order parameter profiles. Close to nematic-smectic phase transition, our results indicate that the thermal Casimir force has a significant enhancement which reinforces the predominance of the fluctuationinduced interaction as compared to standard van der Waals interaction in thin smectic films. In temperatures where the smectic phase is well established, we investigate how the interplay of the surface order and the external field induced order affect the Casimirlike force. For asymmetrically anchored films, the fluctuation-induced interaction energy obeys a law of corresponding states and can change its nature from attractive to repulsive through variations of an external field. We discuss the possible relevance of this field effect in smectic wetting transitions. With concern to the dynamical properties, we investigate how surface operators modify the relaxation dynamics of hexatic-B liquid crystal films. In particular, we study how a surface ordering field modifies the damping rate of the orientational modes in the system. In a purely diffusive regime, we demonstrate that a surface tilted order drives the slowest relaxation mode from hydrodynamical to non-hydrodynamical character. In the viscous regime, the hydrodynamical character of the slowest relaxation mode persists even for a surface tilted order. However, the normal modes develop an oscillatory-exponential relaxation. Finally, we use the photon correlation spectroscopy technique to investigate the dynamic properties of free-standing films close to smectic-A - crystal-B transition. We observe that the experimental data indicate the existence of a non-hydrodynamic mode and measure the temperature dependence of the damping rate. We considered a simplified model that incorporates the gradient velocity field effects which reproduces qualitatively the experimental measurements. / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / As propriedades térmicas e dinâmicas de filmes de cristais líquidos na fase esmética são extremamente dependentes das condições de contorno e da presença de campos externos. Utilizando diferentes modelagens teóricas e a técnica de espectroscopia de fotocorrelação, estudamos como as condiçõoes de contorno e a presença de um campo externo afetam a dinâmica de relaxação, a energia de interação induzida por flutuações e as transições de fase envolvendo a fase esmética. Utilizando uma extensão para o modelo de McMillan, estudamos como o ancoramento homeotrópico estabiliza a ordem esmética acima da temperatura de transição do sistema. Em particular, determinamos como a temperatura de transição depende da intensidade do ancoramento superficial e da espessura do filme. Identificamos um ancoramento característico para o qual a temperatura de transição independe da espessura. Para ancoramentos fortes, observamos que a depend encia da temperatura de transição com a espessura do filme segue aproximadamente uma lei de potência, em concordância com uma série de resultados experimentais existentes na literatura. Baseado em uma teoria funcional Gaussiana para o funcional energia livre, investigamos tamb´em como a força induzida por flutuações esméticas depende do perfil dos parâmetros de ordem nemático e esmético. Nas proximidades da transição nemática esmética, nossos resultados indicam que a força de Casimir térmica cresce significativamente, podendo ser mais relevante que a força de van der Waals usual. Em temperaturas onde a fase esmética é bem estabelecida, investigamos como a competição entre a ordem superficial e a ordem induzida por um campo externo se reflete nas características da força de Casimir. Obtivemos que, para filmes com ancoramentos superficiais assimétricos, a força de Casimir térmica obedece a uma lei de estados correspondentes e pode mudar sua natureza de atrativa para repulsiva através de variações de um campo externo. Discutimos como este comportamento pode influenciar as transições de umedecimento da fase esmética. No que diz respeito às propriedades dinâmicas, investigamos como operadores de superfície modificam a dinâmica de relaxação de filmes na fase hexática-B. Em particular estudamos como um campo de ordenamento superficial modifica a taxa de amortecimento dos modos orientacionais do sistema. Num regime puramente difusivo, nós demonstramos que uma ordem superficial com o vetor diretor não paralelo à direção normal das camadas faz com que os modos de relaxação tornem-se não-hidrodinâmicos. No regime viscoso, sempre existirão modos hidrodinâmicos e a dinâmica de relaxação é sempre lenta. Entretanto, os modos normais podem apresentar um decaimento oscilatório. Por fim, usamos a técnica de espectroscopia de fotocorrelação para investigar as propriedades dinâmicas de filmes livremente suspensos nas proximidades da transição esmética-A - cristal-B. Observamos que os dados experimentais indicam a existência de um modo não-hidrodinâmico e medimos a dependência da taxa de relaxação com a temperatura. Propusemos um modelo que incorpora a influência do gradiente do campo de velocidades que reproduz qualitativamente as observações experimentais.

