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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 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Exponential Runge-Kutta Parareal for non-diffusive equations

Parareal is a well-known parallel-in-time algorithm that combines a coarse and fine propagator within a parallel iteration. It allows for large-scale parallelism that leads to significantly reduced computational time compared to serial time-stepping methods. However, like many parallel-in-time methods it can fail to converge when applied to non-diffusive equations such as hyperbolic systems or dispersive nonlinear wave equations. Here, this paper explores the use of exponential integrators within the Parareal iteration. Exponential integrators are particularly interesting candidates for Parareal because of their ability to resolve fast-moving waves, even at the large stepsizes used by coarse propagators. This work begins with an introduction to exponential Parareal integrators followed by several motivating numerical experiments involving the nonlinear Schrödinger equation. These experiments are then analyzed using linear analysis that approximates the stability and convergence properties of the exponential Parareal iteration on nonlinear problems. The paper concludes with two additional numerical experiments involving the dispersive Kadomtsev-Petviashvili equation and the hyperbolic Vlasov-Poisson equation. These experiments demonstrate that exponential Parareal methods offer improved time-to-solution compared to serial exponential integrators when solving certain non-diffusive equations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Accurate modeling and reconstruction of three-dimensional percolating filamentary microstructures from two-dimensional micrographs via dilation-erosion method

Heterogeneous materials are ubiquitous in nature and synthetic situations and have a wide range of important engineering applications. Accurate modeling and reconstructing three-dimensional (3D) microstructure of topologically complex materials from limited morphological information such as a two-dimensional (2D) micrograph is crucial to the assessment and prediction of effective material properties and performance under extreme conditions. Here, we extend a recently developed dilation–erosion method and employ the Yeong–Torquato stochastic reconstruction procedure to model and generate 3D austenitic–ferritic cast duplex stainless steel microstructure containing percolating filamentary ferrite phase from 2D optical micrographs of the material sample. Specifically, the ferrite phase is dilated to produce a modified target 2D microstructure and the resulting 3D reconstruction is eroded to recover the percolating ferrite filaments. The dilation–erosion reconstruction is compared with the actual 3D microstructure, obtained from serial sectioning (polishing), as well as the standard stochastic reconstructions incorporating topological connectedness information. The fact that the former can achieve the same level of accuracy as the latter suggests that the dilation–erosion procedure is tantamount to incorporating appreciably more topological and geometrical information into the reconstruction while being much more computationally efficient. - Highlights: • Spatial correlation functions used to characterize filamentary ferrite phase • Clustering information assessed from 3D experimental structure via serial sectioning • Stochastic reconstruction used to generate 3D virtual structure 2D micrograph • Dilation–erosion method to improve accuracy of 3D reconstruction.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Comparison of three-dimensional morphologies of abnormally growing grains between Monte Carlo simulations and experiments of Fe-3% Si steel

Highlights: • Grains with sub-boundaries grew abnormally in the MC simulation with realistic grain boundary energy. • The experimental 3-D morphology of Goss grain was reconstructed from serially sectioned images. • 2-D sectioned microstructures of the MC simulation and experiment have highly irregular shape. • Both simulated and experimental 3-D morphologies of AGG have similar complicated shapes. - Abstract: Three-dimensional (3-D) Monte Carlo simulations of grain growth with sub-boundaries in the presence of precipitates were performed based on the distribution of realistic grain boundary energy data. The simulated grains with sub-boundaries grew abnormally. The simulated and experimental morphologies of the abnormally growing grains in Fe-3%Si steel were compared. The experimental 3-D morphology was reconstructed from serially sectioned images. Both the simulated and experimental 3-D morphologies of abnormally growing grains have highly irregular and complicated shapes whereas both the simulated and experimental 3-D morphologies of normally growing grains have relatively regular and simple shapes. Growth by wetting is responsible for the highly irregular shape of the experimental abnormally growing grains of Fe-3%Si steel as well as for the highly irregular shape of the simulated abnormally growing grains.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Mid-infrared emissions of Pr{sup 3+}-doped GeS{sub 2}–Ga{sub 2}S{sub 3}–CdI{sub 2} chalcohalide glasses

