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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Muon g-2 reconstruction and analysis framework for the muon anomalous precession frequency

The Muon g-2 experiment at Fermilab, with the aim to measure the muon anomalous magnetic moment to an unprecedented level of 140~ppb, has started beam and detector commissioning in Summer 2017. To deal with incoming data projected to be around tens of petabytes, a robust data reconstruction and analysis chain based on Fermilab's art event-processing framework is developed. Herein, I report the current status of the framework, together with its novel features such as multi-threaded algorithms for online data quality monitor (DQM) and fast-turnaround operation (nearline). Performance of the framework during the commissioning run is also discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
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 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 OSTI2020

amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool

Antimicrobial peptides (AMPs) are promising alternative antimicrobial agents. Currently, however, portable, user-friendly and efficient methods for predicting AMP sequences from genome-scale data are not readily available. In this work, we present amPEPpy, an open-source, multi-threaded command-line application for predicting AMP sequences using a random forest classifier.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

tSFM 1.0: tRNA Structure–Function Mapper

Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation P-values can quantify the significance of CIF divergences between two taxa, their naive Monte Carlo approximation is slow and inaccurate. The Peaks-over-Threshold approach of Knijnenburg et al. (2009) promises improvements to both speed and accuracy of permutation P-values, but has no publicly available API. Here, we present tRNA Structure–Function Mapper (tSFM) v1.0, an open-source, multi-threaded application that efficiently computes, visualizes and assesses significance of single- and paired-site CIFs and their evolutionary divergences for any RNA, protein, gene or genomic element sequence family. Multiple estimators of permutation P-values for CIF evolutionary divergences are provided along with confidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Linear complexity

We present factorization and solution phases for a new linear complexity direct solver designed for concurrent batch operations on fine-grained parallel architectures, for matrices amenable to hierarchical representation. We focus on the strong-admissibility-based $\mathscr{H}^{2}$ format, where strong recursive skeletonization factorization compresses remote interactions. We build upon previous implementations of $\mathscr{H}^{2}$ matrix construction for efficient factorization and solution algorithm design, which are illustrated graphically in stepwise detail. The algorithms are ‘blackbox’ in the sense that the only inputs are the matrix and right-hand side, without analytical or geometrical information about the origin of the system. We demonstrate linear complexity scaling in both time and memory on four representative families of dense matrices up to one million in size. Parallel scaling up to 16 threads is enabled by a multi-level matrix graph coloring and avoidance of dynamic memory allocations thanks to prefix-sum memory management. An experimental backward error analysis is included. We break down the timings of different phases, identify phases that are memory-bandwidth limited, and discuss alternatives for phases that may be sensitive to the trend to employ lower precisions for performance.

Boukaram, Wajih↗
DOE OSTI2023

Magnetorotational instability in a swirling partially ionized gas

ABSTRACT The magnetorotational instability (MRI) has been proposed as the method of angular momentum transport that enables accretion in astrophysical discs. However, for weakly ionized discs, such as protoplanetary discs, it remains unclear whether the combined non-ideal magnetohydrodynamic (MHD) effects of Ohmic resistivity, ambipolar diffusion, and the Hall effect make these discs MRI stable. While much effort has been made to simulate non-ideal MHD MRI, these simulations make simplifying assumptions and are not always in agreement with each other. Furthermore, it is difficult to directly observe the MRI astrophysically because it occurs on small scales. Here, we propose the concept of a swirling gas experiment of weakly ionized argon gas between two concentric cylinders threaded with an axial magnetic field that can be used to study non-ideal MHD MRI. For our proposed experiment, we derive the hydrodynamic equilibrium flow and a dispersion relation for MRI that includes the three non-ideal effects. We solve this dispersion relation numerically for the parameters of our proposed experiment. We find it should be possible to produce a non-ideal MRI in such an experiment because of the Hall effect, which increases the MRI growth rate when the vertical magnetic field is anti-aligned with the rotation axis. As a proof of concept, we also present experimental results for a hydrodynamic flow in an unmagnetized prototype. We find that our prototype has a small, but non-negligible, α-parameter that could serve as a baseline for comparison to our proposed magnetized experiment, which could be subject to additional turbulence from the MRI.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes

Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering method CUPP, Conserved Unique Peptide Patterns. CUPP operates synergistically with the CAZy family/subfamily categorizations to allow systematic exploration of CAZymes by defining small protein groups with shared sequence motifs. The updated CUPP library contains 21,930 of such motif groups including 3,842,628 proteins. The new implementation of the CUPP-webserver, https://cupp.info/, now includes all published fungal and algal genomes from the Joint Genome Institute (JGI), genome resources MycoCosm and PhycoCosm, dynamically subdivided into motif groups of CAZymes. This allows users to browse the JGI portals for specific predicted functions or specific protein families from genome sequences. Thus, a genome can be searched for proteins having specific characteristics. All JGI proteins have a hyperlink to a summary page which links to the predicted gene splicing including which regions have RNA support. The new CUPP implementation also includes an update of the annotation algorithm that uses only a fourth of the RAM while enabling multi-threading, providing an annotation speed below 1 ms/protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structural features underlying recognition and translocation of extracellular polysaccharides

Essentially all living systems produce complex carbohydrates as an energy source, structural component, protective coat or adhesive for cell attachment. Many polysaccharides are displayed on the cell surface or are threaded through proteinaceous tunnels for degradation. Dictated by their chemical composition and mode of polymerization, the physical properties of complex carbohydrates differ substantially, from amphipathic water-insoluble polymers to highly hydrated hydrogel-forming macromolecules. Accordingly, diverse recognition and translocation mechanisms evolved to transport polysaccharides to their final destinations. This review will summarize and compare diverse polysaccharide transport mechanisms implicated in the biosynthesis and degradation of cell surface polymers in pro- and eukaryotes.

biofuels (including algae and biomass), bio-inspir↗
DOE OSTI2025

Proposal for superconducting quantum networks using multioctave transduction to lower frequencies

We propose networking superconducting quantum circuits by transducing their excitations (typically 4–8 GHz) to 200–500 MHz photons for transmission via superconducting cryogenic coaxial cables. This frequency down-conversion reduces transmission losses and, counterintuitively, reduces noise. We introduce a multioctave asymmetrically threaded superconducting quantum interference device circuit capable of the required efficient, high-rate transduction. For a 100-meter cable with 𝑄 𝑖 = 10 5 at 10 mK, we theoretically show that our approach achieves single-photon fidelities of 0.962 at 200 MHz versus 0.772 at 8 GHz, and triples the lower bound on quantum channel capacity. In conclusion, this method enables highly efficient networking of superconducting qubits while maintaining high fidelities, combining improved performance with the practical advantages of flexible, compact coaxial cables.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Parallel general purpose multiobjective optimization framework with application to electron beam dynamics

Particle accelerators are invaluable tools for research in the basic and applied sciences, such as materials science, chemistry, the biosciences, particle physics, nuclear physics and medicine. The design, commissioning, and operation of accelerator facilities is a nontrivial task, due to the large number of control parameters and the complex interplay of several conflicting design goals. The Argonne Wakefield Accelerator facility has some unique challenges resulting from its purpose to carry out advanced accelerator R&D. Individual experiments often have challenging beam requirements, and the physical configuration of the beam lines is often changed to accommodate the variety of supported experiments. The need for rapid deployment of different operational settings further complicates the optimization work that must be done for multiple constraints and challenging operational regimes. One example of this is an independently staged two-beam acceleration experiment which requires the construction of an additional beam line (this is now in progress). The high charge drive beam, well into the space charge regime, must be threaded through small aperture (17.6 mm) decelerating structures. In addition, the bunch length must be sufficiently short to maximize power generation in the decelerator. We propose to tackle this problem by means of multiobjective optimization algorithms which also facilitate a parallel deployment. In order to compute solutions in a meaningful time frame, a fast and scalable software framework is required. In this paper, we present a general-purpose framework for simulation-based multiobjective optimization methods that allows the automatic investigation of optimal sets of machine parameters. Using evolutionary algorithms as the optimizer and opal as the forward solver, validation experiments and results of multiobjective optimization problems in the domain of beam dynamics are presented. Optimized solutions for the new high charge drive beam line found by the framework were used to finish the design of a two beam acceleration experiment. The selected solution along with the associated beam parameters is presented.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Dark magnetohydrodynamics: Black hole accretion in superradiant dark photon clouds

Black holes threaded by massive vector fields can be subject to a superradiant instability, growing a cloud of massive vector particles around it. In this work, we consider what happens if such a dark matter candidate field mimicking a dark photon interacts with an accretion flow onto the black hole. By including a kinetic mixing term with the standard model photon, we extend the commonly used equations of general-relativistic magnetohydrodynamics to a dark photon constituent. The coupling to the dark photon then appears as an effective dynamo term together with a dark Lorentz force acting on the accreting matter. We numerically study the interactions between the superradiant dark photon cloud and the inner accretion flow by solving the coupled system in full numerical relativity. By parameterically varying the mixing parameter between the dark and standard model sector, we provide a first investigation of how the accretion flow could be modified. In conclusion, depending on the coupling strength, our solutions exhibit increased wind launching, as well as oscillation modes in the disk.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Distinguishability of black hole microstates

