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All sourcesNASA NTRSDOE OSTI
NASA NTRS2011

Engineering and Scientific Applications: Using MatLab(Registered Trademark) for Data Processing and Visualization

MatLab(R) (MATrix LABoratory) is a numerical computation and simulation tool that is used by thousands Scientists and Engineers in many cou ntries. MatLab does purely numerical calculations, which can be used as a glorified calculator or interpreter programming language; its re al strength is in matrix manipulations. Computer algebra functionalities are achieved within the MatLab environment using "symbolic" toolbo x. This feature is similar to computer algebra programs, provided by Maple or Mathematica to calculate with mathematical equations using s ymbolic operations. MatLab in its interpreter programming language fo rm (command interface) is similar with well known programming languag es such as C/C++, support data structures and cell arrays to define c lasses in object oriented programming. As such, MatLab is equipped with most ofthe essential constructs of a higher programming language. M atLab is packaged with an editor and debugging functionality useful t o perform analysis of large MatLab programs and find errors. We belie ve there are many ways to approach real-world problems; prescribed methods to ensure foregoing solutions are incorporated in design and ana lysis of data processing and visualization can benefit engineers and scientist in gaining wider insight in actual implementation of their perspective experiments. This presentation will focus on data processing and visualizations aspects of engineering and scientific applicati ons. Specifically, it will discuss methods and techniques to perform intermediate-level data processing covering engineering and scientifi c problems. MatLab programming techniques including reading various data files formats to produce customized publication-quality graphics, importing engineering and/or scientific data, organizing data in tabu lar format, exporting data to be used by other software programs such as Microsoft Excel, data presentation and visualization will be discussed. The presentation will emphasize creating practIcal scripts (pro grams) that extend the basic features of MatLab TOPICS mclude (1) Ma trix and vector analysis and manipulations (2) Mathematical functions (3) Symbolic calculations & functions (4) Import/export data files (5) Program lOgic and flow control (6) Writing function and passing parameters (7) Test application programs

Sen, Syamal K.↗
DOE OSTI2019

Use of Automation in Low Level Waste Storage and Management - 19227

The Australian Nuclear Science and Technology Organisation (ANSTO) generates Low Level Waste (LLW) and Intermediate Level Waste (ILW) from various site operations such as the operation of a research Reactor and the manufacture of Molybdenum 99. The Low Level Solid Waste (LLSW) generated is stored at ANSTO before and after conditioning. The current process flow involves the storage of LLSW waste before conditioning on racks, handled using forklifts. When the unconditioned waste is ready for conditioning, it is transferred to another facility, where volume reduction and packaging is carried out. Once conditioned, the waste is placed in further storage, pending dispatch to the proposed Australian National Radioactive Waste Management Facility (NRWMF). A new purpose built facility has been constructed, adjacent to the LLSW processing facility, for the storage and management of LLSW in both unconditioned and conditioned forms. This new facility will streamline the waste management process and significantly enhance the safety and efficiency of the process. In line with international best practises, the new facility utilises automation solutions to minimise the build footprint, and minimise the use of forklifts and other mobile plant. Most importantly, it applies the principle of ALARA (As Low as Reasonably Achievable) to minimise operator activities in areas where radioactive material is stored and eliminates double handling of the waste. The automation for unconditioned waste utilises an Automated Storage and Retrieval System (ASRS), a vertical stacker crane within high density racking, to provide easy storage and retrieval for processing and/or routine inspections. This system allows operators to control it from outside of the storage area whilst utilising integrated software that allows for the required tracking of the unconditioned waste. From the ASRS storage area, unconditioned waste will have a smooth transition to the processing facility which is located adjacent to the ASRS system. Once conditioned, the waste is catalogued and returned to a designated storage area within the new facility using an automated building gantry crane with a target delivery system to eliminate the need for operators in the main storage bay. The waste will be held here in preparation for dispatch to the future repository. The utilisation of the ASRS for the purpose of storing LLSW is an innovative use of automation that will eliminate operators from active areas, reduce dose rates received and integrate with the waste tracking software. Furthermore, the system has significant advantages with operational efficiencies increased, reduced double handling of nuclear waste and maximum use of building footprint. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS2008

