Exploring space situational awareness using neuromorphic event-based cameras

The orbits around earth are a limited natural resource and one that hosts a vast range of vital space-based systems that support international systems use by both commercial industries, civil organisations, and national defence. The availability of this space resource is rapidly depleting due to the ever-growing presence of space debris and rampant overcrowding, especially in the limited and highly desirable slots in geosynchronous orbit. The field of Space Situational Awareness encompasses tasks aimed at mitigating these hazards to on-orbit systems through the monitoring of satellite traffic. Essential to this task is the collection of accurate and timely observation data. This thesis explores the use of a novel sensor paradigm to optically collect and process sensor data to enhance and improve space situational awareness tasks. Solving this issue is critical to ensure that we can continue to utilise the space environment in a sustainable way. However, these tasks pose significant engineering challenges that involve the detection and characterisation of faint, highly distant, and high-speed targets. Recent advances in neuromorphic engineering have led to the availability of high-quality neuromorphic event-based cameras that provide a promising alternative to the conventional cameras used in space imaging. These cameras offer the potential to improve the capabilities of existing space tracking systems and have been shown to detect and track satellites or ‘Resident Space Objects’ at low data rates, high temporal resolutions, and in conditions typically unsuitable for conventional optical cameras. This thesis presents a thorough exploration of neuromorphic event-based cameras for space situational awareness tasks and establishes a rigorous foundation for event-based space imaging. The work conducted in this project demonstrates how to enable event-based space imaging systems that serve the goals of space situational awareness by providing accurate and timely information on the space domain. By developing and implementing event-based processing techniques, the asynchronous operation, high temporal resolution, and dynamic range of these novel sensors are leveraged to provide low latency target acquisition and rapid reaction to challenging satellite tracking scenarios. The algorithms and experiments developed in this thesis successfully study the properties and trade-offs of event-based space imaging and provide comparisons with traditional observing methods and conventional frame-based sensors. The outcomes of this thesis demonstrate the viability of event-based cameras for use in tracking and space imaging tasks and therefore contribute to the growing efforts of the international space situational awareness community and the development of the event-based technology in astronomy and space science applications

