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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 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data Movement Categories

We have endeavored to classify the commonly seen data movement needs, as observed in data-intensive institutions (both commercial and non-profit), into four categories. Knowing how to map a data movement task into one of the four categories helps select proper data mover tools. For each category, how the data storage is involved, high-level examples and the nature of typical solutions are described. Finally, some general remarks are provided to help further orient readers new to this field - the 4th IT pillar.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2020

Variable Precision Computing (VPC) (Final Report)

The overall goal of the Variable Precision Computing project is exploring and identifying ways to reduce internodal communication cost in production physics simulation experiments running on a distributed-memory systems by compressing data, either in a lossy or lossless way, thus resulting in a significant computational performance increase. Among the several approaches proposed, the one discussed here has been proposed, designed and implemented by me. It concerns the application of information theory-derived metrics to classical molecular dynamics and computational fluid dynamics simulation experiments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Characterization of Tri-lab β-Tin (Sn)

This report documents details of the microstructure and mechanical properties of -tin (Sn), that is used in the Tri-lab (Los Alamos National Laboratory (LANL), Lawrence Livermore National Laboratory (LLNL), Sandia National Laboratories (SNL)) collaboration project on Multi-phase Tin Strength. We report microstructural features detailing the crystallographic texture and grain morphology of as-received -tin from electron back scatter diffraction (EBSD). Temperature and strain rate dependent mechanical behavior was investigated by multiple compression tests at temperatures of 200K to 400K and strain rates of 0.0001 /s to 100 /s. Tri-lab tin showed significant temperature and strain rate dependent strength with no significant plastic anisotropy. A sample to sample material variation was observed from duplicate compression tests and texture measurements. Compression data was used to calibrate model parameters for temperature and rate dependent strength models, Johnson-Cook (JC), Zerilli-Armstrong (ZA) and Preston-Tonks-Wallace (PTW) strength models.

36 MATERIALS SCIENCE↗
DOE OSTI2023

New Sesame Equations of State for Polypropylene, Polyvinylchloride (PVC), and Nylon 66

I built new Sesame equations of state (EOS) for polypropylene (PP), polyvinylchloride (PVC), and nylon 66. PP has the same stoichiometry as polyethylene and TPX but with a density intermediate between the two. Nylon is a polyamide manufactured chiefly in the form of fibers. PP and PVC are the second- and third-most widely produced polymers in the world. All three are thermoplastics. Their monomer units are depicted in Figure 1. I discuss the theory on which the EOS are based in the following section, then compare results to thermal and shock compression data in Section III.

36 MATERIALS SCIENCE↗
DOE OSTI2024

LLNL FESP Theory Highlights: October 2024

I. Novikau, I. Y. Dodin, E. A. Startsev, I. Joseph, Quantum algorithms for simulating dissipative linear and nonlinear dynamics of plasmas. Invited talk at the 66th Annual Meeting of the APS Division of Plasma Physics, Atlanta, Georgia. Novikau I., Dodin I.Y., Startsev E.A., Encoding of linear kinetic plasma problems in quantum circuits via data compression, Journal of Plasma Physics. 2024;90(4):805900401, doi:10.1017/S0022377824000795. We propose an algorithm for encoding linear kinetic plasma problems in quantum circuits. The focus is on modelling electrostatic linear waves in a one-dimensional Maxwellian electron plasma. The waves are described by the linearized Vlasov–Ampère system with a spatially localized external current that drives plasma oscillations. This system is formulated as a boundary-value problem and cast in the form of a linear vector equation to be solved by using the quantum signal processing algorithm. The latter requires encoding of a matrix in a quantum circuit as a sub-block of a unitary matrix. We propose how to encode in a circuit in a compressed form and discuss how the resulting circuit scales with the problem size and the desired precision.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Control of Weld Residual Stress in a Thin Steel Plate through Low Transformation Temperature Welding Consumables

Low transformation temperature welding (LTTW) consumables are characterized by a low martensite start temperature and a large fraction of martensite forming in the weld. It can efficiently reduce the tensile residual stress because the volume expansion associated with the martensitic transformation compensates for the thermal contraction during cooling. In this work, a LTTW wire, designated as EH200B, was created for the arc welding of advanced high-strength steel thin plates. In comparison to conventional ER70S-3 wires, this LTTW wire generated an opposite distortion pattern. Neutron diffraction measurements along the center thickness of the welded plates showed the maximum residual stress along the longitudinal direction (LD) in the weld region, and the heat-affected zone (HAZ) immediately adjacent to the weld region was reduced from ~330 MPa to below 240 MPa by using the LTTW wire. A finite element (FE) model was developed to predict the residual stress distributions of the plates welded under these two wires. The simulation results showed reasonable agreement with the volume-average neutron diffraction data. Compressive residual stress in the weld region using the LTTW wire was predicted by the FE method. Electron backscattered diffraction and x-ray diffraction measurements confirmed ~90% martensite was present in the LTTW weld. The fatigue life of DP980 steel lap joint panels using EH200B wire nearly doubled that of ER70S-3 wire. This improvement was attributed to the high strength and low LD residual stress in the weld and HAZ immediately adjacent to the weld.

36 MATERIALS SCIENCE↗
NASA NTRS1969

Improved first order interpolator

Data compression method enables first order interpolator to operate at higher speeds. Method requires same number of additions and subtractions but fewer multiplications than the conventional method.

Andrews, C. A.↗
NASA NTRS1969

Maximum RMS error comparison of several redundancy techniques

Paper presents mathematical comparison of several techniques with the limiting slope technique for data reduction and reconstruction. Limiting slope method results in maximum possible RMS error versus data compression ratio advantage of 2-to-1 over step and fan methods and 3-to-1 over the two point projection method.

Breaux, J. N.↗