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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 433 records · Page 24

County Level Annual Population Projections for SSP3 and SSP5

This dataset consist of annual (2020-2100) county-level population projections for the United States (U.S.) for Shared Socioeconomic Pathways (SSPs) 3 and 5. The original decadal state-level data is used as an input to the gridded population data model to downscale the state-level projections for each SSP to a 1 km grid. The 1 km data is then aggregated to the county-level using the 2020 TIGER/Line county shapefiles from the U.S. Census Bureau. The two data files are shared as .csv files with the following structure: Rows = Data for individual counties which are identified using their Federal Information Processing Standard (FIPS) code. The FIPS code is stored in the first column. Columns = Each year from 2020-2100 is an individual column. For easier reference, the state name associated with each row is stored in the last column. Values in each cell are the downscaled estimated population for that county-year combination. Values are fractional due to the weighting scheme used in the downscaling. The paper and model source code cited in the "Related Works" section describes the initial source of the population projections.

FIPS↗

Simulation of the spatial shift in detector response for polarized protons within a calorimeter

Measurement of the helicity dependent elastic electron-proton scattering cross section provides a key means of investigating parity violation within the proton. However, such measurements exhibit potential instrumental effects associated with the detection of polarized recoiled protons. In particular, spin-orbit interactions within a massive detector induce a systematic spatial shift in the detector signal. In this study, we determine the size of this shift using the Geant4 simulation toolkit. For a typical hadron calorimeter, we found a polarization dependent shift on the order of 0.01-0.1 mm, multiple orders of magnitude smaller than the typical spatial resolution seen in hadronic calorimeters. Additionally, we provide the custom modifications required of the Geant4 source code to implement the quasi-elastic scattering of polarized protons incident on nuclei in the detector. The modifications are readily extendable to generic matter sources, and can be used for the study of additional spin dependent observables in Geant4.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

gRNA-SeqRET: a universal tool for targeted and genome-scale gRNA design and sequence extraction for prokaryotes and eukaryotes

High-throughput genetic screening is frequently employed to rapidly associate gene with phenotype and establish sequence-function relationships. With the advent of CRISPR technology, and the ability to functionally interrogate previously genetically recalcitrant organisms, non-model organisms can be investigated using pooled guide RNA (gRNA) libraries and sequencing-based assays to quantitatively assess fitness of every targeted locus in parallel. To aid the construction of pooled gRNA assemblies, we have developed an in silico design workflow for gRNA selection using the gRNA Sequence Region Extraction Tool (gRNA-SeqRET). Built upon the previously developed CCTop, gRNA-SeqRET enables automated, scalable design of gRNA libraries that target user-specified regions or whole genomes of any prokaryote or eukaryote. Additionally, gRNA-SeqRET automates the bulk extraction of any regions of sequence relative to genes or other features, aiding in the design of homology arms for insertion or deletion constructs. We also assess in silico the application of a designed gRNA library to other closely related genomes and demonstrate that for very closely related organisms Average Nucleotide Identity (ANI) > 95% a large fraction of the library may be of relevance. The gRNA-SeqRET web application pipeline can be accessed at https://grna.jgi.doe.gov. The source code is comprised of freely available software tools and customized Python scripts, and is available at https://bitbucket.org/berkeleylab/grnadesigner/src/master/ under a modified BSD open-source license (https://bitbucket.org/berkeleylab/grnadesigner).

59 BASIC BIOLOGICAL SCIENCES↗

Machine Learning-enabled Scalable Performance Prediction of Scientific Codes

Hardware architectures become increasingly complex as the compute capabilities grow to exascale. Here, we present the Analytical Memory Model with Pipelines (AMMP) of the Performance Prediction Toolkit (PPT). PPT-AMMP takes high-level source code and hardware architecture parameters as input and predicts runtime of that code on the target hardware platform, which is defined in the input parameters. PPT-AMMP transforms the code to an (architecture-independent) intermediate representation, then (i) analyzes the basic block structure of the code, (ii) processes architecture-independent virtual memory access patterns that it uses to build memory reuse distance distribution models for each basic block, and (iii) runs detailed basic-block level simulations to determine hardware pipeline usage. PPT-AMMP uses machine learning and regression techniques to build the prediction models based on small instances of the input code, then integrates into a higher-order discrete-event simulation model of PPT running on Simian PDES engine. We validate PPT-AMMP on four standard computational physics benchmarks and present a use case of hardware parameter sensitivity analysis to identify bottleneck hardware resources on different code inputs. We further extend PPT-AMMP to predict the performance of a scientific application code, namely, the radiation transport mini-app SNAP. To this end, we analyze multi-variate regression models that accurately predict the reuse profiles and the basic block counts. We validate predicted SNAP runtimes against actual measured times.

