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Entwine Point Tiles for 3D Visualization and Querying of ICESat-2

Point Cloud data from non-optical sensors present challenges in scientific computing in both volume of data and files, even for cloud services environments. As part of the Multi-Mission Algorithm and Analysis Platform (MAAP), a joint open science platform for global biomass modelling, we’ve developed a cloud optimized workflow for using ATL08 (ICESat-2) data as a point cloud. For MAAP, the ATL08 data product is published as Entwine Point Tiles (EPT), allowing users to visualize and query the full extent of this collection interactively without pre-downloading, or preprocessing. The EPT format is a cloud-optimized point cloud data format which re-organizes points into a cloud friendly spatially indexed data structure. MAAP uses AWS S3 to store these point clouds and serves them over OGC specified APIs, 3DTiles for visualization, and WFS for querying. This workflow allows for interactive 3D visualizations in a web browser, including notebook environments and facilitates on the fly subsetting for interactive data exploration, all of which can be applied to other similar sensors.

Alex Mandel↗

DOE OSTI2022

Protein sequence design with a learned potential

The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of a deep neural network model to automate design of sequences onto protein backbones, having learned directly from crystal structure data and without any human-specified priors. The model generalizes to native topologies not seen during training, producing experimentally stable designs. We evaluate the generalizability of our method to a de novo TIM-barrel scaffold. The model produces novel sequences, and high-resolution crystal structures of two designs show excellent agreement with in silico models. Our findings demonstrate the tractability of an entirely learned method for protein sequence design.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

A velocity/stress mixed stabilized nodal finite element for elastodynamics: Analysis and computations with strongly and weakly enforced boundary conditions

A new nodal mixed finite element is proposed for the simulation of linear elastodynamics and wave propagation problems in time domain. Our method is based on equal-order interpolation discrete spaces for both the velocity (or displacement) and stress (or strain) tensor variables. The mixed form is derived using either the velocity/stress or velocity/strain pair of unknowns, the latter being instrumental in extensions of the method to nonlinear mechanics. The proposed approach works equally well on hexahedral or tetrahedral grids and, for this reason, it is suitable for time-domain engineering applications in complex geometry. The peculiarity of the proposed approach is the use of the rate form of the stress update equation, which yields a set of governing equations with the structure of a non-dissipative space/time Friedrichs’ system. We complement standard traction boundary conditions for the stress with strongly and weakly enforced boundary conditions for the velocity (or displacement). Weakly enforced boundary conditions are particularly suitable when considering complex geometrical shapes, because they do not require dedicated data structures for the imposition of the boundary degrees of freedom, but, rather, they utilize the structure of the variational formulation. Here we also show how the framework of weakly enforced boundary conditions can be used to develop variational forms for multi-domain simulations of heterogeneous media. A complete analysis including stability and convergence proofs is included, in the case of a space–time variational approach. A series of computational tests are used to demonstrate and verify the performance of the proposed approach.

42 ENGINEERING↗

DOE OSTI2016

A quantitative model of application slow-down in multi-resource shared systems

Scheduling multiple jobs onto a platform enhances system utilization by sharing resources. The benefits from higher resource utilization include reduced cost to construct, operate, and maintain a system, which often include energy consumption. Maximizing these benefits comes at a price-resource contention among jobs increases job completion time. In this study, we analyze slow-downs of jobs due to contention for multiple resources in a system; referred to as dilation factor. We observe that multiple-resource contention creates non-linear dilation factors of jobs. From this observation, we establish a general quantitative model for dilation factors of jobs in multi-resource systems. A job is characterized by a vector-valued loading statistics and dilation factors of a job set are given by a quadratic function of their loading vectors. We demonstrate how to systematically characterize a job, maintain the data structure to calculate the dilation factor (loading matrix), and calculate the dilation factor of each job. We validate the accuracy of the model with multiple processes running on a native Linux server, virtualized servers, and with multiple MapReduce workloads co-scheduled in a cluster. Evaluation with measured data shows that the D-factor model has an error margin of less than 16%. We extended the D-factor model to capture the slow-down of applications when multiple identical resources exist such as multi-core environments and multi-disks environments. Finally, validation results of the extended D-factor model with HPC checkpoint applications on the parallel file systems show that D-factor accurately captures the slow down of concurrent applications in such environments.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1995

A unified multigrid solver for the Navier-Stokes equations on mixed element meshes

