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At least 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

CMS readiness for multi-core workload scheduling

In the present run of the LHC, CMS data reconstruction and simulation algorithms benefit greatly from being executed as multiple threads running on several processor cores. The complexity of the Run 2 events requires parallelization of the code to reduce the memory-per- core footprint constraining serial execution programs, thus optimizing the exploitation of present multi-core processor architectures. The allocation of computing resources for multi-core tasks, however, becomes a complex problem in itself. The CMS workload submission infrastructure employs multi-slot partitionable pilots, built on HTCondor and GlideinWMS native features, to enable scheduling of single and multi-core jobs simultaneously. This provides a solution for the scheduling problem in a uniform way across grid sites running a diversity of gateways to compute resources and batch system technologies. This paper presents this strategy and the tools on which it has been implemented. The experience of managing multi-core resources at the Tier-0 and Tier-1 sites during 2015, along with the deployment phase to Tier-2 sites during early 2016 is reported. The process of performance monitoring and optimization to achieve efficient and flexible use of the resources is also described.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Construction status of the Mu2e crystal calorimeter

The Mu2e experiment at Fermilab will search for the charged-lepton flavor violating neutrino-less conversion of a negative muon into an electron in the field of an aluminum nucleus. The Mu2e detector is composed of a tracker, an electromagnetic calorimeter and an external veto for cosmic rays. The calorimeter plays an important role in providing excellent particle identification capabilities and a fast online trigger filter, while aiding the track reconstruction capabilities. Calorimeter requirements are to provide a large acceptance for 0~10 MeV electrons and reach: i) a time resolution better than 0.5 ns; ii) an energy resolution better than 10%; and iii) a position resolution of 1 cm. The calorimeter consists of two disks, each one made of 674 pure CsI crystals. Each crystal is readout by two large area 2×3 arrays of UV-extended SiPMs of 6×6 mm2 dimensions. A large scale prototype (Module-0) has been tested at an electron beam. We report here the tests done to finalize the calorimeter design, the results obtained with Module-0 and the status of production. At this time, the performance characteristics of 85% of the crystals and all of the SiPMs have been measured. The calorimeter engineering drawings have been completed and the large mechanical components are under fabrication. Analog and digital electronics have been prototyped and tested with irradiation dose. Their serial production is being organized. The calorimeter assembly phase is planned for mid-2020.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Characterization and QC practice of 16-channel ADC ASIC at cryogenic temperature for Liquid Argon TPC front-end readout electronics system in DUNE experiment

ColdADC is a low-noise 16-channel analog-to-digital converter ASIC designed for cold readout electronics of Liquid Argon Time Projection Chambers (LArTPCs) in the Deep Underground Neutrino Experiment (DUNE). ColdADC was specifically designed for operation at cryogenic temperatures (77 K–89 K). Cold electronics is considered to be an enabling technology for liquid argon detectors in neutrino experiments. The main function of the chip is to digitize signals from the 16-channel charge-sensitive amplifier designed at BNL (LArASIC) and send digitized signals to the data aggregator and serializer chip (COLDATA). ColdADC operates with a resolution of 12 bits and a sampling rate of 2 MS/s per channel. A complete characterization of prototype chips was conducted at cryogenic temperature, involving power consumption, noise and linearity performance. In the first DUNE Far-Detector module, 384000 data channels will be read out, corresponding to 24000 ColdADC chips. Therefore, systematic testing of ColdADC chips at cryogenic temperature is vital for the quality and reliability of DUNE Single-Phase modules. We have developed a Quality Control (QC) test stand that includes ColdADC evaluation and characterization at cryogenic temperature. The QC procedure was applied to a first batch of 33 chips, corresponding to 528 data channels. The obtained results meet all the required DUNE specifications for ColdADC. Moreover, the testing outcome allowed us to identify possibilities of performance optimization that are currently being addressed in the design of the next version of the chip. The Quality Control procedure is proved to be successful and will be a reference design for future large-batch production testing of final ColdADC ASICs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Optimizing the hit finding algorithm for liquid argon TPC neutrino detectors using parallel architectures

Neutrinos are particles that interact rarely, so identifying them requires large detectors which produce lots of data. Processing this data with the computing power available is becoming even more difficult as the detectors increase in size to reach their physics goals. Liquid argon time projection chamber (LArTPC) neutrino experiments are expected to grow in the next decade to have 100 times more wires than in currently operating experiments, and modernization of LArTPC reconstruction code, including parallelization both at data- and instruction-level, will help to mitigate this challenge. The LArTPC hit finding algorithm is used across multiple experiments through a common software framework. In this paper we discuss a parallel implementation of this algorithm. Using a standalone setup we find speedup factors of two times from vectorization and 30–100 times from multi-threading on Intel architectures. The new version has been incorporated back into the framework so that it can be used by experiments. On a serial execution, the integrated version is about 10 times faster than the previous one and, once parallelization is enabled, more speedups comparable to the standalone program are achieved.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

