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.

Neural routing circuits for forming invariant representations of visual objects

This thesis presents a biologically plausible model of an attentional mechanism for forming position- and scale-invariant representations of objects in the visual world. The model relies on a set of control neurons to dynamically modify the synaptic strengths of intra-cortical connections so that information from a windowed region of primary visual cortex (Vl) is selectively routed to higher cortical areas. Local spatial relationships (i.e., topography) within the attentional window are preserved as information is routed through the cortex, thus enabling attended objects to be represented in higher cortical areas within an object-centered reference frame that is position and scale invariant. The representation in V1 is modeled as a multiscale stack of sample nodes with progressively lower resolution at higher eccentricities. Large changes in the size of the attentional window are accomplished by switching between different levels of the multiscale stack, while positional shifts and small changes in scale are accomplished by translating and rescaling the window within a single level of the stack. The control signals for setting the position and size of the attentional window are hypothesized to originate from neurons in the pulvinar and in the deep layers of visual cortex. The dynamics of these control neurons are governed by simple differential equations that can be realized by neurobiologically plausible circuits. In pre-attentive mode, the control neurons receive their input from a low-level "saliency map" representing potentially interesting regions of a scene. During the pattern recognition phase, control neurons are driven by the interaction between top-down (memory) and bottom-up (retinal input) sources. The model respects key neurophysiological, neuroanatomical, and psychophysical data relating to attention, and it makes a variety of experimentally testable predictions.

Oceans and human health: Sentinel habitats and sentinel species

The health of the oceans and people are inextricably linked. For many years we focused research and policy on anthropogenic impacts to oceans and coasts. Recently we have started to think about how the health of the oceans affects us. In response to the Oceans and Human Health Act of 2004, a NOAA initiative was created to explore the “One Health” of the oceans and coasts. The Center of Excellence in Oceans and Human Health at Hollings Marine Laboratory (HML) is one of three Centers dedicated to understanding the connections and forecasting changes in ocean and coastal health and human health. The Center at HML is developing new tools and approaches, including sentinel habitats and sentinel species, to evaluate linkages between ecological process and human health and wellbeing. The results provide environmental and public health managers, policy-makers and communities forecasts and assessments to improve ecosystem-based management that protects health and mitigates risks for the oceans, coasts and people.(PDF contains 4 pages)

Coastal resource planning system: Integrating evaluation of ecological integrity and ecosystem services valuation

Efficient and effective coastal management decisions rely on knowledge of the impact of human activities on ecosystem integrity, vulnerable species, and valued ecosystem services—collectively, human impact on environmental quality (EQ). Ecosystem-based management (EBM) is an emerging approach to address the dynamics and complexities of coupled social-ecological systems. EBM “is intended to directly address the long-term sustainable delivery of ecosystem services and the resilience of marine ecosystems to perturbations” (Rosenberg and Sandifer, 2009). The lack of a tool that integrates human choices with the ecological connections between contributing watersheds and nearshore areas, and that incorporates valuation of ecosystem services, is a critical missing piece needed for effective and efficient coastal management. To address the need for an integrative tool for evaluation of human impacts on ecosystems and their services, Battelle developed the EcoVal™ Environmental Quality Evaluation System. The EcoVal system is an updated (2009) version of the EQ Evaluation System for Water Resources developed by Battelle for the U.S. Bureau of Reclamation (Dee et al., 1972). The Battelle EQ evaluation system has a thirty-year history of providing a standard approach to evaluate watershed EQ. This paper describes the conceptual approach and methodology of the updated EcoVal system and its potential application to coastal ecosystems. (PDF contains 4 pages)

Four essays on the empirical analysis of political ideology

This thesis examines four distinct facets and methods for understanding political ideology, and so it includes four distinct chapters with only moderate connections between them. Chapter 2 examines how reactions to emotional stimuli vary with political opinion, and how the stimuli can produce changes in an individuals political preferences. Chapter 3 examines the connection between self-reported fear and item nonresponse on surveys. Chapter 4 examines the connection between political and moral consistency with low-dimensional ideology, and Chapter 5 develops a technique for estimating ideal points and salience in a low-dimensional ideological space.