Hardware Architecture Study for NASA's Space Software Defined Radios

This study defines a hardware architecture approach for software defined radios to enable commonality among NASA space missions. The architecture accommodates a range of reconfigurable processing technologies including general purpose processors, digital signal processors, field programmable gate arrays (FPGAs), and application-specific integrated circuits (ASICs) in addition to flexible and tunable radio frequency (RF) front-ends to satisfy varying mission requirements. The hardware architecture consists of modules, radio functions, and and interfaces. The modules are a logical division of common radio functions that comprise a typical communication radio. This paper describes the architecture details, module definitions, and the typical functions on each module as well as the module interfaces. Trade-offs between component-based, custom architecture and a functional-based, open architecture are described. The architecture does not specify the internal physical implementation within each module, nor does the architecture mandate the standards or ratings of the hardware used to construct the radios.

Reinhart, Richard C.↗
NASA NTRS2015

Avionics Configuration Assessment for Flightdeck Interval Management: A Comparison of Avionics and Notification Methods

Flightdeck Interval Management is one of the NextGen operational concepts that FAA is sponsoring to realize requisite National Airspace System (NAS) efficiencies. Interval Management will reduce variability in temporal deviations at a position, and thereby reduce buffers typically applied by controllers - resulting in higher arrival rates, and more efficient operations. Ground software generates a strategic schedule of aircraft pairs. Air Traffic Control (ATC) provides an IM clearance with the IM spacing objective (i.e., the TTF, and at which point to achieve the appropriate spacing from this aircraft) to the IM aircraft. Pilots must dial FIM speeds into the speed window on the Mode Control Panel in a timely manner, and attend to deviations between actual speed and the instantaneous FIM profile speed. Here, the crew is assumed to be operating the aircraft with autothrottles on, with autopilot engaged, and the autoflight system in Vertical Navigation (VNAV) and Lateral Navigation (LNAV); and is responsible for safely flying the aircraft while maintaining situation awareness of their ability to follow FIM speed commands and to achieve the FIM spacing goal. The objective of this study is to examine whether three Notification Methods and four Avionics Conditions affect pilots' performance, ratings on constructs associated with performance (workload, situation awareness), or opinions on acceptability. Three Notification Methods (alternate visual and aural alerts that notified pilots to the onset of a speed target, conformance deviation from the required speed profile, and reminded them if they failed to enter the speed within 10 seconds) were examined. These Notification Methods were: VVV (visuals for all three events), VAV (visuals for all three events, plus an aural for speed conformance deviations), and AAA (visual indications and the same aural to indicate all three of these events). Avionics Conditions were defined by the instrumentation (and location) used to present IM information to crews: (1) Integrated (IM information is embedded in extant PFD (Primary Flight Display), ND (Navigation Display), EICAS (Engine Indicating and Crew Alerting System) displays); (2) EFB_Aft (IM information is only supplied in an EFB and mounted in location similar to that for MITRE's UPS work); (3) EFB_Fore (IM information is only supplied in an EFB which is mounted more forward, under the side window), and (4) EFB_Aft plus use of an AGD (the same IM information is supplied in an EFB and on an AGD, both mounted in locations similar to that in MITRE's UPS work ). Twelve commercial pilot crews flew descent scenarios (VNAV Speed with the mode control panel (MCP) speed window open until flaps extended, then VNAV Path) in a commercial transport flight simulator with realistic visual scene and communications. The results of this study serve three practical aims: (1) contribute to the down-select of avionics configuration for future assessment of the ASTAR spacing algorithm at NASA; (2) provide information useful to the FAA Human Factors Division (ANG-C1)'s mission to identify issues pertinent to flight certification of, and flight standards; (3) identify methodological considerations in support of future FIM human-in-the-loop (HITL) investigations.