System design and prototyping for the CMS Level-1 Trigger at the High-Luminosity LHC

For the High-Luminosity Large Hadron Collider, the trigger and data acquisition system of the CMS experiment will be entirely replaced. Novel design choices have been explored, including ATCA prototyping platforms with SoC controllers and newly available interconnect technologies with serial optical links with data rates up to 28 Gb/s. Trigger analyses will be performed through sophisticated algorithms, including widespread use of Machine Learning, in large FPGAs, such as the Xilinx Ultrascale family. The system will process over 50 Tb/s of detector data with an event rate of 750 kHz. Here, we describe system design and prototyping and review trigger algorithm exemplars.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

RD53 pixel readout integrated circuits for ATLAS and CMS HL-LHC upgrades

The RD53 collaboration has since 2013 developed new hybrid pixel detector chips with 50 × 50 μm2 pixels for the HL-LHC upgrades of the ATLAS and CMS experiments at CERN. A common architecture, design and verification framework has been developed to enable final pixel chips of different sizes to be designed, verified and tested to handle extreme hit rates of 3 GHz/cm2 (up to 12 GHz per chip) together with an increased trigger rate of 1 MHz and efficient readout of up to 5.12 Gbits/s per pixel chip. Tolerance to an extremely hostile radiation environment with 1 Grad over 10 years and induced SEU (Single Event Upset) rates of up to 100 upsets per second per chip have been major challenges to make reliable pixel chips. Three generations of pixel chips, and many specific mixed signal building blocks and radiation test chips, have been submitted and extensively tested to get to final production chips. The large, complex and high rate pixel chips have been developed with a strong emphasis on low power consumption together with a concurrent development and qualification of novel serial powering at chip, module and system level, to minimize detector material budget.

Alimonti, G↗
DOE OSTI2025

How transparent is graphene? A surface science perspective on remote epitaxy

Remote epitaxy is the synthesis of a single crystalline film on a graphene-covered substrate, where the film adopts epitaxial registry to the substrate as if the graphene is transparent. Despite many exciting applications for flexible electronics, strain engineering, and heterogeneous integration, an understanding of the fundamental synthesis mechanisms remains elusive. Here we offer a perspective on the synthesis mechanisms, focusing on the foundational assumption of graphene transparency. We identify challenges for quantifying the strength of the remote substrate potential that permeates through graphene, and propose Fourier and beating analysis as a bias-free method for decomposing the lattice potential contributions from the substrate, from graphene, and from surface reconstructions, each at different frequencies. We highlight the importance of graphene-induced reconstructions on epitaxial templating, drawing comparison to moiré epitaxy. We highlight the role of the remote potential in tuning surface diffusion and adatom kinetics on graphene, which are crucial for navigating the competition between remote epitaxy and defect-seeded mechanisms like pinhole epitaxy. In light of this weak remote potential, we re-evaluate the current state-of-the-art experimental evidence, highlighting why it remains challenging to experimentally validate a ‘remote’ epitaxy mechanism that cannot be explained by alternatives, such as pinhole-seeded epitaxy or serial van der Waals epitaxy. We end with one experimental example that, to out knowledge, cannot be explained by competing mechanisms: a different long-range epitaxial relationship for GdPtSb films grown on graphene/sapphire, compared to direct epitaxy on sapphire. We suggest for future experiments that directly measure the remote potential and impact of tuneable growth kinetics.

epitaxy↗
DOE OSTI2021

Half-life of 67 Cu

The half-life of 67 Cu was determined through serial gamma-ray spectrometry measurements of the dominant gamma emission (E γ : 184.6 keV; branching ratio: 48.7%) produced following β- decay. Data were collected consecutively for 1000 s per measurement, with a total of 3063 measurements over the duration of 36 days. The incidence rate for the 184.6 keV gamma-ray was determined from the spectral peak area and duration of each measurement. This rate was then corrected to account for detector dead-time, radioactive decay during each acquisition and drift in the computer clock in comparison to NIST nuclear clock. Least-squares regression analysis was performed to determine the half-life of 67 Cu. The result was 61.761 ± 0.004 h, which is the highest precision measurement to date, and marks a 24-fold precision improvement over the current Nuclear Data Sheets value.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Fluorescent and Bioluminescent Reporter Mouse-Adapted Ebola Viruses Maintain Pathogenicity and Can Be Visualized in Vivo

