Design and Implementation of a Framework for the Interconnection of Cellular Automata in Software and Hardware

There has been a move recently in academia, industry, and the consumer space towards the use of unsupervised parallel computation and distributed networks (i.e., networks of computing elements working together to achieve a global outcome with only local knowledge). To fully understand the types of problems that these systems are applied to regularly, a representative member of this group of unsupervised parallel and distributed systems is needed to allow the development of generalizable results. Although not the only potential candidate, the field of cellular automata is an excellent choice for analyzing how these systems work as it is one of the simplest members of this group in terms of design specification. The current ability of the field of cellular automata to represent the realm of unsupervised parallel and distributed systems is limited to only a subset of the possible systems, which leads to the main goal of this work of finding a method of allowing cellular automata to represent a much larger range of systems. To achieve this goal, a conceptual framework has been developed that allows the definition of interconnected systems of cellular automata that can represent most, if not all, unsupervised parallel and distributed systems. The framework introduces the concept of allowing the boundary conditions of a cellular automaton to be defined by a separately specified system, which can be any system that is capable of producing the information needed, including another cellular automaton. Using this interconnection concept, two forms of computational simplification are enabled: the deconstruction of a large system into smaller, modular pieces; and the construction of a large system built from a heterogeneous set of smaller pieces. This framework is formally defined using an interconnection graph, where edges signify the flow of information from one node to the next and the nodes are the various systems involved. A library has been designed which implements the interconnection graphs defined by the framework for a subset of the possible nodes, primarily to allow an exploration of the field of cellular automata as a potential representational member of unsupervised parallel and distributed systems. This library has been developed with a number of criteria in mind that will allow it to be instantiated on both hardware and software using an open and extendable architecture to enable interaction with external systems and future expansion to take into account novel research. This extendability is discussed in terms of combining the library with genetic algorithms to find an interconnected system that will satisfy a specific computational goal. There are also a number of novel components of the library that further enhance the capabilities of potential research, including methods for automatically building interconnection graphs from sets of cellular automata and the ability to skip over static regions of a given cellular automaton in an intelligent way to reduce computation time. With a particular set of cellular automaton parameters, the use of this feature reduced the computation time by 75%. As a demonstration of the usefulness of both the library and the framework that it implements, a hardware application has been developed which makes use of many of the novel aspects that have been introduced to produce an interactive art installation named 'Aurora'. This application has a number of design requirements that are directly achieved through the use of library components and framework definitions. These design requirements included a lack of centralized control or data storage, a need for visibly dynamic behaviour in the installation, and the desire for the visitors to the installation to be able to affect the visible movement of patterns across the surface of the piece. The success of the library in this application was heavily dependent on its instantiation on a mixture of hardware and software, as well as the ability to extend the library to suit particular needs and aspects of the specific application requirements. The main goal of this thesis research, finding a method that allows cellular automata to represent a much larger range of unsupervised parallel and distributed systems, has been partially achieved in the creation of a novel framework which defines the concept of interconnection, and the design of an interconnection graph using this concept. This allows the field of cellular automata, in combination with the framework, to be an excellent representational member of an extended set of unsupervised parallel and distributed systems when compared to the field alone. A library has been developed that satisfies a broad set of design criteria that allow it to be used in any future research built on the use of cellular automata as this representational member. A hardware application was successfully created that makes use of a number of novel aspects of both the framework and the library to demonstrate their applicability in a real world situation