Structure- and Ligand-Based Design of Novel Antimicrobial Agents

The use of computer based techniques in the design of novel therapeutic agents is a rapidly emerging field. Although the drug-design techniques utilized by Computational Medicinal Chemists vary greatly, they can roughly be classified into structure-based and ligand-based approaches. Structure-based methods utilize a solved structure of the design target, protein or DNA, usually obtained by X-ray or NMR methods to design or improve compounds with activity against the target. Ligand-based methods use active compounds with known affinity for a target that may yet be unresolved. These methods include Pharmacophore-based searching for novel active compounds or Quantitative Structure-Activity Relationship (QSAR) studies. The research presented here utilized both structure and ligand-based methods against two bacterial targets: Bacillus anthracis and Mycobacterium tuberculosis. The first part of this thesis details our efforts to design novel inhibitors of the enzyme dihydropteroate synthase from B. anthracis using crystal structures with known inhibitors bound. The second part describes a QSAR study that was performed using a series of novel nitrofuranyl compounds with known, whole-cell, inhibitory activity against M. tuberculosis. Dihydropteroate synthase (DHPS) catalyzes the addition of p-amino benzoic acid (pABA) to dihydropterin pyrophosphate (DHPP) to form pteroic acid as a key step in bacterial folate biosynthesis. It is the traditional target of the sulfonamide class of antibiotics. Unfortunately, bacterial resistance and adverse effects have limited the clinical utility of the sulfonamide antibiotics. Although six bacterial crystal structures are available, the flexible loop regions that enclose pABA during binding and contain key sulfonamide resistance sites have yet to be visualized in their functional conformation. To gain a new understanding of the structural basis of sulfonamide resistance, the molecular mechanism of DHPS action, and to generate a screening structure for high-throughput virtual screening, molecular dynamics simulations were applied to model the conformations of the unresolved loops in the active site. Several series of molecular dynamics simulations were designed and performed utilizing enzyme substrates and inhibitors, a transition state analog, and a pterin-sulfamethoxazole adduct. The positions of key mutation sites conserved across several bacterial species were closely monitored during these analyses. These residues were shown to interact closely with the sulfonamide binding site. The simulations helped us gain new understanding of the positions of the flexible loops during inhibitor binding that has allowed the development of a DHPS structural model that could be used for high-through put virtual screening (HTVS). Additionally, insights gained on the location and possible function of key mutation sites on the flexible loops will facilitate the design of new, potent inhibitors of DHPS that can bypass resistance mutations that render sulfonamides inactive. Prior to performing high-throughput virtual screening, the docking and scoring functions to be used were validated using established techniques against the B. anthracis DHPS target. In this validation study, five commonly used docking programs, FlexX, Surflex, Glide, GOLD, and DOCK, as well as nine scoring functions, were evaluated for their utility in virtual screening against the novel pterin binding site. Their performance in ligand docking and virtual screening against this target was examined by their ability to reproduce a known inhibitor conformation and to correctly detect known active compounds seeded into three separate decoy sets. Enrichment was demonstrated by calculated enrichment factors at 1% and Receiver Operating Characteristic (ROC) curves. The effectiveness of post-docking relaxation prior to rescoring and consensus scoring were also evaluated. Of the docking and scoring functions evaluated, Surflex with SurflexScore and Glide with GlideScore performed best overall for virtual screening against the DHPS target. The next phase of the DHPS structure-based drug design project involved high-throughput virtual screening against the DHPS structural model previously developed and docking methodology validated against this target. Two general virtual screening methods were employed. First, large, virtual libraries were pre-filtered by 3D pharmacophore and modified Rule-of-Three fragment constraints. Nearly 5 million compounds from the ZINC databases were screened generating 3,104 unique, fragment-like hits that were subsequently docked and ranked by score. Second, fragment docking without pharmacophore filtering was performed on almost 285,000 fragment-like compounds obtained from databases of commercial vendors. Hits from both virtual screens with high predicted affinity for the pterin binding pocket, as determined by docking score, were selected for in vitro testing. Activity and structure-activity relationship of the active fragment compounds have been developed. Several compounds with micromolar activity were identified and taken to crystallographic trials. Finally, in our ligand-based research into M. tuberculosis active agents, a series of nitrofuranylamide and related aromatic compounds displaying potent activity was investigated utilizing 3-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR) techniques. Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) methods were used to produce 3D-QSAR models that correlated the Minimum Inhibitory Concentration (MIC) values against M. tuberculosis with the molecular structures of the active compounds. A training set of 95 active compounds was used to develop the models, which were then evaluated by a series of internal and external cross-validation techniques. A test set of 15 compounds was used for the external validation. Different alignment and ionization rules were investigated as well as the effect of global molecular descriptors including lipophilicity (cLogP, LogD), Polar Surface Area (PSA), and steric bulk (CMR), on model predictivity. Models with greater than 70% predictive ability, as determined by external validation and high internal validity (cross validated r2 \u3e .5) were developed. Incorporation of lipophilicity descriptors into the models had negligible effects on model predictivity. The models developed will be used to predict the activity of proposed new structures and advance the development of next generation nitrofuranyl and related nitroaromatic anti-tuberculosis agents

Design and application of an automated system for camera photogrammetric calibration

This work presents the development of a novel Automatic Photogrammetric Camera Calibration System (APCCS) that is capable of calibrating cameras, regardless of their Field of View (FOV), resolution and sensitivity spectrum. Such calibrated cameras can, despite lens distortion, accurately determine vectors in a desired reference frame for any image coordinate, and map points in the reference frame to their corresponding image coordinates. The proposed system is based on a robotic arm which presents an interchangeable light source to the camera in a sequence of known discrete poses. A computer captures the camera's image for each robot pose and locates the light source centre in the image for each point in the sequence. Careful selection of the robot poses allows cost functions dependant on the captured poses and light source centres to be formulated for each of the desired calibration parameters. These parameters are the Brown model parameters to convert from the distorted to the undistorted image (and vice versa), the focal length, and the camera's pose. The pose is split into the camera pose relative to its mount and the mount's pose relative to the reference frame to aid subsequent camera replacement. The parameters that minimise each cost function are deter- mined via a combination of coarse global and fine local optimisation techniques: genetic algorithms and the Leapfrog algorithm, respectively. The real world applicability of the APCCS is assessed by photogrammetrically stitching cameras of differing resolutions, FOVs and spectra into a single multi- spectral panorama. The quality of these panoramas are deemed acceptable after both subjective and quantitative analyses. The quantitative analysis compares the stitched position of matched image feature pairs found with the Shape Invariant Feature Tracker (SIFT) and Speeded Up Robust Features (SURF) algorithms and shows the stitching to be accurate to within 0.3°. The noise sensitivity of the APCCS is assessed via the generation of synthetic light source centres and robot poses. The data is realistically created for a hy- pothetical camera pair via the corruption of ideal data using seven noise sources emulating the robot movement, camera mounting and image processing errors. The calibration and resulting stitching accuracies are shown to be largely independent of the noise magnitudes in the operational ranges tested. The APCCS is thus found to be robust to noise. The APCCS is shown to meet all its requirements by determining a novel combination of calibration parameters for cameras regardless of their properties in a noise resilient manner

