Testing the performance and feasibility of Bluetooth communications in pervasive systems

Smart and mobile environments require seamless connections. However, due to the frequent process of ''discovery'' and disconnection of mobile devices while data interchange is happening, wireless connections are often interrupted. To minimize this drawback, a protocol that enables an easy and fast synchronization is crucial. Bearing this in mind, Bluetooth technology appears to be a suitable solution to carry on such connections due to the discovery and pairing capabilities it provides. Nonetheless, the time and energy spent when several devices are being discovered and used at the same time still needs to be managed properly. It is essential that this process of discovery takes as little time and energy as possible. In addition to this, it is believed that the performance of the communications is not constant when the transmission speeds and throughput increase, but this has not been proved formally. Therefore, the purpose of this project is twofold: Firstly, to design and build a framework-system capable of performing controlled Bluetooth device discovery, pairing and communications. Secondly, to analyze and test the scalability and performance of the \emph{classic} Bluetooth standard under different scenarios and with various sensors and devices using the framework developed. To achieve the first goal, a generic Bluetooth platform will be used to control the test conditions and to form a ubiquitous wireless system connected to an Android Smartphone. For the latter goal, various stress-tests will be carried on to measure the consumption rate of battery life as well as the quality of the communications between the devices involved.

Various algorithms for optimization and learning in adaptive systems

This thesis discusses various methods for learning and optimization in adaptive systems. Overall, it emphasizes the relationship between optimization, learning, and adaptive systems; and it illustrates the influence of underlying hardware upon the construction of efficient algorithms for learning and optimization. Chapter 1 provides a summary and an overview.

Chapter 2 discusses a method for using feed-forward neural networks to filter the noise out of noise-corrupted signals. The networks use back-propagation learning, but they use it in a way that qualifies as unsupervised learning. The networks adapt based only on the raw input data-there are no external teachers providing information on correct operation during training. The chapter contains an analysis of the learning and develops a simple expression that, based only on the geometry of the network, predicts performance.

Chapter 3 explains a simple model of the piriform cortex, an area in the brain involved in the processing of olfactory information. The model was used to explore the possible effect of acetylcholine on learning and on odor classification. According to the model, the piriform cortex can classify odors better when acetylcholine is present during learning but not present during recall. This is interesting since it suggests that learning and recall might be separate neurochemical modes (corresponding to whether or not acetylcholine is present). When acetylcholine is turned off at all times, even during learning, the model exhibits behavior somewhat similar to Alzheimer's disease, a disease associated with the degeneration of cells that distribute acetylcholine.

Chapters 4, 5, and 6 discuss algorithms appropriate for adaptive systems implemented entirely in analog hardware. The algorithms inject noise into the systems and correlate the noise with the outputs of the systems. This allows them to estimate gradients and to implement noisy versions of gradient descent, without having to calculate gradients explicitly. The methods require only noise generators, adders, multipliers, integrators, and differentiators; and the number of devices needed scales linearly with the number of adjustable parameters in the adaptive systems. With the exception of one global signal, the algorithms require only local information exchange.

Analysis and optimization of stress wave propagation in two-dimensional granular crystals with defects

Granular crystals are compact periodic assemblies of elastic particles in Hertzian contact whose dynamic response can be tuned from strongly nonlinear to linear by the addition of a static precompression force. This unique feature allows for a wide range of studies that include the investigation of new fundamental nonlinear phenomena in discrete systems such as solitary waves, shock waves, discrete breathers and other defect modes. In the absence of precompression, a particularly interesting property of these systems is their ability to support the formation and propagation of spatially localized soliton-like waves with highly tunable properties. The wealth of parameters one can modify (particle size, geometry and material properties, periodicity of the crystal, presence of a static force, type of excitation, etc.) makes them ideal candidates for the design of new materials for practical applications. This thesis describes several ways to optimally control and tailor the propagation of stress waves in granular crystals through the use of heterogeneities (interstitial defect particles and material heterogeneities) in otherwise perfectly ordered systems. We focus on uncompressed two-dimensional granular crystals with interstitial spherical intruders and composite hexagonal packings and study their dynamic response using a combination of experimental, numerical and analytical techniques. We first investigate the interaction of defect particles with a solitary wave and utilize this fundamental knowledge in the optimal design of novel composite wave guides, shock or vibration absorbers obtained using gradient-based optimization methods.

