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Ramen

Many computationally unintensive models for material process-structure-property connections exist in the literature (e.g. journal articles and textbooks). However, to our knowledge there is no existing compilation of these models in one package. Many industrially and research relevant workflows involve combinations of many of these models and if the models have inconsistent interfaces, building these workflows can be challenging. Ramen provides a collection of computationally unintensive models for calculating material process-structure-property relationships from the literature, as well as related tools (e.g. for plotting results). These models use a consistent interface structure and all leverage material data files and data structures from the Mist library (also developed at ORNL). Ramen provides a structured package for combining many standard models in one place, with a standardized interface. This approach makes combining models in long/complex chains easy and straightforward.

DeWitt, Stephen [Oak Ridge National Laboratory (OR↗

Visualization of three-dimensional CFD solutions

The implementation is described of the FLOWVIS flow visualization package on a graphics supercomputer that provides real-time interactive investigation of three-dimensional CFD solutions on structured and unstructured meshes. The data structures are briefly described and the methods of visualizing flow fields are examined, including surface plots, particle paths, and planar displays in the flow field. Preliminary results using the package and work in progress are discussed.

Modiano, David L.↗

Aerodynamic Characteristics of a Proposed Personnel Launch System (PLS) Lifting-Body Configuration at Mach Numbers from 0.05 to 20.3

A wind-tunnel investigation was performed to determine the aerodynamic characteristics of a proposed lifting-body personnel launch system (PLS) configuration over a Mach range of 0.05 to 20.3. The test configuration had a low-aspect-ratio body with a flat undersurface and three fins on the upper aft body. Data are presented with a minimum of analysis. All of the experimental data were placed in a structured data base using the R:BASE system and are included on a CD-ROM available with this report.

Cruz, Christopher I.↗

MODIS Technical Report Series. Volume 4: MODIS data access user's guide: Scan cube format

The software described in this document provides I/O functions to be used with Moderate Resolution Spectroradiometer (MODIS) level 1 and 2 data, and could be easily extended to other data sources. This data is in a scan cube data format: a 3-dimensional ragged array containing multiple bands which have resolutions ranging from 250 to 1000 meters. The complexity of the data structure is handled internally by the library. The I/O calls allow the user to access any pixel in any band through 'C' structure syntax. The high MODIS data volume (approaching half a terabyte per day) has been a driving factor in the library design. To avoid recopying data for user access, all I/O is performed through dynamic 'C' pointer manipulation. This manual contains background material on MODIS, several coding examples of library usage, in-depth discussions of each function, reference 'man' type pages, and several appendices with details of the included files used to customize a user's data product for use with the library.

Kalb, Virginia L.↗

Aerodynamic Characteristics of a Proposed Personnel Launch System (PLS) Lifting-Body Configuration at Mach Numbers from 0.05 to 20.3. Supplement

A wind-tunnel investigation was performed to determine the aerodynamic characteristics of a proposed lifting-body personnel launch system (PLS) configuration over a Mach range of 0.05 to 20.3. The test configuration had a low-aspect-ratio body with a flat undersurface and three fins on the upper aft body. Data are presented with a minimum of analysis. All of the experimental data were placed in a structured data base using the R:BASE system. This is the CD-ROM that is available for this report.

Cruz, Christopher I.↗

Online Time Series Analysis of Land Products over Asia Monsoon Region via Giovanni

Time series analysis is critical to the study of land cover/land use changes and climate. Time series studies at local-to-regional scales require higher spatial resolution, such as 1km or less, data. MODIS land products of 250m to 1km resolution enable such studies. However, such MODIS land data files are distributed in 10ox10o tiles, due to large data volumes. Conducting a time series study requires downloading all tiles that include the study area for the time period of interest, and mosaicking the tiles spatially. This can be an extremely time-consuming process. In support of the Monsoon Asia Integrated Regional Study (MAIRS) program, NASA GES DISC (Goddard Earth Sciences Data and Information Services Center) has processed MODIS land products at 1 km resolution over the Asia monsoon region (0o-60oN, 60o-150oE) with a common data structure and format. The processed data have been integrated into the Giovanni system (Goddard Interactive Online Visualization ANd aNalysis Infrastructure) that enables users to explore, analyze, and download data over an area and time period of interest easily. Currently, the following regional MODIS land products are available in Giovanni: 8-day 1km land surface temperature and active fire, monthly 1km vegetation index, and yearly 0.05o, 500m land cover types. More data will be added in the near future. By combining atmospheric and oceanic data products in the Giovanni system, it is possible to do further analyses of environmental and climate changes associated with the land, ocean, and atmosphere. This presentation demonstrates exploring land products in the Giovanni system with sample case scenarios.

Shen, Suhung↗

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here.

59 BASIC BIOLOGICAL SCIENCES↗

Leiomodin creates a leaky cap at the pointed end of actin-thin filaments

Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a “swinging gate” allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.