Latorella, Kara A.↗
DOE OSTI2026

CodeScribe Agent

SF-26-086 CodeScribe introduces a structured, multi-stage pipeline that combines deterministic program analysis with LLM-powered translation to enable incremental, testable Fortran-to-C++ migration. First, `code-scribe index` traverses the project directory tree and produces `scribe.yaml` metadata files recording all modules, subroutines, and functions at each level, giving the LLM accurate structural context instead of a hallucinated codebase model. Second, `code-scribe draft` performs the deterministic portion of translation — converting Fortran types to C++ equivalents, replacing `use` statements with `#include` and `using namespace` directives, and detecting constructs requiring special handling — while embedding`scribe-prompt` annotations that guide the LLM through non-trivial cases such as statement-function-to-lambda conversions and `extern "C"` wrapper generation. Third, `code-scribe translate` applies project-specific TOML-based few-shot prompt templates and submits the composed prompt to a pluggable LLM backend (OpenAI, Anthropic, Argonne ARGO, any OpenAI-compatible endpoint, or local Hugging Face checkpoints), producing a C++ source file, a header, and a Fortran-C++ interface file for each translated routine so the codebase compiles and runs correctly throughout the migration. Beyond translation, CodeScribe includes a tool-using coding agent (`code-scribe agent`) with read, bash, edit, and write capabilities, and a bounded loop mode (`code-scribe loop`) that runs repeated stateless agent sessions over a task file with restricted tool access — enabling sustained, auditable software development workflows for broader scientific computing tasks.

Dhruv, Akash [Argonne National Laboratory (ANL), A↗
DOE OSTI2020

PAL Experimental Report Form

We constructed the first simultaneous dark- and bright-field X-ray microscope in this experiment, coupling it to simultaneous measurements of the wide-angle Xray diffraction, and the XFEL pulse intensity and energy spectrum on each shot. This experiment established proof of concept for this new advanced measurement technique and demonstrated DFXM at an XFEL for the first time. Within this complex experiment, we also acquired data that advanced our research goals within materials science and mathematics. These included: A preliminary study of how local effects reduce the X-ray damage threshold in diamond; A preliminary study of how X-ray radiation imparts heat into materials based on irreversible phase transitions that occur in boric acid with increasing temperature (based on hydration); A study of X-ray radiation damage from ultrafast thermal cycling and nonthermal melting in bismuth selenide; We also began developing software to automate alignment of compound refractive lenses (CRLs) using stochastic Nelder-Mead optimization methods. This work will expedite and improve the accuracy of alignments for many future experiments using CRLs.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Interactive Mesh Generation and Comparison Tools for Nuclear Energy Advanced Modeling & Simulation Phase I. Final Report

The promise of computer simulations for nuclear reactor designs is the opportunity to speed up the design process while also improving safety, providing more detail and higher fidelity, reducing cost, minimizing schedule risk, and avoiding many other potential problems; because simulations have the potential to be much less expensive and time-consuming than traditional development – where scale models and physical tests require construction and long lead times – it is possible to consider more alternatives and complete more comprehensive assessments before the design is finalized and constructed. As more design scenarios are studied by simulation, the speed that simulations promise is only available as long as bottlenecks are addressed for these scenarios. A frequent bottleneck is the amount of human labor required to describe the shape of the objects being designed and decompose the shape into simple elements, such as hexahedra, that are small enough to capture the physical phenomena of interest without being so small that even fast computers cannot perform the simulation in a reasonable amount of time. Recently, techniques for creating all-hexahedral decompositions have been developed, but they require some human input. Many simulation codes prefer all-hexahedral decompositions, so we proposed to evaluate the feasibility of these techniques on nuclear reactor geometries to see whether they required too much human input to be commercially viable. Our study concluded that they can be made viable with some additional software tools to reduce the amount of user input required.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
NASA NTRS2003