Quantum interference in laser-induced nonsequential double ionization in diatomic molecules: Role of alignment and orbital symmetry

We address the influence of the orbital symmetry and the molecular alignment with respect to the laser-field polarization on laser-induced nonsequential double ionization of diatomic molecules, in the length and velocity gauges. We work within the strong-field approximation and assume that the second electron is dislodged by electron-impact ionization, and also consider the classical limit of this model. We show that the electron-momentum distributions exhibit interference maxima and minima due to electron emission at spatially separated centers. The interference patterns survive integration over the transverse momenta for a small range of alignment angles, and are sharpest for parallel-aligned molecules. Due to the contributions of the transverse-momentum components, these patterns become less defined as the alignment angle increases, until they disappear for perpendicular alignment. This behavior influences the shapes and the peaks of the electron-momentum distributions.

Quantum computation based on a quantum switch in cavity QED

A feasible scheme for constructing quantum logic gates is proposed on the basis of quantum switches in cavity QED. It is shown that the light field which is fed into the cavity due to the passage of an atom in a certain state can be used to manipulate the conditioned quantum logical gate. In our scheme, the quantum information is encoded in the states of Rydberg atoms and the cavity mode is not used as logical qubits or as a communicating "bus"; thus, the effect of atomic spontaneous emission can be neglected and the strict requirements for the cavity can be relaxed.

Random propagation in complex systems : nonlinear matrix recursions and epidemic spread

This dissertation studies long-term behavior of random Riccati recursions and mathematical epidemic model. Riccati recursions are derived from Kalman filtering. The error covariance matrix of Kalman filtering satisfies Riccati recursions. Convergence condition of time-invariant Riccati recursions are well-studied by researchers. We focus on time-varying case, and assume that regressor matrix is random and identical and independently distributed according to given distribution whose probability distribution function is continuous, supported on whole space, and decaying faster than any polynomial. We study the geometric convergence of the probability distribution. We also study the global dynamics of the epidemic spread over complex networks for various models. For instance, in the discrete-time Markov chain model, each node is either healthy or infected at any given time. In this setting, the number of the state increases exponentially as the size of the network increases. The Markov chain has a unique stationary distribution where all the nodes are healthy with probability 1. Since the probability distribution of Markov chain defined on finite state converges to the stationary distribution, this Markov chain model concludes that epidemic disease dies out after long enough time. To analyze the Markov chain model, we study nonlinear epidemic model whose state at any given time is the vector obtained from the marginal probability of infection of each node in the network at that time. Convergence to the origin in the epidemic map implies the extinction of epidemics. The nonlinear model is upper-bounded by linearizing the model at the origin. As a result, the origin is the globally stable unique fixed point of the nonlinear model if the linear upper bound is stable. The nonlinear model has a second fixed point when the linear upper bound is unstable. We work on stability analysis of the second fixed point for both discrete-time and continuous-time models. Returning back to the Markov chain model, we claim that the stability of linear upper bound for nonlinear model is strongly related with the extinction time of the Markov chain. We show that stable linear upper bound is sufficient condition of fast extinction and the probability of survival is bounded by nonlinear epidemic map.

New insights into the formation and modification of carbonate-bearing minerals and methane gas in geological systems using multiply substituted isotopologues

This thesis describes the use of multiply-substituted stable isotopologues of carbonate minerals and methane gas to better understand how these environmentally significant minerals and gases form and are modified throughout their geological histories. Stable isotopes have a long tradition in earth science as a tool for providing quantitative constraints on how molecules, in or on the earth, formed in both the present and past. Nearly all studies, until recently, have only measured the bulk concentrations of stable isotopes in a phase or species. However, the abundance of various isotopologues within a phase, for example the concentration of isotopologues with multiple rare isotopes (multiply substituted or 'clumped' isotopologues) also carries potentially useful information. Specifically, the abundances of clumped isotopologues in an equilibrated system are a function of temperature and thus knowledge of their abundances can be used to calculate a sample’s formation temperature. In this thesis, measurements of clumped isotopologues are made on both carbonate-bearing minerals and methane gas in order to better constrain the environmental and geological histories of various samples.

