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At least 469 records · Page 26

Neural-network accelerated coupled core-pedestal simulations with self-consistent transport of impurities and compatible with ITER IMAS

pedestal structure, current profile, and plasma equilibrium physics has been developed and tested against a DIII-D discharge. Here, key features of the achieved core-pedestal coupled workflow are its ability to account for the transport of impurities in the plasma self-consistently, as well as its use of machine learning accelerated models for the pedestal structure and for the turbulent transport physics. Notably, the coupled workflow is implemented within the OMFIT framework, and makes use of the ITER integrated modeling and analysis suite (IMAS) data structure for exchanging data among the physics codes that are involved in the simulations. Such technical advance has been facilitated by the development of a new numerical library named OMAS.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Spacelab uplink/downlink data flow and formats

The results of an analysis of the Spacelab (SL) data uplink/downlink structure and those data system elements associated with the support of this data flow are presented. Specific objectives of this report are to present the results of the following analyses: (1) operations of the SL high rate multiplexer, including format structure, data rates, format combinations, format switching, etc.; (2) operations of SL data recorders to include the definition of modes, data rates and forms; (3) operations of the high rate demultiplexer as described above; (4) potential experiment data formats defining formatting parameters to be considered in decommutation analysis; (5) SL computer input/output (I/O) decommutation channels, including the definition of structure, quantity and use of this I/O data; (6) detailed requirements of the data quality monitoring philosophy for this function.

Kandefer, F.↗

Cryo-EM structure of substrate-bound human telomerase holoenzyme

Telomerase adds telomeric repeats to chromosome ends to balance incomplete replication. Telomerase regulation is implicated in cancer, aging and other human diseases, but progress towards telomerase clinical manipulation is hampered by the lack of structural data. Here we present the cryo-electron microscopy structure of substrate-bound human telomerase holoenzyme at subnanometer resolution, describing two flexibly RNA-tethered lobes: the catalytic core with telomerase reverse transcriptase (TERT) and conserved motifs of telomerase RNA (hTR), and an H/ACA ribonucleoprotein (RNP). In the catalytic core, RNA encircles TERT, adopting a well-ordered tertiary structure with surprisingly limited protein-RNA interactions. The H/ACA RNP lobe comprises two sets of heterotetrameric H/ACA proteins and one Cajal body protein, TCAB1, representing a pioneering structure of a large eukaryotic family of ribosome and spliceosome biogenesis factors. Our findings provide a structural framework for understanding human telomerase disease mutations and represent an important step towards telomerase-related clinical therapeutics

59 BASIC BIOLOGICAL SCIENCES↗

ATDM LANL FleCSI: Topology and Execution Framework

FleCSI is a compile-time configurable C++ framework designed to support multi-physics application development. As such, FleCSI attempts to provide a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. This means that FleCSI is potentially useful to many different ECP projects. Current support includes multidimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures (to identify data dependencies between distributed-memory address spaces). FleCSI introduces a functional programming model with control, execution, and data abstractions that are consistent with state-of-the-art task-based runtimes such as Legion and Charm++. The model also provides support for fine-grained, data-parallel execution with backend support for runtimes such as OpenMP and C++17. The FleCSI abstraction layer provides the developer with insulation from the underlying runtimes, while allowing support for multiple runtime systems, including conventional models like asynchronous MPI. The intent is to give developers a concrete set of user-friendly programming tools that can be used now, while allowing flexibility in choosing runtime implementations and optimizations that can be applied to architectures and runtimes that arise in the future. This project is essential to the ECP Ristra Next-Generation Code project, part of ASC ATDM, because it provides a hierarchically parallel programming model that is consistent with the design of modern system architectures, but which allows for the straightforward expression of algorithmic parallelism in a portably performant manner.

97 MATHEMATICS AND COMPUTING↗

Asynchronous Graphs (Final Report)

The most performant massive-scale distributed graph analytic engines were essentially unusable for anything but the analytic they were tuned to solve. The project team had previously developed HavoqGT and used this project to demonstrate it as a flexible graph framework, aiming to extend algorithmic capabilities, improve underlying data structures, and develop novel communication paradigms to enable new data analysis missions. Highlights of the technology developed include (a) a new distributed communication paradigm dubbed You’ve Got Mail (YGM), (b) a performant exact and fuzzy HPC graph pattern matching approach, and (c) a distributed biased random walk simulation capability. The project was successful on several measurable fronts, including advancing computer science (reflected by publishing 14 peer-reviewed research papers yielding 4 publication awards and over 16 conference presentations), contributing tangibly to LLNL recruiting rare talent, and obtaining follow-on funding. These technologies were transferred to several FY19-20 programmatic projects and will continue to be leveraged by new research projects for several years.