Experiments with an EVA Assistant Robot

Human missions to the Moon or Mars will likely be accompanied by many useful robots that will assist in all aspects of the mission, from construction to maintenance to surface exploration. Such robots might scout terrain, carry tools, take pictures, curate samples, or provide status information during a traverse. At NASA/JSC, the EVA Robotic Assistant (ERA) project has developed a robot testbed for exploring the issues of astronaut-robot interaction. Together with JSC's Advanced Spacesuit Lab, the ERA team has been developing robot capabilities and testing them with space-suited test subjects at planetary surface analog sites. In this paper, we describe the current state of the ERA testbed and two weeks of remote field tests in Arizona in September 2002. A number of teams with a broad range of interests participated in these experiments to explore different aspects of what must be done to develop a program for robotic assistance to surface EVA. Technologies explored in the field experiments included a fuel cell, new mobility platform and manipulator, novel software and communications infrastructure for multi-agent modeling and planning, a mobile science lab, an "InfoPak" for monitoring the spacesuit, and delayed satellite communication to a remote operations team. In this paper, we will describe this latest round of field tests in detail.

Burridge, Robert R.↗
NASA NTRS2002

REACH: Real-Time Data Awareness in Multi-Spacecraft Missions

Missions have been proposed that will use multiple spacecraft to perform scientific or commercial tasks. Indeed, in the commercial world, some spacecraft constellations already exist. Aside from the technical challenges of constructing and flying these missions, there is also the financial challenge presented by the tradition model of the flight operations team (FOT) when it is applied to a constellation mission. Proposed constellation missions range in size from three spacecraft to more than 50. If the current ratio of three-to-five FOT personnel per spacecraft is maintained, the size of the FOT becomes cost prohibitive. The Advanced Architectures and Automation Branch at the Goddard Space Flight Center (GSFC Code 588) saw the potential to reduce the cost of these missions by creating new user interfaces to the ground system health-and-safety data. The goal is to enable a smaller FOT to remain aware and responsive to the increased amount of ground system information in a multi-spacecraft environment. Rather than abandon the tried and true, these interfaces were developed to run alongside existing ground system software to provide additional support to the FOT. These new user interfaces have been combined in a tool called REACH. REACH-the Real-time Evaluation and Analysis of Consolidated Health-is a software product that uses advanced visualization techniques to make spacecraft anomalies easy to spot, no matter how many spacecraft are in the constellation. REACH reads a real-time stream of data from the ground system and displays it to the FOT such that anomalies are easy to pick out and investigate. Data visualization has been used in ground system operations for many years. To provide a unique visualization tool, we developed a unique source of data to visualize: the REACH Health Model Engine. The Health Model Engine is rule-based software that receives real-time telemetry information and outputs "health" information related to the subsystems and spacecraft that the telemetry belong to. The Health Engine can run out-of-the-box or can be tailored with a scripting language. Out of the box, it uses limit violations to determine the health of subsystems and spacecraft; when tailored, it determines health using equations combining the values and limits of any telemetry in the spacecraft. The REACH visualizations then "roll up" the information from the Health Engine into high level, summary displays. These summary visualizations can be "zoomed" into for increasing levels of detail. Currently REACH is installed in the Small Explorer (SMEX) lab at GSFC, and is monitoring three of their five spacecraft. We are scheduled to install REACH in the Mid-sized Explorer (MIDEX) lab, which will allow us to monitor up to six more spacecraft. The process of installing and using our "research" software in an operational environment has provided many insights into which parts of REACH are a step forward and which of our ideas are missteps. Our paper explores both the new concepts in spacecraft health-and-safety visualization, the difficulties of such systems in the operational environment, and the cost and safety issues of multi-spacecraft missions.

Maks, Lori↗
NASA NTRS2015

Face Sheet/Core Disbond Growth in Honeycomb Sandwich Panels Subjected to Ground-Air-Ground Pressurization and In-Plane Loading

