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Proceedings of the Second NASA Formal Methods Symposium

This publication contains the proceedings of the Second NASA Formal Methods Symposium sponsored by the National Aeronautics and Space Administration and held in Washington D.C. April 13-15, 2010. Topics covered include: Decision Engines for Software Analysis using Satisfiability Modulo Theories Solvers; Verification and Validation of Flight-Critical Systems; Formal Methods at Intel -- An Overview; Automatic Review of Abstract State Machines by Meta Property Verification; Hardware-independent Proofs of Numerical Programs; Slice-based Formal Specification Measures -- Mapping Coupling and Cohesion Measures to Formal Z; How Formal Methods Impels Discovery: A Short History of an Air Traffic Management Project; A Machine-Checked Proof of A State-Space Construction Algorithm; Automated Assume-Guarantee Reasoning for Omega-Regular Systems and Specifications; Modeling Regular Replacement for String Constraint Solving; Using Integer Clocks to Verify the Timing-Sync Sensor Network Protocol; Can Regulatory Bodies Expect Efficient Help from Formal Methods?; Synthesis of Greedy Algorithms Using Dominance Relations; A New Method for Incremental Testing of Finite State Machines; Verification of Faulty Message Passing Systems with Continuous State Space in PVS; Phase Two Feasibility Study for Software Safety Requirements Analysis Using Model Checking; A Prototype Embedding of Bluespec System Verilog in the PVS Theorem Prover; SimCheck: An Expressive Type System for Simulink; Coverage Metrics for Requirements-Based Testing: Evaluation of Effectiveness; Software Model Checking of ARINC-653 Flight Code with MCP; Evaluation of a Guideline by Formal Modelling of Cruise Control System in Event-B; Formal Verification of Large Software Systems; Symbolic Computation of Strongly Connected Components Using Saturation; Towards the Formal Verification of a Distributed Real-Time Automotive System; Slicing AADL Specifications for Model Checking; Model Checking with Edge-valued Decision Diagrams; and Data-flow based Model Analysis.

Munoz, Cesar↗

Adaptive Wavelength Scanning Lidar (AWSL) for 3D Mapping from Space

We present the design and performance of an adaptive wavelength scanning lidar (AWSL) for highly efficient mapping from low Earth orbit (LEO). Mapping is accomplished by steering a laser beam across 1,200 resolvable spots using wavelength tuning and grating dispersion. Any subset of these 1,200 spots can be selected by wavelength switching. The design is validated with an 1550-nm prototype using a fast wavelength-tuned (500-kHz) pulsed (2-ns) fiber laser with the beam dispersed by gratings for beam steering. Reflected pulses are detected with an eight-pixel detector array with single-photon sensitivity. Eight lidar returns are time-multiplexed to one output that is digitized with a single 1-GSPS-digitizer, to save power. A grating spectrometer rejects solar background noise spatially and spectrally, and images laser footprints on to the detector array. The gratings retain the fiber laser beam quality. We are developing a 1030-nm AWSL intended for a LEO SmallSat platform.

Guangning Yang↗

RF Sheath-Enhanced Plasma Surface Interaction Studies using Beryllium Optical Emission Spectroscopy in JET ITER-Like Wall

A dedicated study on JET-ILW, deploying two types of ICRH antennas and spectroscopic observation spots at two outboard, beryllium limiters, has provided insight on long-range (up to 6m) RFenhanced plasma-surface interactions (RF-PSI) due to near-antenna electric fields. To aid in the interpretation of optical emission measurements of these effects, the antenna near-fields are computed using the TOPICA code, specifically run for the ITER-like antenna (ILA); similar modelling already existed for the standard JET antennas (A2). In the experiment, both antennas were operated in current drive mode, as RF-PSI tends to be higher in this phasing and at similar power (~0.5 MW). When sweeping the edge magnetic field pitch angle, peaked RF-PSI effects, in the form of 2-4 fold increase in the local Be source,are consistently measured with the observation spots magnetically connect to regions of TOPICAL-calculated high near-fields, particularly at the near-antenna limiters. It is also found that similar RF-PSI effects are produced by the two types of antenna on similarly distant limiters. Although this mapping of calculated near-fields to enhanced RF-PSI gives only qualitative interpretion of the data, the present dataset is expected to provide a sound experimental basis for emerging RF sheath simulation model validation.