97 MATHEMATICS AND COMPUTING↗

BASIN-3D Data Integration for Selected ARM Data Field Campaign Report

The purpose of this data services request was to demonstrate integration of the Atmospheric Radiation Measurement (ARM) User Facility’s “met” datastreams with time series data from other earth science data sources using the BASIN-3D data synthesis software tool. BASIN-3D is an open-source Python library that enables researchers to integrate data across configured public and private data sources. It provides a common query language for researchers to request measurement locations and time series data based on specified locations, variables, time period, statistics, aggregation, and data quality. BASIN-3D acquires the data that match the query from each configured data source and translates the results into harmonized vocabularies, thus reducing researchers' data-wrangling effort. In addition, because the queries are executed on demand, researchers can easily regenerate their synthesized data sets as new data and/or data updates become available, eliminating one-off data products. BASIN-3D can output data using a variety of different data structures for end-user applications including Python pandas data frames and hdf5 output formats.

54 ENVIRONMENTAL SCIENCES↗

Evaluation of a data dictionary system

The usefulness was investigated of a data dictionary/directory system for achieving optimum benefits from existing and planned investments in computer data files in the Data Systems Development Branch and the Institutional Data Systems Division. Potential applications of the data catalogue system are discussed along with an evaluation of the system. Other topics discussed include data description, data structure, programming aids, programming languages, program networks, and test data.

Driggers, W. G.↗

Data acquisition for a real time fault monitoring and diagnosis knowledge-based system for space power system

The design and implementation of the real-time data acquisition and processing system employed in the AMPERES project is described, including effective data structures for efficient storage and flexible manipulation of the data by the knowledge-based system (KBS), the interprocess communication mechanism required between the data acquisition system and the KBS, and the appropriate data acquisition protocols for collecting data from the sensors. Sensor data are categorized as critical or noncritical data on the basis of the inherent frequencies of the signals and the diagnostic requirements reflected in their values. The critical data set contains 30 analog values and 42 digital values and is collected every 10 ms. The noncritical data set contains 240 analog values and is collected every second. The collected critical and noncritical data are stored in separate circular buffers. Buffers are created in shared memory to enable other processes, i.e., the fault monitoring and diagnosis process and the user interface process, to freely access the data sets.

Wilhite, Larry D.↗

Optimal expression evaluation for data parallel architectures

A data parallel machine represents an array or other composite data structure by allocating one processor (at least conceptually) per data item. A pointwise operation can be performed between two such arrays in unit time, provided their corresponding elements are allocated in the same processors. If the arrays are not aligned in this fashion, the cost of moving one or both of them is part of the cost of the operation. The choice of where to perform the operation then affects this cost. If an expression with several operands is to be evaluated, there may be many choices of where to perform the intermediate operations. An efficient algorithm is given to find the minimum-cost way to evaluate an expression, for several different data parallel architectures. This algorithm applies to any architecture in which the metric describing the cost of moving an array is robust. This encompasses most of the common data parallel communication architectures, including meshes of arbitrary dimension and hypercubes. Remarks are made on several variations of the problem, some of which are solved and some of which remain open.

Gilbert, John R.↗

Development of a Simulated Data Set for the SeaWiFS Mission

A realistic simulated data set is essential for mission readiness preparations and can potentially assist in all phases of ground support for a future mission. Such a data set was created for the Sea-viewing Wide Field-of-view Sensor (SeaWiFS), a global ocean color mission due for launch in 1997. This data set incorporates a representation of virtually every known aspect of the flight mission. Thus, it provides a high fidelity data set for testing most phases of the ground system, Including data processing, data transfers, calibration and validation, quality control, and mission operations. The data set is constructed for a seven-day period, March 25-31, 1994. Specific features of the data set: it includes Global Area Coverage (GAC), recorded Local Area Coverage (LAC), and real-time High Resolution Picture Transmission (HRFIT) data for the seven-day period; it includes a realistic orbit which is propagated using a Brouwer-Lyddane model with drag; the data correspond to a command schedule based on the orbit for this seven-day period; it includes total (at-satellite) radiances for ocean, land, clouds, and ice; it utilizes a high-resolution land/sea mask; it includes actual SeaWiFS spectral responses; it includes the actual sensor saturation responses; it is formatted according to current onboard data structures; and it includes corresponding telemetry (instrument and spacecraft) data. The methods are described and some examples of the output are given.

