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All sources NASA NTRS DOE OSTI

DOE OSTI2018

Non-heme High-Spin {FeNO} 6–8 Complexes: One Ligand Platform Can Do It All

Heme and non-heme iron-nitrosyl complexes are important intermediates in biology. While there are numerous examples of low-spin heme iron-nitrosyl complexes in different oxidation states, much less is known about high-spin (hs) non-heme iron-nitrosyls in oxidation states other than the formally ferrous NO adducts ({FeNO} 7 in the Enemark-Feltham notation). In this study, we present a complete series of hs-{Fe-NO} 6-8 complexes using the TMG 3 tren coligand. Redox transformations from the hs-{FeNO} 7 complex [Fe(TMG 3 tren)(NO)] 2+ to its {FeNO} 6 and {FeNO} 8 analogs do not alter the coordination environment of the iron center, allowing for detailed comparisons between these species. Here, we present new MCD, NRVS, XANES/EXAFS and Mössbauer data, demonstrating that these redox transformations are metal based, which allows us to access hs-Fe(II)-NO¯, Fe(III)-NO¯ and Fe(IV)-NO¯ complexes. Vibrational data, analyzed by NCA, directly quantify changes in Fe-NO bonding along this series. Optical data allow for the identification of a “spectator” charge-transfer transition that, together with Mössbauer and XAS data, directly monitors electronic changes of the Fe center. Using EXAFS, we are also now able to provide structural data for all complexes. The magnetic properties of the complexes are further analyzed (from magnetic Mössbauer). The properties of our hs-{FeNO} 6-8 complexes are then contrasted to corresponding, low-spin iron-nitrosyl complexes, where redox transformations are generally NO-centered. The hs-{FeNO} 8 complex can further be protonated by weak acids, and the product of this reaction is characterized. Altogether, these results provide unprecedented insight into the properties of biologically relevant non-heme iron-nitrosyl complexes in three relevant oxidation states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Separating the effects of nucleotide and EB binding on microtubule structure

Microtubules (MTs) are polymers assembled from αβ-tubulin heterodimers that display the hallmark behavior of dynamic instability. MT dynamics are driven by GTP hydrolysis within the MT lattice, and are highly regulated by a number of MT-associated proteins (MAPs). How MAPs affect MTs is still not fully understood, partly due to a lack of high-resolution structural data on undecorated MTs, which need to serve as a baseline for further comparisons. Here we report three structures of MTs in different nucleotide states (GMPCPP, GDP, and GTPγS) at near-atomic resolution and in the absence of any binding proteins. These structures allowed us to differentiate the effects of nucleotide state versus MAP binding on MT structure. Kinesin binding has a small effect on the extended, GMPCPP-bound lattice, but hardly affects the compacted GDP-MT lattice, while binding of end-binding (EB) proteins can induce lattice compaction (together with lattice twist) in MTs that were initially in an extended and more stable state. We propose a MT lattice-centric model in which the MT lattice serves as a platform that integrates internal tubulin signals, such as nucleotide state, with outside signals, such as binding of MAPs or mechanical forces, resulting in global lattice rearrangements that in turn affect the affinity of other MT partners and result in the exquisite regulation of MT dynamics.

Science & Technology - Other Topics↗

DOE OSTI2019

A JSON to CMake tool

As part of the conversion of the MCNP®testing system to CTest, a tool was needed to generate CMake variables from JSON formatted data structure. The system was first implemented using the JSON to CMake parser which with some slight modifications provided data useful for the MCNP CTest testing system. Upon further evaluation, we found it to be slow when setting up the 1600 tests during the CMake configuration step. Not only was it slow, it did not validate the JSON files during configuration allowing for unexpected behavior. Upon some web searching we came across a simple recursive python example that would provide the same capability needed by our testing system. This python example was effectively wrapped into a single python script that was used to convert the JSON data into CMake variables. This tool is attached as json_to_cmake.py and is listed in the appendix. In essence, the tool provides single variables for each value defined within the JSON file. The name for the variable is constructed by using the associated object names and array indicies needed to deference the variable itself. In the following sections, examples are provided to better describe how this is done.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1984

Data engineering systems: Computerized modeling and data bank capabilities for engineering analysis

The Data Engineering System (DES) is a computer-based system that organizes technical data and provides automated mechanisms for storage, retrieval, and engineering analysis. The DES combines the benefits of a structured data base system with automated links to large-scale analysis codes. While the DES provides the user with many of the capabilities of a computer-aided design (CAD) system, the systems are actually quite different in several respects. A typical CAD system emphasizes interactive graphics capabilities and organizes data in a manner that optimizes these graphics. On the other hand, the DES is a computer-aided engineering system intended for the engineer who must operationally understand an existing or planned design or who desires to carry out additional technical analysis based on a particular design. The DES emphasizes data retrieval in a form that not only provides the engineer access to search and display the data but also links the data automatically with the computer analysis codes.