Typical damage modes in light honeycomb sandwich structures include face sheet/core disbonding and core fracture, both of which can pose a threat to the structural integrity of a component. These damage modes are of particular interest to aviation certification authorities since several in-service occurrences, such as rudder structural failure and other control surface malfunctions, have been attributed to face sheet/core disbonding. Extensive studies have shown that face sheet/core disbonding and core fracture can lead to damage propagation caused by internal pressure changes in the core. The increasing use of composite sandwich construction in aircraft applications makes it vitally important to understand the effect of ground-air-ground (GAG) cycles and conditions such as maneuver and gust loads on face sheet/core disbonding. The objective of the present study was to use a fracture mechanics based approach developed earlier to evaluate the loading at the disbond front caused by ground-air-ground pressurization and in-plane loading. A honeycomb sandwich panel containing a circular disbond at one face sheet/core interface was modeled with three-dimensional (3D) solid finite elements. The disbond was modeled as a discrete discontinuity and the strain energy release rate along the disbond front was computed using the Virtual Crack Closure Technique (VCCT). Special attention was paid to the pressure-deformation coupling which can decrease the pressure load within the disbonded sandwich section significantly when the structure is highly deformed. The commercial finite element analysis software, Abaqus/Standard, was used for the analyses. The recursive pressure-deformation coupling problem was solved by representing the entrapped air in the honeycomb cells as filled cavities in Abaqus/Standard. The results show that disbond size, face sheet thickness and core thickness are important parameters that determine crack tip loading at the disbond front. Further, the pressure-deformation coupling was found to have an important load decreasing effect [6]. In this paper, a detailed problem description is provided first. Second, the analysis methodology is presented. The fracture mechanics approach used is described and the specifics of the finite element model, including the fluid-filled cavities, are introduced. Third, the initial model verification and validation are discussed. Fourth, the findings from a closely related earlier study [6] are summarized. These findings provided the basis for the current investigation. Fifth, an aircraft ascent scenario from 0 to 12192 m (0 to 40000 ft) is considered and the resulting crack tip loading at the disbond front is determined. In-plane loading to simulate maneuvers and gust conditions are also considered. Sixth, the results are shown for a curved panel, which was used to simulate potential fuselage applications. Finally, a brief summary of observations is presented and recommendations for improvement are provided.

Chen, Zhi M.↗
NASA NTRSDate not supplied

Microwave Structure Construction Capability Year One Accomplishments

The Microwave Structure Construction Capability (MSCC) element, part of the Moon to Mars Planetary Autonomous Construction Project (MMPACT) was initiated in 2020. MSCC is responsible for creating horizontal and vertical infrastructure on the moon using microwave energy. Microwave energy was selected since it is the only method to volumetrically heat the regolith. All other sintering/melting methods rely on thermal conduction through the very low conductivity surface, resulting in an inefficient process. Advances were achieved in materials characterization and understanding, microwave sintering in vacuum, and microwave design and analyses. Two dielectric property testing systems have been developed at Radiance Technologies and JPL. These will examine dielectric properties at cryogenic temperatures and over a broad frequency range. Permittivity and permeability testing at -60 ̊C in vacuum from 0.05 to 3 GHz has been generated at JPL. Additional modifications will be made to go to -190 ̊C (LN2). Radiance Technologies created a test system to measure dielectric properties at greater than 10 GHz and initiated work on developing a vacuum capable, portable test system to measure dielectric properties of Apollo regolith and simulants from 100 MHz to 18 GHz. These tests are to identify optimal heating frequencies and protocols. During microwave sintering at about 1100 ̊C, volatiles were creating difficulty in achieving a reasonably dense specimen. Due to processing in vacuum and the nature of the lunar regolith, some volatiles and porosity are expected. However, the Earth produced simulants have non-lunar materials in them that create volatiles that aren’t representative of lunar regolith. Therefore, a five month effort was conducted to establish a heat treat method to remove these non-lunar materials. Tests were conducted using TGA mass spectrometry, heating in vacuum and conducting mass spectrometry, dielectric and DTA, Raman, BET, particle size analysis, morphological analysis, carbon and sulfur chemical content determination and microscopy. The process has been scaled-up to 6 kg batch size and undergoing evaluation. A 36 kg batch size is the target for JSC-1A and other limited availability simulants. These calcining protocols will be standard for NASA and beyond. MSCC has also created scalable processes for fabricating synthetic lunar materials. Processes to fabricate Anorthite (plagioclase CaAl2Si2O8), Diopside (pyroxene CaMgSi₂O₆), and Enstatite (pyroxene Mg2Si2O6) have been generated. These materials will enable generation of microwave sintering models to bound various composition ranges anticipated on the Moon, therefore mitigating the need for a precise simulant with respect to location on the Moon. Successful microwave sintering in air using a horn applicator was demonstrated. All previous microwave vacuum sintering in the literature was at small scale and in a contained enclosure thus taking advantage of reflections. This is the first to use a lunar like microwave applicator to sinter ceramic in a bed as it would be done on the Moon. Small scale and inert sintering were conducted to assist in developing protocols with quicker turnaround times than larger scale testing. Testing has anchored thermal analysis predicting heat flow in vacuum during microwave sintering. Thermal conductivity testing was also initiated. Microwave coupling to the regolith has been modeled by multiple organizations and with different software packages. At least six horn designs and applicator configurations for both magnetron and solid state sources are being examined. Optimal simulant container designs for microwaves have also been generated. The power and electronics design for the solid state microwave system has been initiated. Concept designs for a lander based microwave sintering have been evaluated.

