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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Ligand placement based on prior structures: the guided ligand-replacement method

A new module, Guided Ligand Replacement (GLR), has been developed in Phenix to increase the ease and success rate of ligand placement when prior protein-ligand complexes are available. The process of iterative structure-based drug design involves the X-ray crystal structure determination of upwards of 100 ligands with the same general scaffold (i.e. chemotype) complexed with very similar, if not identical, protein targets. In conjunction with insights from computational models and assays, this collection of crystal structures is analyzed to improve potency, to achieve better selectivity and to reduce liabilities such as absorption, distribution, metabolism, excretion and toxicology. Current methods for modeling ligands into electron-density maps typically do not utilize information on how similar ligands bound in related structures. Even if the electron density is of sufficient quality and resolution to allow de novo placement, the process can take considerable time as the size, complexity and torsional degrees of freedom of the ligands increase. A new module, Guided Ligand Replacement (GLR), was developed in Phenix to increase the ease and success rate of ligand placement when prior protein–ligand complexes are available. At the heart of GLR is an algorithm based on graph theory that associates atoms in the target ligand with analogous atoms in the reference ligand. Based on this correspondence, a set of coordinates is generated for the target ligand. GLR is especially useful in two situations: (i) modeling a series of large, flexible, complicated or macrocyclic ligands in successive structures and (ii) modeling ligands as part of a refinement pipeline that can automatically select a reference structure. Even in those cases for which no reference structure is available, if there are multiple copies of the bound ligand per asymmetric unit GLR offers an efficient way to complete the model after the first ligand has been placed. In all of these applications, GLR leverages prior knowledge from earlier structures to facilitate ligand placement in the current structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

Simulation Toolkit for Renewable Energy Advanced Materials Modeling

STREAMM is a collection of python classes and scripts that enables and eases the setup of input files and configuration files for simulations of advanced energy materials. The core STREAMM python classes provide a general framework for storing, manipulating and analyzing atomic/molecular coordinates to be used in quantum chemistry and classical molecular dynamics simulations of soft materials systems. The design focuses on enabling the interoperability of materials simulation codes such as GROMACS, LAMMPS and Gaussian.

Sides, Scott↗
NASA NTRS2008

Model of Image Artifacts from Dust Particles

A mathematical model of image artifacts produced by dust particles on lenses has been derived. Machine-vision systems often have to work with camera lenses that become dusty during use. Dust particles on the front surface of a lens produce image artifacts that can potentially affect the performance of a machine-vision algorithm. The present model satisfies a need for a means of synthesizing dust image artifacts for testing machine-vision algorithms for robustness (or the lack thereof) in the presence of dust on lenses. A dust particle can absorb light or scatter light out of some pixels, thereby giving rise to a dark dust artifact. It can also scatter light into other pixels, thereby giving rise to a bright dust artifact. For the sake of simplicity, this model deals only with dark dust artifacts. The model effectively represents dark dust artifacts as an attenuation image consisting of an array of diffuse darkened spots centered at image locations corresponding to the locations of dust particles. The dust artifacts are computationally incorporated into a given test image by simply multiplying the brightness value of each pixel by a transmission factor that incorporates the factor of attenuation, by dust particles, of the light incident on that pixel. With respect to computation of the attenuation and transmission factors, the model is based on a first-order geometric (ray)-optics treatment of the shadows cast by dust particles on the image detector. In this model, the light collected by a pixel is deemed to be confined to a pair of cones defined by the location of the pixel s image in object space, the entrance pupil of the lens, and the location of the pixel in the image plane (see Figure 1). For simplicity, it is assumed that the size of a dust particle is somewhat less than the diameter, at the front surface of the lens, of any collection cone containing all or part of that dust particle. Under this assumption, the shape of any individual dust particle artifact is the shape (typically, circular) of the aperture, and the contribution of the particle to the attenuation factor for a given pixel is the fraction of the cross-sectional area of the collection cone occupied by the particle. Assuming that dust particles do not overlap, the net transmission factor for a given pixel is calculated as one minus the sum of attenuation factors contributed by all dust particles affecting that pixel. In a test, the model was used to synthesize attenuation images for random distributions of dust particles on the front surface of a lens at various relative aperture (F-number) settings. As shown in Figure 2, the attenuation images resembled dust artifacts in real test images recorded while the lens was aimed at a white target.