La précipitation et la dissolution du carbonate de calcium (CaCO3) sont des processus clés dans les systèmes naturels en raison de leur association intime avec le cycle du carbone terrestre. La précipitation se produit généralement sur des substrats étrangers en abaissant les barrières énergétiques qui contrôlent la nucléation. Ce processus appelé nucléation hétérogène résulte d'une interaction entre la sursaturation du fluide et les différentes énergies d’interface entre substrat-noyau-fluide. Malgré l’importance des énergies d’interface sur le devenir de la nucléation hétérogène, la littérature actuelle reste rare dans leurs valeurs absolues, limitant la précision de la modélisation du transport réactif. La formation des biominéraux constitue un réservoir majeur des carbonates dans la lithosphère. Des études récentes ont révélé des nucléations par multi-étapes impliquant la formation du carbonate de calcium amorphe (ACC), un intermédiaire métastable durant les premiers stades de la formation des biominéraux. De tels précurseurs amorphes permettent de réaliser les formes complexes des biominéraux, tandis que leur stabilité et leur cinétique de cristallisation sont contrôlées par de multiples facteurs. L'élucidation des mécanismes sous-jacents est bénéfique pour le développement de matériaux biomimétiques.Le premier objectif est de développer une compréhension prédictive des valeurs d'énergie d’interface régissant la nucléation hétérogène du CaCO3 en fonction des propriétés physico-chimiques spécifiques des substrats, comme l'hydrophobicité. Cette dernière est étudiée en utilisant de la phlogopite avec et sans substitution par le fluor produisant des substrats hydrophobes et hydrophiles. La technique de diffusion des rayons X aux petits angles en incidence rasante a été employée in situ pour obtenir des valeurs d’énergie effective d’interface. Il est intéressant de noter que les valeurs extraites pour les deux substrats sont similaires, et thermodynamiquement les deux fournissent un bon modèle pour la nucléation, alors que leurs mécanismes sont différents. La caractérisation ex situ par microscopie à force atomique a montré que le substrat hydrophile favorise la formation et la stabilisation d’ACC, tandis que le substrat hydrophobe favorise la formation de calcite. Ces résultats soulignent la flexibilité structurelle intrinsèque du CaCO3 et son avantage dans les processus de nucléation hétérogènes.Le deuxième objectif est de fournir une description atomistique de l'hydrophobicité du substrat. L'adsorption d'eau sur la phlogopite a été réalisée in situ par spectroscopie de photoélectrons à pression ambiante pour étudier l'effet de la substitution par le fluor et de différents types de contre-ions (K+, Na+ vs. Cs+). Ces résultats ont été interprétés par des simulations de dynamique moléculaire et la théorie de bond-valence. La combinaison de ces techniques montre que l'hydrophobicité du substrat provient d'une compétition entre deux facteurs: l'hydratation des contre-ions par rapport à celle du substrat.Le but final est d'étudier les mécanismes moléculaires par lesquels Mg2+, une impureté chez les précurseurs amorphes biogéniques, augmente la persistance cinétique d’ACC. La technique de diffusion inélastique incohérente des neutrons a été combinée avec la spectroscopie de corrélation de photons X pour élucider la dynamique à l'échelle nanométrique de l'eau et des ions dans les ACC. Les résultats montrent que la présence de Mg2+ augmente la diffusion atomique dans le solide tout en amplifiant la rigidité du réseau des liaisons hydrogène. Ces résultats contre-intuitifs sont abordés en considérant différents facteurs cinétiques inclus dans l’équation décrivant le taux de nucléation au sein de la théorie classique de la nucléation. Dans l'ensemble, ces résultats indiquent l'importance de l'eau comme stabilisant cinétique de la structure amorphe et de l'existence de barrières stériques qui abaissent le taux de cristallisation. / Precipitation and dissolution of calcium carbonate (CaCO3) are key processes in both natural and engineered systems due to their intimate association with the Earth’s carbon cycle. Precipitation usually occurs on foreign substrates since they lower the energetic barriers controlling nucleation events. This so-called heterogeneous nucleation results from the interplay between the fluid supersaturation and the interfacial free energies present at the substrate-nucleus-fluid interfaces. Despite the relevance of interfacial energies for the fate of heterogeneous nucleation, the current literature remains scarce in their absolute values, which limits the accuracy of reactive transport modelling. Of particular relevance to the carbon cycle, the formation of biominerals accounts for a major reservoir of the carbonate minerals in the lithosphere. Recent studies have revealed the existence of multistep nucleation pathways that involve formation of amorphous calcium carbonate (ACC), a metastable intermediate during the early stages of biomineral formation. Such amorphous precursors allow molding of the intricate shapes of biominerals, while their stability and crystallization kinetics are effectively controlled by multiple factors. Elucidating