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At least 487 records · Page 27

All sources NASA NTRS DOE OSTI

DOE OSTI2015

3D numerical simulation of the long range propagation of acoustical shock waves through a heterogeneous and moving medium

Many situations involve the propagation of acoustical shock waves through flows. Natural sources such as lightning, volcano explosions, or meteoroid atmospheric entries, emit loud, low frequency, and impulsive sound that is influenced by atmospheric wind and turbulence. The sonic boom produced by a supersonic aircraft and explosion noises are examples of intense anthropogenic sources in the atmosphere. The Buzz-Saw-Noise produced by turbo-engine fan blades rotating at supersonic speed also propagates in a fast flow within the engine nacelle. Simulating these situations is challenging, given the 3D nature of the problem, the long range propagation distances relative to the central wavelength, the strongly nonlinear behavior of shocks associated to a wide-band spectrum, and finally the key role of the flow motion. With this in view, the so-called FLHOWARD (acronym for FLow and Heterogeneous One-Way Approximation for Resolution of Diffraction) method is presented with three-dimensional applications. A scalar nonlinear wave equation is established in the framework of atmospheric applications, assuming weak heterogeneities and a slow wind. It takes into account diffraction, absorption and relaxation properties of the atmosphere, quadratic nonlinearities including weak shock waves, heterogeneities of the medium in sound speed and density, and presence of a flow (assuming a mean stratified wind and 3D turbulent ? flow fluctuations of smaller amplitude). This equation is solved in the framework of the one-way method. A split-step technique allows the splitting of the non-linear wave equation into simpler equations, each corresponding to a physical effect. Each sub-equation is solved using an analytical method if possible, and finite-differences otherwise. Nonlinear effects are solved in the time domain, and others in the frequency domain. Homogeneous diffraction is handled by means of the angular spectrum method. Ground is assumed perfectly flat and rigid. Due to the 3D aspect, the code was massively parallelized using the single program, multiple data paradigm with the Message Passing Interfaces (MPI) for distributed memory architectures. This allows us to handle problems in the order of a thousand billion mesh points in the four dimensions (3 dimensions of space plus time). The validity of the method has been thoroughly evaluated on many cases with known solutions: linear piston, scattering of plane wave by a heterogeneous sphere, propagation in a waveguide with a shear flow, scattering by a finite amplitude vortex and nonlinear propagation in a thermoviscous medium. This validation process allows for a detailed assessment of the advantages and limitations of the method. Finally, applications to atmospheric propagation of shock waves will be presented.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A Reference Implementation for a Quantum Message Passing Interface

Practical applications of quantum computing are currently limited by the number of qubits that can be set with reasonable fidelities for each system. Therefore, a distributed quantum computing system with multiple quantum computers coherently connected is highly demanding. To realize the internode communication of quantum information, the software interface, Quantum Message Passing Interface (QMPI), leveraging the framework built for classical MPI but taking advantage of quantum teleportation to communicate between different quantum nodes was proposed. In this project, we develop the QMPI with point-to-point and collective operations in Qiskit and characterize its performance by demonstrating the application implementations. Moreover, we developed a new technique for optimizing collective communication of the distributed quantum programs with Multi-Controlled Toffoli gates. This technique beats the state-of-the-art in terms of fidelity and the number of remote EPR pairs consumed in both simulations and experiments.

Shi, Yue↗

DOE OSTI2025

An open-access simulated earthquake ground-motion database for an M7 Hayward Fault earthquake in the San Francisco Bay Region