97 MATHEMATICS AND COMPUTING↗

Metabolomics Collision Cross Section Database and Server

This is a the code and data for a website created to display collision cross section data for metabolites and small molecules. This repository hosts two things. First is the source code (js) for a website created to display collision cross section data for metabolites and other small molecules. The second is the underlying CCS dataset. The growing interest in metabolomic and exposomic studies is also inciting a need for new techniques to analyze these diverse molecules. Mass spectrometry-based studies are often preferred for the confident identification of small molecules. Ion mobility spectrometry (IMS) is capable of separating molecules that have the same m/z but different conformational arrangements, which is very useful in metabolomic and exposomic analyses. As the desire for IMS measurements of metabolites continues to grow, so does the need for high quality collision cross section (CCS) values.

Payne, Sam↗

NOS3: NASA Operational Simulator for Small Satellites

The NASA Operational Simulator for Small Satellites (NOS3) is a suite of open-source software tools to aid in areas such as software development, integration & test (I&T), mission operations/training, verification and validation (V&V), and software systems check-out. NOS3 provides a software development environment, a multi-target build system, operational interface/ground software, dynamics and environment simulations, and software-based hardware models. NOS3 has just recently been open-sourced by NASA and is available for immediate use. It enables the development of flight software (FSW) early in the project life cycle when hardware availability is limited. Small satellite development suffers from extensive lead times on many of the commercial-off-the-shelf (COTS) components as well as limited funding for engineering test units (ETUs). To alleviate the need to provide a hardware test-bed for each developer/tester, NOS3 hardware models are based upon characteristic data or manufacturer's data sheets for each individual component. The NOS3 hardware models' fidelity is such that FSW executes unaware that physical hardware is not present. This allows FSW binaries to be compiled for both the simulation environment and the flight computer without changing the FSW source code. For hardware models that provide data which is dependent upon the environment and spacecraft dynamics, such as a GPS receiver or magnetometer, an open-source tool from NASA GSFC (42 Spacecraft Simulator) is used to provide the necessary data. The underlying infrastructure used to transfer messages between FSW and the hardware models can also be used to monitor, intercept, and inject messages, which has proven to be beneficial for V&V of larger missions such as James Webb Space Telescope (JWST). As hardware is selected and becomes available, drivers can be added to the NOS3 environment to enable hardware-in-the-loop (HWIL) testing. When strict time synchronization is not vital, any number of combinations of hardware components and software-based models can be tested. NOS3 was actively used for FSW development and component testing of the Simulation-to-Flight 1 (STF-1) CubeSat and the Lunar IceCube CubeSat. As NOS3 matures, hardware models have been added for common small satellite components such as GPS receivers, electrical power systems and batteries, and antenna systems.

Suder, Mark↗

Reformulation RELAP5-3D in FORTRAN 95 and Results

RELAP5-3D is a nuclear power plant code used worldwide for safety analysis, design, and operator training. In keeping with ongoing developments in the computing industry, we have re-architected the code in the FORTRAN 95 language, the current, fully-available, FORTRAN language. These changes include a complete reworking of the database and conversion of the source code to take advantage of new constructs. The improvements and impacts to the code are manifold. It is a completely machine-independent code that produces machine independent fluid property and plot files and expands to the exact size needed to accommodate the user’s input. Runtime is generally better for larger input models. Other impacts of code conversion are improved code readability, reduced maintenance and development time, increased adaptability to new computing platforms, and increased code longevity. The conversion methodology, code improvements and testing upgrades are presented in a manner that will be useful to future conversion projects for other such large codes. Comparison between the pre- and post-conversion code are made on the basis of code metrics and code performance.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Nuclear Energy Advanced Modeling and Simulation (NEAMS) waste Integrated Performance and Safety Codes (IPSC) : gap analysis for high fidelity and performance assessment code development.