Graphical abstract: ∼4.6 μm mid-infrared fluorescence emission from Pr{sup 3+} in the sulfide glass is successfully observed at room temperature excited by a 2.01 μm Tm{sup 3+}:YAG ceramic laser system. - Highlights: • Serial Pr{sup 3+}-doped GeS{sub 2}–Ga{sub 2}S{sub 3}–CdI{sub 2} chalcohalide glasses were synthesized. • ∼4.6 μm mid-infrared fluorescence from Pr{sup 3+} was observed at room temperature. • The compositional dependence of luminescence properties was studied. • Radiative properties have been determined using the Judd–Ofelt theory. - Abstract: For elucidation of the glass composition’s influence on the spectroscopic properties in the chalcohalide system and the discovery of a new material for applications in mid-infrared fiber-lasers, a serial Pr{sup 3+}-doped (100 − x)(0.8GeS{sub 2}·0.2Ga{sub 2}S{sub 3})xCdI{sub 2} (x = 5, 10, 15 and 20) chalcohalide glasses were prepared. ∼4.6 μm mid-infrared fluorescence emission from Pr{sup 3+} in the sulfide glass is successfully observed at room temperature excited by a 2.01 μm Tm{sup 3+}:YAG ceramic laser system, and the effective line-width of fluorescence band is 106–227 nm. Intense compositional dependence of mid-infrared emissions is found. The radiative rates of Pr{sup 3+} ions in these glasses were calculated by using the Judd–Ofelt theory.

36 MATERIALS SCIENCE↗
DOE OSTI2025

gRASPA

GPU Monte Carlo Simulation Code with a taste of RASPA We present enhancements in Monte Carlo simulation speed and functionality within an open-source code, gRASPA, which uses graphical processing units (GPUs) to achieve significant performance improvements compared to serial, CPU implementations of Monte Carlo. The code supports a wide range of Monte Carlo simulations, including canonical ensemble (NVT), grand canonical, NVT Gibbs, Widom test particle insertions, and continuous-fractional component Monte Carlo. Implementation of grand canonical transition matrix Monte Carlo (GC-TMMC) and a novel feature to allow different moves for the different components of metal-organic framework (MOF) structures exemplify the capabilities of gRASPA for precise free energy calculations and enhanced adsorption studies, respectively. The introduction of a High-Throughput Computing (HTC) mode permits many Monte Carlo simulations on a single GPU device for accelerated materials discovery. The code can incorporate machine learning (ML) potentials. The open-source nature of gRASPA promotes reproducibility and openness in science, and users may add features to the code and optimize it for their own purposes. The code is written in CUDA/C++ and SYCL/C++ to support different GPU vendors. The gRASPA code is publicly available at https://github.com/snurr-group/gRASPA.

Li, Zhao [Purdue/Northwestern/Notre Dame Universit↗
DOE OSTI2020

High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States

Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O 2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. Furthermore, this study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source

High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

12 GeV detector technology at Jefferson Lab

The Thomas Jefferson National Accelerator Facility (JLab) is presently in the middle of an upgrade to increase the energy of its CW electron beam from 6 GeV to 12 GeV along with the addition of a fourth experimental hall. Driven both by necessity and availability, novel detectors and electronics modules have been used in the upgrade. One such sensor is the Silicon Photomultiplier (SiPM), specifically a Multi-Pixel Photon Counter (MPPC), which is an array of avalanche photodiode pixels operating in Geiger mode that are used to sense photons. The SiPMs replace conventional photomultiplier tubes and have several distinct advantages including the safe operation in a magnetic field and the lack of need for high voltage. Another key to 12 GeV success is advanced fast electronics. Jlab will use custom 250 MHz and 125 MHz 12-bit analog to digital converters (ADCs) and time to digital converters (TDCs) all of which take advantage of VME Switched Serial (VXS) bus with its GB/s high bandwidth readout capability. These new technologies will be used to readout drift chambers, calorimeters, spectrometers and other particle detectors at Jlab once the 12 GeV upgrade is complete. The largest experiment at Jlab utilizing these components is GlueX - an experiment in the newly constructed Hall D that will study the photoproduction of light mesons in the search for hybrid mesons. The performance of these components and their respective detectors will be presented.