Agarici, G.↗

Comparative Analysis of Empirical and Machine Learning Models for Chla Extraction Using Sentinel-2 and Landsat OLI Data: Opportunities, Limitations, and Challenges

Remote retrieval of near-surface chlorophyll-a (Chla) concentration in small inland waters is challenging due to substantial optical interferences of various water constituents and uncertainties in the atmospheric correction (AC) process. Although various algorithms have been developed to estimate Chla from moderate-resolution terrestrial missions (∼10–60 m), the production of both accurate distribution maps and time series of Chla has proven challenging, limiting the use of remote analyses for lake monitoring. Here, we develop a support vector regression (SVR) model, which uses satellite-derived remote-sensing reflectance spectra () from Sentinel-2 and Landsat-8 images as input for Chla retrieval in a representative eutrophic prairie lake, Buffalo Pound Lake (BPL), Saskatchewan, Canada. Validated against in situ Chla from seven ice-free seasons (N ∼ 200; 2014–2020), the SVR model outperformed both locally tuned, -fed empirical models (Normalized Difference Chlorophyll Index, 2- and 3-band, and OC3) and Mixture Density Networks (MDNs) by 15–65%, while exhibiting comparable performance to a locally trained MDN, with an error of ∼35%. Comparison of Chla retrieval models, AC processors (iCOR, ACOLITE), and radiometric products (Rayleigh-corrected, surface, and top-of-atmosphere reflectance) showed that the best Chla maps and optimal time series (up to 100 mg m−3) were produced using a coupled SVR-iCOR system.

algal blooms↗

Information system of rice planting calendar based on ten-day (Dasarian) rainfall prediction

This paper describes information system of rice planting calendar to help farmers in determining the time for rice planting. The information includes rainfall prediction in ten days (dasarian) scale overlaid to map of rice field to produce map of rice planting in village level. The rainfall prediction was produced by stochastic modeling using Fast Fourier Transform (FFT) and Non-Linier Least Squares methods to fit the curve of function to the rainfall data. In this research, the Fourier series has been modified become non-linear function to follow the recent characteristics of rainfall that is non stationary. The results have been also validated in 4 steps, including R-Square, RMSE, R-Skill, and comparison with field data. The development of information system (cyber extension) provides information such as rainfall prediction, prediction of the planting time, and interactive space for farmers to respond to the information submitted. Interfaces for interactive response will be critical to the improvement of prediction accuracy of information, both rainfall and planting time. The method used to get this information system includes mapping on rice planting prediction, converting the format file, developing database system, developing website, and posting website. Because of this map was overlaid with the Google map, the map files must be converted to the .kml file format.

60 APPLIED LIFE SCIENCES↗

TH-CD-202-06: A Method for Characterizing and Validating Dynamic Lung Density Change During Quiet Respiration

Purpose: To obtain a functional relationship that calibrates the lung tissue density change under free breathing conditions through correlating Jacobian values to the Hounsfield units. Methods: Free-breathing lung computed tomography images were acquired using a fast helical CT protocol, where 25 scans were acquired per patient. Using a state-of-the-art deformable registration algorithm, a set of the deformation vector fields (DVF) was generated to provide spatial mapping from the reference image geometry to the other free-breathing scans. These DVFs were used to generate Jacobian maps, which estimate voxelwise volume change. Subsequently, the set of 25 corresponding Jacobian and voxel intensity in Hounsfield units (HU) were collected and linear regression was performed based on the mass conservation relationship to correlate the volume change to density change. Based on the resulting fitting coefficients, the tissues were classified into parenchymal (Type I), vascular (Type II), and soft tissue (Type III) types. These coefficients modeled the voxelwise density variation during quiet breathing. The accuracy of the proposed method was assessed using mean absolute difference in HU between the CT scan intensities and the model predicted values. In addition, validation experiments employing a leave-five-out method were performed to evaluate the model accuracy. Results: The computed mean model errors were 23.30±9.54 HU, 29.31±10.67 HU, and 35.56±20.56 HU, respectively, for regions I, II, and III, respectively. The cross validation experiments averaged over 100 trials had mean errors of 30.02 ± 1.67 HU over the entire lung. These mean values were comparable with the estimated CT image background noise. Conclusion: The reported validation experiment statistics confirmed the lung density modeling during free breathing. The proposed technique was general and could be applied to a wide range of problem scenarios where accurate dynamic lung density information is needed. This work was supported in part by NIH R01 CA0096679.

