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At least 649 records · Page 36

SeaWiFS Science Algorithm Flow Chart

This flow chart describes the baseline science algorithms for the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) Data Processing System (SDPS). As such, it includes only processing steps used in the generation of the operational products that are archived by NASA's Goddard Space Flight Center (GSFC) Distributed Active Archive Center (DAAC). It is meant to provide the reader with a basic understanding of the scientific algorithm steps applied to SeaWiFS data. It does not include non-science steps, such as format conversions, and places the greatest emphasis on the geophysical calculations of the level-2 processing. Finally, the flow chart reflects the logic sequences and the conditional tests of the software so that it may be used to evaluate the fidelity of the implementation of the scientific algorithm. In many cases however, the chart may deviate from the details of the software implementation so as to simplify the presentation.

Darzi, Michael↗

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.

Biomedical applications↗

A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation

Estimating the thermochemical properties of systems is important in many fields such as material science and catalysis. The Python multiscale thermochemistry toolbox (pMuTT) is a Python software library developed to streamline the conversion of ab-initio data to thermochemical properties using statistical mechanics, to perform thermodynamic analysis, and to create input files for kinetic modeling software. Its open-source implementation in Python leverages existing scientific codes, encourages users to write scripts for their needs, and allows the code to be expanded easily. The core classes developed include a statistical mechanical model in which energy modes can be included or excluded to suit the application, empirical models for rapid thermodynamic property estimation, and a reaction model to calculate kinetic parameters or changes in thermodynamic properties. In addition, pMuTT supports other features, such as Brønsted–Evans–Polanyi (BEP) relationships, coverage effects, and ab-initio phase diagrams.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗

UQpy Version 4.2: Uncertainty quantification with Python

We introduce a new module for the UQpy software package which extends its capabilities into the field of Scientific Machine Learning. This module builds on PyTorch to create a flexible and robust platform for uncertainty quantification in machine learning. The scientific machine learning module of UQpy introduces custom layers, neural networks, and neural network trainers that are compatible with torch version 2.2.2 and allow for “plug and play” integration into existing torch code.

Neural networks↗

Quantitative analysis of total reflection X-ray fluorescence from finely layered structures using XeRay

Total reflection x-ray fluorescence (TXRF) is a widely applicable experimental technique for studying chemical element distributions across finely layered structures at extremely high sensitivity. To promote and facilitate scientific discovery using TXRF, we developed a MATLAB-based software package with a graphical user interface, named XeRay, for quick, accurate, and intuitive data analysis. XeRay lets the user model any layered system, each layer with its independent chemical composition and thickness, and enables fine-tuned data fitting. The accuracy of XeRay has been tested in the analysis of TXRF data from both air/liquid interface and liquid/liquid interfacial studies and has been compared to literature results. In an air/liquid interface study, Ca 2+ sequestration was measured at a Langmuir monolayer of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidic acid (SOPA) on a buffer solution of 1 mM CaCl2 at pH 7.5. Data analysis with XeRay reveals that each 1 nm2 of interfacial area contains 2.38 ± 0.06 Ca 2+ ions, which corresponds to a 1:1 ratio between SOPA headgroups and Ca 2+ ions, consistent with several earlier reports. For the liquid/liquid interface study of Sr 2+ enrichment at the dodecane/surfactant/water interface, analysis using XeRay gives a surface enrichment of Sr 2+ at $68^{+6}_{-5}$ Å 2 per ion, consistent with the result published for the same dataset.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Dynamic Transmission Line Switching Amid Wildfire-Prone Weather Under Decision-Dependent Uncertainty