Abstract Ebola virus (EBOV) causes lethal disease in humans but not in mice. Here, we generated recombinant mouse-adapted (MA) EBOVs, including 1 based on the previously reported serially adapted strain (rMA-EBOV), along with single-reporter rMA-EBOVs expressing either fluorescent (ZsGreen1 [ZsG]) or bioluminescent (nano-luciferase [nLuc]) reporters, and dual-reporter rMA-EBOVs expressing both ZsG and nLuc. No detriment to viral growth in vitro was seen with inclusion of MA-associated mutations or reporter proteins. In CD-1 mice, infection with MA-EBOV, rMA-EBOV, and single-reporter rMA-EBOVs conferred 100% lethality; infection with dual-reporter rMA-EBOV resulted in 73% lethality. Bioluminescent signal from rMA-EBOV expressing nLuc was detected in vivo and ex vivo using the IVIS Spectrum CT. Fluorescent signal from rMA-EBOV expressing ZsG was detected in situ using handheld blue-light transillumination and ex vivo through epi-illumination with the IVIS Spectrum CT. These data support the use of reporter MA-EBOV for studies of Ebola virus in animal disease models.

Immunology↗
DOE OSTI2018

GALARIO: a GPU accelerated library for analysing radio interferometer observations

We present GALARIO, a computational library that exploits the power of modern graphical processing units (GPUs) to accelerate the analysis of observations from radio interferometers like Atacama Large Millimeter and sub-millimeter Array or the Karl G. Jansky Very Large Array. GALARIO speeds up the computation of synthetic visibilities from a generic 2D model image or a radial brightness profile (for axisymmetric sources). On a GPU, GALARIO is 150 faster than standard PYTHON and 10 times faster than serial C++ code on a CPU. Highly modular, easy to use, and to adopt in existing code, GALARIO comes as two compiled libraries, one for Nvidia GPUs and one for multicore CPUs, where both have the same functions with identical interfaces. GALARIO comes with PYTHON bindings but can also be directly used in C or C++. The versatility and the speed of GALARIO open new analysis pathways that otherwise would be prohibitively time consuming, e.g. fitting high-resolution observations of large number of objects, or entire spectral cubes of molecular gas emission. It is a general tool that can be applied to any field that uses radio interferometer observations. The source code is available online at http://github.com/mtazzari/galario under the open source GNU Lesser General Public License v3.

Astronomy & Astrophysics↗
DOE OSTI2017

Phylodynamic Inference across Epidemic Scales

Within-host genetic diversity and large transmission bottlenecks confound phylodynamic inference of epidemiological dynamics. Conventional phylodynamic approaches assume that nodes in a time-scaled pathogen phylogeny correspond closely to the time of transmission between hosts that are ancestral to the sample. However, when hosts harbor diverse pathogen populations, node times can substantially pre-date infection times. Imperfect bottlenecks can cause lineages sampled in different individuals to coalesce in unexpected patterns. To address realistic violations of standard phylodynamic assumptions we developed a new inference approach based on a multi-scale coalescent model, accounting for nonlinear epidemiological dynamics, heterogeneous sampling through time, non-negligible genetic diversity of pathogens within hosts, and imperfect transmission bottlenecks. We apply this method to HIV-1 and Ebola virus (EBOV) outbreak sequence data, illustrating how and when conventional phylodynamic inference may give misleading results. Within-host diversity of HIV-1 causes substantial upwards bias in the number of infected hosts using conventional coalescent models, but estimates using the multi-scale model have greater consistency with reported number of diagnoses through time. In contrast, we find that within-host diversity of EBOV has little influence on estimated numbers of infected hosts or reproduction numbers, and estimates are highly consistent with the reported number of diagnoses through time. The multi-scale coalescent also enables estimation of within-host effective population size using single sequences from a random sample of patients. We find within-host population genetic diversity of HIV-1 p17 to be 2Nμ=0.012 (95% CI 0.0066–0.023), which is lower than estimates based on HIV envelope serial sequencing of individual patients.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs

Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Deciphering the altered conformational states of bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus

Abstract The thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle represents one of the most efficient mechanisms for CO2 fixation discovered to date. Within this cycle, the enzyme encoded by Nmar_1308 from Nitrosopumilus maritimus SCM1 plays a crucial role due to its dual functionality as both a crotonyl-CoA hydratase (CCAH) and a 3-hydroxypropionyl-CoA dehydratase (3HPD). Although the importance of a bifunctional enzyme for lowering the cost of biosynthesis, the details of structural dynamics are still missing. Here, in addition to our cryogenic temperature structures, we determined the first ambient temperature structures of the Nmar_1308 protein by Serial Femtosecond X-ray Crystallography (SFX). The determined structures capture previously unobserved conformational dynamics of the Nmar_1308 protein, providing invaluable information for future synthetic biology applications.