60 APPLIED LIFE SCIENCES↗

Alignment Measurements of the Microwave Anisotropy Probe (MAP) Instrument in a Thermal/Vacuum Chamber Using Photogrammetry

The Microwave Anisotropy Probe (MAP) Observatory, scheduled for a late 2000 launch, is designed to measure temperature fluctuations (anisotropy) and produce a high sensitivity and high spatial resolution (< 0.3 deg at 90 GHz.) map of the cosmic microwave background (CMB) radiation over the entire sky between 22 and 90 GHz. MAP utilizes back-to-back Gregorian telescopes to focus the microwave signals into 10 differential microwave receivers, via 20 feed horns. Proper alignment of the telescope reflectors and the feed horns at the operating temperature of 90 K is a critical element to ensure mission success. We describe the hardware and methods used to validate the displacement/deformation predictions of the reflectors and the microwave feed horns during thermal/vacuum testing of the reflectors and the microwave instrument. The smallest deformations to be resolved by the measurement system were on the order of +/- 0.030 inches (0.762 mm). Performance of these alignment measurements inside a thermal/vacuum chamber with conventional alignment equipment posed several limitations. A photogrammetry (PG) system was chosen to perform the measurements since it is a non-contact measurement system, the measurements can be made relatively quickly and accurately, and the photogrammetric camera can be operated remotely. The hardware and methods developed to perform the MAP alignment measurements using PG proved to be highly successful. The PG measurements met the desired requirements, enabling the desired deformations to be measured and even resolved to an order of magnitude smaller than the imposed requirements. Viable data were provided to the MAP Project for a full analysis of the on-orbit performance of the Instrument's microwave system.

Hill, Michael D.↗

INVERSIONS FOR AVERAGE SUPERGRANULAR FLOWS USING FINITE-FREQUENCY KERNELS

I analyze the maps recording the travel-time shifts caused by averaged plasma anomalies under an 'average supergranule', constructed by means of statistical averaging over 5582 individual supergranules with large divergence signals detected in two months of Helioseismic and Magnetic Imager Dopplergrams. By utilizing a three-dimensional validated time-distance inversion code, I measure a peak vertical velocity of 117 {+-} 2 m s{sup -1} at depths around 1.2 Mm in the center of the supergranule and a root-mean-square vertical velocity of 21 m s{sup -1} over the area of the supergranule. A discrepancy between this measurement and the measured surface vertical velocity (a few m s{sup -1}) can be explained by the existence of the large-amplitude vertical flow under the surface of supergranules with large divergence signals, recently suggested by Duvall and Hanasoge.

79 ASTRONOMY AND ASTROPHYSICS↗

Chaotic dynamics of flexible Euler-Bernoulli beams

Mathematical modeling and analysis of spatio-temporal chaotic dynamics of flexible simple and curved Euler-Bernoulli beams are carried out. The Kármán-type geometric non-linearity is considered. Algorithms reducing partial differential equations which govern the dynamics of studied objects and associated boundary value problems are reduced to the Cauchy problem through both Finite Difference Method with the approximation of O(c{sup 2}) and Finite Element Method. The obtained Cauchy problem is solved via the fourth and sixth-order Runge-Kutta methods. Validity and reliability of the results are rigorously discussed. Analysis of the chaotic dynamics of flexible Euler-Bernoulli beams for a series of boundary conditions is carried out with the help of the qualitative theory of differential equations. We analyze time histories, phase and modal portraits, autocorrelation functions, the Poincaré and pseudo-Poincaré maps, signs of the first four Lyapunov exponents, as well as the compression factor of the phase volume of an attractor. A novel scenario of transition from periodicity to chaos is obtained, and a transition from chaos to hyper-chaos is illustrated. In particular, we study and explain the phenomenon of transition from symmetric to asymmetric vibrations. Vibration-type charts are given regarding two control parameters: amplitude q{sub 0} and frequency ω{sub p} of the uniformly distributed periodic excitation. Furthermore, we detected and illustrated how the so called temporal-space chaos is developed following the transition from regular to chaotic system dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Cryo_fit : Democratization of flexible fitting for cryo-EM

Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in hardware and software. Flexible fitting of atomic models to three-dimensional (3D) cryo-EM reconstructions by molecular dynamics (MD) simulation is a popular technique but often requires technical expertise in computer simulation. This work introduces cryo_fit, a package for the automatic flexible fitting of atomic models in cryo-EM maps using MD simulation. Additionally, the package is integrated with the Phenix software suite. The module was designed to automate the multiple steps of MD simulation in a reproducible manner, as well as facilitate refinement and validation through Phenix. Through the use of cryo_fit, scientists with little experience in MD simulation can produce high quality atomic models automatically and better exploit the potential of cryo-EM.

59 BASIC BIOLOGICAL SCIENCES↗

Chloride Insertion Enhances the Electrochemical Oxidation of Iron Hydroxide Double-Layer Hydroxide into Oxyhydroxide in Alkaline Iron Batteries

Rechargeable alkaline iron batteries that constitute environmentally benign electrolytes and earth-abundant industrial materials are desirable green solutions for large-scale energy storage. As one of the most abundant metal elements in the earth’s crust, iron (Fe) can satisfy nearly all criteria for low-cost and safe battery electrodes. However, challenges in achieving reversible Fe redox impede their extensive implementation in modern energy supply systems. Here, this study revealed that Cl-anion insertion into Fe(OH) 2 layered double hydroxide (LDH) formed a green rust intermediate phase with the formula [Fe 2 2+ Fe 1 3+ (HO – ) 6 ] + [Cl] – , which assisted a high Fe(OH) 2 /FeOOH conversion reaction (64.7%) and improved cycling stability. This new iron redox chemistry was validated by operando X-ray diffraction, electrochemical testing, X-ray absorption spectroscopy (XAS), X-ray photoelectron spectroscopy (XPS) analysis, scanning transmission electron microscopy–energy-dispersive X-ray spectroscopy (STEM-EDS) mapping, and molecular dynamics (MD) simulations. Our study provides new insight into designing LDH materials for high-capacity alkaline iron batteries.

36 MATERIALS SCIENCE↗

Inspection design using 2D phased array, TFM and cueMAP software

A simulation suite, cueMAP, has been developed to facilitate the design of inspection processes and sparse 2D array configurations. At the core of cueMAP is a Total Focusing Method (TFM) imaging algorithm that enables computer assisted design of ultrasonic inspection scenarios, including the design of bespoke array configurations to match the inspection criteria. This in-house developed TFM code allows for interactive evaluation of image quality indicators of ultrasonic imaging performance when utilizing a 2D phased array working in FMC/TFM mode. The cueMAP software uses a series of TFM images to build a map of resolution, contrast and sensitivity of imaging performance of a simulated reflector, swept across the inspection volume. The software takes into account probe properties, wedge or water standoff, and effects of specimen curvature. In the validation process of this new software package, two 2D arrays have been evaluated on 304n stainless steel samples, typical of the primary circuit in nuclear plants. Thick section samples have been inspected using a 1MHz 2D matrix array. Due to the processing efficiency of the software, the data collected from these array configurations has been used to investigate the influence sub-aperture operation on inspection performance.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Simulating energetic particle losses in JET plasmas with a reverse integration biasing scheme