Beyond Watson and Crick : programming the self-assembly and reconfiguration of DNA nanostructures based on stacking interactions

Life is the result of the execution of molecular programs: like how an embryo is fated to become a human or a whale, or how a person’s appearance is inherited from their parents, many biological phenomena are governed by genetic programs written in DNA molecules. At the core of such programs is the highly reliable base pairing interaction between nucleic acids. DNA nanotechnology exploits the programming power of DNA to build artificial nanostructures, molecular computers, and nanomachines. In particular, DNA origami—which is a simple yet versatile technique that allows one to create various nanoscale shapes and patterns—is at the heart of the technology. In this thesis, I describe the development of programmable self-assembly and reconfiguration of DNA origami nanostructures based on a unique strategy: rather than relying on Watson-Crick base pairing, we developed programmable bonds via the geometric arrangement of stacking interactions, which we termed stacking bonds. We further demonstrated that such bonds can be dynamically reconfigurable.

The first part of this thesis describes the design and implementation of stacking bonds. Our work addresses the fundamental question of whether one can create diverse bond types out of a single kind of attractive interaction—a question first posed implicitly by Francis Crick while seeking a deeper understanding of the origin of life and primitive genetic code. For the creation of multiple specific bonds, we used two different approaches: binary coding and shape coding of geometric arrangement of stacking interaction units, which are called blunt ends. To construct a bond space for each approach, we performed a systematic search using a computer algorithm. We used orthogonal bonds to experimentally implement the connection of five distinct DNA origami nanostructures. We also programmed the bonds to control cis/trans configuration between asymmetric nanostructures.

The second part of this thesis describes the large-scale self-assembly of DNA origami into two-dimensional checkerboard-pattern crystals via surface diffusion. We developed a protocol where the diffusion of DNA origami occurs on a substrate and is dynamically controlled by changing the cationic condition of the system. We used stacking interactions to mediate connections between the origami, because of their potential for reconfiguring during the assembly process. Assembling DNA nanostructures directly on substrate surfaces can benefit nano/microfabrication processes by eliminating a pattern transfer step. At the same time, the use of DNA origami allows high complexity and unique addressability with six-nanometer resolution within each structural unit.

The third part of this thesis describes the use of stacking bonds as dynamically breakable bonds. To break the bonds, we used biological machinery called the ParMRC system extracted from bacteria. The system ensures that, when a cell divides, each daughter cell gets one copy of the cell’s DNA by actively pushing each copy to the opposite poles of the cell. We demonstrate dynamically expandable nanostructures, which makes stacking bonds a promising candidate for reconfigurable connectors for nanoscale machine parts.

Convex analysis for minimizing and learning submodular set functions

The connections between convexity and submodularity are explored, for purposes of minimizing and learning submodular set functions.

First, we develop a novel method for minimizing a particular class of submodular functions, which can be expressed as a sum of concave functions composed with modular functions. The basic algorithm uses an accelerated first order method applied to a smoothed version of its convex extension. The smoothing algorithm is particularly novel as it allows us to treat general concave potentials without needing to construct a piecewise linear approximation as with graph-based techniques.

Second, we derive the general conditions under which it is possible to find a minimizer of a submodular function via a convex problem. This provides a framework for developing submodular minimization algorithms. The framework is then used to develop several algorithms that can be run in a distributed fashion. This is particularly useful for applications where the submodular objective function consists of a sum of many terms, each term dependent on a small part of a large data set.

Lastly, we approach the problem of learning set functions from an unorthodox perspective---sparse reconstruction. We demonstrate an explicit connection between the problem of learning set functions from random evaluations and that of sparse signals. Based on the observation that the Fourier transform for set functions satisfies exactly the conditions needed for sparse reconstruction algorithms to work, we examine some different function classes under which uniform reconstruction is possible.

State-dependent modulation of neuronal circuits in C. elegans sleep

C. elegans is a compact system of 302 neurons with identifiable and mapped connections that makes it ideal for systems analysis. This work is a demonstration of what I have been able to learn about the nature of state-specific modulation and reversibility during a state called lethargus, a sleep-like state in the worm. I begin with description about the nervous system of the worm, the nature of sleep in the worm, the questions about behavior and its apparent circuit properties, the tools available and used to manipulate the nervous system, and what I have been able to learn from these studies. I end with clues that the physiology helps to teach us about the dynamics of state specific modulation, what makes sleep so different from other states, and how we can use these measurements to understand which modulators, neurotransmitters, and channels can be used to create different dynamics in a simple model system.