microwave↗
DOE OSTI2016

SU-F-I-15: Evaluation of a New MR-Compatible Respiratory Motion Device at 3T

Purpose: Recent advances in MRI-guided radiotherapy has inspired the development of MRI-compatible motion devices that simulate patient periodic motion in the scanner, particularly respiratory motion. Most commercial devices rely on non MR-safe ferromagnetic stepper motors which are not practical for regular QA testing. This work evaluates the motion performance of a new fully MRI compatible respiratory motion device at 3T. Methods: The QUASAR™ MRI-compatible respiratory motion phantom has been recently developed by Modus QA Inc., London, ON, Canada. The prototype is constructed from diamagnetic materials with linear motion generated using MRI-compatible piezoelectric motors that can be safely inserted in the scanner bore. The tumor was represented by a fillable sphere and is attached to the linear motion generator. The spherical tumor-representative and its surroundings were filled with different concentrations of MnCl2 to produce realistic relaxation times. The motion was generated along the longitudinal (H/F) axis of the bore using sinusoidal reference waveform (amplitude = 15 mm, frequency 0.25 Hz). Imaging was then performed on 3T Philips Achieva using a 32-channel cardiac coil. Fast 2D spoiled gradient-echo was used with a spatial resolution of 1.8 × 1.8 mm{sup 2} and slice thickness of 4 mm. The motion waveform was then measured on the resultant image series by tracking the centroid of the sphere through the time series. This image-derived measured motion was compared to the software-generated reference waveform. Results: No visible distortions from the device were observed on the images. Excellent agreement between the measured and the reference waveforms were obtained. Negligible motion was observed in the lateral (R/L) direction. Conclusion: Our investigation demonstrates that this piezo-electric motor design is effective at simulating periodic motion and is a potential candidate for MRI-radiotherapy respiratory motion simulation. Future work should focus on evaluating non-sinusoidal waveforms, fast 3D pulse sequences, and perform dosimetric QA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

WE-FG-BRA-04: A Portable Confocal Microscope to Image Live Cell Damage Response Induced by Therapeutic Radiation