We report that an integrated energetic particle transport model has been constructed in JET plasmas constrained by experimental fast ion loss measurements. The model incorporates a synthetic fast ion loss detector identical to JET’s thin-foil Faraday cup fast ion loss detector array. The loss model combines analyses from the TRANSP and ORBIT-kick codes with enhanced features for producing the synthetic diagnostic. Extensions to the ORBIT code framework allow a full-orbit representation within the vacuum region that can map particles directly to an installed detector geometry. Since synthetic fast ion loss detectors are plagued by weak loss statistics, a novel reverse integration biasing scheme has been implemented to boost computational efficiency. The model is validated against experimental loss measurements induced by long-lived kink modes and is found to be in good agreement. This confirms the development of a fully integrated transport/loss model which can be quantitatively verified against experiment allowing for future validation and predictive studies. The model is particularly useful for more complicated plasma scenarios that involve multiple fast ion species such as JET’s 2021 DT-campaign.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Entropy and Boundary Based Adversarial Learning for Large Scale Unsupervised Domain Adaptation

Supervised semantic segmentation methods provide state-of-the-art performance, but their performance is limited by the amount of quality labeled data they need for training. Scarcity of labeled data and non-transferablity of models, due to cross-domain discrepancy makes it a bigger challenge for remote sensing imagery analysis. In this work, we approach this problem through adversarial learning, driven by entropy and boundary of region-of-interest for unsupervised domain adaptation. This concept helps with better boundary prediction and encourages target domain entropy maps (probability/uncertainty maps) to be similar to source domains. In particular, we showed that deriving informative entropy through the adversarial learning is essential to enable the adaptation. We used a large scale cross country building extraction dataset to validate the framework. The experimental results show the usefulness of considering boundary and entropy driven adversarial learning for adaptation.

Makkar, Nikhil↗

SU-G-TeP4-04: An Automated Monte Carlo Based QA Framework for Pencil Beam Scanning Treatments

Purpose: Prior to treating new PBS field, multiple (three) patient-field-specific QA measurements are performed: two 2D dose distributions at shallow depth (M1) and at the tumor depth (M2) with treatment hardware at zero gantry angle; one 2D dose distribution at iso-center (M3) without patient specific devices at the planned gantry angle. This patient-specific QA could be simplified by the use of MC model. The results of MC model commissioning for a spot-scanning system and the fully automated TOPAS/MC-based QA framework will be presented. Methods: We have developed in-house MC interface to access a TPS (Astroid) database from a computer cluster remotely. Once a plan is identified, the interface downloads information for the MC simulations, such as patient images, apertures points, and fluence maps and initiates calculations in both the patient and QA geometries. The resulting calculations are further analyzed to evaluate the TPS dose accuracy and the PBS delivery. Results: The Monte Carlo model of our system was validated within 2.0 % accuracy over the whole range of the dose distribution (proximal/shallow part, as well as target dose part) due to the location of the measurements. The averaged range difference after commissioning was 0.25 mm over entire treatment ranges, e.g., 6.5 cm to 31.6 cm. Conclusion: As M1 depths range typically from 1 cm to 4 cm from the phantom surface, The Monte Carlo model of our system was validated within +− 2.0 % in absolute dose level over a whole treatment range. The averaged range difference after commissioning was 0.25 mm over entire treatment ranges, e.g., 6.5 cm to 31.6 cm. This work was supported by NIH/NCI under CA U19 21239.

60 APPLIED LIFE SCIENCES↗

Comprehensive characterization of extracellular vesicles produced by environmental (Neff) and clinical (T4) strains of Acanthamoeba castellanii

We conducted a comprehensive comparative analysis of extracellular vesicles (EVs) from two Acanthamoeba castellanii strains, Neff (environmental) and T4 (clinical). Morphological analysis via transmission electron microscopy revealed slightly larger Neff EVs (average = 194.5 nm) compared to more polydisperse T4 EVs (average = 168.4 nm). Nanoparticle tracking analysis (NTA) and dynamic light scattering validated these differences. Proteomic analysis of the EVs identified 1,352 proteins, with 1,107 common, 161 exclusive in Neff, and 84 exclusively in T4 EVs. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) mapping revealed distinct molecular functions and biological processes and notably, the T4 EVs enrichment in serine proteases, aligned with its pathogenicity. Lipidomic analysis revealed a prevalence of unsaturated lipid species in Neff EVs, particularly triacylglycerols, phosphatidylethanolamines (PEs), and phosphatidylserine, while T4 EVs were enriched in diacylglycerols and diacylglyceryl trimethylhomoserine, phosphatidylcholine and less unsaturated PEs, suggesting differences in lipid metabolism and membrane permeability. Metabolomic analysis indicated Neff EVs enrichment in glycerolipid metabolism, glycolysis, and nucleotide synthesis, while T4 EVs, methionine metabolism. Furthermore, RNA-seq of EVs revealed differential transcript between the strains, with Neff EVs enriched in transcripts related to gluconeogenesis and translation, suggesting gene regulation and metabolic shift, while in the T4 EVs transcripts were associated with signal transduction and protein kinase activity, indicating rapid responses to environmental changes. In this novel study, data integration highlighted the differences in enzyme profiles, metabolic processes, and potential origins of EVs in the two strains shedding light on the diversity and complexity of A. castellanii EVs and having implications for understanding host-pathogen interactions and developing targeted interventions for Acanthamoeba-related diseases.