From bilateral two-way to unilateral one-way flow link-formation

Documento de trabajo

Wireless parylene-based retinal implant

The degeneration of the outer retina usually causes blindness by affecting the photoreceptor cells. However, the ganglion cells, which consist of optic nerves, on the middle and inner retina layers are often intact. The retinal implant, which can partially restore vision by electrical stimulation, soon becomes a focus for research. Although many groups worldwide have spent a lot of effort on building devices for retinal implant, current state-of-the-art technologies still lack a reliable packaging scheme for devices with desirable high-density multi-channel features. Wireless flexible retinal implants have always been the ultimate goal for retinal prosthesis. In this dissertation, the reliable packaging scheme for a wireless flexible parylene-based retinal implants has been well developed. It can not only provide stable electrical and mechanical connections to the high-density multi-channel (1000+ channels on 5 mm × 5 mm chip area) IC chips, but also survive for more than 10 years in the human body with corrosive fluids.

The device is based on a parylene-metal-parylene sandwich structure. In which, the adhesion between the parylene layers and the metals embedded in the parylene layers have been studied. Integration technology for high-density multi-channel IC chips has also been addressed and tested with dummy and real 268-channel and 1024-channel retinal IC chips. In addition, different protection schemes have been tried in application to IC chips and discrete components to gain the longest lifetime. The effectiveness has been confirmed by the accelerated and active lifetime soaking test in saline solution. Surgical mockups have also been designed and successfully implanted inside dog's and pig's eyes. Additionally, the electrodes used to stimulate the ganglion cells have been modified to lower the interface impedance and shaped to better fit the retina. Finally, all the developed technologies have been applied on the final device with a dual-metal-layer structure.

Damage detection in civil structures using high-frequency seismograms

The dynamic properties of a structure are a function of its physical properties, and changes in the physical properties of the structure, including the introduction of structural damage, can cause changes in its dynamic behavior. Structural health monitoring (SHM) and damage detection methods provide a means to assess the structural integrity and safety of a civil structure using measurements of its dynamic properties. In particular, these techniques enable a quick damage assessment following a seismic event. In this thesis, the application of high-frequency seismograms to damage detection in civil structures is investigated.

Two novel methods for SHM are developed and validated using small-scale experimental testing, existing structures in situ, and numerical testing. The first method is developed for pre-Northridge steel-moment-resisting frame buildings that are susceptible to weld fracture at beam-column connections. The method is based on using the response of a structure to a nondestructive force (i.e., a hammer blow) to approximate the response of the structure to a damage event (i.e., weld fracture). The method is applied to a small-scale experimental frame, where the impulse response functions of the frame are generated during an impact hammer test. The method is also applied to a numerical model of a steel frame, in which weld fracture is modeled as the tensile opening of a Mode I crack. Impulse response functions are experimentally obtained for a steel moment-resisting frame building in situ. Results indicate that while acceleration and velocity records generated by a damage event are best approximated by the acceleration and velocity records generated by a colocated hammer blow, the method may not be robust to noise. The method seems to be better suited for damage localization, where information such as arrival times and peak accelerations can also provide indication of the damage location. This is of significance for sparsely-instrumented civil structures.

The second SHM method is designed to extract features from high-frequency acceleration records that may indicate the presence of damage. As short-duration high-frequency signals (i.e., pulses) can be indicative of damage, this method relies on the identification and classification of pulses in the acceleration records. It is recommended that, in practice, the method be combined with a vibration-based method that can be used to estimate the loss of stiffness. Briefly, pulses observed in the acceleration time series when the structure is known to be in an undamaged state are compared with pulses observed when the structure is in a potentially damaged state. By comparing the pulse signatures from these two situations, changes in the high-frequency dynamic behavior of the structure can be identified, and damage signals can be extracted and subjected to further analysis. The method is successfully applied to a small-scale experimental shear beam that is dynamically excited at its base using a shake table and damaged by loosening a screw to create a moving part. Although the damage is aperiodic and nonlinear in nature, the damage signals are accurately identified, and the location of damage is determined using the amplitudes and arrival times of the damage signal. The method is also successfully applied to detect the occurrence of damage in a test bed data set provided by the Los Alamos National Laboratory, in which nonlinear damage is introduced into a small-scale steel frame by installing a bumper mechanism that inhibits the amount of motion between two floors. The method is successfully applied and is robust despite a low sampling rate, though false negatives (undetected damage signals) begin to occur at high levels of damage when the frequency of damage events increases. The method is also applied to acceleration data recorded on a damaged cable-stayed bridge in China, provided by the Center of Structural Monitoring and Control at the Harbin Institute of Technology. Acceleration records recorded after the date of damage show a clear increase in high-frequency short-duration pulses compared to those previously recorded. One undamage pulse and two damage pulses are identified from the data. The occurrence of the detected damage pulses is consistent with a progression of damage and matches the known chronology of damage.