A unified multigrid solution technique is presented for solving the Euler and Reynolds-averaged Navier-Stokes equations on unstructured meshes using mixed elements consisting of triangles and quadrilaterals in two dimensions, and of hexahedra, pyramids, prisms, and tetrahedra in three dimensions. While the use of mixed elements is by no means a novel idea, the contribution of the paper lies in the formulation of a complete solution technique which can handle structured grids, block structured grids, and unstructured grids of tetrahedra or mixed elements without any modification. This is achieved by discretizing the full Navier-Stokes equations on tetrahedral elements, and the thin layer version of these equations on other types of elements, while using a single edge-based data-structure to construct the discretization over all element types. An agglomeration multigrid algorithm, which naturally handles meshes of any types of elements, is employed to accelerate convergence. An automatic algorithm which reduces the complexity of a given triangular or tetrahedral mesh by merging candidate triangular or tetrahedral elements into quadrilateral or prismatic elements is also described. The gains in computational efficiency afforded by the use of non-simplicial meshes over fully tetrahedral meshes are demonstrated through several examples.

Mavriplis, D. J.↗

DOE OSTI2017

Design and implementation of HuREX analysis supporting interface - 171

Human error is recognized as one of the main causes to affect to the socio-technical system including nuclear power plant. Therefore, reducing human error through human reliability analysis (HRA) is a critical issue. Moreover, sufficient and reliable human performance data collection is a prerequisite for ensuring the safety of nuclear power plants. Korea Atomic Energy Research Institute developed the HuREX (Human Reliability data Extraction) framework to collect and analyze the responses of human operators from simulator training records of nuclear power plant. Thus, the development and computer software interfaces of the database are essential to efficiently support human reliability analysis. In this study, OPERA database was developed in accordance with the following process. First, the essential data required for the HRA analysis (e.g., plant data, procedures, system and equipment info, operating crews, results of simulator experiments, and so forth) was stored in the database. In addition, standardized procedures and related items were stored in the database to support HRA quantification. A data structure was developed to store crew responses conducted by operators to cope with an emergency situation during simulator experiments. In addition, various interfaces that escalate efficiency of the HuREX applications were developed. The HuREX analysis support interface was developed with HuREX Video Analyzer for observation of simulator collection data (e.g., audio-visual records, plant parameters, operator's action logs) and HuREX Data Analyzer for analysis of operator's conducted task. By using the OPERA database and HuREX analysis support interface developed through this research, maximizing the efficiency of human reliability analysis based on simulator training data. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2017

Ensemble averaged structure–function relationship for nanocrystals: effective superparamagnetic Fe clusters with catalytically active Pt skin [Ensemble averaged structure-function relationship for composite nanocrystals: magnetic bcc Fe clusters with catalytically active fcc Pt skin]

Practical applications require the production and usage of metallic nanocrystals (NCs) in large ensembles. Besides, due to their cluster-bulk solid duality, metallic NCs exhibit a large degree of structural diversity. This poses the question as to what atomic-scale basis is to be used when the structure–function relationship for metallic NCs is to be quantified precisely. In this paper, we address the question by studying bi-functional Fe core-Pt skin type NCs optimized for practical applications. In particular, the cluster-like Fe core and skin-like Pt surface of the NCs exhibit superparamagnetic properties and a superb catalytic activity for the oxygen reduction reaction, respectively. We determine the atomic-scale structure of the NCs by non-traditional resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Using the experimental structure data we explain the observed magnetic and catalytic behavior of the NCs in a quantitative manner. Lastly, we demonstrate that NC ensemble-averaged 3D positions of atoms obtained by advanced X-ray scattering techniques are a very proper basis for not only establishing but also quantifying the structure–function relationship for the increasingly complex metallic NCs explored for practical applications.

36 MATERIALS SCIENCE↗

NASA NTRS1998

Isosurface Extraction in Time-Varying Fields Using a Temporal Hierarchical Index Tree

Many high-performance isosurface extraction algorithms have been proposed in the past several years as a result of intensive research efforts. When applying these algorithms to large-scale time-varying fields, the storage overhead incurred from storing the search index often becomes overwhelming. this paper proposes an algorithm for locating isosurface cells in time-varying fields. We devise a new data structure, called Temporal Hierarchical Index Tree, which utilizes the temporal coherence that exists in a time-varying field and adoptively coalesces the cells' extreme values over time; the resulting extreme values are then used to create the isosurface cell search index. For a typical time-varying scalar data set, not only does this temporal hierarchical index tree require much less storage space, but also the amount of I/O required to access the indices from the disk at different time steps is substantially reduced. We illustrate the utility and speed of our algorithm with data from several large-scale time-varying CID simulations. Our algorithm can achieve more than 80% of disk-space savings when compared with the existing techniques, while the isosurface extraction time is nearly optimal.