59 BASIC BIOLOGICAL SCIENCES↗

Component Importance and Interdependence Analysis for Transmission, Distribution and Communication Systems

For critical infrastructure restoration planning, the real-time scheduling and coordination of system restoration efforts, the key in decision-making is to prioritize those critical components that are out of service during the restoration. For this purpose, there is a need for component importance analysis. While it has been investigated extensively for individual systems, component importance considering interdependence among transmission, distribution and communication (T&D&C) systems has not been systematically analyzed and widely adopted. In this study, we propose a component importance assessment method in the context of interdependence between T&D&C networks. Analytic methods for multilayer networks and a set of metrics have been applied for assessing the component importance and interdependence between T&D&C networks based on their physical characteristics. The proposed methodology is further validated with integrated synthetic Illinois regional transmission, distribution, and communication (T&D&C) systems, the results reveal the unique characteristics of component/node importance, which are strongly affected by the network topologies and cross-domain node mapping.

24 POWER TRANSMISSION AND DISTRIBUTION↗

SAM Plug-in Development (Phase I Final Report)

The DOE Office of Nuclear Energy (NE) has created an extensive set of advanced modeling and simulation tools for nuclear engineering analysis. The advanced capabilities of these newer analysis codes require more in-depth training, skills, and knowledge in order to effectively utilize them for the design, analysis, and licensing of advanced nuclear systems and experiments. A high learning curve for inexperienced users may deter organizations from incorporating these tools into their internal processes. This project involved development of a plug-in to the Symbolic Nuclear Analysis Package (SNAP) for the System Analysis Module (SAM) tool. SAM is an advanced system analysis tool for reactor transient analyses being developed at Argonne National Laboratory under the U.S. DOE Office of Nuclear Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. SAM utilizes an object-oriented application framework (MOOSE), and its underlying meshing and finite-element library (libMesh) and linear and non-linear solvers (PETSc), to leverage modern advanced software environments and numerical methods. SNAP provides a highly flexible framework for creating, modifying and documenting input for engineering analysis codes such as SAM as well as extensive functionality for submitting, monitoring, and interacting with the codes through an intuitive graphical user interface (GUI). The common user interface provided by SNAP minimizes the learning curve for engineers starting with a new analysis code and provides an intuitive framework for transitioning between different analysis codes. SNAP provides a powerful but intuitive interface to facilitate access to advanced modeling and simulation tools for inexperienced users. Unlike many “form based” GUI’s, SNAP maps each engineering code’s component input to an internal database which manages all component input parameters along with component interconnections. This level of abstraction permits SNAP to support several advanced capabilities such as renodalization, model validation and consistency checks, embedded documentation, model notebook generation, data ownership and reviewer tracking, and variable assignment for inputs to name a few. SNAP includes a built-in Python interpreter and is interfaced to several commercial and open source packages including CPython, MATLAB/OCTAVE, Microsoft Office, Open Office, and SANDIA’s DAKOTA package which provides Uncertainty Quantification analysis through the SNAP plug-ins. Phase I of this project involved development a fully functional basic SAM plug-in to SNAP. This plug-in provides the ability to import existing models, graphically construct, edit and submit models using SNAP’s extensive functionality.

99 GENERAL AND MISCELLANEOUS↗