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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

U.S. Department of Energy: National Virtual Biotechnology Laboratory (Technical Report)

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. The NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply shortages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. As part of the NVBL framework, DOE rapidly assembled five project teams to (1) identify new targets for medical therapeutics; (2) develop innovations in testing capabilities; (3) provide epidemiological and logistical support; (4) understand viral fate and transport in the environment; and (5) address supply chain bottlenecks by harnessing extensive additive manufacturing capabilities. Each research team was charged with defining high-impact projects that could be completed in a 6-month sprint while coordinating their developments with academia, other government agencies, and the private sector. Within months, NVBL teams used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported efforts by the U.S. Food and Drug Administration, Centers for Disease Control and Prevention, and U.S. Department of Defense to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. To minimize virus uptake and protect human health, NVBL teams studied how to control indoor virus movement. Researchers also produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment, creating nearly 1,000 new jobs. Through its NVBL framework, DOE has contributed significantly to the nation’s COVID response, demonstrating in only a few months the critical impact of its national laboratories. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development solutions. Going forward, the NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, DOE will continue to be an integral component of agency-wide efforts to prepare for and respond to biorisks and other crises. This technical report describes the goals, progress, and results of NVBL’s five project teams—Molecular Design for COVID-19 Therapeutics, COVID-19 Testing, Epidemiological Modeling, Viral Fate and Transport, and Materials and Manufacturing of Critical Supplies—and lists each team’s publications and research output.

42 ENGINEERING↗
DOE OSTI2015

Combined Spectroscopic and Electrochemical Detection of a NiI•••H–N Bonding Interaction with Relevance to Electrocatalytic H2 Production

The [Ni(PR2NR’2)2]2+ family of complexes are exceptionally active catalysts for proton reduction to H2. In this manuscript, we explore the first protonation step of the proposed catalytic cycle by using a catalytically inactive NiI complex possessing a sterically demanding variation of the ligand. Due to the paramagnetic nature of the NiI oxidation state, the protonated NiI intermediate has been characterized through a combination of cyclic voltammetry, ENDOR, and HYSCORE spectroscopy. Both the electrochemical and spectroscopic studies indicate that the NiI complex is protonated at a pendant amine that is endo to Ni, which suggests the presence of an intramolecular NiI•••HN bonding interaction. Using density functional theory, the proton was found to hydrogen bond to three doubly-occupied, localized molecular orbitals: the 3dxz, 3dz2, and 3dyz orbitals of nickel. These studies provide the first direct experimental evidence for this critical catalytic intermediate, and implications for catalytic H2 production are discussed. Research was supported by the Max Planck Society (EPR, ENDOR, and HYSCORE spectroscopy, computational studies), and as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (electrochemistry, NMR spectroscopy). Pacific Northwest National Laboratory is operated by Battelle for DOE.

electrocatalysis↗
DOE OSTI2014

Characterizing and Modeling Cloud Applications/Jobs on a Google Data Center

In this paper, we characterize and model Google applications and jobs, based on a 1-month Google trace from a large-scale Google data center. We address four contributions: (1) we compute the valuable statistics about task events and resource utilization for Google applications, based on various types of resources and execution types; (2) we analyze the classification of applications via a K-means clustering algorithm with optimized number of sets, based on task events and resource usage; (3) we study the correlation of Google application properties and running features (e.g., job priority and scheduling class); (4) we finally build a model that can simulate Google jobs/tasks and dynamic events, in accordance with Google trace. Experiments show that the tasks simulated based on our model exhibit fairly analogous features with those in Google trace. 95+ % of tasks' simulation errors are 20 %, confirming a high accuracy of our simulation model.

Di, Sheng↗
DOE OSTI2015

Evaluations of secondary cancer risk in spine radiotherapy using 3DCRT, IMRT, and VMAT: A phantom study

This study evaluated the secondary cancer risk from volumetric-modulated arc therapy (VMAT) for spine radiotherapy compared with intensity-modulated radiotherapy (IMRT) and 3-dimensional conformal radiotherapy (3DCRT). Computed tomography images of an Radiological Physics Center spine anthropomorphic phantom were exported to a treatment planning system (Pinnacle{sup 3}, version 9.4). Radiation treatment plans for spine were prepared using VMAT (dual-arc), 7-field IMRT (beam angles: 110°, 130°, 150°, 180°, 210°, 230°, and 250°), and 4-field 3DCRT technique. The mean and maximum doses, dose-volume histograms, and volumes receiving more than 2 and 4 Gy to organs at risk (OARs) were calculated and compared. The lifetime risk for secondary cancers was estimated according to the National Cancer Registry Programme Report 116. VMAT delivered the lowest maximum dose to the esophagus (4.03 Gy), bone (8.11 Gy), heart (2.11 Gy), spinal cord (6.45 Gy), and whole lung (5.66 Gy) as compared with other techniques (IMRT and 3DCRT). The volumes of OAR (esophagus) receiving more than 4 Gy were 0% for VMAT, 27.06% for IMRT, and up to 32.35% for 3DCRT. The estimated risk for secondary cancer in the respective OAR is considerably lower in VMAT compared with other techniques. The results of maximum doses and volumes of OARs suggest that the risk of secondary cancer induction for the spine in VMAT is lower than IMRT and 3DCRT, whereas VMAT has the best target coverage compared with the other techniques.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2026