Shen, Han-Wei↗

DOE OSTI2022

Microgrid Communications Using the Open-Source Open Field Message Bus (OpenFMB) Framework Applied to a 480V, 100kW Laboratory Microgrid

Microgrids require an extensive communication infrastructure to allow interoperability between the microgrid controller and assets. However, the lack of standardization of data structures combined with the variety of communication protocols poses several challenges to the implementation of a communication network. This paper presents an application of the open-source Open Field Message Bus (OpenFMB) framework to simplify the communication layer in microgrids. This work leverages the OpenFMB protocol translation and data model extensions to reduce the complexity in the microgrid communications. Conducted in a laboratory microgrid, the case study demonstrates how the OpenFMB provides predefined data models and simplifies the communication layer by providing information exchange between multiple legacy communication protocols.

Ferrari Maglia, Max↗

DOE OSTI2020

Algorithms for Efficient Reproducible Floating Point Summation

We define “reproducibility” as getting bitwise identical results from multiple runs of the same program, perhaps with different hardware resources or other changes that should not affect the answer. Many users depend on reproducibility for debugging or correctness. However, dynamic scheduling of parallel computing resources, combined with nonassociative floating point addition, makes reproducibility challenging even for summation, or operations like the BLAS. We describe a “reproducible accumulator” data structure (the “binned number”) and associated algorithms to reproducibly sum binary floating point numbers, independent of summation order. We use a subset of the IEEE Floating Point Standard 754-2008 and bitwise operations on the standard representations in memory. Our approach requires only one read-only pass over the data, and one reduction in parallel, using a 6-word reproducible accumulator (more words can be used for higher accuracy), enabling standard tiling optimization techniques. Summing n words with a 6-word reproducible accumulator requires approximately 9 n floating point operations (arithmetic, comparison, and absolute value) and approximately 3 n bitwise operations. The final error bound with a 6-word reproducible accumulator and our default settings can be up to 2 29 times smaller than the error bound for conventional (recursive) summation on ill-conditioned double-precision inputs.

Computer Science↗

NASA NTRS1986

Block rotations in the Rio Grande Rift, New Mexico

Paleomagnetic data from 13 sites of intrusive and extrusive rocks associated with the Oligocene Espinaso Formation around the Ortiz mountains, New Mexico, indicate mean magnetic directions of I = 42.1 deg and D = 337.8 deg, with a corresponding pole position of 67.9 deg N latitude and 142.3 deg E longitude. From comparison with the expected Oligocene direction, 17.8 + or - 11.3 deg of counterclockwise rotation is found, and the similar rotations for Oligocene and Pliocene age rocks suggests that motion has occurred in the past 5 m.y. Data support the previously suggested diamond-shaped crustal block extending from the San Luis basin southward to the Albuquerque basin bounded by well-defined recently active fault zones. The size of the block, the counterclockwise nature of rotation and the timing of motion are supported by geologic and structural data. The counterclockwise rotation of the block has resulted in uplift at the acute ends of the block and subsidence at the obtuse ends, and the driving mechanism may be left slip along the rift.

Brown, L. L.↗

NASA NTRS2016

GPS and Galileo Developments on Board the International Space Station With the Space Communications and Navigation (SCaN) Testbed