2D-NMR↗

Extending the Blockchain: Ensuring Transactional Integrity in Relational Data via Blockchain Technology

The idea of combining a relational database with concepts associated with blockchain technology is being examined. The use case outlined herein concurrently utilizes relational and blockchain data structures to facilitate the sharing of complex data among untrusted users without the participation of a trusted third party. By capturing the transactions that result in data being stored in a relational database and placing those transactions in a blockchain structure, users can be assured that the information has not been created, altered, or destroyed without the knowledge of all users of the data. Capturing relational database transactions via a blockchain structure presents several challenges. Among them are increased storage capacity requirements, transaction ordering prior to placement on the blockchain within a multiuser database, use of existing or creation of new consensus mechanisms, and timely data verification. Addressing these challenges, although not unsurmountable, will introduce trade-offs (e.g., increased system sizing, slower transaction execution) that might or might not be acceptable based upon the envisioned use. If these trade-offs are acceptable, then this concept of extending the blockchain is a powerful method to provide both applications and their users immutable, trusted, well-defined, and consistent data.

Ray, Brian↗

Sequential Principal Component Analysis -An Optimal and Hardware-Implementable Transform for Image Compression

This paper presents the JPL-developed Sequential Principal Component Analysis (SPCA) algorithm for feature extraction / image compression, based on "dominant-term selection" unsupervised learning technique that requires an order-of-magnitude lesser computation and has simpler architecture compared to the state of the art gradient-descent techniques. This algorithm is inherently amenable to a compact, low power and high speed VLSI hardware embodiment. The paper compares the lossless image compression performance of the JPL's SPCA algorithm with the state of the art JPEG2000, widely used due to its simplified hardware implementability. JPEG2000 is not an optimal data compression technique because of its fixed transform characteristics, regardless of its data structure. On the other hand, conventional Principal Component Analysis based transform (PCA-transform) is a data-dependent-structure transform. However, it is not easy to implement the PCA in compact VLSI hardware, due to its highly computational and architectural complexity. In contrast, the JPL's "dominant-term selection" SPCA algorithm allows, for the first time, a compact, low-power hardware implementation of the powerful PCA algorithm. This paper presents a direct comparison of the JPL's SPCA versus JPEG2000, incorporating the Huffman and arithmetic coding for completeness of the data compression operation. The simulation results show that JPL's SPCA algorithm is superior as an optimal data-dependent-transform over the state of the art JPEG2000. When implemented in hardware, this technique is projected to be ideally suited to future NASA missions for autonomous on-board image data processing to improve the bandwidth of communication.

Duong, Tuan A.↗

Emulation automation and model checking

A method of automating emulations is provided. The method comprising collecting publicly available network data over a predefined time interval, wherein the collected network data might comprise structured and unstructured data. Any unstructured data is converted into structured data. The original and converted structured data is stored in a database and compared to known network vulnerabilities. An emulated network is created according to the collected network data and the comparison of the structured data with known vulnerabilities. Virtual machines are created to run on the emulated network. Director programs and guest actor programs are run on the virtual machines, wherein the actor programs imitate real user behavior on the emulated network. The director programs deliver task commands to the guest actor programs to imitate real user behavior. The imitated behavior is presented to a user via an interface.

Urias, Vincent↗

An approach for management of geometry data

The strategies for managing Integrated Programs for Aerospace Design (IPAD) computer-based geometry are described. The computer model of geometry is the basis for communication, manipulation, and analysis of shape information. IPAD's data base system makes this information available to all authorized departments in a company. A discussion of the data structures and algorithms required to support geometry in IPIP (IPAD's data base management system) is presented. Through the use of IPIP's data definition language, the structure of the geometry components is defined. The data manipulation language is the vehicle by which a user defines an instance of the geometry. The manipulation language also allows a user to edit, query, and manage the geometry. The selection of canonical forms is a very important part of the IPAD geometry. IPAD has a canonical form for each entity and provides transformations to alternate forms; in particular, IPAD will provide a transformation to the ANSI standard. The DBMS schemas required to support IPAD geometry are explained.

Dube, R. P.↗

Nuclear Data Sheets for A=39☆

Experimental nuclear structure data from various reactions and decays have been evaluated for all known nuclides of mass 39 (Mg, Al, Si, P, S, Cl, Ar, K, Ca, Sc, Ti). Detailed evaluated nuclear structure information is presented for each reaction and decay and the best values combining all available data are recommended for level energies, half-lives, γ-ray energies and intensities, decay properties (energies, intensities and placement of radiations), and other spectroscopic data. The {sup 39}K, {sup 39}Ca and {sup 39}Ar are the most extensively studied nuclides; no excited states are known in {sup 39}Mg and {sup 39}Ti. This work supersedes the earlier full evaluation of A=39 by B. Singh and J. Cameron (2006Si02).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Nuclear Data Sheets for A=138☆