Destan, Ebru (ORCID:0000000231290827)↗
DOE OSTI2022

Size Effect of Local Current-Voltage Characteristics of MX 2 Nanoflakes: Local Density of States Reconstruction from Scanning Tunneling Microscopy Experiments

Local current-voltage characteristics for low-dimensional transition-metal dichalcogenides (LDTMD), as well as the reconstruction of their local density of states (LDOS) from scanning tunneling microscopy (STM) experiments, are of fundamental interest and can be useful for advanced applications. Most of the existing models either have limited applicability for complex-shaped LDTMDs (e.g., those based on the Simmons approach) or require solving of an ill-defined integral equation to deconvolute the unknown LDOS (e.g., those based on the Tersoff approach). Using a serial expansion of the Tersoff formulas, we propose a flexible method to reconstruct the LDOS from local current-voltage characteristics measured in STM experiments. We establish a set of key physical parameters, which characterize the tunneling current of a STM-probe–sample contact and the sample LDOS expanded in Gaussian functions. Using a direct variational method coupled with probabilistic analysis, we determine these parameters from the STM experiments for MoS2 nanoflakes with different numbers of layers. The main result is the reconstruction of the LDOS in a relatively wide energy range around the Fermi level, which allows us to gain insight into the local band structure of LDTMDs. The reconstructed LDOS reveal pronounced size effects for the single-layer, two-layer, and three-layer MoS 2 nanoflakes, which we relate to the low dimensionality and strong bending or corrugation of the nanoflakes. We hope that the proposed elaboration of the Tersoff approach, allowing LDOS reconstruction, will be of critical interest for the quantitative description of STM experiments and also of use to better understand the microscopic physical aspects of the surface, strain, and bending contributions to the LDTMDs’ electronic properties.

42 ENGINEERING↗
DOE OSTI2022

Asymptotic optimality of twist-untwist protocols for Heisenberg scaling in atom-based sensing

Twist-untwist protocols for quantum metrology consist of a serial application of (1) unitary nonlinear dynamics (e.g., spin squeezing or Kerr nonlinearity), (2) parameterized dynamics U ( φ ) (e.g., a collective rotation or phase space displacement), and (3) time reversed application of step 1. Such protocols are known to produce states that allow Heisenberg scaling for experimentally accessible estimators of φ even when the nonlinearities are applied for times much shorter than required to produce Schrödinger cat states. In this work, we prove that, asymptotically in the number of particles, twist-untwist protocols provide the lowest estimation error among quantum metrology protocols that utilize two calls to a weakly nonlinear evolution and a readout involving only first and second moments of a total spin operator n → · J → . We consider the following physical settings: all-to-all interactions generated by one-axis twisting J z 2 (e.g., interacting Bose gases), constant finite range spin-spin interactions of distinguishable or bosonic atoms (e.g., trapped ions or Rydberg atoms, or lattice bosons). In these settings, we further show that the optimal twist-untwist protocols asymptotically achieve 85% and 92% of the respective quantum Cramér-Rao bounds. We show that the error of a twist-untwist protocol can be decreased by a factor of L without an increase in the noise of the spin measurement if the twist-untwist protocol can be noiselessly iterated as an L layer quantum alternating operator ansatz.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

In vacuo X-ray data collection from graphene-wrapped protein crystals

A method is reported for collecting room-temperature data from protein crystals under vacuum by protecting them with a thin graphene layer. The measurement of diffraction data from macromolecular crystal samples held in vacuo holds the promise of a very low X-ray background and zero absorption of incident and scattered beams, leading to better data and the potential for accessing very long X-ray wavelengths (>3 Å) for native sulfur phasing. Maintaining the hydration of protein crystals under vacuum is achieved by the use of liquid jets, as with serial data collection at free-electron lasers, or is side-stepped by cryocooling the samples, as implemented at new synchrotron beamlines. Graphene has been shown to protect crystals from dehydration by creating an extremely thin layer that is impermeable to any exchanges with the environment. Furthermore, owing to its hydrophobicity, most of the aqueous solution surrounding the crystal is excluded during sample preparation, thus eliminating most of the background caused by liquid. Here, it is shown that high-quality data can be recorded at room temperature from graphene-wrapped protein crystals in a rough vacuum. Furthermore, it was observed that graphene protects crystals exposed to different relative humidities and a chemically harsh environment.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

IOTA : integration optimization, triage and analysis tool for the processing of XFEL diffraction images

Serial femtosecond crystallography (SFX) uses an X-ray free-electron laser to extract diffraction data from crystals not amenable to conventional X-ray light sources owing to their small size or radiation sensitivity. However, a limitation of SFX is the high variability of the diffraction images that are obtained. As a result, it is often difficult to determine optimal indexing and integration parameters for the individual diffraction images. Presented here is a software package, called IOTA , which uses a grid-search technique to determine optimal spot-finding parameters that can in turn affect the success of indexing and the quality of integration on an image-by-image basis. Integration results can be filtered using a priori information about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.

Chemistry↗