Clumped-isotope-based measurements of ancient carbonate-bearing minerals, including apatites, have opened up paleotemperature reconstructions to a variety of systems and time periods. However, a critical issue when using clumped-isotope based measurements to reconstruct ancient mineral formation temperatures is whether the samples being measured have faithfully recorded their original internal isotopic distributions. These original distributions can be altered, for example, by diffusion of atoms in the mineral lattice or through diagenetic reactions. Understanding these processes quantitatively is critical for the use of clumped isotopes to reconstruct past temperatures, quantify diagenesis, and calculate time-temperature burial histories of carbonate minerals. In order to help orient this part of the thesis, Chapter 2 provides a broad overview and history of clumped-isotope based measurements in carbonate minerals.

In Chapter 3, the effects of elevated temperatures on a sample’s clumped-isotope composition are probed in both natural and experimental apatites (which contain structural carbonate groups) and calcites. A quantitative model is created that is calibrated by the experiments and consistent with the natural samples. The model allows for calculations of the change in a sample’s clumped isotope abundances as a function of any time-temperature history.

In Chapter 4, the effects of diagenesis on the stable isotopic compositions of apatites are explored on samples from a variety of sedimentary phosphorite deposits. Clumped isotope temperatures and bulk isotopic measurements from carbonate and phosphate groups are compared for all samples. These results demonstrate that samples have experienced isotopic exchange of oxygen atoms in both the carbonate and phosphate groups. A kinetic model is developed that allows for the calculation of the amount of diagenesis each sample has experienced and yields insight into the physical and chemical processes of diagenesis.

The thesis then switches gear and turns its attention to clumped isotope measurements of methane. Methane is critical greenhouse gas, energy resource, and microbial metabolic product and substrate. Despite its importance both environmentally and economically, much about methane’s formational mechanisms and the relative sources of methane to various environments remains poorly constrained. In order to add new constraints to our understanding of the formation of methane in nature, I describe the development and application of methane clumped isotope measurements to environmental deposits of methane. To help orient the reader, a brief overview of the formation of methane in both high and low temperature settings is given in Chapter 5.

In Chapter 6, a method for the measurement of methane clumped isotopologues via mass spectrometry is described. This chapter demonstrates that the measurement is precise and accurate. Additionally, the measurement is calibrated experimentally such that measurements of methane clumped isotope abundances can be converted into equivalent formational temperatures. This study represents the first time that methane clumped isotope abundances have been measured at useful precisions.

In Chapter 7, the methane clumped isotope method is applied to natural samples from a variety of settings. These settings include thermogenic gases formed and reservoired in shales, migrated thermogenic gases, biogenic gases, mixed biogenic and thermogenic gas deposits, and experimentally generated gases. In all cases, calculated clumped isotope temperatures make geological sense as formation temperatures or mixtures of high and low temperature gases. Based on these observations, we propose that the clumped isotope temperature of an unmixed gas represents its formation temperature — this was neither an obvious nor expected result and has important implications for how methane forms in nature. Additionally, these results demonstrate that methane-clumped isotope compositions provided valuable additional constraints to studying natural methane deposits.

Scheme for unconventional geometric quantum computation in cavity QED

In this paper, we present a scheme for implementing the unconventional geometric two-qubit phase gate with nonzero dynamical phase based on two-channel Raman interaction of two atoms in a cavity. We show that the dynamical phase and the total phase for a cyclic evolution are proportional to the geometric phase in the same cyclic evolution; hence they possess the same geometric features as does the geometric phase. In our scheme, the atomic excited state is adiabatically eliminated, and the operation of the proposed logic gate involves only the metastable states of the atoms; thus the effect of the atomic spontaneous emission can be neglected. The influence of the cavity decay on our scheme is examined. It is found that the relations regarding the dynamical phase, the total phase, and the geometric phase in the ideal situation are still valid in the case of weak cavity decay. Feasibility and the effect of the phase fluctuations of the driving laser fields are also discussed.