How Does Metal Spin State Affect Electronic Communication in Mixed-Valence Dimers? Insights from Ultrafast Near-Infrared and Soft X-ray Transient Absorption Spectroscopy

Recent advancements in photocatalysis, photovoltaics, and quantum information science take advantage of electron spin, and determining how spin multiplicity affects electron transfer is key to understanding these phenomena. Here, in this study, we examine how metal spin state affects electronic communication in an organometallic mixed-valence dimer, ferrocenyl cobaltocenium ([Fe II Cp 2 Co III Cp 2 ] + ). This complex can be photoexcited from its low-spin singlet Fe II ground state to form intermediate-spin triplet Fe II and high-spin quintet Fe II excited states. Using femtosecond optical transient absorption (OTA) spectroscopy with visible (vis), near-infrared (NIR), and short-wave IR (SWIR) probes, supported by time-dependent density functional theory (TD-DFT) calculations, we measure Fe II Co III →Fe III Co II intervalence charge transfer (IVCT) bands in each of the Fe II spin states. Mulliken–Hush analysis of the excited-state IVCT bands was used to compute the electronic coupling between the metal centers in all three spin states, which increased as quintet < triplet < singlet. Meanwhile, the peak energy of the bands, and thus the ΔG of the IVCT transition, increased as triplet < quintet < singlet. Then, to directly probe the electronic structure at each metal center, we employed picosecond soft X-ray transient absorption (XTA) spectroscopy at the Fe and Co L 3 edges. Our results show that the low-spin and high-spin states of [Fe II Cp 2 Co III Cp 2 ] + are valence-localized, while the intermediate-spin state is partially delocalized. The differences in charge delocalization are attributed to differences in orbital occupation and geometry that affect the free energy and superexchange coupling.

Burke, John H. [Univ. of Illinois at Urbana-Champa↗
DOE OSTI2022

Neural Network for Principle of Least Action

The principle of least action is the cornerstone of classical mechanics, theory of relativity, quantum mechanics, and thermodynamics. Here, we describe how a neural network (NN) learns to find the trajectory for a Lennard-Jones (LJ) system that maintains balance in minimizing the Onsager–Machlup (OM) action and maintaining the energy conservation. The phase-space trajectory thus calculated is in excellent agreement with the corresponding results from the “ground-truth” molecular dynamics (MD) simulation. Furthermore, we show that the NN can easily find structural transformation pathways for LJ clusters, for example, the basin-hopping transformation of an LJ 38 from an incomplete Mackay icosahedron to a truncated face-centered cubic octahedron. Unlike MD, the NN computes atomic trajectories over the entire temporal domain in one fell swoop, and the NN time step is a factor of 20 larger than the MD time step. The NN approach to OM action is quite general and can be adapted to model morphometrics in a variety of applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Elastic Properties of Plasma-Exposed Tungsten Predicted by Molecular-Dynamics Simulations

We report results of systematic molecular-dynamics computations of the elastic properties of single-crystalline tungsten containing structural defects, voids and overpressurized He nanobubbles, related to plasma exposure of tungsten serving as a plasma- facing component (PFC) in nuclear fusion devices. Our computations reveal that the empty voids are centers of dilatation resulting in development of tensile stress in the tungsten matrix, whereas He-filled voids (nanobubbles) introduce compressive stress in the plasma-exposed tungsten. We find that the dependence of the elastic moduli of plasma-exposed tungsten, namely, the bulk, Young, and shear modulus, on its void fraction follows a universal exponential scaling relation. We also find that the elastic moduli of plasma-exposed tungsten soften substantially as a function of He content in the tungsten matrix, following an exponential scaling relation; this He-induced exponential softening is in addition to the softening caused in the matrix with increasing temperature. A systematic characterization of the dependence of the elastic moduli on the He bubble size reveals that He bubble growth affects significantly both the bulk modulus and the Poisson ratio of plasma-exposed tungsten, while its effect on the Young and shear moduli of the plasma-exposed material is weak. Our findings contribute directly to the development of a structure-properties database that is required for the predictive modeling of the dynamical response of PFCs in nuclear fusion devices.

