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At least 1,063 records · Page 59

CRITICA: coding region identification tool invoking comparative analysis

Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

Non-NASA Center↗

Computational Methods for Structural Mechanics and Dynamics

Topics addressed include: transient dynamics; transient finite element method; transient analysis in impact and crash dynamic studies; multibody computer codes; dynamic analysis of space structures; multibody mechanics and manipulators; spatial and coplanar linkage systems; flexible body simulation; multibody dynamics; dynamical systems; and nonlinear characteristics of joints.

Stroud, W. Jefferson↗

Testing and Performance Analysis of the Multichannel Error Correction Code Decoder

This report provides the test results and performance analysis of the multichannel error correction code decoder (MED) system for a regenerative satellite with asynchronous, frequency-division multiple access (FDMA) uplink channels. It discusses the system performance relative to various critical parameters: the coding length, data pattern, unique word value, unique word threshold, and adjacent-channel interference. Testing was performed under laboratory conditions and used a computer control interface with specifically developed control software to vary these parameters. Needed technologies - the high-speed Bose Chaudhuri-Hocquenghem (BCH) codec from Harris Corporation and the TRW multichannel demultiplexer/demodulator (MCDD) - were fully integrated into the mesh very small aperture terminal (VSAT) onboard processing architecture and were demonstrated.

Soni, Nitin J.↗

REGAL International Program: Analysis of experimental data for depletion code validation

The Rod-Extremity and Gadolinia AnaLysis (REGAL) Program is a joint international effort to expand the nuclide inventory experimental data for irradiated nuclear fuel, with a specific focus on addressing two challenging needs associated with the characterization of modern, high duty, nuclear fuel. The first challenge is filling the gaps in experimental nuclide inventory data for gadolinia (UO 2 –Gd 2 O 3 ) fuel rods. The huge absorption cross sections of Gd-155 and Gd-157 in the Gd dopant in these rods lead to atypical spatial self-shielding patterns and have an impact on the neutronic environment within the fuel assembly compared to regular UO 2 fuel rods. Additionally, the second challenge is investigating the impact of burnup gradients at rod extremities on fuel composition and neutron leakage, to provide relevant experimental data for assessing computational capabilities to model such impact. A benchmark has been defined as a first step in the development of best-estimate models in the preliminary phase of the experimental data evaluation. Comparison of experimental results obtained in Phase I of the program for two measured pressurized water reactor (PWR) samples, one UO 2 and one UO 2 –Gd 2 O 3 sample, with calculated results obtained with different computational tools based on the defined benchmark are presented and discussed.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Fuel Performance Evaluation of THOR-C Experiments

The Temperature Heatsink Overpower Response Commissioning (THOR-C) and THOR-Metal (THOR-M) experiments will be performed as part of an ongoing project for testing sodium fast reactor fuels with the Japan Atomic Energy Agency (JAEA). The THOR-C experiments consist of fresh metallic fuel pins and have been analyzed using the ABAQUS, Ansys codes and the BISON fuel performance code. THOR-M-Loss of Flow-1 (THOR-M-LOF-1) is designed to test an EBR-II irradiated fuel pin under LOF conditions. Simulation of the THOR-MLOF-1 experiment required first simulating the base irradiation of the fuel pin in EBR-II. MFUEL module of SAS4A/SASSYS-1 [1] is a physics-based metallic fuel performance model applicable to the normal operation, transient scenarios and fuel failure modeling including scenarios with bulk fuel melting. The model has been validated using EBR-II normal operation, separate effect transient tests as well as TREAT M-Series transient tests [2]. In this study, MFUEL models has been utilized together with a new capsule heat transfer model developed in this project. The new heat transfer model was necessary due to (1) significant amount of heat losses that required 2D heat transfer, (2) the presence of a titanium heat sink, rejecting a significant amount of heat, and (3) stagnant coolant conditions, which are inconsistent with SAS4A/SASSYS-1 (SAS) heat transfer model. Updates to SAS4A/SASSYS-1 and MFUEL has been described below, followed by a preliminary validation effort using the results from THOR-C-2 fresh fuel capsule experiment. A previous study for THOR-C-2 analysis using BISON code is also utilized in this study to model this test [3]. [1] D. O’Grady, A. J. Brunett, L. Ibarra, A. Karahan, T. Kim, T. S. Sumner, R. Thomas, T. H. Fanning, “The SAS4A/SASSYS-2 Version 5.7 Safety Analysis Code System,” Argonne National Laboratory,ANL/NSE-SAS/5.7, (2023). [2] A. Karahan, T. Kim, T. Fanning, D. O’Grady, “Validation of MFUEL Metal Fuel Performance Models of SAS4A/SASSYS-1,” Argonne National Laboratory, ANL/NSE-23/11, (2023). [3] M. Mihelish, A. Zabriskie, K. Paaren, P. Medvedev, C. Jensen, “Fuel Performance Predictions for the TREAT THOR-C Experiments,” Idaho National Laboratory, INL/RPT-23-73397, Revision 0, (2023)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Construction of a Code Verification Matrix for Heat Conduction With Finite Element Code Applications