Comprehensive understanding of earthquake ground motions, particularly in the near-fault region of large-magnitude events, is limited by gaps in strong-motion data. This challenge is prominent in areas with high seismic hazard but infrequent large earthquakes where data is sparse and difficult to interpret. These data limitations lead to uncertainties in the development of site-specific ground motions, which are crucial for engineering risk assessments. To address these challenges, physics-based regional-scale ground-motion simulations have been developed. With the emergence of exaflop-scale computing ecosystems, it is now possible to simulate regional earthquake processes at unprecedented fidelity and generate the large number of fault rupture realizations necessary to characterize both intra- and inter-event ground-motion variability. This article introduces a new database of simulated earthquake ground motions, created for applications in earthquake engineering, earthquake planning, and emergency response. The inaugural version of the database features simulated ground motions for a magnitude 7 Hayward Fault earthquake in the San Francisco Bay Region (SFBR), using the EarthQuake SIMulation (EQSIM) simulation framework and the Graves–Pitarka kinematic rupture model. The aim is to provide high-fidelity, spatially dense, three-component motions generated on the Department of Energy’s (DOE) newest generation of graphics processing unit (GPU)-accelerated supercomputers. These motions are being made openly available to the engineering, scientific, and disaster planning communities. In addition, this work develops protocols for the efficient dissemination of these large data sets and emphasizes community engagement to build confidence in their application. This article discusses the methodology behind the data, underlying software verification and validation, scalable data management, and a user interface for data access. The goal is to facilitate widespread use and elicit expert feedback to maximize the utility and exploitation of simulated motions. While the initial focus is on the San Francisco Region, simulations for additional regions will be added as the DOE program progresses.

Simulated ground-motion database↗

DOE OSTI2014

Enabling a systems biology knowledgebase with gaggle and firegoose

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is an open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Programmed Nanomaterial Assemblies in Large Scales: Applications of Synthetic and Genetically- Engineered Peptides to Bridge Nano-Assemblies and Macro-Assemblies

Work is reported in these areas: Large-scale & reconfigurable 3D structures of precise nanoparticle assemblies in self-assembled collagen peptide grids; Binary QD-Au NP 3D superlattices assembled with collagen-like peptides and energy transfer between QD and Au NP in 3D peptide frameworks; Catalytic peptides discovered by new hydrogel-based combinatorial phage display approach and their enzyme-mimicking 2D assembly; New autonomous motors of metal-organic frameworks (MOFs) powered by reorganization of self-assembled peptides at interfaces; Biomimetic assembly of proteins into microcapsules on oil-in-water droplets with structural reinforcement via biomolecular recognition-based cross-linking of surface peptides; and Biomimetic fabrication of strong freestanding genetically-engineered collagen peptide films reinforced by quantum dot joints. We gained the broad knowledge about biomimetic material assembly from nanoscale to microscale ranges by coassembling peptides and NPs via biomolecular recognition. We discovered: Genetically-engineered collagen-like peptides can be self-assembled with Au NPs to generate 3D superlattices in large volumes (> μm{sup 3}); The assembly of the 3D peptide-Au NP superstructures is dynamic and the interparticle distance changes with assembly time as the reconfiguration of structure is triggered by pH change; QDs/NPs can be assembled with the peptide frameworks to generate 3D superlattices and these QDs/NPs can be electronically coupled for the efficient energy transfer; The controlled assembly of catalytic peptides mimicking the catalytic pocket of enzymes can catalyze chemical reactions with high selectivity; and, For the bacteria-mimicking swimmer fabrication, peptide-MOF superlattices can power translational and propellant motions by the reconfiguration of peptide assembly at the MOF-liquid interface.

36 MATERIALS SCIENCE↗

DOE OSTI2020

A Framework for the Analysis of Compiler Optimizations

Compilers transform program source code to machine executable code. During this transformation, they perform a number of compiler optimizations to improve the performance of the generated executable code. Importantly, applying those optimizations depends on the source code structure, such as the parallel programming model used to parallelize an algorithm. Often, implementations of the same algorithm with different programming models have vastly different performance because the compiler optimized them differently. We create FAROS, a framework to structure and automate the analysis of compiler optimizations on programs. FAROS automates the building process, execution profiling, and analysis of compiler optimization of programs, through a configuration interface. It outputs compiler optimization reports to show which optimizations applied to which line of source code, leveraging compilation remarks output by the compiler. Also, FAROS supports benchmarking performance of different program versions by collecting execution time results. In this first release of FAROS, we provide a configuration file to analyze compiler optimization differences for sequential vs OpenMP compilation, including 38 programs consisting of HPC proxy/mini/large applications, and NAS and Rodina kernels for analysis.