Improving Wifi Sensing And Networking With Channel State Information

In recent years, WiFi has a very rapid growth due to its high throughput, high efficiency, and low costs. Multiple-Input Multiple-Output (MIMO) and Orthogonal Frequency-Division Multiplexing (OFDM) are two key technologies for providing high throughput and efficiency for WiFi systems. MIMO-OFDM provides Channel State Information (CSI) which represents the amplitude attenuation and phase shift of each transmit-receiver antenna pair of each carrier frequency. CSI helps WiFi achieve high throughput to meet the growing demands of wireless data traffic. CSI captures how wireless signals travel through the surrounding environment, so it can also be used for wireless sensing purposes. This dissertation presents how to improve WiFi sensing and networking with CSI. More specifically, this dissertation proposes deep learning models to improve the performance and capability of WiFi sensing and presents network protocols to reduce CSI feedback overhead for high efficiency WiFi networking. For WiFi sensing, there are many wireless sensing applications using CSI as the input in recent years. To get a better understanding of existing WiFi sensing technologies and future WiFi sensing trends, this dissertation presents a survey of signal processing techniques, algorithms, applications, performance results, challenges, and future trends of CSI-based WiFi sensing. CSI is widely used for gesture recognition and sign language recognition. Existing methods for WiFi-based sign language recognition have low accuracy and high costs when there are more than 200 sign gestures. The dissertation presents SignFi for sign language recognition using CSI and Convolutional Neural Networks (CNNs). SignFi provides high accuracy and low costs for run-time testing for 276 sign gestures in the lab and home environments. For WiFi networking, although CSI provides high throughput for WiFi networks, it also introduces high overhead. WiFi transmitters need CSI feedback for transmit beamforming and rate adaptation. The size of CSI packets is very large and it grows very fast with respect to the number of antennas and channel width. CSI feedback introduces high overhead which reduces the performance and efficiency of WiFi systems, especially mobile and hand-held WiFi devices. This dissertation presents RoFi to reduce CSI feedback overhead based on the mobility status of WiFi receivers. CSI feedback compression reduces overhead, but WiFi receivers still need to send CSI feedback to the WiFi transmitter. The dissertation presents EliMO for eliminating CSI feedback without sacrificing beamforming gains

Molecular-Level Characterisation of Crystal-Solution Interfaces

The shape of solution-grown crystal particles is largely dependent on the relative growth rate of the morphologically dominant crystal faces, which is known to be affected by the solvent. Developing accurate models for predicting crystal morphologies requires a molecular-level understanding of the solid-liquid interface. Using a combination of molecular dynamics simulations and enhanced sampling methods, this work carries out a comprehensive study on the dynamics and thermodynamics of crystal-solution interfaces for the case of ibuprofen, focusing on aspects often neglected in mesoscopic models for crystal growth. An investigation on the conformational isomerism of ibuprofen shows that conformational rearrangements at the crystal-solution interface are governed by specific surface-solvent interactions and can have a non-negligible impact on the surface growth/dissolution kinetics. An unsupervised clustering algorithm is proposed to extend the study of conformational isomerism for systems with a large number of conformationally relevant degrees of freedom. By assessing thermodynamic and kinetic information on the solvent in contact with crystal surfaces, surface-solvent interactions are found to be solvent- and face-specific. Following this analysis, a computational screening procedure is proposed for identifying solvents which can significantly affect the relative growth rate of the crystal facets and hence, the growth morphology of the crystal. To gain an in-depth understanding into the role of the solvent on the ease of association/dissociation of solute molecules at the crystal surface, a study on the formation of a vacancy on the morphologically dominant crystal faces of ibuprofen is carried out. Thermodynamics of the process reveal a distinct solvent-dependency for several faces, indicating in such cases desolvation-dominated defect formation. The research subject of this dissertation contributes to developing general and computationally-affordable workflows necessary to obtain a comprehensive and quantitative understanding of molecular processes, impacting the solid-liquid interface, which will contribute towards the formulation of detailed mesoscopic growth and dissolution models