Kopp, H.↗

NASA NTRS1993

High performance FORTRAN without templates: An alternative model for distribution and alignment

Language extensions of FORTRAN are being developed which permit the user to map data structures to the individual processors of distributed memory machines. These languages allow a programming style in which global data references are used. Current efforts are focussed on designing a common basis for such languages, the result of which is known as High Performance Fortran (HPF). One of the central debates in the HPF effort revolves around the concept of templates, introduced as an abstract index space to which data could be aligned. A model for the mapping of data which provides the functionality of High Performance Fortran distributions without the use of templates is presented.

Chapman, Barbara↗

DOE OSTI2017

Block-Parallel Data Analysis with DIY2

DIY2 is a programming model and runtime for block-parallel analytics on distributed-memory machines. Its main abstraction is block-structured data parallelism: data are decomposed into blocks; blocks are assigned to processing elements (processes or threads); computation is described as iterations over these blocks, and communication between blocks is defined by reusable patterns. By expressing computation in this general form, the DIY2 runtime is free to optimize the movement of blocks between slow and fast memories (disk and flash vs. DRAM) and to concurrently execute blocks residing in memory with multiple threads. This enables the same program to execute in-core, out-of-core, serial, parallel, single-threaded, multithreaded, or combinations thereof. This paper describes the implementation of the main features of the DIY2 programming model and optimizations to improve performance. DIY2 is evaluated on benchmark test cases to establish baseline performance for several common patterns and on larger complete analysis codes running on large-scale HPC machines.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Neural network representation of electronic structure from ab initio molecular dynamics

Despite their rich information content, electronic structure data amassed at high volumes in ab initio molecular dynamics simulations are generally under-utilized. Here we introduce a transferable high-fidelity neural network representation of such data in the form of tight-binding Hamiltonians for crystalline materials. This predictive representation of ab initio electronic structure, combined with machine-learning boosted molecular dynamics, enables efficient and accurate electronic evolution and sampling. When it is applied to a one-dimension charge-density wave material, carbyne, we are able to compute the spectral function and optical conductivity in the canonical ensemble. The spectral functions evaluated during soliton-antisoliton pair annihilation process reveal significant renormalization of low-energy edge modes due to retarded electron-lattice coupling beyond the Born–Oppenheimer limit. The availability of an efficient and reusable surrogate model for the electronic structure dynamical system will enable calculating many interesting physical properties, paving the way to previously inaccessible or challenging avenues in materials modeling.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2016

Cadmium(II) inhibition of human uracil-DNA glycosylase by catalytic water supplantation

Toxic metals are known to inhibit DNA repair but the underlying mechanisms of inhibition are still not fully understood. DNA repair enzymes such as human uracil-DNA glycosylase (hUNG) perform the initial step in the base excision repair (BER) pathway. In this work, we showed that cadmium [Cd(II)], a known human carcinogen, inhibited all activity of hUNG at 100 μM. Computational analyses based on 2 μs equilibrium, 1.6 μs steered molecular dynamics (SMD), and QM/MM MD determined that Cd(II) ions entered the enzyme active site and formed close contacts with both D145 and H148, effectively replacing the catalytic water normally found in this position. Geometry refinement by density functional theory (DFT) calculations showed that Cd(II) formed a tetrahedral structure with D145, P146, H148, and one water molecule. This work for the first time reports Cd(II) inhibition of hUNG which was due to replacement of the catalytic water by binding the active site D145 and H148 residues. Comparison of the proposed metal binding site to existing structural data showed that D145:H148 followed a general metal binding motif favored by Cd(II). The identified motif offered structural insights into metal inhibition of other DNA repair enzymes and glycosylases.