Horizontal Bloch line motion in magnetic bubble materials

The purpose of this work is to extend experimental and theoretical understanding of horizontal Bloch line (HBL) motion in magnetic bubble materials. The present theory of HBL motion is reviewed, and then extended to include transient effects in which the internal domain wall structure changes with time. This is accomplished by numerically solving the equations of motion for the internal azimuthal angle ɸ and the wall position q as functions of z, the coordinate perpendicular to the thin-film material, and time. The effects of HBL's on domain wall motion are investigated by comparing results from wall oscillation experiments with those from the theory. In these experiments, a bias field pulse is used to make a step change in equilibrium position of either bubble or stripe domain walls, and the wall response is measured by using transient photography. During the initial response, the dynamic wall structure closely resembles the initial static structure. The wall accelerates to a relatively high velocity (≈20 m/sec), resulting in a short (≈22 nsec ) section of initial rapid motion. An HBL gradually forms near one of the film surfaces as a result of local dynamic properties, and moves along the wall surface toward the film center. The presence of this structure produces low-frequency, triangular-shaped oscillations in which the experimental wall velocity is nearly constant, v_s≈ 5-8 m/sec. If the HBL reaches the opposite surface, i.e., if the average internal angle reaches an integer multiple of π, the momentum stored in the HBL is lost, and the wall chirality is reversed. This results in abrupt transitions to overdamped motion and changes in wall chirality, which are observed as a function of bias pulse amplitude. The pulse amplitude at which the n^th punch- through occurs just as the wall reaches equilibrium is given within 0.2 0e by H_n = (2v_sH'/γ)^1/2 • (nπ)^1/2 + H_sv), where H' is the effective field gradient from the surrounding domains, and H_sv is a small (less than 0.03 0e), effective drag field. Observations of wall oscillation in the presence of in-plane fields parallel to the wall show that HBL formation is suppressed by fields greater than about 40 0e (≈2πM_s), resulting in the high-frequency, sinusoidal oscillations associated with a simple internal wall structure.

On the Role of Delays in Biological Systems : Analysis and Design

This work quantifies the nature of delays in genetic regulatory networks and their effect on system dynamics. It is known that a time lag can emerge from a sequence of biochemical reactions. Applying this modeling framework to the protein production processes, delay distributions are derived in a stochastic (probability density function) and deterministic setting (impulse function), whilst being shown to be equivalent under different assumptions. The dependence of the distribution properties on rate constants, gene length, and time-varying temperatures is investigated. Overall, the distribution of the delay in the context of protein production processes is shown to be highly dependent on the size of the genes and mRNA strands as well as the reaction rates. Results suggest longer genes have delay distributions with a smaller relative variance, and hence, less uncertainty in the completion times, however, they lead to larger delays. On the other hand large uncertainties may actually play a positive role, as broader distributions can lead to larger stability regions when this formalization of the protein production delays is incorporated into a feedback system.

Furthermore, evidence suggests that delays may play a role as an explicit design into existing controlling mechanisms. Accordingly, the reccurring dual-feedback motif is also investigated with delays incorporated into the feedback channels. The dual-delayed feedback is shown to have stabilizing effects through a control theoretic approach. Lastly, a distributed delay based controller design method is proposed as a potential design tool. In a preliminary study, the dual-delayed feedback system re-emerges as an effective controller design.

Quantum superchemistry in an output coupler of coherent matter waves

We investigate the quantum superchemistry or Bose-enhanced atom-molecule conversions in a coherent output coupler of matter waves, as a simple generalization of the two-color photoassociation. The stimulated effects of molecular output step and atomic revivals are exhibited by steering the rf output couplings. The quantum noise-induced molecular damping occurs near a total conversion in a levitation trap. This suggests a feasible two-trap scheme to make a stable coherent molecular beam.