Three-dimensional nonlinear inelastic analysis of steel moment-frame buildings damaged by earthquake excitations

The Northridge earthquake of January 17, 1994, highlighted the two previously known problems of premature fracturing of connections and the damaging capabilities of near-source ground motion pulses. Large ground motions had not been experienced in a city with tall steel moment-frame buildings before. Some steel buildings exhibited fracture of welded connections or other types of structural degradation.

A sophisticated three-dimensional nonlinear inelastic program is developed that can accurately model many nonlinear properties commonly ignored or approximated in other programs. The program can assess and predict severely inelastic response of steel buildings due to strong ground motions, including collapse.

Three-dimensional fiber and segment discretization of elements is presented in this work. This element and its two-dimensional counterpart are capable of modeling various geometric and material nonlinearities such as moment amplification, spread of plasticity and connection fracture. In addition to introducing a three-dimensional element discretization, this work presents three-dimensional constraints that limit the number of equations required to solve various three-dimensional problems consisting of intersecting planar frames.

Two buildings damaged in the Northridge earthquake are investigated to verify the ability of the program to match the level of response and the extent and location of damage measured. The program is used to predict response of larger near-source ground motions using the properties determined from the matched response.

A third building is studied to assess three-dimensional effects on a realistic irregular building in the inelastic range of response considering earthquake directivity. Damage levels are observed to be significantly affected by directivity and torsional response.

Several strong recorded ground motions clearly exceed code-based levels. Properly designed buildings can have drifts exceeding code specified levels due to these ground motions. The strongest ground motions caused collapse if fracture was included in the model. Near-source ground displacement pulses can cause columns to yield prior to weaker-designed beams. Damage in tall buildings correlates better with peak-to-peak displacements than with peak-to-peak accelerations.

Dynamic response of tall buildings shows that higher mode response can cause more damage than first mode response. Leaking of energy between modes in conjunction with damage can cause torsional behavior that is not anticipated.

Various response parameters are used for all three buildings to determine what correlations can be made for inelastic building response. Damage levels can be dramatically different based on the inelastic model used. Damage does not correlate well with several common response parameters.

Realistic modeling of material properties and structural behavior is of great value for understanding the performance of tall buildings due to earthquake excitations.

Expression of eph-family receptor tyrosine kinases and ephrins in the tadpole of the frog Xenopus laevis, and possible roles in the development of retinotectal topography

Assembling a nervous system requires exquisite specificity in the construction of neuronal connectivity. One method by which such specificity is implemented is the presence of chemical cues within the tissues, differentiating one region from another, and the presence of receptors for those cues on the surface of neurons and their axons that are navigating within this cellular environment.

Connections from one part of the nervous system to another often take the form of a topographic mapping. One widely studied model system that involves such a mapping is the vertebrate retinotectal projection-the set of connections between the eye and the optic tectum of the midbrain, which is the primary visual center in non-mammals and is homologous to the superior colliculus in mammals. In this projection the two-dimensional surface of the retina is mapped smoothly onto the two-dimensional surface of the tectum, such that light from neighboring points in visual space excites neighboring cells in the brain. This mapping is implemented at least in part via differential chemical cues in different regions of the tectum.

The Eph family of receptor tyrosine kinases and their cell-surface ligands, the ephrins, have been implicated in a wide variety of processes, generally involving cellular movement in response to extracellular cues. In particular, they possess expression patterns-i.e., complementary gradients of receptor in retina and ligand in tectum- and in vitro and in vivo activities and phenotypes-i.e., repulsive guidance of axons and defective mapping in mutants, respectively-consistent with the long-sought retinotectal chemical mapping cues.

