Describing the FPGA-Based Hardware Architecture of Systemic Computation (HAoS)

his paper presents HAoS, the first hardware architecture of the bio-inspired computational paradigm known as Systemic Computation (SC). SC was designed to support the modelling of biological processes inherently by defining a massively parallel non-conventional computer architecture and a model of natural behaviour. In this work we describe a novel custom digital design, which addresses the SC architecture parallelism requirement by exploiting the inbuilt parallelism of a Field Programmable Gate Array (FPGA) and by using the highly efficient matching capability of a Ternary Content Addressable Memory (TCAM). Basic processing capabilities are embedded in HAoS in order to minimize time-demanding data transfers. Its custom instruction set can be expanded based on user requirements, since the optional use of a CPU provides high-level processing support if required. We demonstrate a functional simulation-verified prototype, which takes into consideration programmability and scalability, and review various communication interfaces between HAoS and the CPU. Analysis shows that the proposed architecture provides an effective solution in terms of efficiency versus flexibility trade-off and can potentially outperform prior implementations

Assessment of Multispectral Imaging System for UAS Navigation in a GPS-denied Environment

NPS NRP Technical ReportMultispectral (MS) imaging systems have been used for the detection, identification, and quantification in numerous environmental and military applications already. It is proposed to analyze feasibility of utilizing this emerging technology on small unmanned aerial vehicles (sUAS) for the purpose of enhancing accuracy and precision of object detection (identification), classification and tracking (DCT) that may contribute to a variety of downstream applications including threat detection, forensics, battle damage-assessment, additional/alternative aid to navigation (ATON) in the GPS-degraded or GPS-denied environments. This study assesses applicability and benefits of using a MS sensor as opposed to standard infrared (IR) and/or electro-optical (EO) sensors for DCT applications. It also includes an assessment of the computer-vision (CV) and artificial intelligence (AI) algorithms to quickly and reliably process the sensor output data. It is envisioned that a MicaSense RedEdge-MX or Altum like high-resolution global-shutter 5-band MS sensor integrated with a commercial-of-the-shelf (COTS) Group 1 or Group2 sUAS will be used to collect data to train a deep-learning (DL) convolutional neural network (DCNN) capable to handle one or two specific DCT problems to address the following research questions: Whether using multiple spectral bands has any benefits compared to a standard EO sensor or EO sensor combined with IR sensor? That includes benefits of having a spectral profile of surrounding background area and objects from the standpoint of more reliable/precise DCT. What are the limitations of using MS sensors and CV/AI algorithms to process data from the standpoint of operating environment, terrain, altitudes, object size and material, time of the day, weather, number of spectral bands, resolution, narrow field of view, addition of a downwelling light sensor)? What computational resources would be required to enable DTS capability aboard COTS sUAS The study will look at the requirements to such a system and its CONOPS, followed by conducting numerical experiments and field testing to gather and analyze data coming out of a MS imaging sensor. It is expected to involve SE, OC and CS students, and summarize all the findings in the final report.Naval Special Warfare Command (NAVSPECWARCOM)N9 - Warfare SystemsThis research is supported by funding from the Naval Postgraduate School, Naval Research Program (PE 0605853N/2098). https://nps.edu/nrpChief of Naval Operations (CNO)Approved for public release. Distribution is unlimited.

Single Molecule Studies of Myosin-Ib

Myosin-Is are the single-headed, membrane-associated members of the myosin superfamily that are found in many eukaryotic cells. These actin-based motors have been shown to play important roles in powering membrane dynamics, defining cytoskeletal structure, and regulating mechanical signal-transduction. However, many molecular details of myosin-I function are not known. My goal has been to determine the mechanical and kinetic properties of a myosin-I isoform (myo1b) as it undergoes its force-generating power stroke under physiological tension and when external mechanical loads are applied to it. We therefore characterized the force dependence of myo1b splice isoforms using an optical trap and a novel isometric force clamp. Myo1b is alternatively spliced within the regulatory domain of the molecule, yielding motors that have “lever-arms” with different lengths. We found the actin-attachment kinetics of all myo1b splice isoforms to be highly force sensitive, with forces of \u3c 2 pN decreasing the rate of actin detachment \u3e 75 fold. However, we found that the magnitude of the tension sensitivities depend on the splice isoform. Therefore, we propose that the tension sensing properties of myo1b are transcriptionally regulated. Finally, we found the tension sensitivity of myo1b to be regulated by calcium, such that micromolar calcium concentrations effectively uncouple the myosin active site from lever arm rotation. Taken together, this work supports a model in which myosin-Is play roles in generating and sustaining membrane tension, and that the mechanochemical properties of this protein are regulated by alternative splicing and calcium