We use the Holevo information to estimate distinguishability of microstates of a black hole in anti-de Sitter space by measurements one can perform on a subregion of a Cauchy surface of the dual conformal field theory. We find that microstates are not distinguishable at all until the subregion reaches a certain size and that perfect distinguishability can be achieved before the subregion covers the entire Cauchy surface. We will then compare our results with expectations from the entanglement wedge reconstruction, tensor network models, and the bit threads interpretation of the Ryu-Takayanagi formula.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Hofstadter Topology: Noncrystalline Topological Materials at High Flux

he Hofstadter problem is the lattice analog of the quantum Hall effect and is the paradigmatic example of topology induced by an applied magnetic field. Conventionally, the Hofstadter problem involves adding ~10 4 T magnetic fields to a trivial band structure. In this work, we show that when a magnetic field is added to an initially topological band structure, a wealth of possible phases emerges. Remarkably, we find topological phases that cannot be realized in any crystalline insulators. We prove that threading magnetic flux through a Hamiltonian with a nonzero Chern number or mirror Chern number enforces a phase transition at fixed filling and that a 2D Hamiltonian with a nontrivial Kane–Mele invariant can be classified as a 3D topological insulator (TI) or 3D weak TI phase in periodic flux. We then study fragile topology protected by the product of twofold rotation and time reversal and show that there exists a higher order TI phase where corner modes are pumped by flux. We show that a model of twisted bilayer graphene realizes this phase. Our results rely primarily on the magnetic translation group that exists at rational values of the flux. The advent of Moiré lattices renders our work relevant experimentally. Due to the enlarged Moiré unit cell, it is possible for laboratory-strength fields to reach one flux per plaquette and allow access to our proposed Hofstadter topological phase.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Measuring Topological Constraint Relaxation in Ring-Linear Polymer Blends

Polymers are an effective test bed for studying topological constraints in condensed matter due to a wide array of synthetically available chain topologies. When linear and ring polymers are blended together, emergent rheological properties are observed as the blend can be more viscous than either of the individual components. This emergent behavior arises since ring-linear blends can form long-lived topological constraints as the linear polymers thread the ring polymers. Here, in this work, we demonstrate how the Gauss linking integral can be used to efficiently evaluate the relaxation of topological constraints in ring-linear polymer blends. For majority-linear blends, the relaxation rate of topological constraints depends primarily on reptation of the linear polymers, resulting in the diffusive time τ d,R for rings of length N R blended with linear chains of length N l to scale as τ d,R ~ N$^2_R$N$^{3.4}_L$.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

High-pressure lithium as an elemental topological semimetal

Topological semimetals generally contain heavy elements. Using density-functional theoretic calculations, we predict that three dense lithium polymorphs in the pressure range 200–360 GPa display nontrivial semimetallic electronic structure. Specifically, these high-pressure phases exhibit Fermi pockets which are degenerate over a loop in k space, around which an encircling k-space path is threaded by ±π Berry phase. Accordingly, these dense lithium phases are topological nodal loop semimetals involving a single light element.

36 MATERIALS SCIENCE↗
DOE OSTI2023

TomocuPy – efficient GPU-based tomographic reconstruction with asynchronous data processing

Fast 3D data analysis and steering of a tomographic experiment by changing environmental conditions or acquisition parameters require fast, close to real-time, 3D reconstruction of large data volumes. Here a performance-optimized TomocuPy package is presented as a GPU alternative to the commonly used central processing unit (CPU) based TomoPy package for tomographic reconstruction. TomocuPy utilizes modern hardware capabilities to organize a 3D asynchronous reconstruction involving parallel read/write operations with storage drives, CPU–GPU data transfers, and GPU computations. In the asynchronous reconstruction, all the operations are timely overlapped to almost fully hide all data management time. Since most cameras work with less than 16-bit digital output, the memory usage and processing speed are furthermore optimized by using 16-bit floating-point arithmetic. As a result, 3D reconstruction with TomocuPy became 20–30 times faster than its multi-threaded CPU equivalent. Full reconstruction (including read/write operations and methods initialization) of a 2048 3 tomographic volume takes less than 7 s on a single Nvidia Tesla A100 and PCIe 4.0 NVMe SSD, and scales almost linearly increasing the data size. To simplify operation at synchrotron beamlines, TomocuPy provides an easy-to-use command-line interface. Efficacy of the package was demonstrated during a tomographic experiment on gas-hydrate formation in porous samples, where a steering option was implemented as a lens-changing mechanism for zooming to regions of interest.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