The Space Communications and Navigation (SCaN) is a facility developed by NASA and hosted on board the International Space Station (ISS) on an external truss since 2013.It has the objective of testing navigation and communication experimentations with a Software Defined Radio (SDR) approach, which permits software updates for testing new experimentations.NASA has developed the Space Telecommunications Radio System (STRS) architecture standard for SDRs used in space and ground-based platforms to provide commonality among radio developments to provide enhanced capability. The hardware is equipped with both L band front-end radios and the NASA space network communicates with it using S-band, Ku-band and Ka-band links.In May 2016 Qascom started GARISS (GPS and Galileo Receiver for the ISS), an activity of experimentation in collaboration with ESA and NASA that has the objective to develop and validate the acquisition and processing of combined GPS and Galileo signals on board the ISS SCaN testbed. This paper has the objective to present the mission, and provide preliminary details about the challenges in the design, development and verification of the waveform that will be installed on equipment with limited resources. GARISS is also the first attempt to develop a waveform for the ISS as part of an international collaboration between US and Europe. Although the final mission objective is to target dual frequency processing, initial operations will foresee a single frequency processing. Initial results and trade-off between the two options, as well as the final decision will be presented and discussed. The limited resources on board the SCaN with respect to the challenging requirements to acquire and track contemporaneously two satellite navigation systems, with different modulations and data structure, led to the need to assess the possibility of aiding from ground through the S-band. This option would allow assistance to the space receiver in order to provide knowledge of GNSS orbits and reduce the processing on board. Trade off and various options for telemetry and uplink data are presented and discussed. Finally, integration and validation of the waveform are one of the major challenges of GARISS: The Experiment Development System (EDS) and the the Ground Integration Unit (GIU) for VV will be used prior to conducting the experiment on the ISS. The EDS can be used in lab environment and allows prototyping and verification activities with the simulator, but does not include all hardware components. The GIU on the other side is the flight model which replicates the flying equipment, but has limited flexibility for testing.As conclusion, the project is now approaching the Preliminary Design Review (PDR) and indeed only preliminary results are available. This paper is an opportunity to present the GARISS mission as part of an International cooperation between ESA, NASA and Qascom. The preliminary results include GPS and Galileo processing from space signals, the challenges and trade off decisions, the high level STRS architecture and foreseen experimentation campaign. Detailed results from the test campaigns are expected in 2017.

space navigation↗

NASA NTRS2002

Defining the Relationship Between Human Error Classes and Technology Intervention Strategies

One of the main factors in all aviation accidents is human error. The NASA Aviation Safety Program (AvSP), therefore, has identified several human-factors safety technologies to address this issue. Some technologies directly address human error either by attempting to reduce the occurrence of errors or by mitigating the negative consequences of errors. However, new technologies and system changes may also introduce new error opportunities or even induce different types of errors. Consequently, a thorough understanding of the relationship between error classes and technology "fixes" is crucial for the evaluation of intervention strategies outlined in the AvSP, so that resources can be effectively directed to maximize the benefit to flight safety. The purpose of the present project, therefore, was to examine the repositories of human factors data to identify the possible relationship between different error class and technology intervention strategies. The first phase of the project, which is summarized here, involved the development of prototype data structures or matrices that map errors onto "fixes" (and vice versa), with the hope of facilitating the development of standards for evaluating safety products. Possible follow-on phases of this project are also discussed. These additional efforts include a thorough and detailed review of the literature to fill in the data matrix and the construction of a complete database and standards checklists.

Wiegmann, Douglas A.↗

DOE OSTI2018

Structure of the HIV-1 Full-Length Capsid Protein in a Conformationally Trapped Unassembled State Induced by Small-Molecule Binding

The capsid (CA) protein plays crucial roles in HIV infection and replication, essential to viral maturation. The absence of high-resolution structural data on unassembled CA hinders the development of antivirals effective in inhibiting assembly. Unlike enzymes that have targetable, functional substrate-binding sites, the CA does not have a known site that affects catalytic or other innate activity, which can be more readily targeted in drug development efforts. We report the crystal structure of the HIV-1 CA, revealing the domain organization in the context of the wild-type full-length (FL) unassembled CA. The FL CA adopts an antiparallel dimer configuration, exhibiting a domain organization sterically incompatible with capsid assembly. A small compound, generated in situ during crystallization, is bound tightly at a hinge site ('H site'), indicating that binding at this interdomain region stabilizes the ADP conformation. Electron microscopy studies on nascent crystals reveal both dimeric and hexameric lattices coexisting within a single condition, in agreement with the interconvertibility of oligomeric forms and supporting the feasibility of promoting assembly-incompetent dimeric states. Solution characterization in the presence of the H-site ligand shows predominantly unassembled dimeric CA, even under conditions that promote assembly. Our structure elucidation of the HIV-1 FL CA and characterization of a potential allosteric binding site provides three-dimensional views of an assembly-defective conformation, a state targeted in, and thus directly relevant to, inhibitor development. Based on our findings, we propose an unprecedented means of preventing CA assembly, by 'conformationally trapping' CA in assembly-incompetent conformational states induced by H-site binding.