43 PARTICLE ACCELERATORS↗
DOE OSTI2014

Multichannel low power time-to-digital converter card with 21 ps precision and full scale range up to 10 μs

We present a Time-to-Digital Converter (TDC) card with a compact form factor, suitable for multichannel timing instruments or for integration into more complex systems. The TDC Card provides 10 ps timing resolution over the whole measurement range, which is selectable from 160 ns up to 10 μs, reaching 21 ps rms precision, 1.25% LSB rms differential nonlinearity, up to 3 Mconversion/s with 400 mW power consumption. The I/O edge card connector provides timing data readout through either a parallel bus or a 100 MHz serial interface and further measurement information like input signal rate and valid conversion rate (typically useful for time-correlated single-photon counting application) through an independent serial link.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2014

Mode-space energy distribution in instability-driven plasma turbulence

Energy transfer to damped modes in gyrokinetic ion temperature gradient driven turbulence is studied to understand the transfer dynamics and find scaling representations for the heavily populated mode space. Proper orthogonal and linear eigenmode decompositions are introduced and examined to assess whether modes are well-resolved and what scales they encompass. It is observed that damped modes across a range of inhomogeneous scales receive energy simultaneously and directly from the unstable mode, constituting a form of parallel transfer, distinct from the serial mode-to-mode transfer of the wavenumber cascade of hydrodynamic turbulence. Controlling for modes that are well resolved and labeling the modes of the linear decomposition in order of damping rate, energy transfer in the mode space satisfies an equipartition of the energy dissipation rate, leading to a simple rule for the distribution of energy in the space of damped modes. Energy dissipation rate equipartition is the form that the canonical nonlinear invariance of energy transfer assumes in a dissipation range with parallel rather than serial transfer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Note: Design of a full photon-timing recorder down to 1-ns resolution for fluorescence fluctuation measurements

A photon timing recorder was realized in a field programmable gate array to capture all timing data of photons on multiple channels with down to a 1-ns resolution and to transfer all data to a host computer in real-time through universal serial bus with more than 10 M events/s transfer rate. The main concept is that photon time series can be regarded as a serial communication data stream. This recorder was successfully applied for simultaneous measurements of fluorescence fluctuation and lifetime of near-infrared dyes in solution. This design is not only limited to the fluorescence fluctuation measurement but also applicable to any kind of photon counting experiments in a nanosecond time range because of the simple and easily modifiable design.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Demonstration of femtosecond X-ray pump X-ray probe diffraction on protein crystals

The development of X-ray free-electron lasers (XFELs) has opened the possibility to investigate the ultrafast dynamics of biomacromolecules using X-ray diffraction. Whereas an increasing number of structures solved by means of serial femtosecond crystallography at XFELs is available, the effect of radiation damage on protein crystals during ultrafast exposures has remained an open question. We used a split-and-delay line based on diffractive X-ray optics at the Linac Coherent Light Source XFEL to investigate the time dependence of X-ray radiation damage to lysozyme crystals. For these tests, crystals were delivered to the X-ray beam using a fixed-target approach. The presented experiments provide probe signals at eight different delay times between 19 and 213 femtoseconds after a single pump event, thereby covering the time-scales relevant for femtosecond serial crystallography. Even though significant impact on the crystals was observed at long time scales after exposure with a single X-ray pulse, the collected diffraction data did not show significant signal reduction that could be assigned to beam damage on the crystals in the sampled time window and resolution range. This observation is in agreement with estimations of the applied radiation dose, which in our experiment was clearly below the values expected to cause damage on the femtosecond time scale. The experiments presented here demonstrate the feasibility of time-resolved pump-multiprobe X-ray diffraction experiments on protein crystals.