Evolutionary Dynamics of Rapid, Microgeographic Adaptation in an Amphibian Metapopulation

Wild organisms can rapidly adapt to changing environments, even at fine spatial scales. This fact prompts hope that contemporary local adaptation may buffer some of the negative anthropogenic impacts to ecosystems. However, there are limits to the pace of adaptation. Understanding the adaptive potential—and limitations—of individual species at fine-resolution is an important task if we hope to accurately predict the repercussions of future climate and landscape change on biodiversity. My dissertation takes advantage of an uncommonly long-observed and closely-studied system to paint a comprehensive picture of evolution over time in association with shifts in ecological contexts. In this dissertation, I show evidence of rapid, microgeographic evolution in response to climate within a metapopulation of wood frogs (Rana sylvatica). Critically, I show that populations separated by tens to hundreds of meters—well within the dispersal ability of the species—exhibited considerable shifts in development rates over a period of two decades, or roughly 6-9 generations. Using historical climate data and new methods of assessing landscape change, I show that these changes were mainly a response to warming climates. The ecological contexts experienced by the metapopulation are associated with the evolution of physiological rates. Specifically, I show that climate change seems to have caused a counter-intuitive delay in spring breeding phenology while drought and warming later in the larval development period correspond with a shift toward earlier metamorphosis. The picture that emerges is of a contracting developmental window, which is expected to select for faster intrinsic development rates. Superimposed on the metapopulation-wide shift to faster development was a pattern of counter-gradient variation reflecting a similar pattern seen two decades prior. Furthermore, I empirically demonstrate a trade-off between faster development and a swimming performance trait that strongly contributes to fitness. This trade-off helps to explain why intrinsic development rates vary spatially with pond temperatures, but in the opposite direction of the relationship with temperature over time. Though the evidence for rapid adaptation to climate change presented in this dissertation reveals that evolution can buffer populations from extinction, it also entreats caution. There is a clear trend of demographic decline among wood frog populations that experienced greater magnitudes of environmental change. In fact, the three populations that suffered local extinctions over the 20-year course of observations inhabited ponds characterized by the greatest change in temperature or canopy

Evaluation of NorESM-OC (versions 1 and 1.2), the ocean carbon-cycle stand-alone configuration of the Norwegian Earth System Model (NorESM1)

Idealised and hindcast simulations performed with the stand-alone ocean carbon-cycle configuration of the Norwegian Earth System Model (NorESM-OC) are described and evaluated. We present simulation results of two different model versions at different grid resolutions and using two different atmospheric forcing data sets. Model version NorESM-OC1 corresponds to the version that is included in the fully coupled model NorESM-ME1, which participated in CMIP5. The main update between NorESM-OC1 and NorESM-OC1.2 is the addition of two new options for the treatment of sinking particles. We find that using a constant sinking speed, which has been the standard in NorESM's ocean carbon cycle module HAMOCC (HAMburg Ocean Carbon Cycle model) does not transport enough particulate organic carbon (POC) into the deep ocean below approximately 2000 m depth. The two newly implemented parameterisations, a particle aggregation scheme with prognostic sinking speed, and a simpler scheme prescribing a linear increase of sinking speed with depth, provide better agreement with observed POC fluxes. Additionally, reduced deep ocean biases of oxygen and remineralised phosphate indicate a better performance of the new parameterisations. For model version 1.2, a re-tuning of the ecosystem parameterisation has been performed, which (i) reduces previously too high primary production in high latitudes, (ii) consequently improves model results for surface nutrients, and (iii) reduces alkalinity and dissolved inorganic carbon biases at low latitudes. We use hindcast simulations with prescribed observed and constant (pre-industrial) atmospheric CO2 concentrations to derive the past and contemporary ocean carbon sink. For the period 1990–1999 we find an average ocean carbon uptake ranging from 2.01 to 2.58 Pg C yr-1 depending on model version, grid resolution and atmospheric forcing data set