During dry and windy seasons, environmental conditions significantly increase the risk of wildfires, exposing power grids to disruptions caused by transmission line failures. Wildfire propagation exacerbates grid vulnerability, potentially leading to prolonged power outages. To address this challenge, we propose a multistage optimization model that dynamically adjusts transmission grid topology in response to wildfire propagation, aiming to develop an optimal response policy. By accounting for decision-dependent uncertainty, where line survival probabilities depend on usage, we employ distributionally robust optimization to model uncertainty in line survival distributions. We adapt the stochastic nested decomposition algorithm and derive a deterministic upper bound for its finite convergence. To enhance computational efficiency, we exploit the Lagrangian dual problem structure for a faster generation of Lagrangian cuts. Using realistic data from the California transmission grid, we demonstrate the superior performance of dynamic response policies against two-stage alternatives through a comprehensive case study. In addition, after solving the multistage formulation, we construct easy-to-implement policies that significantly reduce computational burden while maintaining good performance in real-time deployment. History: Accepted by Russell Bent, Area Editor for Network Optimization: Algorithms and Applications. Funding: This work was supported by the U.S. Department of Energy, Office of Electricity [Grant DE-AC02-05CH11231]. The work of R. Jiang was supported in part by the U.S. National Science Foundation, Division of Electrical, Communications and Cyber Systems [Grant ECCS-1845980] and the U.S. Air Force Office of Scientific Research [Grant FA9550-23-1-0323]. Supplemental Material: The software that supports the findings of this study is available within the paper and its Supplemental Information ( https://pubsonline.informs.org/doi/suppl/10.1287/ijoc.2025.1210 ) as well as from the IJOC GitHub software repository ( https://github.com/INFORMSJoC/2025.1210 ). The complete IJOC Software and Data Repository is available at https://informsjoc.github.io/ .

Estrada-Garcia, Juan-Alberto↗

Final Report: Correctness Tools for Petascale Computing

In the course of developing parallel programs for leadership computing systems, subtle programming errors often arise that are extremely difficult to diagnose without tools. To meet this challenge, University of Maryland, the University of Wisconsin—Madison, and Rice University worked to develop lightweight tools to help code developers pinpoint a variety of program correctness errors that plague parallel scientific codes. The aim of this project was to develop software tools that help diagnose program errors including memory leaks, memory access errors, round-off errors, and data races. Research at Rice University focused on developing algorithms and data structures to support efficient monitoring of multithreaded programs for memory access errors and data races. This is a final report about research and development work at Rice University as part of this project.

97 MATHEMATICS AND COMPUTING↗

Hardening DOE R&D Software Tools for Web-based Visualization SBIR Phase I Final Report

Ubiquitous web-based visualization is essential to delivering large-scale data visualization to various stakeholders, from the scientist to the board member. These stakeholders will not tolerate a stalled application or a pop-up window asking them to wait for the processing to complete. They require a responsive and interactive visualization environment with high-quality imagery suitable for detailed analysis and boardroom presentations. At Kitware, Inc., we have accomplished web visualization to this point, leveraging state-of-the-art tools like HTML5, CSS3, SVG, Canvas, and WebGL. Solutions that leverage a combination of these technologies are necessary to handle workloads that vary significantly in data size efficiently. However, it is not always practical to move large data to the web client for visualization. Kitware's ParaView as a Service combines client-side visualization using both distributed processing and remote rendering on big data impractical to move. Existing distributed processing and remote rendering solution's interactivity is below the expectations of web-based applications. Our project examined proposed solutions to the areas outlined above in ParaView as a Service. We have investigated concurrent pipelines, streaming images, progressive rendering, and optimization of algorithms and data movement to address these concerns. For the Phase I project, we completed the proposed work plan. As a result, the project produced three prototypes of essential importance for web visualization and the ParaView as a Service community. We created a simple desktop application for an interactive streamline placement prototype, a web-based interactive streamline placement prototype, and a web-based progressive rendering utilizing raytracing prototype. These prototypes relied on the hardening of emerging software toolkits funded by the Department of Energy (DOE) Advanced Scientific Computing Research (ASCR) program (such as ParaView, VTK-m, and Mochi). We blended these components into web-based visualization prototypes that meet the industry's expectations for interactivity and responsiveness. The Phase I project had four essential focus areas: 1. Develop prototype ParaView as a Service backend server using asynchronous, non-blocking design principles. 2. Develop a prototype web application that uses the ParaView as a Service backend server for remote data visualization. 3. Implement image streaming with encoding/compression and progressive rendering capabilities in the proposed platform. 4. Evaluate the prototype developed and summarize observations, including the challenges and pitfalls of our approach. After our successful completion of Phase I, we are strongly positioned to propose a successful Phase II project.

Geveci, Berk↗

OASIS: Open-Source AI Software Infrastructure for Science-SBIR Phase I

OASIS: Open source AI Software Infrastructure for Science is developed for researchers in the scientific domain. OASIS provides a data API to ingest and serve scientific data formats and annotations within AI workflows. It delivers a unique integration of features such as coupling of data to AI models, scalable training, cloud deployment into a cohesive web and command-line interface, and state-of-the-art techniques to debug and enhance AI models.