Willson, Reg↗
DOE OSTI2023

Generating MCNP Input Files for Unstructured Mesh Geometries

The Los Alamos National Laboratory’s (LANL) Monte Carlo N-Particle (MCNP)1 transport code version 6.3 (also known as MCNP6.3) has the capability for tracking particles on unstructured mesh (UM) geometry models embedded into constructive solid geometry (CSG) cells. This feature has been developed for performing calculations of complex geometry models because manually creating CSG models is time-consuming and error-prone as the complexities of geometries increase. A UM geometry model is a collection of finite elements representing a solid geometry. The first step of the MCNP UM calculation is using other software packages to create a finite element mesh representation of a solid 3D geometry because the MCNP code cannot be used to generate a UM model. Computer-aided design (CAD) software is typically used to create a solid geometry model, which is later imported into mesh generation software to create a UM model. Some mesh generation software packages may also be used to create solid geometries and thus CAD files are not needed. The MCNP UM feature was originally designed for models generated by the Abaqus/CAE software suite. The MCNP code version 6.0 and later can process UM models formatted as Abaqus input files. Starting with a 6.3 version, the MCNP code can process HDF5 mesh input files. We only focus on the UM models formatted as Abaqus input files in this report since currently no external software can be used to generate HDF5 mesh input files for MCNP UM calculations. The MCNP code version 6.3 can be used to convert the Abaqus mesh input files into the HDF5 mesh input files, but this option is typically used by the MCNP code development team to test the HDF5 mesh input file feature. Several software packages (such as Abaqus, Attila4MC, or Cubit) can be used to create the Abaqus input files for MCNP UM calculations. An MCNP UM calculation using an Abaqus model requires two input file types: MCNP and Abaqus input files. The Abaqus input files needed for MCNP UM calcu lations must have the correct Abaqus syntax and meet the additional requirements by the MCNP code. The MCNP code can process only Abaqus input files that make use of part and assembly definitions, where elements in each part must be grouped into one or more element sets (i.e., elset) using *Elset keyword lines with specified naming formats. The MCNP and Abaqus input files required for MCNP UM simulations must be related; pseudo-cells in an MCNP input file must be constructed from mesh model data from an Abaqus input file. For large complex UM models, it is tedious to manually create MCNP UM input files. The um pre op (unstructured mesh pre operations) program with the -m option can be used to create a skeleton MCNP input file from an Abaqus input file [6]. Since the um pre op program was written in Fortran and was not written for optimized performance, this program is a deprecated feature in the MCNP code version 6.3 and may be removed in the next release of the code. To improve calculation flow of multiphysics calculations, a Python3 code called write mcnp um input has been developed to generate an MCNP input file instead of using the um_pre_op -m option. This Python code was initially released to the public in 2020. We have updated this Python code for MCNP6.3 and it was used to generate the MCNP input files used to verify the MCNP6.3 code. The write_mcnp_um_input code is included with the MCNP6.3 code package which will be released to the public through the Radiation Safety Information Computational Center (RSICC) at Oak Ridge National Laboratory. This report is a revision of LA-UR-20-27139 report.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Improving representation of drought stress and fire emissions in climate carbon models: measurements and modeling with a focus on the western USA

The objective of the proposed research was to collect data and develop models to improve our understanding of the role of drought and fire impacts on the terrestrial carbon cycle in the western US, including impacts associated with urban systems as they impacted regional carbon cycles. Using data we collected and a synthesis of other measurements, we developed new ways (a) to evaluate the representation of drought stress and fire emissions in the Community Land Model, (b) to model net ecosystem exchange combining ground level atmospheric observations with boundary layer theory, (c) to model upstream impacts of fire and fossil fuel emissions on atmospheric carbon dioxide observations, and (d) to model carbon dioxide observations within urban systems and at the urban-wildland interfaces of forest ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Modeling Soot Oxidation and Gasification with Bayesian Statistics