MYO1C Binds to PiP2 With High Affinity Through a Putative Ph Domain

Myo1c is a member of the myosin superfamily that links the dynamic actin cytoskeleton to the membrane, and plays roles in mechano-signal transduction and membrane trafficking. We located and characterized two distinct membrane binding sites within the regulatory and tail domains of this myosin. We found that the tail domain binds tightly and specifically to PIP2 in a non-cooperative manner. It binds with slightly higher affinity to Ins(1,4,5)P3 as well as other inositol phosphates which may act as inhibitors to membrane binding in the cell. By sequence and secondary structure analysis, we identified this phosphatidylinositol binding site in the tail to be a putative pleckstrin homology (PH) domain. Point mutations of residues known to be essential for phosphatidylinositol binding in previously characterized PH domains inhibit myo1c binding to PIP2 in vitro and eradicate correct localization and membrane binding in vivo. The extended sequence of this binding site is conserved within many other myosin-Is across species, suggesting they also contain a putative PH domain. We also characterized a previously identified membrane binding site within the IQ motifs in the regulatory domain. This region is not phosphatidylinositol specific, but binds anionic phospholipids in a Ca2+ dependent manner; nevertheless, this site is not essential for in vivo membrane binding. As a result, we have determined that myo1c contains two lipid binding sites, a polybasic region that binds to high levels of PS in a Ca2+ dependent manner and a putative PH domain that binds tightly and specifically to phosphatidylinositols

A Practical Hardware Implementation of Systemic Computation

It is widely accepted that natural computation, such as brain computation, is far superior to typical computational approaches addressing tasks such as learning and parallel processing. As conventional silicon-based technologies are about to reach their physical limits, researchers have drawn inspiration from nature to found new computational paradigms. Such a newly-conceived paradigm is Systemic Computation (SC). SC is a bio-inspired model of computation. It incorporates natural characteristics and defines a massively parallel non-von Neumann computer architecture that can model natural systems efficiently. This thesis investigates the viability and utility of a Systemic Computation hardware implementation, since prior software-based approaches have proved inadequate in terms of performance and flexibility. This is achieved by addressing three main research challenges regarding the level of support for the natural properties of SC, the design of its implied architecture and methods to make the implementation practical and efficient. Various hardware-based approaches to Natural Computation are reviewed and their compatibility and suitability, with respect to the SC paradigm, is investigated. FPGAs are identified as the most appropriate implementation platform through critical evaluation and the first prototype Hardware Architecture of Systemic computation (HAoS) is presented. HAoS is a novel custom digital design, which takes advantage of the inbuilt parallelism of an FPGA and the highly efficient matching capability of a Ternary Content Addressable Memory. It provides basic processing capabilities in order to minimize time-demanding data transfers, while the optional use of a CPU provides high-level processing support. It is optimized and extended to a practical hardware platform accompanied by a software framework to provide an efficient SC programming solution. The suggested platform is evaluated using three bio-inspired models and analysis shows that it satisfies the research challenges and provides an effective solution in terms of efficiency versus flexibility trade-off

Quantitative Mass Spectrometric Analysis of RNA-Protein Cross-Links

In recent times much emphasis has been laid on revealing the composition and regulation of various RNP complexes. The structural studies of the RNP complexes provide a valuable insight into the binding modes and functional implications of interactions between the RNAs and RNA binding proteins within the complexes. To investigate the interactions of the RNA-binding proteins within RNP complexes, UV-induced cross-linking followed by mass spectrometry (MS) has proved to be a promising and straightforward technique. But the limitations of most of the purification methods as well as the intricate mass spectrometric data analysis have hampered the study of these RNP complexes. During the course of this study, the protocol was modified and optimized for the interaction analysis of large RNP complex assemblies like RNP complexes isolated from the HeLa nuclear extract which led to the identification of predicted as well as unknown RBMs. Moreover, the qualitative analysis of the protein-RNA cross-links derived from in vitro assembled Brat-NHL-hb RNA complex and CWC2-U6/U4 snRNAs complexes was also carried out. Based on the qualitative analysis of CWC2-U6/U4 cross-links, the quantitative analysis of protein-RNA cross-links has been established. The studies conducted during the research work have contributed in the identification and characterization of protein-RNA interactions within the aforementioned complexes and also provided the quantitative insight into the protein-RNA interactions.2020-03-0

Human Enhancement Technologies and Our Merger with Machines

A cross-disciplinary approach is offered to consider the challenge of emerging technologies designed to enhance human bodies and minds. Perspectives from philosophy, ethics, law, and policy are applied to a wide variety of enhancements, including integration of technology within human bodies, as well as genetic, biological, and pharmacological modifications. Humans may be permanently or temporarily enhanced with artificial parts by manipulating (or reprogramming) human DNA and through other enhancement techniques (and combinations thereof). We are on the cusp of significantly modifying (and perhaps improving) the human ecosystem. This evolution necessitates a continuing effort to re-evaluate current laws and, if appropriate, to modify such laws or develop new laws that address enhancement technology. A legal, ethical, and policy response to current and future human enhancements should strive to protect the rights of all involved and to recognize the responsibilities of humans to other conscious and living beings, regardless of what they look like or what abilities they have (or lack). A potential ethical approach is outlined in which rights and responsibilities should be respected even if enhanced humans are perceived by non-enhanced (or less-enhanced) humans as “no longer human” at all