Purpose: To construct a custom and portable fluorescence confocal laser-scanning microscope (FCLSM) that can be placed in the path of therapeutic radiation beams to study real-time radiation-induced damage response in live cells. Methods: We designed and constructed a portable FCLSM with three laser diodes for excitation (405, 488, and 635 nm). An objective lens focuses the excitation light and collects fluorescence from the sample. A pair of galvanometer mirrors scans/collects the laser beam/fluorescence along the focal plane (x/y-directions). A stepper motor stage scans in the axial direction and positions the x/y of the image field. Barrier filters and dichroic mirrors are used to route the spectral emission bands to the appropriate photodetector. An avalanche photodiode collects near-infrared fluorescence; a photodiode collects back-reflected 635 nm light; and a photomultiplier tube collects green fluorescence in the range of eGFP/eYFP. A 200-µm diameter pinhole was used to implement the confocal geometry for near-infrared and red channels and a 150-µm diameter pinhole for the green channel. Data acquisition and system control were achieved using a high-throughput data acquisition card. In-house software developed in LabVIEW was used to control the hardware, collect data from the photodetectors and reconstruct the confocal images. Results: 6 frames/s can be acquired for a 25 µm{sup 2} (128×128 pixels) field of view, visualizing the entire volume of the cell nucleus (∼10 µm depth) in <10 s. To demonstrate the usefulness of our FCLSM, we imaged gold nanoshells in live cells, radiation-induced damage in fibrosarcoma cells expressing eGFP tagged to a DNA repair protein, and neurons expressing eGFP. The system can also image particle tracks in fluorescent nuclear track detectors. Conclusion: We developed a versatile and portable FCLSM that allows radiobiology studies in live cells exposed to therapeutic radiation. The FCLSM can be placed in any vertical beam line for top-to-bottom exposures. This research was supported by the Sister Institution Network Fund and the Center for Radiation Oncology Research at The University of Texas MD Anderson Cancer Center and Cancer Prevention and Research Institute of Texas. Gabriel Sawakuchi has research support from Elekta Inc.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Validation of general purpose mathematical efficiency modeling with ISOCS - 15579

Gamma spectroscopy is a commonly used method for radioactive waste characterization and activity determination in in-situ objects. The gamma rays emitted by radionuclides in the waste container matrix are highly penetrating and can be measured using one or more gamma ray detectors, thus allowing for a passive nondestructive assay. One problem is that a source based calibration of full energy peak efficiency can be difficult or impractical because of the large size and/or an unusual shape of the sample geometry. One attractive solution is to use mathematical efficiency modeling to calculate the full energy peak efficiency. The In-Situ Object Calibration Software (ISOCS) has successfully been used for more than a decade for mathematical efficiency modeling of template based geometries. Templates include the most common objects in waste characterization and D and D, including but not limited to: boxes, drums, and pipes with hotspots, beams, tanks and walls. Scenarios exist where these templates cannot model the desired measurement geometry. Canberra has developed a general purpose version of ISOCS where primitive objects can be combined into practically any geometry. The primitive objects are right circular cylinder, right elliptical cylinder, right circular cone, right elliptical cone, sphere, spheroid, ellipsoid, box (rectangular parallelepiped), torus, and beaker (any cylindrical symmetric object). Multiple primitive objects can be combined using the priority scheme and cut by planes into almost any desired shape. In addition, multiple objects can be defined in the same scene, for example cylinders next to each other or a pipe and a box. Collimators can be constructed as easily as in template based ISOCS. The ray tracing algorithm in ISOCS has been extended to support the new primitive objects for attenuation calculation between the radioactive source and the detector end cap. The new version uses the same vacuum efficiency response, or characterization, in the energy range 10 - 7000 keV of individual detectors to be able to calculate the efficiency as accurately as possible. MCNP has been shown to be able to calculate detection efficiencies for any geometry and the new version of ISOCS have been validated to MCNP. The vacuum efficiency is based on an MCNP model and this model was the base for constructing an identical model in MCNP as in ISOCS. The calculated efficiencies from the two codes have been compared and the agreement is within 3% except for the lowest energies for one geometry. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2026

pyEF: A Python Framework for QM and QM/MM Atom-Wise Electric Field Analysis

We introduce pyEF, a software package for computing molecular electric fields, electrostatic interaction energies, and electrostatic potentials from quantum mechanical (QM) atom-centered multipole expansions with atom-wise decomposable contributions. We demonstrate the computational efficiency and accuracy of this QM-derived electric field evaluation tool through several tests. To assess the influence of the underlying QM method and charge partitioning scheme on these electrostatic quantities, we analyze over 250 configurations of an acetone solute molecule in five solvents of variable polarity. We find that electric field calculations are highly sensitive to the choice of charge partitioning method. Even among real-space charge schemes, acetone Stark tuning rates differ by up to a factor of 2. Benchmarking computed solvent dipole moments against experimental bulk values, we conclude that the CM5, ADCH, and Hirshfeld-I charge schemes most reliably capture solvent electrostatics and therefore provide a more faithful foundation for computing electric fields. When constructed from these real-space charges, electric fields are nearly insensitive to basis set size and monotonically increase in magnitude with higher Fock exchange. We also demonstrate efficient convergence of QM electrostatics when more distant molecules are represented solely by MM point charges, reducing computational overhead. Leveraging these findings, we demonstrate the use of pyEF to deduce environmental effects on a transition metal complex from a Ga 4 L 6 12– nanocage and quantify the dominant role of organic linkers in orchestrating electrostatic preorganization.