When establishing the pedigree of a simulation tool, code verification is used to ensure that the implemented numerical algorithm is a faithful representation of its underlying mathematical model. During this process, numerical results on various meshes are systematically compared to a reference analytic solution. The selection of analytic solutions can be a laborious process, as it is difficult to establish adequate code confidence without performing redundant work. In this report we address this issue by applying a physics-based process that establishes a set of reference problems. In this process, code simulation options are categorized and systematically tested, which ensures that gaps in testing are easily identified and addressed. The resulting problems are primarily intended for code verification analysis but may also be useful for comparison to other simulation codes, troubleshooting activities, or training exercises. The process is used to select fifteen code verification problems relevant for the one-dimensional steady-state heat conduction equation. These problems are applicable to a wide variety of simulation tools, but, in this work, a demonstration is performed using the finite element-based nuclear fuel performance code BISON. Convergence to the analytic solution at the theoretical rate is quantified for a selection of the problems, which establishes a baseline pedigree for the code. Not only can this standard set of conduction solutions be used for verification of other codes, but also the physics-based process for selecting problems can be utilized to quantify and expand testing for any simulation tool.

42 ENGINEERING↗

Verification and Validation of the PLTEMP/ANL Code for Thermal-Hydraulic Analysis of Experimental and Test Reactors

The document compiles in a single volume the verification and validation works done for the PLTEMP/ANL code during the years of its development and improvement. The verification of sixteen capabilities of the PLTEMP/ANL Version 4.3 code that were identified by research reactor analysts as frequently used in their thermal-hydraulic analysis are described and documented. Each chapter of the document deals with the verification or validation of a specific model. The model verification is usually done by comparing the code with hand calculation, Microsoft spreadsheet calculation, or Mathematica calculation. The model validation is done by comparing the code with experimental data or a widely tested code like the RELAP5 code. In addition, some PLTEMP/ANL verification works that are available in the open literature are simply referenced and not included in the document. PLTEMP/ANL has been used in conversion safety analysis reports of several US and foreign research reactors that have been licensed and converted. A list of such reactors is given.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

High-Fidelity Buckling Analysis of Composite Cylinders Using the STAGS Finite Element Code

Results from previous shell buckling studies are presented that illustrate some of the unique and powerful capabilities in the STAGS finite element analysis code that have made it an indispensable tool in structures research at NASA over the past few decades. In particular, prototypical results from the development and validation of high-fidelity buckling simulations are presented for several unstiffened thin-walled compression-loaded graphite-epoxy cylindrical shells along with a discussion on the specific methods and user-defined subroutines in STAGS that are used to carry out the high-fidelity simulations. These simulations accurately account for the effects of geometric shell-wall imperfections, shell-wall thickness variations, local shell-wall ply-gaps associated with the fabrication process, shell-end geometric imperfections, nonuniform applied end loads, and elastic boundary conditions. The analysis procedure uses a combination of nonlinear quasi-static and transient dynamic solution algorithms to predict the prebuckling and unstable collapse response characteristics of the cylinders. Finally, the use of high-fidelity models in the development of analysis-based shell-buckling knockdown (design) factors is demonstrated.

Hilburger, Mark W.↗

An Object-Oriented Approach to Writing Computational Electromagnetics Codes

Presently, most computer software development in the Computational Electromagnetics (CEM) community employs the structured programming paradigm, particularly using the Fortran language. Other segments of the software community began switching to an Object-Oriented Programming (OOP) paradigm in recent years to help ease design and development of highly complex codes. This paper examines design of a time-domain numerical analysis CEM code using the OOP paradigm, comparing OOP code and structured programming code in terms of software maintenance, portability, flexibility, and speed.