This paper presents a statistical method for model calibration using data collected from literature. The method is used to calibrate parameters for global models of soot consumption in combustion systems. This consumption is broken into two different submodels: first for oxidation where soot particles are attacked by certain oxidizing agents; second for gasification where soot particles are attacked by H 2 O or CO 2 molecules. Rate data were collected from 19 studies in the literature and evaluated using Bayesian statistics to calibrate the model parameters. Bayesian statistics are valued in their ability to quantify uncertainty in modeling. The calibrated consumption model with quantified uncertainty is presented here along with a discussion of associated implications. The oxidation results are found to be consistent with previous studies. Significant variation is found in the CO 2 gasification rates.

01 COAL, LIGNITE, AND PEAT↗
NASA NTRS1983

Scattering from randomly oriented circular discs with application to vegetation

A vegetation layer is modeled by a collection of randomly oriented circular discs over a half space. The backscattering coefficient from such a half space is computed using the radiative transfer theory. It is shown that significantly different results are obtained from this theory as compared with some earlier investigations using the same modeling approach but with restricted disc orientations. In particular, the backscattered cross-polarized returns cannot have a fast increasing angular trend which is inconsistent with measurements. By setting the appropriate angle of orientation to zero the theory reduces to previously published results. Comparisons are shown with measurements taken from milo, corn and wheat and good agreements are obtained for both polarized and cross-polarized returns.

Karam, M. A.↗
NASA NTRS1984

Scattering from randomly oriented circular discs with application to vegetation

A vegetation layer is modeled by a collection of randomly oriented circular discs over a half space. The backscattering coefficient from such a half space is computed using the radiative transfer theory. It is shown that significantly different results are obtained from this theory as compared with some earlier investigations using the same modeling approach but with restricted disc orientations. In particular, the backscattered cross polarized returns cannot have a fast increasing angular trend which is inconsistent with measurements. By setting the appropriate angle of orientation to zero the theory reduces to previously published results. Comparisons are shown with measurements taken from milo, corn and wheat and good agreements are obtained for both polarized and cross polarized returns.

Karam, M. A.↗
DOE OSTI2019

The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases

Model organisms are essential experimental platforms for discovering gene functions, defining protein and genetic networks, uncovering functional consequences of human genome variation, and for modeling human disease. For decades, researchers who use model organisms have relied on Model Organism Databases (MODs) and the Gene Ontology Consortium (GOC) for expertly curated annotations, and for access to integrated genomic and biological information obtained from the scientific literature and public data archives. Through the development and enforcement of data and semantic standards, these genome resources provide rapid access to the collected knowledge of model organisms in human readable and computation-ready formats that would otherwise require countless hours for individual researchers to assemble on their own. Since their inception, the MODs for the predominant biomedical model organisms [Mus sp (laboratory mouse), Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, and Rattus norvegicus] along with the GOC have operated as a network of independent, highly collaborative genome resources. In 2016, these six MODs and the GOC joined forces as the Alliance of Genome Resources (the Alliance). By implementing shared programmatic access methods and data-specific web pages with a unified "look and feel," the Alliance is tackling barriers that have limited the ability of researchers to easily compare common data types and annotations across model organisms. To adapt to the rapidly changing landscape for evaluating and funding core data resources, the Alliance is building a modern, extensible, and operationally efficient "knowledge commons" for model organisms using shared, modular infrastructure.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2017