43 PARTICLE ACCELERATORS↗
DOE OSTI2013

Heterogeneous Seeding of a Prion Structure by a Generic Amyloid Form of the Fungal Prion-forming Domain HET-s(218-289)

The fungal prion-forming domain HET-s(218–289) forms infectious amyloid fibrils at physiological pH that were shown by solid-state NMR to be assemblies of a two-rung β-solenoid structure. Under acidic conditions, HET-s(218–289) has been shown to form amyloid fibrils that have very low infectivity in vivo, but structural information about these fibrils has been very limited. We show by x-ray fiber diffraction that the HET-s(218–289) fibrils formed under acidic conditions have a stacked β-sheet architecture commonly found in short amyloidogenic peptides and denatured protein aggregates. At physiological pH, stacked β-sheet fibrils nucleate the formation of the infectious β-solenoid prions in a process of heterogeneous seeding, but do so with kinetic profiles distinct from those of spontaneous or homogeneous (seeded with infectious β-solenoid fibrils) fibrillization. Several serial passages of stacked β-sheet-seeded solutions lead to fibrillization kinetics similar to homogeneously seeded solutions. Our results directly show that structural mutation can occur between substantially different amyloid architectures, lending credence to the suggestion that the processes of strain adaptation and crossing species barriers are facilitated by structural mutation.

Wan, William↗
DOE OSTI2024

Multi-amplifier Sensing Charge-coupled Devices for Next Generation Spectroscopy

We present characterization results and performance of a prototype Multiple-Amplifier Sensing (MAS) silicon charge-coupled device (CCD) sensor with 16 channels potentially suitable for faint object astronomical spectroscopy and low-signal, photon-limited imaging. The MAS CCD is designed to reach sub-electron readout noise by repeatedly measuring charge through a line of amplifiers during the serial transfer shifts. Using synchronized readout electronics based on the Dark Energy Spectroscopic Instrument CCD controller, we report a read noise of 1.03 e$^{−}$ rms pix$^{−1}$ at a speed of 26 μs pix$^{−1}$ with a single-sample readout scheme where charge in a pixel is measured only once for each output stage. At these operating parameters, we find the amplifier-to-amplifier charge transfer efficiency (ACTE) to be >0.9995 at low counts for all amplifiers but one for which the ACTE is 0.997. This charge transfer efficiency falls above 50,000 electrons for the read-noise optimized voltage configuration we chose for the serial clocks and gates. The amplifier linearity across a broad dynamic range from ∼300 to 35,000 e$^{−}$ was also measured to be ±2.5%. We describe key operating parameters to optimize on these characteristics and describe the specific applications for which the MAS CCD may be a suitable detector candidate.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

A 20 Gbps PAM4 data transmitter ASIC for particle physics experiments

We present the design and test results of a novel data transmitter ASIC operating up to 20.48 Gbps with 4-level Pulse-Amplitude-Modulation (PAM4) for particle physics experiments. This ASIC, named GBS20, is fabricated in a 65 nm CMOS technology. Two serializers share a 5.12 GHz Phase Locked Loop (PLL) clock. The outputs from the serializers are combined into a PAM4 signal that directly drives a Vertical-Cavity-Surface-Emitting-Laser (VCSEL). The input data channels, each at 1.28 Gbps, are scrambled with an internal 2$^{7}$-1 Pseudo-Random Binary Sequence (PRBS), which also serves as a frame aligner. GBS20 is tested to work at 10.24 and 20.48 Gbps with a VCSEL-based Transmitter-Optical-Subassembly (TOSA). The power consumption of GBS20 is below 238 mW and reduced to 164 mW in the low-power mode.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