Gregg, Watson W.↗

Advanced Data Format (ADF) Software Library and Users Guide

The "CFD General Notation System" (CGNS) consists of a collection of conventions, and conforming software, for the storage and retrieval of Computational Fluid Dynamics (CFD) data. It facilitates the exchange of data between sites and applications, and helps stabilize the archiving of aerodynamic data. This effort was initiated in order to streamline the procedures in exchanging data and software between NASA and its customers, but the goal is to develop CGNS into a National Standard for the exchange of aerodynamic data. The CGNS development team is comprised of members from Boeing Commercial. Airplane Group, NASA-Ames, NASA-Langley, NASA-Lewis, McDonnell-Douglas Corporation (now Boeing-St. Louis), Air Force-Wright Lab., and ICEM-CFD Engineering. The elements of CGNS address all activities associated with the storage of data on external media and its movement to and from application programs. These elements include: 1) The Advanced Data Format (ADF) Database manager, consisting of both a file format specification and its 1/0 software, which handles the actual reading and writing of data from and to external storage media; 2) The Standard Interface Data Structures (SIDS), which specify the intellectual content of CFD data and the conventions governing naming and terminology; 3) The SIDS-to-ADF File Mapping conventions, which specify the exact location where the CFD data defined by the SIDS is to be stored within the ADF file(s); and 4) The CGNS Mid-level Library, which provides CFD-knowledgeable routines suitable for direct installation into application codes. The ADF is a generic database manager with minimal intrinsic capability. It was written for the purpose of storing large numerical datasets in an efficient, platform independent manner. To be effective, it must be used in conjunction with external agreements on how the data will be organized within the ADF database such defined by the SIDS. There are currently 34 user callable functions that comprise the ADF Core library and are described in the Users Guide. The library is written in C, but each function has a FORTRAN counterpart.

Smith, Matthew↗

CGNS Mid-Level Software Library and Users Guide

The "CFD General Notation System" (CGNS) consists of a collection of conventions, and conforming software, for the storage and retrieval of Computational Fluid Dynamics (CFD) data. It facilitates the exchange of data between sites and applications, and helps stabilize the archiving of aerodynamic data. This effort was initiated in order to streamline the procedures in exchanging data and software between NASA and its customers, but the goal is to develop CGNS into a National Standard for the exchange of aerodynamic data. The CGNS development team is comprised of members from Boeing Commercial Airplane Group, NASA-Ames, NASA-Langley, NASA-Lewis, McDonnell-Douglas Corporation (now Boeing-St. Louis), Air Force-Wright Lab., and ICEM-CFD Engineering. The elements of CGNS address all activities associated with the storage of data on external media and its movement to and from application programs. These elements include: - The Advanced Data Format (ADF) Database manager, consisting of both a file format specification and its I/O software, which handles the actual reading and writing of data from and to external storage media; - The Standard Interface Data Structures (SIDS), which specify the intellectual content of CFD data and the conventions governing naming and terminology; - The SIDS-to-ADF File Mapping conventions, which specify the exact location where the CFD data defined by the SIDS is to be stored within the ADF file(s); and - The CGNS Mid-level Library, which provides CFD-knowledgeable routines suitable for direct installation into application codes. The CGNS Mid-level Library was designed to ease the implementation of CGNS by providing developers with a collection of handy I/O functions. Since knowledge of the ADF core is not required to use this library, it will greatly facilitate the task of interfacing with CGNS. There are currently 48 user callable functions that comprise the Mid-level library and are described in the Users Guide. The library is written in C, but each function has a FORTRAN counterpart.

Poirier, Diane↗

Behavioral Mapless Navigation Using Rings

This paper presents work on the development and implementation of a novel approach to robotic navigation. In this system, map-building and localization for obstacle avoidance are discarded in favor of moment-by-moment behavioral processing of the sonar sensor data. To accomplish this, we developed a network of behaviors that communicate through the passing of rings, data structures that are similar in form to the sonar data itself and express the decisions of each behavior. Through the use of these rings, behaviors can moderate each other, conflicting impulses can be mediated, and designers can easily connect modules to create complex emergent navigational techniques. We discuss the development of a number of these modules and their successful use as a navigation system in the Trinity omnidirectional robot.