Biomechanical Modeling Analysis of Loads Configuration for Squat Exercise

INTRODUCTION: Long duration space travel will expose astronauts to extended periods of reduced gravity. Since gravity is not present to assist loading, astronauts will use resistive and aerobic exercise regimes for the duration of the space flight to minimize loss of bone density, muscle mass and aerobic capacity that occurs during exposure to a reduced gravity environment. Unlike the International Space Station (ISS), the area available for an exercise device in the next generation of spacecraft for travel to the Moon or to Mars is limited and therefore compact resistance exercise device prototypes are being developed. The Advanced Resistive Exercise Device (ARED) currently on the ISS is being used as a benchmark for the functional performance of these new devices. Biomechanical data collection and computational modeling aid the device design process by quantifying the joint torques and the musculoskeletal forces that occur during exercises performed on the prototype devices. METHODS The computational models currently under development utilize the OpenSim [1] software platform, consisting of open source code for musculoskeletal modeling, using biomechanical input data from test subjects for estimation of muscle and joint loads. The OpenSim Full Body Model [2] is used for all analyses. The model incorporates simplified wrap surfaces, a new knee model and updated lower body muscle parameters derived from cadaver measurements and magnetic resonance imaging of young adults. The upper body uses torque actuators at the lumbar and extremity joints. The test subjects who volunteer for this study are instrumented with reflective markers for motion capture data collection while performing squat exercising on the Hybrid Ultimate Lifting Kit (HULK) prototype device (ZIN Technologies, Middleburg Heights, OH). Ground reaction force data is collected with force plates under the feet, and device loading is recorded through load cells internal to the HULK. Test variables include the applied device load and the dual cable long bar or single cable T-bar interface between the test subject and the device. Data is also obtained using free weights with the identical loading for a comparison to the resistively loaded exercise device trials. The data drives the OpenSim biomechanical model, which has been scaled to match the anthropometrics of the test subject, to calculate the body loads. RESULTS Lower body kinematics, joint moments, joint forces and muscle forces are obtained from the OpenSim biomechanical analysis of the squat exercises under different loading conditions. Preliminary results from the model for the loading conditions will be presented as will hypotheses developed for follow on work.

Human Factors Engineering↗
DOE OSTI2022

Y-12 Nuclear Criticality Safety Program Health Model: Development, Use and Benefits

The Y-12 National Security Complex (Y-12) operates seven diverse enriched uranium processing facilities and maintains a comprehensive nuclear criticality safety (NCS) program. Given the magnitude of the hazard, the NCS program receives significant oversight. Describing the scope and health of the Y-12 NCS program to sometimes non-expert stakeholders with limited time had historically focused on recent events and “hot topics” which did not always convey sufficient context (i.e., how to differentiate between an individual performance issue and a systemic concern). Y-12 created the NCS Program Health (NCSPH) Model to provide a complete and holistic framework to quantify and communicate NCS program health. The model is constructed in a tiered fashion with the top tier broken into three (3) Tier 2 elements, fourteen (14) Tier 3 elements, and 104 Tier 4 and 5 elements. This granularity ensures every feature of the NCS Program is accounted for and stakeholders can see how these features support the collective whole. The model is used as the framework for NCS communications including program plans, reports, health surveys, and meeting agendas. The model has substantially improved stakeholder appreciation for the entirety of the NCS program and how events and assessment results factor into an overarching conclusion on NCS program health. While some details are Y-12 specific, the NCSPH model can easily be tailored for any other site with an NCS program.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS2016

A Comparison of Van Allen Belt Radiation Environment Modeling Programs: AE8/AP8 Legacy, AE9/AP9, and SPENVIS

In the space surrounding Earth there exists an active radiation environment consisting mostly of electrons and protons that have been trapped by Earths magnetic field. This radiation, also known as the Van Allen Belts, has the potential to damage man-made satellites in orbit; thus, proper precautions must be taken to shield NASA assets from this phenomenon. Data on the Van Allen Belts has been collected continuously by a multitude of space-based instruments since the beginning of space exploration. Subsequently, using theory to fill in the gaps in the collected data, computer models have been developed that take in the orbital information of a hypothetical mission and output the expected particle fluence and flux for that orbit. However, as new versions of the modeling system are released, users are left wondering how the new version differs from the old. Therefore, we performed a comparison of three different editions of the modeling system: AE8/AP8 (legacy), which is included in the model 9 graphical user interface as an option for ones calculations, AE9/AP9, and the Space Environment Information System (SPENVIS), which is an online-based form of AE8/AP8 developed by NASA and the European Space Agency that changed the code to allow the program to extrapolate data to predict fluence and flux at higher energies. Although this evaluation is still ongoing, it is predicted that the model 8 (legacy) and SPENVIS version will have identical outputs with the exception of the extended energy levels from SPENVIS, while model 9 will provide different fluences than model 8 based on additional magnetic field descriptions and on-orbit data.