The tadpole of Xenopus laevis, the South African clawed frog, is advantageous for in vivo retinotectal studies because of its transparency and manipulability. However, neither the expression patterns nor the retinotectal roles of these proteins have been well characterized in this system. We report here comprehensive descriptions in swimming stage tadpoles of the messenger RNA expression patterns of eleven known Xenopus Eph and ephrin genes, including xephrin-A3, which is novel, and xEphB2, whose expression pattern has not previously been published in detail. We also report the results of in vivo protein injection perturbation studies on Xenopus retinotectal topography, which were negative, and of in vitro axonal guidance assays, which suggest a previously unrecognized attractive activity of ephrins at low concentrations on retinal ganglion cell axons. This raises the possibility that these axons find their correct targets in part by seeking out a preferred concentration of ligands appropriate to their individual receptor expression levels, rather than by being repelled to greater or lesser degrees by the ephrins but attracted by some as-yet-unknown cue(s).

Earthquake response of steel braces and braced steel frames

This thesis consists of three parts. Chapter 2 deals with the dynamic buckling behavior of steel braces under cyclic axial end displacement. Braces under such a loading condition belong to a class of "acceleration magnifying" structural components, in which a small motion at the loading points can cause large internal acceleration and inertia. This member-level inertia is frequently ignored in current studies of braces and braced structures. This chapter shows that, under certain conditions, the inclusion of the member-level inertia can lead to brace behavior fundamentally different from that predicted by the quasi-static method. This result is to have significance in the correct use of the quasi-static, pseudo-dynamic and static condensation methods in the simulation of braces or braced structures under dynamic loading. The strain magnitude and distribution in the braces are also studied in this chapter.

Chapter 3 examines the effect of column uplift on the earthquake response of braced steel frames and explores the feasibility of flexible column-base anchoring. It is found that fully anchored braced-bay columns can induce extremely large internal forces in the braced-bay members and their connections, thus increasing the risk of failures observed in recent earthquakes. Flexible braced-bay column anchoring can significantly reduce the braced bay member force, but at the same time also introduces large story drift and column uplift. The pounding of an uplifting column with its support can result in very high compressive axial force.

Chapter 4 conducts a comparative study on the effectiveness of a proposed non-buckling bracing system and several conventional bracing systems. The non-buckling bracing system eliminates buckling and thus can be composed of small individual braces distributed widely in a structure to reduce bracing force concentration and increase redundancy. The elimination of buckling results in a significantly more effective bracing system compared with the conventional bracing systems. Among the conventional bracing systems, bracing configurations and end conditions for the bracing members affect the effectiveness.

The studies in Chapter 3 and Chapter 4 also indicate that code-designed conventionally braced steel frames can experience unacceptably severe response under the strong ground motions recorded during the recent Northridge and Kobe earthquakes.

Neural network design for switching network control

A neural network is a highly interconnected set of simple processors. The many connections allow information to travel rapidly through the network, and due to their simplicity, many processors in one network are feasible. Together these properties imply that we can build efficient massively parallel machines using neural networks. The primary problem is how do we specify the interconnections in a neural network. The various approaches developed so far such as outer product, learning algorithm, or energy function suffer from the following deficiencies: long training/ specification times; not guaranteed to work on all inputs; requires full connectivity.

Alternatively we discuss methods of using the topology and constraints of the problems themselves to design the topology and connections of the neural solution. We define several useful circuits-generalizations of the Winner-Take-All circuitthat allows us to incorporate constraints using feedback in a controlled manner. These circuits are proven to be stable, and to only converge on valid states. We use the Hopfield electronic model since this is close to an actual implementation. We also discuss methods for incorporating these circuits into larger systems, neural and nonneural. By exploiting regularities in our definition, we can construct efficient networks. To demonstrate the methods, we look to three problems from communications. We first discuss two applications to problems from circuit switching; finding routes in large multistage switches, and the call rearrangement problem. These show both, how we can use many neurons to build massively parallel machines, and how the Winner-Take-All circuits can simplify our designs.

Next we develop a solution to the contention arbitration problem of high-speed packet switches. We define a useful class of switching networks and then design a neural network to solve the contention arbitration problem for this class. Various aspects of the neural network/switch system are analyzed to measure the queueing performance of this method. Using the basic design, a feasible architecture for a large (1024-input) ATM packet switch is presented. Using the massive parallelism of neural networks, we can consider algorithms that were previously computationally unattainable. These now viable algorithms lead us to new perspectives on switch design.