This report describes a gap analysis performed in the process of developing the Waste Integrated Performance and Safety Codes (IPSC) in support of the U.S. Department of Energy (DOE) Office of Nuclear Energy Advanced Modeling and Simulation (NEAMS) Campaign. The goal of the Waste IPSC is to develop an integrated suite of computational modeling and simulation capabilities to quantitatively assess the long-term performance of waste forms in the engineered and geologic environments of a radioactive waste storage or disposal system. The Waste IPSC will provide this simulation capability (1) for a range of disposal concepts, waste form types, engineered repository designs, and geologic settings, (2) for a range of time scales and distances, (3) with appropriate consideration of the inherent uncertainties, and (4) in accordance with rigorous verification, validation, and software quality requirements. The gap analyses documented in this report were are performed during an initial gap analysis to identify candidate codes and tools to support the development and integration of the Waste IPSC, and during follow-on activities that delved into more detailed assessments of the various codes that were acquired, studied, and tested. The current Waste IPSC strategy is to acquire and integrate the necessary Waste IPSC capabilities wherever feasible, and develop only those capabilities that cannot be acquired or suitably integrated, verified, or validated. The gap analysis indicates that significant capabilities may already exist in the existing THC codes although there is no single code able to fully account for all physical and chemical processes involved in a waste disposal system. Large gaps exist in modeling chemical processes and their couplings with other processes. The coupling of chemical processes with flow transport and mechanical deformation remains challenging. The data for extreme environments (e.g., for elevated temperature and high ionic strength media) that are needed for repository modeling are severely lacking. In addition, most of existing reactive transport codes were developed for non-radioactive contaminants, and they need to be adapted to account for radionuclide decay and in-growth. The accessibility to the source codes is generally limited. Because the problems of interest for the Waste IPSC are likely to result in relatively large computational models, a compact memory-usage footprint and a fast/robust solution procedure will be needed. A robust massively parallel processing (MPP) capability will also be required to provide reasonable turnaround times on the analyses that will be performed with the code. A performance assessment (PA) calculation for a waste disposal system generally requires a large number (hundreds to thousands) of model simulations to quantify the effect of model parameter uncertainties on the predicted repository performance. A set of codes for a PA calculation must be sufficiently robust and fast in terms of code execution. A PA system as a whole must be able to provide multiple alternative models for a specific set of physical/chemical processes, so that the users can choose various levels of modeling complexity based on their modeling needs. This requires PA codes, preferably, to be highly modularized. Most of the existing codes have difficulties meeting these requirements. Based on the gap analysis results, we have made the following recommendations for the code selection and code development for the NEAMS waste IPSC: (1) build fully coupled high-fidelity THCMBR codes using the existing SIERRA codes (e.g., ARIA and ADAGIO) and platform, (2) use DAKOTA to build an enhanced performance assessment system (EPAS), and build a modular code architecture and key code modules for performance assessments. The key chemical calculation modules will be built by expanding the existing CANTERA capabilities as well as by extracting useful components from other existing codes.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Tight-Binding-Based Method for Simulations of Complex Materials with Accompanying Database

The NRL-Tight-Binding (NRL-TB) method has been applied successfully to many monatomic, binary, and a few ternary systems. The method consists of a fit to Density Functional Theory (DFT) results and has transferability beyond the fitted DFT database including performing tight-binding molecular dynamics simulations. We are working on a new website with a detailed guide of how to use the method in performing the fit to DFT results (Fitting Code) and obtaining non-orthogonal TB parameters expressed in a polynomial form as environment-dependent Slater-Koster parameters (on-site terms), and neighbor distance-dependent Hamiltonian and Overlap terms. These parameters are then used in a Static Code to verify or make predictions for large systems often beyond the computational capabilities of standard DFT codes. Our starting point was a website developed at NRL some years ago which NRL no longer supports. We have now been augmenting that website with new examples of expanding the original capabilities of the method such as incorporating in the codes f-electron states. Our website (esd.cos.gmu.edu/tb) contains two separate branches: One named NRL-TB with the full documentation of the method including source codes and examples. The other branch, named ESD-dB, is a library of electronic structure calculations for all the monatomic elements (a subset of the elements also found in a recent book by the author of this proposal. See reference 22) and an approximately 700 hundred compounds in specific crystal structures. We discuss below the progress made so far in improving and expanding the capabilities of our TB method and the plans for further extensions of our approach.

36 MATERIALS SCIENCE↗

Coupled 2-dimensional cascade theory for noise an d unsteady aerodynamics of blade row interaction in turbofans. Volume 2: Documentation for computer code CUP2D

A two dimensional linear aeroacoustic theory for rotor/stator interaction with unsteady coupling was derived and explored in Volume 1 of this report. Computer program CUP2D has been written in FORTRAN embodying the theoretical equations. This volume (Volume 2) describes the structure of the code, installation and running, preparation of the input file, and interpretation of the output. A sample case is provided with printouts of the input and output. The source code is included with comments linking it closely to the theoretical equations in Volume 1.