Experimental nuclear structure data from various reactions and decays are compiled and evaluated for all known nuclides with mass number A=138 (Sn,Sb,Te,I,Xe,Cs,Ba,La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb). Detailed evaluated nuclear structure information is presented for each reaction and decay and the best values combining all available data are recommended for level energies, half-lives, γ-ray energies and intensities, decay properties (energies, intensities and placement of radiations), and other spectroscopic properties. This work supersedes the previous full evaluation of A=138 by A.A. Sonzogni (2003So13).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Improved renormalization group computation of likelihood functions for cosmological data sets

Evaluation of likelihood functions for cosmological large scale structure data sets (including CMB, galaxy redshift surveys, etc.) naturally involves marginalization, i.e., integration, over an unknown underlying random signal field. Recently, I showed how a renormalization group method can be used to carry out this integration efficiently by first integrating out the smallest scale structure, i.e., localized structure on the scale of differences between nearby data cells, then combining adjacent cells in a coarse graining step, then repeating this process over and over until all scales have been integrated. Here I extend the formulation in several ways in order to reduce the prefactor on the method's linear scaling with data set size. The key improvement is showing how to integrate out the difference between specific adjacent cells before summing them in the coarse graining step, compared to the original formulation in which small-scale fluctuations were integrated more generally. I suggest some other improvements in details of the scheme, including showing how to perform the integration around a maximum likelihood estimate for the underlying random field. In the end, an accurate likelihood computation for a million-cell Gaussian test data set runs in two minutes on my laptop, with room for further optimization and straightforward parallelization.

79 ASTRONOMY AND ASTROPHYSICS↗

MERRA-2 Data and Analytic Services at NASA GES DISC for Climate Extremes Study

NASA's climate reanalysis datasets from the Modern Era Retrospective-analysis for Research and Applications, Version 2 (MERRA-2) contains numerous long-term atmosphere, land, and ocean data products from 1980-present. MERRA-2 datasets, such as precipitation, soil moisture, and temperature, have been used widely to study extreme events. The native archived MERRA-2 data files are day-file (hourly time interval) and month-file, containing up to 125 parameters in one file. Due to the large number of data files and volumes, it is challenging for users, especially the applications research community, to handle the original hourly data files for long time periods to analyze extreme events. In this presentation, we review MERRA-2 data for studies of extreme conditions, and demonstrate analytic services at the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC). One of the current operational services, 'subsetter', allows users to download only specific data of interest, i.e. data selected by parameter, region, and time period. New services are under development that will provide more 'on-the-fly' statistical calculations when downloading data; improve efficiency when accessing long time-series data. We will provide additional "How-to" resources that include step-by-step instructions on data access and usage. We have tested restructuring of day-files in an optimized data cube, which has significantly improved system performance for accessing long time-series. Overall performance is associated with cube size and structure, data compression method, and how the data are accessed. The optimized data cube structure will enable better online analytic services for statistical analysis and extreme events mining. To demonstrate the service, we use an extreme drought associated with the anomalous 2016 monsoon over southern Asia. This prototype time-series service may be augmented in the cloud infrastructure in the future.

data access↗

Structural isomers of the S 2 state in photosystem II: do they exist at room temperature and are they important for function?

In nature, an oxo‐bridged Mn 4 CaO 5 cluster embedded in photosystem II (PSII), a membrane‐bound multi‐subunit pigment protein complex, catalyzes the water oxidation reaction that is driven by light‐induced charge separations in the reaction center of PSII. The Mn 4 CaO 5 cluster accumulates four oxidizing equivalents to enable the four‐electron four‐proton catalysis of two water molecules to one dioxygen molecule and cycles through five intermediate S‐states, S 0 – S 4 in the Kok cycle. One important question related to the catalytic mechanism of the oxygen‐evolving complex (OEC) that remains is, whether structural isomers are present in some of the intermediate S‐states and if such equilibria are essential for the mechanism of the O‐O bond formation. Here we compare results from electron paramagnetic resonance (EPR) and X‐ray absorption spectroscopy (XAS) obtained at cryogenic temperatures for the S 2 state of PSII with structural data collected of the S 1 , S 2 and S 3 states by serial crystallography at neutral pH (∼6.5) using an X‐ray free electron laser at room temperature. While the cryogenic data show the presence of at least two structural forms of the S 2 state, the room temperature crystallography data can be well‐described by just one S 2 structure. We discuss the deviating results and outline experimental strategies for clarifying this mechanistically important question.

Chatterjee, Ruchira↗

Ambidextrous Helical Nanotubes from Self-Assembly of Designed Helical Hairpin Motifs

Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed two synthetic peptides, HEAT R1 and LRV M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS HEAT) and Leucine- Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high aspect-ratio helical helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. Three dimensional reconstructions from the cryo-EM maps led to atomic models for the HEAT R1 and LRV M3Δ1 filaments at resolutions of 6.0 Å and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT R1 and LRV M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the two filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Furthermore, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.

59 BASIC BIOLOGICAL SCIENCES↗