36 MATERIALS SCIENCE↗
DOE OSTI2015

THE GAMMA-RAY AND NEUTRINO SKY: A CONSISTENT PICTURE OF FERMI-LAT, MILAGRO, AND ICECUBE RESULTS

We compute the γ-ray and neutrino diffuse emission of the Galaxy on the basis of a recently proposed phenomenological model characterized by radially dependent cosmic-ray (CR) transport properties. We show how this model, designed to reproduce both Fermi-LAT γ-ray data and local CR observables, naturally reproduces the anomalous TeV diffuse emission observed by Milagro in the inner Galactic plane. Above 100 TeV our picture predicts a neutrino flux that is about five (two) times larger than the neutrino flux computed with conventional models in the Galactic Center region (full-sky). Explaining in that way up to ∼25% of the flux measured by IceCube, we reproduce the full-sky IceCube spectrum adding an extra-Galactic component derived from the muonic neutrinos flux in the northern hemisphere. We also present precise predictions for the Galactic plane region where the flux is dominated by the Galactic emission.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Advancements in NbTiN based circuits for Superconducting Digital Logic

Superconducting (SC) electronics have emerged as a promising platform for high-speed, energy-efficient computing and quantum information processing. This work, centered on NbTiN, presents recent advances in material science and fabrication methods leading to significant improvements in performance, scalability and vertical integration. We specifically report on fabrication and characterization of key components, including Josephson junctions (JJs), flux trapping structures and SC interconnects. Together, these efforts represent critical steps towards realizing practical, complex, dense and large-scale SC integrated circuits.

Pokhrel, A. [Imec,Heverlee,Belgium]↗
DOE OSTI2014

Advanced Liquid Cooling for a Traction Drive Inverter Using Jet Impingement and Microfinned Enhanced Surfaces: Preprint

Jet impingement on plain and micro-finned enhanced surfaces was compared to a traditional channel flow configuration. The jets provide localized cooling to areas heated by the insulated-gate bipolar transistor and diode devices. Enhanced microfinned surfaces increase surface area and thermal performance. Using lighter materials and designing the fluid path to manage pressure losses increases overall performance while reducing weight, volume, and cost. Powering four diodes in the center power module of the inverter and computational fluid dynamics (CFD) modeling was used to characterize the baseline as well as jet-impingement-based heat exchangers. CFD modeling showed the thermal performance improvements should hold for a fully powered inverter. Increased thermal performance was observed for the jet-impingement configurations when tested at full inverter power (40 to 100 kW output power) on a dynamometer. The reliability of the jets and enhanced surfaces over time was also investigated. Experimentally, the junction-to- coolant thermal resistance was reduced by up to 12.5% for jet impingement on enhanced surfaces s compared to the baseline channel flow configuration. Base plate-to-coolant (convective) resistance was reduced by up to 37.0% for the jet-based configuration compared to the baseline, suggesting that while improvements to the cooling side reduce overall resistance, reducing the passive stack resistance may contribute to lowering overall junction-to-coolant resistance. Full inverter power testing showed reduced thermal resistance from the middle of the module baseplate to coolant of up to 16.5%. Between the improvement in thermal performance and pumping power, the coefficient of performance improved by up to 13% for the jet-based configuration.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2014

SU-E-J-230: Effect of Metal Hip Prosthesis On the Accuracy of Electromagnetic Localization and Tracking

Purpose: To quantify the effect of metal hip prosthesis on the ability to track and localize electromagnetic transponders. Methods: Three Calypso transponders were implanted into two prostate phantoms. The geometric center of the transponders were identified on computed tomography and set as the isocenter. With the phantom stationary on the treatment table and the tracking array 14-cm above the isocenter, data was acquired by the Calypso system at 10 Hz to establish the uncertainty in measurements. Transponder positional data was acquired with unilateral hip prostheses of different metallic compositions and then with bilateral hips placed at variable separation from the phantom. Results: Regardless of hip prosthesis composition, the average vector displacement in the presence of a unilateral prosthesis was < 0.5 mm. The greatest contribution to overall vector displacement occurred in the lateral dimension. With bilateral hip prosthesis, the average vector displacement was 0.3 mm. The displacement in the lateral dimension was markedly reduced compared with a unilateral hip, suggesting that there was a countervailing effect with bilateral hip prosthesis. The greatest average vector displacement was 0.6 mm and occurred when bilateral hip prostheses were placed within 4 cm of the detector array. Conclusion: Unilateral and bilateral hip prostheses did not have any meaningful effect on the ability to accurately track electromagnetic transponders implanted in a prostate phantom. At clinically realistic distances between the hip and detection array, the average tracking error is negligible.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