the underlying mechanisms is beneficial for the development of biomimetic materials.The first goal of this dissertation is to develop a predictive understanding of interfacial energy values governing CaCO3 heterogeneous nucleation as a function of specific physico-chemical properties of the substrates, such as hydrophobicity. This last was investigated using phlogopite, a common mica, with and without fluorine substitution yielding hydrophobic and hydrophilic substrates. In situ time-resolved Grazing-Incidence Small Angle X-ray Scattering experiments were performed to obtain effective interfacial energy values. Interestingly, the extracted values for both substrates were similar, and thermodynamically these substrates provide a good template for nucleation, but the pathways differ. By ex situ Atomic Force Microscopy characterization, the hydrophilic substrate was shown to promote the formation and stabilization of ACC, whereas the hydrophobic one favored the formation of calcite. These results point to the intrinsic structural flexibility of CaCO3 and its advantage in heterogeneous nucleation processes.The second goal is to provide an atomistic description of the substrate hydrophobicity/hydrophilicity. Water adsorption on phlogopite was studied in situ using Near-Ambient Pressure X-ray Photoelectron Spectroscopy to investigate the effect of fluorine substitution and the influence of different types of counterions (K+, Na+ vs. Cs+). The results of the spectroscopy experiments were further interpreted using molecular dynamics simulations and bond-valence theory. The combination of these techniques shows that the substrate hydrophobicity stems from a competition between two factors: hydration of counterions vs. that of substrate.The final goal is to study the molecular mechanisms by which Mg2+, a common impurity in biogenic amorphous precursors, increases the kinetic persistence of ACC. Inelastic Incoherent Neutron Scattering and X-ray Photon Correlation Spectroscopy were combined to elucidate the nanoscale dynamics of water and ions within ACC. The presence of Mg2+ was shown to enhance the atomic diffusion within the solid while simultaneously increasing the stiffness of the hydrogen bond network. These counter-intuitive results are addressed by considering the different factors included in the pre-exponential term of the nucleation rate equation within the framework of the classical nucleation theory. Overall, the results point to the importance of water as a kinetic stabilizer, and to the existence of steric barriers that lower the crystallization rate.

Sonder la matière en utilisant des nanoparticules luminescentes nécessite une compréhension de chaque processus pouvant modifier leurs propriétés optiques. Cette thèse se focalise sur l'influence de l'environnement diélectrique sur la luminescence de deux types de nanoobjets : (i) des boites quantiques colloïdales (QDs), et (ii) des nanobâtonnets d'or. L'objectif est d'évaluer les potentialités de ces nanostructures comme sondes locales de l'environnement diélectrique.L'évolution de la dynamique de relaxation de QDs dans différents environnements diélectriques est interprétée en terme d'indice de réfraction effectif local. Cette étude montre qu'une analyse détaillée de la sensibilité des QDs à l'environnement permet de les utiliser comme nanosondes biologiques d'indice de réfraction. Nous présentons également une nouvelle méthode pour l'encapsulation de QDs en matrice diélectrique solide, à travers le dépôt par laser pulsé. Les émetteurs peuvent être protégés par des films minces et subir des perturbations non-destructives et réversibles de leur environnement proche, à l'échelle de la particule unique, tout en analysant la dynamique de fluorescence. Finalement, la sensibilité de la résonance plasmon de nanobâtonnets d'or à l'approche d'une interface diélectrique est également sondée, puis comparée a celle des boites quantiques / Probing systems using luminescent nanoparticles requires the understanding of all the processes that influence the luminescence properties. This thesis focuses on the influence of the dielectric environment on the luminescence of two types of nanoparticles : (i) colloidal quantum dots (QDs), and (ii) gold nanorods. The aim of this work is to evaluate the potential of these nanostructures to act as local probes of the dielectric environment. The evolution of the relaxation dynamics of QDs in various dielectric media is interpreted in terms of local effective refractive index. This work shows that a detailed analysis of the sensitivity of the QDs to the environment allows their use as biological nanoprobes of refractive index. We furthermore present a new method for the encapsulation of QDs in a solid dielectric matrix, using pulsed laser deposition. The emitters can be incorporated in thin films and their local environment can be modified in a reversible and non-destructive way, while the emission dynamics is investigated at the single emitter level. Finally, the sensitivity of the surface plasmon resonance of gold nanorods to an approching dielectric interface is also studied, and compared to the one found for QDs

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.