Zimmerman, Martin↗

Recent Updates to the Object Reentry Survival Analysis Tool (ORSAT) Version 7.1

The Object Reentry Survival Analysis Tool (ORSAT) code is maintained and used by the NASA Orbital Debris Program Office (ODPO) and has been under continuous development and improvement since the mid-1990s. ORSAT is an object-oriented reentry simulation tool; it models a satellite as a collection of discrete components that follow independent trajectories upon the breakup of the parent object. Version 7.1 of the tool incorporates five years of new thermal and aerodynamic model development, multi-processor parametric study capability, codebase upgrades, and numerous bug-fixes. The thermal demise model was completely rewritten using a forward-time/central-space numerical stencil and incorporating a new pyrolysis model for fiber-reinforced plastic (FRP) materials. New aerodynamic and aeroheating models for hollow cylinders and hollow square prisms were developed using a combination of flow simulations in the direct simulation Monte Carlo (DSMC) Analysis Code (DAC) and Data Parallel Line Relaxation (DPLR) code and free-flight tests in the University of Texas at San Antonio’s Hypersonic Wind Tunnel. The latest version also incorporates a mechanical, strength-based demise model for FRP materials. Minor improvements include an update to the Fortran 2018 codebase; improved integration and speed with the Python-based, multi-core, parametric study tool, AutoORSAT; and fixes for many minor bugs. This new version of ORSAT will enable more accurate reentry risk assessments for modern satellites. This paper presents an overview of these changes and a summary of the verification and validation performed on the final code.

Benton R. Greene↗

Recent Updates to the Object Reentry Survival Analysis Tool (ORSAT) Version 7.1

The Object Reentry Survival Analysis Tool (ORSAT) code is maintained and used by the NASA Orbital Debris Program Office (ODPO) and has been under continuous development and improvement since the mid-1990s. ORSAT is an object-oriented reentry simulation tool; it models a satellite as a collection of discrete components that follow independent trajectories upon the breakup of the parent object. Version 7.1 of the tool incorporates five years of new thermal and aerodynamic model development, multi-processor parametric study capability, codebase upgrades, and numerous bug-fixes. The thermal demise model was completely rewritten using a forward-time/central-space numerical stencil and incorporating a new pyrolysis model for fiber-reinforced plastic (FRP) materials. New aerodynamic and aeroheating models for hollow cylinders and hollow square prisms were developed using a combination of flow simulations in the direct simulation Monte Carlo (DSMC) Analysis Code (DAC) and Data Parallel Line Relaxation (DPLR) code and free-flight tests in the University of Texas at San Antonio’s Hypersonic Wind Tunnel. The latest version also incorporates a mechanical, strength-based demise model for FRP materials. Minor improvements include an update to the Fortran 2018 codebase; improved integration and speed with the Python-based, multi-core, parametric study tool, AutoORSAT; and fixes for many minor bugs. This new version of ORSAT will enable more accurate reentry risk assessments for modern satellites. This paper presents an overview of these changes and a summary of the verification and validation performed on the final code.

Benton R. Greene↗

Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.

Non-NASA Center↗

Transonic airfoil codes

Computer codes for the design and analysis of transonic airfoils are considered. The design code relies on the method of complex characteristics in the hodograph plane to construct shockless airfoil. The analysis code uses artificial viscosity to calculate flows with weak shock waves at off-design conditions. Comparisons with experiments show that an excellent simulation of two dimensional wind tunnel tests is obtained. The codes have been widely adopted by the aircraft industry as a tool for the development of supercritical wing technology.

Garabedian, P. R.↗

Modeling the Deterioration of Engine and Low Pressure Compressor Performance During a Roll Back Event Due to Ice Accretion

The main focus of this study is to apply a computational tool for the flow analysis of the engine that has been tested with ice crystal ingestion in the Propulsion Systems Laboratory (PSL) of NASA Glenn Research Center. A data point was selected for analysis during which the engine experienced a full roll back event due to the ice accretion on the blades and flow path of the low pressure compressor. The computational tool consists of the Numerical Propulsion System Simulation (NPSS) engine system thermodynamic cycle code, and an Euler-based compressor flow analysis code, that has an ice particle melt estimation code with the capability of determining the rate of sublimation, melting, and evaporation through the compressor blade rows. Decreasing the performance characteristics of the low pressure compressor (LPC) within the NPSS cycle analysis resulted in matching the overall engine performance parameters measured during testing at data points in short time intervals through the progression of the roll back event. Detailed analysis of the fan-core and LPC with the compressor flow analysis code simulated the effects of ice accretion by increasing the aerodynamic blockage and pressure losses through the low pressure compressor until achieving a match with the NPSS cycle analysis results, at each scan. With the additional blockages and losses in the LPC, the compressor flow analysis code results were able to numerically reproduce the performance that was determined by the NPSS cycle analysis, which was in agreement with the PSL engine test data. The compressor flow analysis indicated that the blockage due to ice accretion in the LPC exit guide vane stators caused the exit guide vane (EGV) to be nearly choked, significantly reducing the air flow rate into the core. This caused the LPC to eventually be in stall due to increasing levels of diffusion in the rotors and high incidence angles in the inlet guide vane (IGV) and EGV stators. The flow analysis indicating compressor stall is substantiated by the video images of the IGV taken during the PSL test, which showed water on the surface of the IGV flowing upstream out of the engine, indicating flow reversal, which is characteristic of a stalled compressor.