Georgakoudis, Giorgis↗

DOE OSTI2026

OptiMX

OptiMX is a GUI-oriented program with principal aim to be an easy to use, yet comprehensive, interactive accelerator optics design and analysis tool. It was originally developed starting in the 1990s as an MS Windows centric application using the commercial Borland OWL framework. In the spring of 2014, a decision was made to port OptiM to Qt, a modern, portable and open framework. As much as possible, the original interface was preserved.While a significant amount of refactoring was required, the underlying physics has been for the most, left unchanged. The custom plots of the original application have been replaced with functional equivalents based on a stable and well-established library (qwt). With very few minor exceptions the new refactored OptiMX should be a drop-in replacement for the original OWL version.

Lebedev, ValeriA. [Joint Inst. for Nuclear Researc↗

DOE OSTI2021

Interactive Web Application for Traffic Simulation Data Management and Visualization

As traffic simulation software becomes more effective for realistically simulating and analyzing traffic dynamics and vehicle interactions on the mesoscopic and microscopic level, the management, dissemination, and collaborative visualization of traffic simulation results produced by individual transportation planners presents a significant challenge. Existing online content management systems have a very limited capability in allowing users to query specific traffic simulation scenarios and geospatially visualize simulation results through shareable and interactive web interfaces. This paper presents a web-based application for promoting the archiving, sharing, and visualization of large-scale traffic simulation outputs. The application is developed to enhance cyber-physical controls, communications, and public education for collaborative transportation planning. Unique features of the web application include: (a) allowing users to upload their new traffic simulation scenarios (parameters and outputs), as well as search existing scenarios using easily accessible interfaces; (b) optimizing simulation output files with heterogeneous data formats and projected coordinate systems for web-based storage and management using a scalable and searchable data/metadata standard; (c) standardizing user-uploaded simulation outputs using web interfaces and data processing libraries with parallel computing capacity; and (d) providing shareable web visual interfaces for visualizing the traffic flow and signal information stored in simulation outputs (e.g., regional traffic patterns and individual vehicle interactions) and visually comparing multiple simulation outputs both spatially and temporally. Furthermore, the paper presents the conceptual design and implementation of this application, and demonstrates the application’s performance for sharing, comparing, and visualizing simulation outputs from VISSIM and SUMO, two commonly used traffic simulation software programs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2017

PLATO (Parallel Load Assignment Tool): A Parallel Workload Partitioner for Particle-based Methods

A key first step in many large-scale high-performance scientific computing applications is the distribution of the computational domain across all participating processors of a parallel computing platform such as a shared memory machine, cluster or a tightly-coupled supercomputer. The primary goal of such a partitioning step is to ensure that the computational work performed by each process remains load-balanced throughout the execution of the parallel application. In this project, a general-purpose parallel partitioning tool, code-named PLATO, was designed and implemented. PLATO assumes that the workload is a set of points in an n-dimensional metric space. These points are abstractions of computational units that may represent point-like computational units such as celestial objects in astrophysics, atoms in materials sciences and molecules in biology/chemistry, or may represent more abstract computational units such as grid points in finite difference methods, grid elements in finite element methods or n-dimensional points in the feature space of a host of other applications. PLATO supports several key and useful capabilities, namely: (a) multiple load partitioning strategies, (b) support for arbitrary user-defined processor topology, (c) pre-fetching data from neighboring processors based on user-defined parameters, and (d) support for arbitrary number and types of attributes associated with each point in the computational domain. PLATO is implemented in the C programming language using Message Passing Interface (MPI) for inter-processor communications and its parallel performance tested on up to 48 processors of a shared memory machine. This report includes a detailed performance study of PLATO using parallel speedup and iso-efficiency as the two main metrics of parallel performance. In addition, a user manual and DOXYGEN generated code documentation have been included for completeness.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Methodological Aspects of Shielding and Activation Analyses for ITER Diagnostics Systems - Paper 125