Chaudhary, Aashish↗

“Development of Interactive Chemistry in E3SM v2” Final Report (3/1/2023-2/29/2024)

We are pleased to report that the proposed milestones and tasks under this subcontract, or those modified subsequently by the Technical Representative based on project needs, have been met. In general, the accomplishments under this subcontract exceeded the originally proposed milestones and effort, and went from code development to scientific results and high-profile publications, to mission critical software development for the E3SM project.

54 ENVIRONMENTAL SCIENCES↗

The Cloud-resolving model Radar SIMulator (CR-SIM) Version 3.3: description and applications of a virtual observatory

Ground-based observatories use multi-sensor observations to characterize cloud and precipitation properties. One of the challenges is how to design strategies to best use these observations to understand these properties and evaluate weather and climate models. This paper introduces the Cloud resolving model Radar SIMulator (CR-SIM), which uses output from high-resolution cloud resolving models (CRMs) to emulate multi-wavelength, zenith-pointing, and scanning radar observables and multi-sensor (radar and lidar) products. CR-SIM allows direct comparison between an atmospheric model simulation and remote-sensing products using a forward-modeling framework consistent with the microphysical assumptions used in the atmospheric model. CR-SIM has the flexibility to easily incorporate additional microphysical modules, such as microphysical schemes and scattering calculations, and expand the applications to simulate multi-sensor retrieval products. In this paper, we present several applications of CR-SIM for evaluating the representativeness of cloud microphysics and dynamics in a CRM, quantifying uncertainties in radar-lidar integrated cloud products and multi-Doppler wind retrievals, and optimizing radar sampling strategy using observing system simulation experiments. These applications demonstrate the application of CR-SIM as a virtual observatory operator on high-resolution model output for a consistent comparison between model results and observations to aid interpretation of the differences and improve understanding of the representativeness errors due to the sampling limitations of the ground-based measurements. CR-SIM is licensed under the GNU GPL package and both the software and the user guide are publicly available to the scientific community.

54 ENVIRONMENTAL SCIENCES↗

Characterizing the scientific potential of satellite sensors

Eleven thematic mapper (TM) radiometric calibration programs were tested and evaluated in support of the task to characterize the potential of LANDSAT TM digital imagery for scientific investigations in the Earth sciences and terrestrial physics. Three software errors related to integer overflow, divide by zero, and nonexist file group were found and solved. Raw, calibrated, and corrected image groups that were created and stored on the Barker2 disk are enumerated. Black and white pixel print files were created for various subscenes of a San Francisco scene (ID 40392-18152). The development of linear regression software is discussed. The output of the software and its function are described. Future work in TM radiometric calibration, image processing, and software development is outlined.

Source record↗

The Voyager-2 Neptune encounter

Aspects of the encounter of Voyager 2 with Neptune which will occur during the summer of 1989 are discussed. The major scientific objectives and the resulting trajectory characteristics are reviewed. The technological requirements for transmitting the scientific data to earth are addressed, and the hardware and software aboard the satellite which will accomplish the transmission are described.

Kosman, William J.↗

Network upgrades

The NASA Scientific and Technical Information (STI) Project modernization plan covers both software and hardware upgrades. On the hardware side, replacing terminals with PC's will enhance office automation functions, provide mainframe and computer network systems access, and facilitate client/server functions. The modernization plan upgrades will involve commercial off-the-shelf software, user interface and client development tools, and the redesign and integration of application systems and software.