Du, Shoucheng↗

NASA NTRS2000

Fast Particle Methods for Multiscale Phenomena Simulations

We are developing particle methods oriented at improving computational modeling capabilities of multiscale physical phenomena in : (i) high Reynolds number unsteady vortical flows, (ii) particle laden and interfacial flows, (iii)molecular dynamics studies of nanoscale droplets and studies of the structure, functions, and evolution of the earliest living cell. The unifying computational approach involves particle methods implemented in parallel computer architectures. The inherent adaptivity, robustness and efficiency of particle methods makes them a multidisciplinary computational tool capable of bridging the gap of micro-scale and continuum flow simulations. Using efficient tree data structures, multipole expansion algorithms, and improved particle-grid interpolation, particle methods allow for simulations using millions of computational elements, making possible the resolution of a wide range of length and time scales of these important physical phenomena.The current challenges in these simulations are in : [i] the proper formulation of particle methods in the molecular and continuous level for the discretization of the governing equations [ii] the resolution of the wide range of time and length scales governing the phenomena under investigation. [iii] the minimization of numerical artifacts that may interfere with the physics of the systems under consideration. [iv] the parallelization of processes such as tree traversal and grid-particle interpolations We are conducting simulations using vortex methods, molecular dynamics and smooth particle hydrodynamics, exploiting their unifying concepts such as : the solution of the N-body problem in parallel computers, highly accurate particle-particle and grid-particle interpolations, parallel FFT's and the formulation of processes such as diffusion in the context of particle methods. This approach enables us to transcend among seemingly unrelated areas of research.

Koumoutsakos, P.↗

DOE OSTI2024

Capturing the generation and structural transformations of molecular ions

Molecular ions are ubiquitous and play pivotal roles in many reactions, particularly in the context of atmospheric and interstellar chemistry. However, their structures and conformational transitions, particularly in the gas phase, are less explored than those of neutral molecules owing to experimental difficulties. A case in point is the halonium ions, whose highly reactive nature and ring strain make them short-lived intermediates that are readily attacked even by weak nucleophiles and thus challenging to isolate or capture before they undergo further reaction. Here we show that mega-electronvolt ultrafast electron diffraction (MeV-UED), used in conjunction with resonance-enhanced multiphoton ionization, can monitor the formation of 1,3-dibromopropane (DBP) cations and their subsequent structural dynamics forming a halonium ion. We find that the DBP + cation remains for a substantial duration of 3.6 ps in aptly named ‘dark states’ that are structurally indistinguishable from the DBP electronic ground state. The structural data, supported by surface-hopping simulations and ab initio calculations, reveal that the cation subsequently decays to iso-DBP + , an unusual intermediate with a four-membered ring containing a loosely bound bromine atom, and eventually loses the bromine atom and forms a bromonium ion with a three-membered-ring structure. We anticipate that the approach used here can also be applied to examine the structural dynamics of other molecular ions and thereby deepen our understanding of ion chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Tuning magnetic coercivity with external pressure in iron-rhenium based ferrimagnetic double perovskites

We studied the effect of physical pressure on the electronic and magnetic properties of ferrimagnetic double perovskites A 2 FeReO 6 (A = Ca, Ba) using Re L 2,3 edge x-ray absorption spectroscopy and powder diffraction measurements. Volume compression is shown to dramatically increase the magnetic coercivity (H c ) in polycrystalline samples of both compounds with ΔH c /ΔV similar to 150-200 Oe/Å 3 . A nearly eight-fold increase in H c , from 0.2 to 1.55 T, is obtained in Ba 2 FeReO 6 at P = 29 GPa. While no signs of structural phase transitions are seen in either sample to similar to 30 GPa, the structural data points to a pressure-driven increase in tetragonal distortion of ReO 6 octahedra. A sizable but pressure-independent Re orbital-to-spin magnetic moment ratio is observed, pointing to the critical role of spin-orbit interactions at Re sites. We present a J(eff) description of the electronic structure that combines effects of crystal field and spin-orbit coupling on the Re 5d 2 orbitals and use this description to provide insight into the pressure-induced enhancement of magnetic anisotropy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

mzapy : An Open-Source Python Library Enabling Efficient Extraction and Processing of Ion Mobility Spectrometry-Mass Spectrometry Data in the MZA File Format

We have recently reported MZA, a new and simple mass spectrometry data structure based on the broadly supported HDF5 format and created to facilitate software development. While this format is inherently supportive of application development, the availability of a core library with standard mass spectrometry utilities greatly facilitates fast software development. Here, we present a Python library, mzapy, for efficient extraction and processing of mass spectrometry data in the MZA format. In addition to raw data extraction, mzapy contains supporting utilities enabling tasks including calibration, signal processing, peak finding, and generating plots. Being implemented in pure Python with minimal and largely standardized dependencies makes mzapy uniquely suited to application development in the multi-omics domain. The free and open source mzapy is built with extensibility in mind, and future development will support cloud computing and artificial intelligence/machine learning applications. The software source code is freely available at https://github.com/PNNL-m-q/mzapy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