Hanson, Donald B.↗

Proceedings of the Third International Workshop on Proof-Carrying Code and Software Certification

This NASA conference publication contains the proceedings of the Third International Workshop on Proof-Carrying Code and Software Certification, held as part of LICS in Los Angeles, CA, USA, on August 15, 2009. Software certification demonstrates the reliability, safety, or security of software systems in such a way that it can be checked by an independent authority with minimal trust in the techniques and tools used in the certification process itself. It can build on existing validation and verification (V&V) techniques but introduces the notion of explicit software certificates, Vvilich contain all the information necessary for an independent assessment of the demonstrated properties. One such example is proof-carrying code (PCC) which is an important and distinctive approach to enhancing trust in programs. It provides a practical framework for independent assurance of program behavior; especially where source code is not available, or the code author and user are unknown to each other. The workshop wiII address theoretical foundations of logic-based software certification as well as practical examples and work on alternative application domains. Here "certificate" is construed broadly, to include not just mathematical derivations and proofs but also safety and assurance cases, or any fonnal evidence that supports the semantic analysis of programs: that is, evidence about an intrinsic property of code and its behaviour that can be independently checked by any user, intermediary, or third party. These guarantees mean that software certificates raise trust in the code itself, distinct from and complementary to any existing trust in the creator of the code, the process used to produce it, or its distributor. In addition to the contributed talks, the workshop featured two invited talks, by Kelly Hayhurst and Andrew Appel. The PCC 2009 website can be found at http://ti.arc.nasa.gov /event/pcc 091.

Ewen, Denney, W.↗

Improvements, enhancements, and optimizations of COBRA-TF

The Reactor Dynamics and Fuel Management Group (RDFMG) at The Pennsylvania State University (PSU) has become active in the Consortium for Advanced Simulation of Light Water Reactors (CASL) program by delivering, supporting, and further developing CTF, the PSU version of the Coolant Boiling in Rod Arrays - Two Fluids (COBRA-TF) Thermal/Hydraulic (T/H), sub-channel program. New development work on CTF was primarily geared towards decreasing the execution time of the code so that it may eventually be used for performing pin-by-pin, full-core simulations. Great gains have been made through targeting sections of source code for optimization. For example, wall clock time has been reduced for a one-assembly, three-dimensional model, containing {approx}9,400 mesh cells, from 9.2 min to 1 min. A further improvement has been reduction in code memory usage, which was previously prohibitive for large models. In conjunction with the run time speedups, this has enabled the simulation of a refined quarter-core model ({approx}460,000 mesh cells), which saw a reduction in memory usage from over 130 GB to less than 3 GB. In addition to the optimization work, RDFMG has also created a preprocessor utility for the fast and less error-prone generation of CTF input decks. Furthermore, basic post-processing capabilities have been implemented by creating a CTF subroutine for producing Visualization Tool-Kit (VTK) files that output mesh data and associated simulation results. These VTK files can be opened with visualization software. (authors)

97 MATHEMATICS AND COMPUTING↗

Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators

Alquimia v1.0 is a generic interface to geochemical solvers that facilitates development of multiphysics simulators by enabling code coupling, prototyping and benchmarking. The interface enforces the function arguments and their types for setting up, solving, serving up output data and carrying out other common auxiliary tasks while providing a set of structures for data transfer between the multiphysics code driving the simulation and the geochemical solver. Alquimia relies on a single-cell approach that permits operator splitting coupling and parallel computation. We describe the implementation in Alquimia of two widely used open-source codes that perform geochemical calculations: PFLOTRAN and CrunchFlow. We then exemplify its use for the implementation and simulation of reactive transport in porous media by two open-source flow and transport simulators: Amanzi and ParFlow. We also demonstrate its use for the simulation of coupled processes in novel multiphysics applications including the effect of multiphase flow on reaction rates at the pore scale with OpenFOAM, the role of complex biogeochemical processes in land surface models such as the E3SM Land Model (ELM) and the impact of surface–subsurface hydrological interactions on hydrogeochemical export from watersheds with the Advanced Terrestrial Simulator (ATS). These applications make it apparent that the availability of a well-defined yet flexible interface has the potential to improve the software development workflow, freeing up resources to focus on advances in process models and mechanistic understanding of coupled problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability

Aptamers are oligonucleotide receptors that bind to their targets with high affinity. Here, we consider aptamers comprised of single-stranded DNA that undergo target-binding-induced conformational changes, giving rise to unique secondary and tertiary structures. Given a specific aptamer primary sequence, there are well-established computational tools (notably mfold) to predict the secondary structure via free energy minimization algorithms. While mfold generates secondary structures for individual sequences, there is a need for a high-throughput process whereby thousands of DNA structures can be predicted in real-time for use in an interactive setting, when combined with aptamer selections that generate candidate pools that are too large to be experimentally interrogated. We developed a new Python code for high-throughput aptamer secondary structure determination (GMfold). GMfold uses subgraph matching methods to group aptamer candidates by secondary structure similarities. We also improve an open-source code, SeqFold, to incorporate subgraph matching concepts. We represent each secondary structure as a lowest-energy bipartite subgraph matching of the DNA graph to itself. These new tools enable thousands of DNA sequences to be compared based on their secondary structures, using machine-learning algorithms. This process is advantageous when analyzing sequences that arise from aptamer selections via systematic evolution of ligands by exponential enrichment (SELEX). This work is a building block for future machine-learning-informed DNA-aptamer selection processes to identify aptamers with improved target affinity and selectivity and advance aptamer biosensors and therapeutics.

Aptamer↗

Automatic Code Generation for High-Performance Graph Algorithms

Graph problems are common across fields of scientific computing and social sciences. However, despite their importance, implementing graph algorithms effectively on modern computing systems is a challenging task that requires significant programming effort and generally results in customized implementations. Current computing and memory hierarchies are not architected for irregular computations resulting in challenges for graph algorithms to achieve high performance on those architectures. In this paper, we present GraphX, a novel compiler framework and DSL designed to simplify the development of efficient graph algorithms and achieve high performance on modern computing systems. GraphX consists of a DSL for efficient implementation of graph algorithms, various optimizations, such as support for sparse linear algebra and workspace transformations, optimized graph primitives, including semiring and masking, and a high-performance code generation engine. Using GraphX, users can implement graph algorithms using a semantically-rich language with graph-oriented operators. GraphX uses these semantics to automatically generate efficient code for target architectures, increasing performance and portability across architectures. The composable nature of GraphX makes it possible to extend the set of optimizations and architectures without modifying the source code. We demonstrate GraphX outperforms state-of-the-art graph libraries, such as LAGraph, up to $3.7 speedup in semiring operations, $2.19 speedup in an important sparse computational kernel, and $9.05 speedup in graph processing algorithms.

compiler, graph algorithms, semiring, masking, wor↗

Summer Report: Tool Integration for Variable-Precision Computing

This summer I worked in the tools group of the variable-precision computing effort at Lawrence Livermore National Laboratory (LLNL). I coordinated an integration project that combined three existing tools into a single pipeline for automated mixed-precision tuning at the source code level. This involved coordinating efforts between several different project groups and making improvements to all three tools. Two of the tools are already available publicly as open-source projects, and the third has been submitted for release. This document serves as an overview of the summer's efforts, focusing on our contributions as well as ideas for future work.

97 MATHEMATICS AND COMPUTING↗

Sensor Radiance for a Midlatitude Atmospheric Model

The Herman radiative transfer code which iteratively traces solar radiance through a discrete number of scattering angles and many atmospheric layers was transferred to a personnal computer to reduce time in recompiling the source code. The code was then used to predict what ground reflectance would saturate the TM sensor output given a standard midlatitude atmospheric model. Output radiance is tabulated for the first four bands. Plots show radiance at the sensor as a function of solar zenith angle from a visibility of 40 km; solar zenith angle as a function of time of year for four latitudes over a typical portion of the descending node of a LANDSAT orbit; and values of ground reflectance required to saturate the TM sensor from three different aerosol loading conditions (corresponding to about 20 km, 40 km. and greater than 100 km visibility).

Source record↗

Sandia Simple Particle Tracking (Sandia SPT) v. 1.0

Sandia SPT is designed as software to accompany a book chapter being published a methods chapter which provides an introduction on how to label and track individual proteins. The Sandia Simple Particle Tracking code uses techniques common to the image processing community, where its value is that it facilitates implementing the methods described in the book chapter by providing the necessary open-source code. The code performs single particle spot detection (or segmentation and localization) followed by tracking (or connecting the detected particles into trajectories). The book chapter, which along with the headers in each file, constitutes the documentation for the code is: Anthony, S.M.; Carroll-Portillo, A.; Timlon, J.A., Dynamics and Interactions of Individual Proteins in the Membrane of Living Cells. In Anup K. Singh (Ed.) Single Cell Protein Analysis Methods in Molecular Biology. Springer

Anthony, StephenM.↗