Dynamic Balance and Gait Metrics for Robotic Bipeds

For legged robots to be useful in the real world, they must be able to balance and walk reliably. Both of these abilities improve when a system is more effective at moving itself around relative to its contacts (i.e., its feet). Achieving this type of movement depends both on the controller used to perform the motion and the physical properties of the system. Although much work has been done on the development of dynamic controllers for balance and gait, only limited research exists on how to quantify a system’s physical balance capabilities or how to modify the system to improve those capabilities. From the control perspective, there are three strategies for maintaining balance in bipeds: flexing, leaning, and stepping. Both stepping and leaning strategies typically depend on balance points (critical points used for maintaining or regaining balance) to determine whether or not a step is needed, and if so, where to step. Although several balance point estimators exist, the majority of these methods make undesirable assumptions (e.g., ignoring the impact dynamics, assuming massless legs, planar motion, etc.). From the physical design perspective, one promising approach for analyzing system performance is a set of dynamic ratios called velocity and momentum gains, which are dependent only on the (scale-invariant) dynamic parameters and instantaneous configuration of a system, enabling entire classes of mechanisms to be analyzed at the same time. This thesis makes four key contributions towards improving biped balancing capabilities. First, a dynamic bipedal controller is proposed which uses a 3D balance point estimator both to respond to disturbances and produce reliable stepping. Second, a novel balance point estimator is proposed that facilitates stepping while combining and expanding the features of existing 2D and 3D estimators to produce a generalized 3D formulation. Third, the momentum gain formulation is extended to general 2D and 3D systems, then both gains are compared to centroidal momentum via a spatial formulation and incorporated into a generalized gain definition. Finally, the gains are used as a metric in an optimization framework to design parameterized balancing mechanisms within a given configuration space. Effectively, this enables an optimization of how well a system could balance without the need to pre-specify or co-generate controllers and/or trajectories. To validate the control contributions, simulated bipeds are subjected to external disturbances while standing still and walking. For the gain contributions, the framework is used to compare gain-optimized mechanisms to those based on the cost of transport metric. Through the combination of gain-based physical design optimization and the use of predictive, real-time balance point estimators within dynamic controllers, bipeds and other legged systems will soon be able to achieve reliable balance and gait in the real world

Virtualization for a Network Processor Runtime System

The continuing ossification of the Internet is slowing the pace of network innovation. Network diversification presents one solution to this problem, by virtualizing the network at multiple layers. Diversified networks consist of a shared physical substrate, virtual routers (metarouters), and virtual links (metalinks). Virtualizing routers enables smooth and incremental upgrades to new network services. Our current priority for a diversified router prototype is to enable reserved slices of the network for researchers to perform repeatable, high-speed network experiments. General-purpose processors have well established techniques for virtualization, but do not scale efficiently to multi-gigabit speeds. To achieve these speeds, we employ network processors (NPs), typically consisting of multicore, multi-threaded processors with asymmetric, heterogeneous memories. The complexity and lack of hardware thread isolation in NP’s, combined with a lack of simple programming models, creates numerous challenges for effective sharing between metarouters. In this paper, we detail strategies for enabling NP virtualization at the link, memory, and processor levels, to better enable a research infrastructure for network innovation

The peptidoglycan-associated protein NapA plays an important role in the envelope integrity and in the pathogenesis of the lyme disease spirochete.

The bacterial pathogen responsible for causing Lyme disease, Borrelia burgdorferi, is an atypical Gram-negative spirochete that is transmitted to humans via the bite of an infected Ixodes tick. In diderms, peptidoglycan (PG) is sandwiched between the inner and outer membrane of the cell envelope. In many other Gram-negative bacteria, PG is bound by protein(s), which provide both structural integrity and continuity between envelope layers. Here, we present evidence of a peptidoglycan-associated protein (PAP) in B. burgdorferi. Using an unbiased proteomics approach, we identified Neutrophil Attracting Protein A (NapA) as a PAP. Interestingly, NapA is a Dps homologue, which typically functions to bind and protect cellular DNA from damage during times of stress. While B. burgdorferi NapA is known to be involved in the oxidative stress response, it lacks the critical residues necessary for DNA binding. Biochemical and cellular studies demonstrate that NapA is localized to the B. burgdorferi periplasm and is indeed a PAP. Cryo-electron microscopy indicates that mutant bacteria, unable to produce NapA, have structural abnormalities. Defects in cell-wall integrity impact growth rate and cause the napA mutant to be more susceptible to osmotic and PG-specific stresses. NapA-linked PG is secreted in outer membrane vesicles and augments IL-17 production, relative to PG alone. Using microfluidics, we demonstrate that NapA acts as a molecular beacon-exacerbating the pathogenic properties of B. burgdorferi PG. These studies further our understanding of the B. burgdorferi cell envelope, provide critical information that underlies its pathogenesis, and highlight how a highly conserved bacterial protein can evolve mechanistically, while maintaining biological function