electric fields↗
DOE OSTI2015

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

The cMonkey integrated biclustering algorithm identifies conditionally co-regulated modules of genes (biclusters). cMonkey integrates various orthogonal pieces of information which support evidence of gene co-regulation, and optimizes biclusters to be supported simultaneously by one or more of these prior constraints. The algorithm served as the cornerstone for constructing the first global, predictive Environmental Gene Regulatory Influence Network (EGRIN) model for a free-living cell, and has now been applied to many more organisms. However, due to its computational inefficiencies, long run-time and complexity of various input data types, cMonkey was not readily usable by the wider community. To address these primary concerns, we have significantly updated the cMonkey algorithm and refactored its implementation, improving its usability and extendibility. These improvements provide a fully functioning and user-friendly platform for building co-regulated gene modules and the tools necessary for their exploration and interpretation. We show, via three separate analyses of data for E. coli, M. tuberculosis and H. sapiens, that the updated algorithm and inclusion of novel scoring functions for new data types (e.g. ChIP-seq and transcription factor over-expression [TFOE]) improve discovery of biologically informative co-regulated modules. The complete cMonkey2 software package, including source code, is available at https://github.com/baliga-lab/cmonkey2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Build Optimization Software Tools (BOOST) v2.0.0

Build Optimization Software Tools (BOOST) accelerate the design of DNA, RNA and protein sequences for their synthesis and assembly in an automated and scalable fashion. The BOOST Juggler automates the following two design tasks: - Reverse-Translation of protein sequences into DNA sequences - Codon Juggling of DNA sequences The BOOST Polisher provides the following design tasks: - The Verification of DNA sequences against DNA synthesis constraints - The Modification of DNA sequences in case they violate any DNA synthesis constraint In addition, the BOOST Polisher can be instructed to verify and modify DNA sequences against sequence patterns, such as restriction sites. The BOOST Partitioner supports both Gibson/chewback and Yeast assembly (also known as Transformation-Associated Recombination, or TAR) methods when performing the decomposition of large sequences that exceed the maximum length of DNA synthesis into synthesizable building blocks. The Partitioner can be instructed to find building blocks with appropriate overlap sequences, making their assembly into the complete construct more efficient. BOOST Workflows enable, in a customized fashion, the execution of the Juggler, Polisher, and Partitioner tools on a batch of sequences.

Sharkey, Michael↗
NASA NTRS2005

Seeing the Invisible: Embedding Tests in Code That Cannot be Modified

The difficulty of characterizing and observing valid software behavior during testing can be very difficult in flight systems. To address this issue, we evaluated several approaches to increasing test observability on the Shuttle Abort Flight Management (SAFM) system. To increase test observability, we added probes into the running system to evaluate the internal state and analyze test data. To minimize the impact of the instrumentation and reduce manual effort, we used Aspect-Oriented Programming (AOP) tools to instrument the source code. We developed and elicited a spectrum of properties, from generic to application specific properties, to be monitored via the instrumentation. To evaluate additional approaches, SAFM was ported to Linux, enabling the use of gcov for measuring test coverage, Valgrind for looking for memory usage errors, and libraries for finding non-normal floating point values. An in-house C++ source code scanning tool was also used to identify violations of SAFM coding standards, and other potentially problematic C++ constructs. Using these approaches with the existing test data sets, we were able to verify several important properties, confirm several problems and identify some previously unidentified issues.

O'Malley, Owen↗