Veres, Joseph P.↗

Modeling the Deterioration of Engine and Low Pressure Compressor Performance During a Roll Back Event Due to Ice Accretion

The main focus of this study is to apply a computational tool for the flow analysis of the engine that has been tested with ice crystal ingestion in the Propulsion Systems Laboratory (PSL) of NASA Glenn Research Center. A data point was selected for analysis during which the engine experienced a full roll back event due to the ice accretion on the blades and flow path of the low pressure compressor. The computational tool consists of the Numerical Propulsion System Simulation (NPSS) engine system thermodynamic cycle code, and an Euler-based compressor flow analysis code, that has an ice particle melt estimation code with the capability of determining the rate of sublimation, melting, and evaporation through the compressor blade rows. Decreasing the performance characteristics of the low pressure compressor (LPC) within the NPSS cycle analysis resulted in matching the overall engine performance parameters measured during testing at data points in short time intervals through the progression of the roll back event. Detailed analysis of the fan-core and LPC with the compressor flow analysis code simulated the effects of ice accretion by increasing the aerodynamic blockage and pressure losses through the low pressure compressor until achieving a match with the NPSS cycle analysis results, at each scan. With the additional blockages and losses in the LPC, the compressor flow analysis code results were able to numerically reproduce the performance that was determined by the NPSS cycle analysis, which was in agreement with the PSL engine test data. The compressor flow analysis indicated that the blockage due to ice accretion in the LPC exit guide vane stators caused the exit guide vane (EGV) to be nearly choked, significantly reducing the air flow rate into the core. This caused the LPC to eventually be in stall due to increasing levels of diffusion in the rotors and high incidence angles in the inlet guide vane (IGV) and EGV stators. The flow analysis indicating compressor stall is substantiated by the video images of the IGV taken during the PSL test, which showed water on the surface of the IGV flowing upstream out of the engine, indicating flow reversal, which is characteristic of a stalled compressor.

Jorgenson, Philip C. E.↗

Decoding Resilience by Modeling Outage and Restoration Processes in Distribution Grids: A Pittsburgh Case Study

Climate-induced extreme weather events, such as floods and heatwaves, pose significant challenges to the resilience of urban power distribution grids. This paper examines the outage and restoration dynamics of Pittsburgh's power grid during the flood event in April 2024 and three heatwaves in June, July, and August 2024. We introduce a comprehensive modeling framework that integrates outage and restoration processes, enabling the quantification of resilience metrics, including total customer-hours of power outage, maximum residual values, and restoration durations across various ZIP codes. Our analysis highlights spatial disparities in outage impacts and restoration efficiencies, with ZIP Code 15222 experiencing the highest cumulative disruptions, while ZIP Code 15217 shows lower susceptibility. By linking statistical trends with weather events, this study underscores the critical need for targeted infrastructure upgrades and advanced restoration strategies. Furthermore, the proposed framework offers valuable insights for planning and managing resilient power systems in the face of increasing climate stress.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Report on PTT Imaging of Defects in AM Metallic Materials-Part 2

Metal Additive Manufacturing (AM) is a promising method for cost-efficient fabrication of complex shape structures for applications in harsh environment, such as in a nuclear reactor. However, internal defects (pores) occur in high-strength AM alloys, which are manufactured with Laser Powder Bed Fusion (LPBF) AM method. Pulsed Infrared Thermography (PIT) is an efficient nondestructive evaluation (NDE) method to examine actual structures, because this method offers one-sided non-contact measurements, and fast processing of large sample areas. However, imaging of material defects, particularly defects with sizes at microscopic level, is challenging. In this report, we benchmark the performance of several Unsupervised Learning (UL) algorithms designed to enhance imaging of microscopic defects in metals with PIT. UL aims to learn the latent principal patterns (dictionaries) in PIT data to detect defects with minimal human supervision. Performance of Independent Component Analysis (ICA), Sparse Coding (SC), Principal Component Analysis (PCA) and Exploratory Factor Analysis (EFA) was compared using F-score, UL model training time and defects reconstruction time. We obtained the average F-score of 0.75, and a highest F-score of 0.89 for the EFA algorithm. Overall, EFA outperforms other UL algorithms considered in this study.

36 MATERIALS SCIENCE↗