A Logical Model of Homology for Comparative Biology

There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for the skeletal elements of vertebrate fins and limbs from the Phenoscape Knowledgebase. Using seven competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms (REA) homology model and the Ancestral Value Axioms (AVA) homology model. The AVA model returned all user-expected results in addition to the search term and any of its subclasses. The AVA model also returns any superclass of the query term in which a homology relationship has been asserted. The REA model returned the user-expected results for five out of seven queries. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Sendai virus intra-host population dynamics and host immunocompetence influence viral virulence during in vivo passage

In vivo serial passage of non-pathogenic viruses has been shown to lead to increased viral virulence, and although the precise mechanism(s) are not clear, it is known that both host and viral factors are associated with increased pathogenicity. Under- or overnutrition leads to a decreased or dysregulated immune response and can increase viral mutant spectrum diversity and virulence. The objective of this study was to identify the role of viral mutant spectra dynamics and host immunocompetence in the development of pathogenicity during in vivo passage. Because the nutritional status of the host has been shown to affect the development of viral virulence, the diet of animal model reflected two extremes of diets which exist in the global population, malnutrition and obesity. Sendai virus was serially passaged in groups of mice with differing nutritional status followed by transmission of the passaged virus to a second host species, guinea pigs. Viral population dynamics were characterized using deep sequence analysis and computational modeling. Histopathology, viral titer and cytokine assays were used to characterize viral virulence. Viral virulence increased with passage and the virulent phenotype persisted upon passage to a second host species. Additionally, nutritional status of mice during passage influenced the phenotype. Sequencing revealed the presence of several non-synonymous changes in the consensus sequence associated with passage, a majority of which occurred in the hemagglutinin-neuraminidase and polymerase genes, as well as the presence of persistent high frequency variants in the viral population. In particular, an N1124D change in the consensus sequences of the polymerase gene was detected by passage 10 in a majority of the animals. In vivo comparison of an 1124D plaque isolate to a clone with 1124N genotype indicated that 1124D was associated with increased virulence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Three-Dimensional Ultrastructure of Arabidopsis Cotyledons Infected with Colletotrichum higginsianum

We used serial block-face scanning electron microscopy (SBF-SEM) to study the host–pathogen interface between Arabidopsis cotyledons and the hemibiotrophic fungus Colletotrichum higginsianum. By combining high-pressure freezing and freeze-substitution with SBF-SEM, followed by segmentation and reconstruction of the imaging volume using the freely accessible software IMOD, we created 3D models of the series of cytological events that occur during the Colletotrichum–Arabidopsis susceptible interaction. We found that the host cell membranes underwent massive expansion to accommodate the rapidly growing intracellular hypha. As the fungal infection proceeded from the biotrophic to the necrotrophic stage, the host cell membranes went through increasing levels of disintegration culminating in host cell death. Intriguingly, we documented autophagosomes in proximity to biotrophic hyphae using transmission electron microscopy (TEM) and a concurrent increase in autophagic flux between early to mid/late biotrophic phase of the infection process. Occasionally, we observed osmiophilic bodies in the vicinity of biotrophic hyphae using TEM only and near necrotrophic hyphae under both TEM and SBF-SEM. Overall, we established a method for obtaining serial SBF-SEM images, each with a lateral ( x-y) pixel resolution of 10 nm and an axial ( z) resolution of 40 nm, that can be reconstructed into interactive 3D models using the IMOD. Application of this method to the Colletotrichum–Arabidopsis pathosystem allowed us to more fully understand the spatial arrangement and morphological architecture of the fungal hyphae after they penetrate epidermal cells of Arabidopsis cotyledons and the cytological changes the host cell undergoes as the infection progresses toward necrotrophy. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Biochemistry & Molecular Biology↗