Modeling Programs↗
DOE OSTI2021

Model Soil Consortium 2 (MSC-2) Bacterial Isolate Genomes

Model Soil Consortium 2 (MSC-2) bacterial isolate genome collections are derived from the soil consortium MSC-1 multi-species cultured isolate genome collections from a previously reported WA-IsoC_MSC1.1.0 collection of a naturally evolved, model soil consortia (10.25584/WAIsoCMSC1/1635272). This collection contains 8 different isolate species cultivated under variable carbon and nitrogen sources, originating from the IAREC grassland soil field site located in Prosser, WA, USA. Genomic sequencing of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names of a given organism within a natural environment. The version described here is the first version.

Soil microbiome, defined community, chitin↗
NASA NTRS2016

Carbon Monoxide Accumulation in the Extravehicular Mobility Unit

Introduction: Life support technology in large closed systems like submarines and space stations catalyzes carbon monoxide (CO) to carbon dioxide, which is easily removed. However, in a small system like the Extravehicular Mobility Unit (EMU), spacesuit, CO from exogenous (contaminated oxygen (O (sub 2) supply) and endogenous (human metabolism) sources will accumulate in the free suit volume. The free volume becomes a sink for CO that is rebreathed by the astronaut. The accumulation through time depends on many variables: the amount absorbed by the astronaut, the amount produced by the astronaut (between 0.28 and 0.34 moles per hour per kilogram)[1], the amount that enters the suit from contaminated O (sub 2), the amount removed through suit leak, the free volume of the suit, and the O (sub 2) partial pressure[2], just to list a few. Contamination of the EMU O (sub 2) supply with no greater than 1 part per million CO was the motivation for empirical measurements from CO pulse oximetry (SpCO) as well as mathematical modeling of the EMU as a rebreather for CO. Methods: We developed a first-order differential mixing equation as well as an iterative method to compute CO accumulation in the EMU. Pre-post measurements of SpCO (Rad-57, Masimo Corporation) from EMU ground training and on-orbit extravehicular activities (EVAs) were collected. Results: Initial modeling without consideration of the astronaut as a sink but only the source of CO showed that after 8 hours breathing 100 percent O (sub 2) with a 10 milliliter per minute (760 millimeters Hg at 21 degrees Centigrade standard) suit leak, an endogenous production rate of 0.23 moles per hour per kilogram for a 70 kilogram person with 42 liters (1.5 cubic feet) free suit volume resulted in a peak CO partial pressure (pCO) of 0.047 millimeters Hg at 4.3 pounds per square inch absolute (222 millimeters Hg). Preliminary results based on a 2008 model[3] with consideration of the astronaut as a sink and source of CO suggests that most of the rebreathed CO stays bound to hemoglobin and myoglobin and; therefore, pCO only increased to 0.002 millimeters Hg in the EMU. Hemoglobin saturation after 8 hours was an insignificant 0.4 percent compared to about 4 percent for cigarette smokers in the general population. This preliminary modeling result supplements 11 pre-post index finger SpCO measurements from EMU ground training (mean 0.5 percent versus 1 percent, probability equal to 0.41 from paired t-test) and 10 on-orbit pre-post EVAs (mean 1.5 percent versus 1.1 percent, probability equal to 0.17 from paired t-test) that showed no consistent increase, at least no increase outside the accuracy of the oximeter (1 percent display resolution with plus or minus 3 percent Standard Deviation). Discussion: Simulations continue, but a preliminary conclusion is that rebreathing endogenous CO accumulating in the EMU is not a serious medical issue during EVA. The absence of CO poisoning signs or symptoms following hundreds of EVAs is also good empirical evidence that corroborates the limited SpCO measurements and preliminary modeling results.

Conkin, J.↗