Ridgeway, Roland↗

Spinoff 2010

Topics covered include: Burnishing Techniques Strengthen Hip Implants; Signal Processing Methods Monitor Cranial Pressure; Ultraviolet-Blocking Lenses Protect, Enhance Vision; Hyperspectral Systems Increase Imaging Capabilities; Programs Model the Future of Air Traffic Management; Tail Rotor Airfoils Stabilize Helicopters, Reduce Noise; Personal Aircraft Point to the Future of Transportation; Ducted Fan Designs Lead to Potential New Vehicles; Winglets Save Billions of Dollars in Fuel Costs; Sensor Systems Collect Critical Aerodynamics Data; Coatings Extend Life of Engines and Infrastructure; Radiometers Optimize Local Weather Prediction; Energy-Efficient Systems Eliminate Icing Danger for UAVs; Rocket-Powered Parachutes Rescue Entire Planes; Technologies Advance UAVs for Science, Military; Inflatable Antennas Support Emergency Communication; Smart Sensors Assess Structural Health; Hand-Held Devices Detect Explosives and Chemical Agents; Terahertz Tools Advance Imaging for Security, Industry; LED Systems Target Plant Growth; Aerogels Insulate Against Extreme Temperatures; Image Sensors Enhance Camera Technologies; Lightweight Material Patches Allow for Quick Repairs; Nanomaterials Transform Hairstyling Tools; Do-It-Yourself Additives Recharge Auto Air Conditioning; Systems Analyze Water Quality in Real Time; Compact Radiometers Expand Climate Knowledge; Energy Servers Deliver Clean, Affordable Power; Solutions Remediate Contaminated Groundwater; Bacteria Provide Cleanup of Oil Spills, Wastewater; Reflective Coatings Protect People and Animals; Innovative Techniques Simplify Vibration Analysis; Modeling Tools Predict Flow in Fluid Dynamics; Verification Tools Secure Online Shopping, Banking; Toolsets Maintain Health of Complex Systems; Framework Resources Multiply Computing Power; Tools Automate Spacecraft Testing, Operation; GPS Software Packages Deliver Positioning Solutions; Solid-State Recorders Enhance Scientific Data Collection; Computer Models Simulate Fine Particle Dispersion; Composite Sandwich Technologies Lighten Components; Cameras Reveal Elements in the Short Wave Infrared; Deformable Mirrors Correct Optical Distortions; Stitching Techniques Advance Optics Manufacturing; Compact, Robust Chips Integrate Optical Functions; Fuel Cell Stations Automate Processes, Catalyst Testing; Onboard Systems Record Unique Videos of Space Missions; Space Research Results Purify Semiconductor Materials; and Toolkits Control Motion of Complex Robotics.

Source record↗

NASA Tech Briefs, December 2006

Topic include: Inferring Gear Damage from Oil-Debris and Vibration Data; Forecasting of Storm-Surge Floods Using ADCIRC and Optimized DEMs; User Interactive Software for Analysis of Human Physiological Data; Representation of Serendipitous Scientific Data; Automatic Locking of Laser Frequency to an Absorption Peak; Self-Passivating Lithium/Solid Electrolyte/Iodine Cells; Four-Quadrant Analog Multipliers Using G4-FETs; Noise Source for Calibrating a Microwave Polarimeter; Hybrid Deployable Foam Antennas and Reflectors; Coating MCPs with AlN and GaN; Domed, 40-cm-Diameter Ion Optics for an Ion Thruster; Gesture-Controlled Interfaces for Self-Service Machines; Dynamically Alterable Arrays of Polymorphic Data Types; Identifying Trends in Deep Space Network Monitor Data; Predicting Lifetime of a Thermomechanically Loaded Component; Partial Automation of Requirements Tracing; Automated Synthesis of Architecture of Avionic Systems; SSRL Emergency Response Shore Tool; Wholly Aromatic Ether-Imides as n-Type Semiconductors; Carbon-Nanotube-Carpet Heat-Transfer Pads; Pulse-Flow Microencapsulation System; Automated Low-Gravitation Facility Would Make Optical Fibers; Alignment Cube with One Diffractive Face; Graphite Composite Booms with Integral Hinges; Tool for Sampling Permafrost on a Remote Planet; and Special Semaphore Scheme for UHF Spacecraft Communications.

Source record↗

Pandora Operation and Analysis Software

Pandora Operation and Analysis Software controls the Pandora Sun- and sky-pointing optical head and built-in filter wheels (neutral density, UV bandpass, polarization filters, and opaque). The software also controls the attached spectrometer exposure time and thermoelectric cooler to maintain the spectrometer temperature to within 1 C. All functions are available through a GUI so as to be easily accessible by the user. The data are automatically stored on a miniature computer (netbook) for automatic download to a designated server at user defined intervals (once per day, once per week, etc.), or to a USB external device. An additional software component reduces the raw data (spectrometer counts) to preliminary scientific products for quick-view purposes. The Pandora systems are built from off-the-shelf commercial parts and from mechanical parts machined using electronic machine shop drawings. The Pandora spectrometer system is designed to look at the Sun (tracking to within 0.1 ), or to look at the sky at any zenith or azimuth angle, to gather information about the amount of trace gases or aerosols that are present.

Herman, Jay↗