A new method for tracking organ motion on diagnostic ultrasound images

Purpose: Respiratory-gated irradiation is effective in reducing the margins of a target in the case of abdominal organs, such as the liver, that change their position as a result of respiratory motion. However, existing technologies are incapable of directly measuring organ motion in real-time during radiation beam delivery. Hence, the authors proposed a novel quantitative organ motion tracking method involving the use of diagnostic ultrasound images; it is noninvasive and does not entail radiation exposure. In the present study, the authors have prospectively evaluated this proposed method. Methods: The method involved real-time processing of clinical ultrasound imaging data rather than organ monitoring; it comprised a three-dimensional ultrasound device, a respiratory sensing system, and two PCs for data storage and analysis. The study was designed to evaluate the effectiveness of the proposed method by tracking the gallbladder in one subject and a liver vein in another subject. To track a moving target organ, the method involved the control of a region of interest (ROI) that delineated the target. A tracking algorithm was used to control the ROI, and a large number of feature points and an error correction algorithm were used to achieve long-term tracking of the target. Tracking accuracy was assessed in terms of how well the ROI matched the center of the target. Results: The effectiveness of using a large number of feature points and the error correction algorithm in the proposed method was verified by comparing it with two simple tracking methods. The ROI could capture the center of the target for about 5 min in a cross-sectional image with changing position. Indeed, using the proposed method, it was possible to accurately track a target with a center deviation of 1.54 ± 0.9 mm. The computing time for one frame image using our proposed method was 8 ms. It is expected that it would be possible to track any soft-tissue organ or tumor with large deformations and changing cross-sectional position using this method. Conclusions: The proposed method achieved real-time processing and continuous tracking of the target organ for about 5 min. It is expected that our method will enable more accurate radiation treatment than is the case using indirect observational methods, such as the respiratory sensor method, because of direct visualization of the tumor. Results show that this tracking system facilitates safe treatment in clinical practice.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Unified Performance and Power Modeling of Scientific Workloads

It is expected that scientific applications executing on future large-scale HPC must be optimized not only in terms of performance, but also in terms of power consumption. As power and energy become increasingly constrained resources, researchers and developers must have access to tools that will allow for accurate prediction of both performance and power consumption. Reasoning about performance and power consumption in concert will be critical for achieving maximum utilization of limited resources on future HPC systems. To this end, we present a unified performance and power model for the Nek-Bone mini-application developed as part of the DOE's CESAR Exascale Co-Design Center. Our models consider the impact of computation, point-to-point communication, and collective communication

Modeling techniques↗
DOE OSTI2016

Error Detection and Correction LDMS Plugin Version 1.0

Sandia's Lightweight Distributed Metric Service (LDMS) is a data collection and transport system used at Livermore Computing to gather performance data across the center. While Sandia has a set of plugins available, they do not include all the data we need to capture. The ECAC plugin that we have developed enables collection of the Error Detection and Correction (EDAC) counters.

Shoga, Kathleen↗
DOE OSTI2015

Physically motivated global alignment method for electron tomography

Electron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop a new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

Solar Position Model for use in DIORAMA

The DIORAMA code requires the solar position relative to earth in order to compute GPS satellite orientation. The present document describes two functions that compute the unit vector from either the center of the Earth to the Sun or from any observer’s position to the Sun at some specified time. Another function determines if a satellite lies within the Earth’s shadow umbra. Similarly, functions determine the position of the moon and whether a satellite lies within the Moon’s shadow umbra.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Final Technical Report for DOE Award SC0006616

This report summarizes research carried out by the project "Collaborative Research, Type 1: Decadal Prediction and Stochastic Simulation of Hydroclimate Over Monsoonal Asia. This collaborative project brought together climate dynamicists (UCLA, IRI), dendroclimatologists (LDEO Tree Ring Laboratory), computer scientists (UCI), and hydrologists (Columbia Water Center, CWC), together with applied scientists in climate risk management (IRI) to create new scientific approaches to quantify and exploit the role of climate variability and change in the growing water crisis across southern and eastern Asia. This project developed new tree-ring based streamflow reconstructions for rivers in monsoonal Asia; improved understanding of hydrologic spatio-temporal modes of variability over monsoonal Asia on interannual-to-centennial time scales; assessed decadal predictability of hydrologic spatio-temporal modes; developed stochastic simulation tools for creating downscaled future climate scenarios based on historical/proxy data and GCM climate change; and developed stochastic reservoir simulation and optimization for scheduling hydropower, irrigation and navigation releases.

54 ENVIRONMENTAL SCIENCES↗