Science & Technology - Other Topics↗

DOE OSTI2017

Polycomb repressive complex 2 in an autoinhibited state

Polycomb-group proteins control many fundamental biological processes, such as anatomical development in mammals and vernalization in plants. Polycomb repressive complex 2 (PRC2) is responsible for methylation of histone H3 lysine 27 (H3K27), and trimethylated H3K27 (H3K27me3) is implicated in epigenetic gene silencing. Recent genomic, biochemical, and structural data indicate that PRC2 is broadly conserved from yeast to human in many aspects. Here, we determined the crystal structure of an apo-PRC2 from the fungus Chaetomium thermophilum captured in a bona fide autoinhibited state, which represents a novel conformation of PRC2 associated with enzyme regulation in light of the basal and stimulated states that we reported previously. We found that binding by the cofactor S-adenosylmethionine mitigates this autoinhibited structural state. Using steady-state enzyme kinetics, we also demonstrated that disrupting the autoinhibition results in a vastly activated enzyme complex. Autoinhibition provides a novel structural platform that may enable control of PRC2 activity in response to diverse transcriptional states and chromatin contexts and set a ground state to allow PRC2 activation by other cellular mechanisms as well.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1984

Technology for the product and process data base

The computerized product and process data base is increasingly recognized to be the cornerstone component of an overall system aimed at the integrated automation of the industrial processes of a given company or enterprise. The technology needed to support these more effective computer integrated design and manufacturing methods, especially the concept of 3-D computer-sensible product definitions rather than engineering drawings, is not fully available and rationalized. Progress is being made, however, in bridging this technology gap with concentration on the modeling of sophisticated information and data structures, high-performance interactive user interfaces and comprehensive tools for managing the resulting computerized product definition and process data base.

Barnes, R. D.↗

NASA NTRS1991

Maintaining consistency in distributed systems

In systems designed as assemblies of independently developed components, concurrent access to data or data structures normally arises within individual programs, and is controlled using mutual exclusion constructs, such as semaphores and monitors. Where data is persistent and/or sets of operation are related to one another, transactions or linearizability may be more appropriate. Systems that incorporate cooperative styles of distributed execution often replicate or distribute data within groups of components. In these cases, group oriented consistency properties must be maintained, and tools based on the virtual synchrony execution model greatly simplify the task confronting an application developer. All three styles of distributed computing are likely to be seen in future systems - often, within the same application. This leads us to propose an integrated approach that permits applications that use virtual synchrony with concurrent objects that respect a linearizability constraint, and vice versa. Transactional subsystems are treated as a special case of linearizability.

Birman, Kenneth P.↗

NASA NTRS1994

Directions in parallel programming: HPF, shared virtual memory and object parallelism in pC++

Fortran and C++ are the dominant programming languages used in scientific computation. Consequently, extensions to these languages are the most popular for programming massively parallel computers. We discuss two such approaches to parallel Fortran and one approach to C++. The High Performance Fortran Forum has designed HPF with the intent of supporting data parallelism on Fortran 90 applications. HPF works by asking the user to help the compiler distribute and align the data structures with the distributed memory modules in the system. Fortran-S takes a different approach in which the data distribution is managed by the operating system and the user provides annotations to indicate parallel control regions. In the case of C++, we look at pC++ which is based on a concurrent aggregate parallel model.

Bodin, Francois↗

NASA NTRS2006

Using Image Tour to Explore Multiangle, Multispectral Satellite Image

This viewgraph presentation reviews the use of Image Tour to explore the multiangle, multispectral satellite imagery. Remote sensing data are spatial arrays of p-dimensional vectors where each component corresponds to one of p variables. Applying the same R(exp p) to R(exp d) projection to all pixels creates new images, which may be easier to analyze than the original because d < p. Image grand tour (IGT) steps through the space of projections, and d=3 outputs a sequence of RGB images, one for each step. In this talk, we apply IGT to multiangle, multispectral data from NASA's MISR instrument. MISR views each pixel in four spectral bands at nine view angles. Multiple views detect photon scattering in different directions and are indicative of physical properties of the scene. IGT allows us to explore MISR's data structure while maintaining spatial context; a key requirement for physical interpretation. We report results highlighting the uniqueness of multiangle data and how IGT can exploit it.

visualization↗

NASA NTRS2010

The Monotonic Lagrangian Grid for Fast Air-Traffic Evaluation

This paper describes the continued development of a dynamic air-traffic model, ATMLG, intended for rapid evaluation of rules and methods to control and optimize transport systems. The underlying data structure is based on the Monotonic Lagrangian Grid (MLG), which is used for sorting and ordering positions and other data needed to describe N moving bodies, and their interactions. In ATMLG, the MLG is combined with algorithms for collision avoidance and updating aircraft trajectories. Aircraft that are close to each other in physical space are always near neighbors in the MLG data arrays, resulting in a fast nearest-neighbor interaction algorithm that scales as N. In this paper, we use ATMLG to examine how the ability to maintain a required separation between aircraft decreases as the number of aircraft in the volume increases. This requires keeping track of the primary and subsequent collision avoidance maneuvers necessary to maintain a five mile separation distance between all aircraft. Simulation results show that the number of collision avoidance moves increases exponentially with the number of aircraft in the volume.