It is expected that the diagnostics systems of the ITER tokamak will provide valuable measurement data about the first in its kind D-T fusion plasma with emission of 14 MeV neutrons. These systems must withstand the neutron and secondary photon radiation along the ITER operation. Under the neutron irradiation the ITER materials are getting radioactive and therefore an adequate shielding must be provided along all the time of ITER operation and shut-down for the reliable machine operation and for the safe personnel access to its components, such as the diagnostics ports. These are the prerequisites for the shielding and activation analysis of the ITER diagnostics systems discussed in this paper. This paper provides insight into the current tasks of neutronics support for the development of ITER diagnostics systems. The tasks themselves range from relatively straightforward ones such as Monte Carlo radiation transport calculations for shielding analyses of the diagnostics systems, to more advanced tasks of Shut-Down Dose Rate (SDDR) analyses for which the dedicated Rigorous 2-Step mesh-based (R2Smesh) and Direct 1-Step (D1S) methodologies were applied. The accuracy and precision of the ITER neutronics analysis is dependent on the methodological approaches and the implying modeling assumptions. In addition to the SDDR challenges, another distinguishing feature of fusion neutronics is a wide use of CAD-based neutronics modeling to design components of fusion devices such as ITER and DEMO. Basically, there are two possibilities of CAD geometry settings in Monte Carlo (MC) radiation transport models, either by the geometry format conversion of CAD models into the format of MC models by means of the interface programs such as McCad and MCAM or by the direct use of CAD geometry engine in MC calculations such as it was realized in the DAGMC code approach. Several conversion interfaces and the DAGMC software library have been tested on the 3D ITER model developed for the CAD-MCNP benchmark. It was concluded that the considered approaches have reached the maturity level to allow their application to real ITER design analyses.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2024

AdvEP

AdvEP is a code repository which contains PyTorch implementations of various adversarial attacks on a deep neural network trained with Equilibrium Propagation (EP), which is a neuromorphic learning framework. AdvEP allows for the training, testing, and conducting white/black-box attacks of EP models on a wide variety of applications and datasets. AdvEP is based on the open-source code https://github.com/Laborieux-Axel/Equilibrium-Propagation which was developed to train energy models. AdvEP was created by modifying the original code to perform and test against adversarial attacks. AdvEP was developed in Python, a high-level programming language that takes advantage of the Python ecosystem of high-quality open-source packages for machine learning. AdvEP interfaces heavily with the open-source PyTorch Python package as well as the open-source Adversarial Robustness Toolbox (ART) package.

Mansingh, Siddarth↗

DOE OSTI2022

Novel Harsh Environment Materials and Fabrication Techniques for Wireless Sensor Applications (Final Report)

The overarching goal of this project is to establish a center of excellence program at the University of Maine that is focused on Harsh Environmental Materials and Fabrication Techniques for Wireless Sensor Applications. UMaine is well-positioned to build on previous successes in the areas of materials science research and sensor engineering. Since 1980, the Laboratory for Surface Science & Technology (LASST) has been a very successful interdisciplinary UMaine research center with a well-established infrastructure to investigate surfaces, interfaces, thin films, and micro/nano-fabrication. This infrastructure established through NSF, DOE, DOD, NASA, the State of Maine, and industry includes (i) a 3,500 ft2 clean room with nano/microfabrication and photolithography instrumentation, (ii) thin film synthesis, processing and characterization, (iii) surface and thin film analytical chemistry tools, and (iv) device packaging, electronic testing, wireless devices, system fabrication, and sensor test facilities. This strong foundation is the basis for a planned significant growth in R&D capacity currently underway. To that end, since the start of this project in the Fall of 2019, LASST has undergone a transition to become a new interdisciplinary center at UMaine, named the Frontier Institute for Research in Sensor Technologies (FIRST). This new focus represents a commitment and investment by UMaine that aligns with the proposed DOE-EPSCoR theme, capitalizing on the state-of-the-art instrumentation to form an energized group of faculty and students pursuing advances in sensor materials, devices, and applications.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Flexible Computer Science Infrastructure (FleCSI)

FleCSI is a compile-time configurable 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. Current support includes multi-dimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures. FleCSI also introduces a functional programming model with control, execution, and data abstractions that are consistent with both MPI and state-of-the-art task-based runtimes such as Legion and Charm++. The FleCSI abstraction layer provides the developer with insulation from the underlying runtime, 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. The control and execution models in FleCSI also provide formal nomenclature for describing poorly understood concepts like kernels and tasks.