Monroe, Randall P.↗

ISS Squat and Deadlift Kinematics on the Advanced Resistive Exercise Device

Visual assessment of exercise form on the Advanced Resistive Exercise Device (ARED) on orbit is difficult due to the motion of the entire device on its Vibration Isolation System (VIS). The VIS allows for two degrees of device translational motion, and one degree of rotational motion. In order to minimize the forces that the VIS must damp in these planes of motion, the floor of the ARED moves as well during exercise to reduce changes in the center of mass of the system. To help trainers and other exercise personnel better assess squat and deadlift form a tool was developed that removes the VIS motion and creates a stick figure video of the exerciser. Another goal of the study was to determine whether any useful kinematic information could be obtained from just a single camera. Finally, the use of these data may aid in the interpretation of QCT hip structure data in response to ARED exercises performed in-flight. After obtaining informed consent, four International Space Station (ISS) crewmembers participated in this investigation. Exercise was videotaped using a single camera positioned to view the side of the crewmember during exercise on the ARED. One crewmember wore reflective tape on the toe, heel, ankle, knee, hip, and shoulder joints. This technique was not available for the other three crewmembers, so joint locations were assessed and digitized frame-by-frame by lab personnel. A custom Matlab program was used to assign two-dimensional coordinates to the joint locations throughout exercise. A second custom Matlab program was used to scale the data, calculate joint angles, estimate the foot center of pressure (COP), approximate normal and shear loads, and to create the VIS motion-corrected stick figure videos. Kinematics for the squat and deadlift vary considerably for the four crewmembers in this investigation. Some have very shallow knee and hip angles, and others have quite large ranges of motion at these joints. Joint angle analysis showed that crewmembers do not return to a normal upright stance during squat, but remain somewhat bent at the hips. COP excursions were quite large during these exercises covering the entire length of the base of support in most cases. Anterior-posterior shear was very pronounced at the bottom of the squat and deadlift correlating with a COP shift to the toes at this part of the exercise. The stick figure videos showing a feet fixed reference frame have made it visually much easier for exercise personnel and trainers to assess exercise kinematics. Not returning to fully upright, hips extended position during squat exercises could have implications for the amount of load that is transmitted axially along the skeleton. The estimated shear loads observed in these crewmembers, along with a concomitant reduction in normal force, may also affect bone loading. The increased shear is likely due to the surprisingly large deviations in COP. Since the footplate on ARED moves along an arced path, much of the squat and deadlift movement is occurring on a tilted foot surface. This leads to COP movements away from the heel. The combination of observed kinematics and estimated kinetics make squat and deadlift exercises on the ARED distinctly different from their ground-based counterparts. CONCLUSION This investigation showed that some useful exercise information can be obtained at low cost, using a single video camera that is readily available on ISS. Squat and deadlift kinematics on the ISS ARED differ from ground-based ARED exercise. The amount of COP shift during these exercises sometimes approaches the limit of stability leading to modifications in the kinematics. The COP movement and altered kinematics likely reduce the bone loading experienced during these exercises. Further, the stick figure videos may prove to be a useful tool in assisting trainers to identify exercise form and make suggestions for improvements

Newby, N.↗

Facilities Asset Mobile Environment (FAME): From Old School to World Class - 18224

Newport News Shipbuilding (NNS) is on a mission to achieve and sustain world-class performance and maintenance excellence for Facilities Support. Our Computerized Maintenance Management System (CMMS) installation was 17 years old, and legacy data structures were inadequate to support collection of accurate reliability data. The Facilities Asset Mobile Environment (FAME) project includes three major segments - Mobile Hardware, Information, and Process Upgrades supported by the CMMS. By implementing the FAME project, NNS is making significant strides in improving Mean Time Between Failures (MTBF) and Mean Time To Repair (MTTR). (authors)

97 MATHEMATICS AND COMPUTING↗

RCSB Protein Data Bank 1D tools and services

Abstract Motivation Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function. Results Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web. Availabilityand implementation https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning

The 2024 Nobel Prize in Chemistry was awarded in part for de novo protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and three-dimensional structure data. AlphaFold2 and related models, including RoseTTAFold and ESMFold, employ specialized neural network architectures driven by attention mechanisms to infer relationships between sequence and structure. At a fundamental level, these AI/ML models operate on the long-standing hypothesis that the structure of a protein is determined by its amino acid sequence. More recently, AlphaFold2 has been adapted for the prediction of multiple protein conformations by subsampling multiple sequence alignments. Herein, we provide an overview of the deterministic relationship between sequence and structure, which was hypothesized over half a century ago with profound implications for the biological sciences ever since. We postulate that protein conformational dynamics are also determined, at least in part, by amino acid sequence and that this relationship may be leveraged for construction of AI/ML models dedicated to predicting protein conformational ensembles. Accordingly, we describe a conceptual model architecture, which may be trained on sequence data in combination with conformationally sensitive structural information, coming primarily from nuclear magnetic resonance (NMR) spectroscopy. Notwithstanding certain limitations in this context, NMR offers abundant structural heterogeneity conducive to conformational ensemble prediction. As NMR and other data continue to accumulate, sequence-informed prediction of protein structural dynamics with AI/ML has the potential to emerge as a transformative capability across the biological sciences.

Artificial intelligence↗

Microphone Phased Array NetCDF/HDF5 Archival Files: Application Program Interface Reference

An application program interface (API) has been developed for the creation and access of structured data files generated by microphone phased arrays utilized in aeroacoustics research. Two structured binary file formats are supported, namely NetCDF (Network Common Data Form) and HDF5 (Hierarchical Data Format) files. The API consists of a library of routines callable from C, Fortran or Matlab, with native versions of the API provided for each language. The libraries are divided into categories for file handling, file definition and initialization, data writing, data recovery, and error handling. The API is intended to provide a mechanism for generating self-describing binary files for long-term archiving of raw and processed data generated by phased array systems.

Humphreys, William M., Jr.↗