Alexandrov, Natalia↗

NASA NTRS2010

Updates of Land Surface and Air Quality Products in NASA MAIRS and NEESPI Data Portals

Following successful support of the Northern Eurasia Earth Sciences Partner Initiative (NEESPI) project with NASA satellite remote sensing data, from Spring 2009 the NASA GES DISC (Goddard Earth Sciences Data and Information Services Center) has been working on collecting more satellite and model data to support the Monsoon Asia Integrated Regional Study (MAIRS) project. The established data management and service infrastructure developed for NEESPI has been used and improved for MAIRS support.Data search, subsetting, and download functions are available through a single system. A customized Giovanni system has been created for MAIRS.The Web-based on line data analysis and visualization system, Giovanni (Goddard Interactive Online Visualization ANd aNalysis Infrastructure) allows scientists to explore, quickly analyze, and download data easily without learning the original data structure and format. Giovanni MAIRS includes satellite observations from multiple sensors and model output from the NASA Global Land Data Assimilation System (GLDAS), and from the NASA atmospheric reanalysis project, MERRA. Currently, we are working on processing and integrating higher resolution land data in to Giovanni, such as vegetation index, land surface temperature, and active fire at 5km or 1km from the standard MODIS products. For data that are not archived at the GESDISC,a product metadata portal is under development to serve as a gateway for providing product level information and data access links, which include both satellite, model products and ground-based measurements information collected from MAIRS scientists.Due to the large overlap of geographic coverage and many similar scientific interests of NEESPI and MAIRS, these data and tools will serve both projects.

Shen, Suhung↗

NASA NTRSDate not supplied

Developmental Flight Instrumentation: Review of Space Shuttle, Ares I-X, and Artemis I

Ascent vehicles in the developmental stages of the program are instrumented with Developmental Flight Instrumentation (DFI) sensors. These sensors establish a link between a vehicle and engineers on the ground to communicate conditions experienced during the ascent. These data are then compared to pre-flight predictions used in the design process. The aerodynamic, acoustic, thermal, and structural data are either telemetered to ground stations during the ascent or stored on the vehicle for post-flight recovery and archived at the Huntsville Operations Support Center (HOSC). Following NASA's Artemis I Space Launch System (SLS) launch on November 16, 2020, data from three separate programs are available at the HOSC: Space Shuttle Program (Space Transport System (STS)), Constellation Program (Ares I-X), and Artemis Program (SLS). Availability of these data presents a unique opportunity to examine DFI data from three distinct vehicles and analyze the broad impact of the DFI data on the understanding of transonic aerodynamics. Classical spectrogram and Empirical Mode Decomposition techniques were used to present data in aerodynamically analogous regions on each vehicle. On the SLS and Ares I-X, a region downstream of the Launch Abort System motors was chosen. Comparing SLS and the STS, a region downstream of booster Froward Attach Hardware was selected as analogous flow region. Some other regions of interest were also identified. Although similarities in flow features on three vehicles were identified, some challenges in the comparison were also encountered, especially due to poor temporal and spatial resolution of Shuttle measurements.

Space Shuttle↗

NASA NTRSDate not supplied

Developmental Flight Instrumentation: Review of Space Shuttle, Ares I-X, and Artemis I

Space Shuttle↗

DOE OSTI2025

Structural Evidence of Interanionic Hydrogen Bonding in Phosphoric Acid Solutions

Interanionic hydrogen bonding (IAHB) is a noncovalent interaction between like-charged ions that challenges conventional electrostatic understanding. This study provides direct structural evidence of IAHB in concentrated aqueous phosphoric acid (PA) solutions, which exhibit >60% dissociation under these conditions. Oxygen K-edge X-ray absorption fine structure spectroscopy, combined with electron affinity time-dependent density functional theory calculations, reveals the formation of stable, cyclic phosphate-phosphate IAHB dimers at PA concentrations ≥7 M. Extended X-ray absorption fine structure data show distinct long-range ordering consistent with these dimers, and near-edge X-ray absorption fine structure spectra confirm a concentration-dependent transition from monomeric to dimeric species. Energy decomposition analysis through density functional theory shows that the formation of solution-phase IAHB is energetically favored and is attributed to polarization of and the charge transfer between the two fragments driven by the surrounding solvent molecules, in addition to the permanent electrostatics. These findings offers crucial structural insights into the H-bonded networks in concentrated PA, highlighting the critical role of solvent in facilitating anion–anion association.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