Moss, Nicholas↗

DOE OSTI2016

Flexible Computer Science Infrastructure (FleCSI)

Bergen, Ben↗

DOE OSTI2026

Programmable Phase Selection between Altermagnetic and Noncentrosymmetric Polymorphs of MnTe on InP via Molecular Beam Epitaxy

Phase selecting nearly degenerate crystalline polymorphs during epitaxial growth can be challenging yet critical to targeting physical properties for specific applications. Here, we establish how phase selectivity of altermagnetic and noncentrosymmetric polymorphs of MnTe can be programmed by subtle changes to the surface of lattice-matched InP substrates in molecular beam epitaxy growth. Bulk altermagnetic MnTe is thermodynamically stable in the hexagonal NiAs-structure and is synthesized here on the polar (111)A surface (In-terminated) of InP, while the noncentrosymmetric, cubic ZnS-structure with wide band gap (>3 eV), which epitaxially matches III–V materials, is stabilized on the (111)B surface (P-terminated). Electron microscopy, X-ray photoemission spectroscopy, and reflection high-energy electron diffraction indicate that phase selection is triggered at the interface and proceeds along the growing surface. First-principles calculations suggest that interfacial termination and strain have a significant effect on the interfacial energy; stabilizing the NiAs polymorph on the In-terminated surface and the ZnS structure on the P-terminated surface. Here, selectively grown, high-quality, phase pure films of both MnTe polymorphs will enable our understanding of the novel properties of these materials, thereby facilitating their use in new applications ranging from spintronics to microelectronic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

NSR&D Program Fiscal Year 2015 Funded Research Stochastic Modeling of Radioactive Material Releases Final Report

Nonreactor nuclear facilities operating under the approval authority of the U.S. Department of Energy use unmitigated hazard evaluations to determine if potential radiological doses associated with design basis events challenge or exceed dose evaluation guidelines. Unmitigated design basis events that sufficiently challenge dose evaluation guidelines or exceed the guidelines for members of the public or workers, merit selection of safety structures, systems, or components or other controls to prevent or mitigate the hazard. Idaho State University, in collaboration with Idaho National Laboratory, has developed a portable and simple to use software application called SODA (Stochastic Objective Decision-Aide) that stochastically calculates the radiation dose distribution associated with hypothetical radiological material release scenarios. Rather than producing a point estimate of the dose, SODA produces a dose distribution result to allow a deeper understanding of the dose potential. SODA allows users to select the distribution type and parameter values for all of the input variables used to perform the dose calculation. Users can also specify custom distributions through a user defined distribution option. SODA then randomly samples each distribution input variable and calculates the overall resulting dose distribution. In cases where an input variable distribution is unknown, a traditional single point value can be used. SODA, developed using the MATLAB coding framework, has a graphical user interface and can be installed on both Windows and Mac computers. SODA is a standalone software application and does not require MATLAB to function. SODA provides improved risk understanding leading to better informed decision making associated with establishing nuclear facility material-at-risk limits and safety structure, system, or component selection. It is important to note that SODA does not replace or compete with codes such as MACCS or RSAC; rather it is viewed as an easy to use supplemental tool to help improve risk understanding and support better informed decisions. The SODA development project was funded through a grant from the DOE Nuclear Safety Research and Development Program.

42 ENGINEERING↗

DOE OSTI2019

MPI Stages : A Serializable MPI Library

MPI library that supports serializing (and check-pointing) its MPI Stages is a communication library that allows nodes and programs in a computer cluster to communicate via the Message-Passing Interface (MPI). The internal data objects of the library are serializable, i.e., the user can convert the MPI state or objects, such as groups or communicators, into byte streams and save them into a checkpoint file. Later users can load the checkpoint file and de-serialize previous objects into the library. Serialization/de-serialization is useful in MPI applications to recover from node failures.

Ruefenacht, Martin↗