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DOE OSTI2012

A spectrum slicing method for the Kohn–Sham problem

Solving the Kohn–Sham equation, which arises in density functional theory, is a standard procedure to determine the electronic structure of atoms, molecules, and condensed matter systems. The solution of this nonlinear eigenproblem is used to predict the spatial and energetic distribution of electronic states. However, obtaining a solution for large systems is computationally intensive because the problem scales super-linearly with the number of atoms. Here we demonstrate a divide and conquer method that partitions the necessary eigenvalue spectrum into slices and computes each partial spectrum on an independent group of processors in parallel. We focus on the elements of the spectrum slicing method that are essential to its correctness and robustness such as the choice of filter polynomial, the stopping criterion for a vector iteration, and the detection of duplicate eigenpairs computed in adjacent spectral slices. Some of the more prominent aspects of developing an optimized implementation are discussed.

Computer Science↗

DOE OSTI2014

Applicability of rat precision-cut lung slices in evaluating nanomaterial cytotoxicity, apoptosis, oxidative stress, and inflammation

The applicability of rat precision-cut lung slices (PCLuS) in detecting nanomaterial (NM) toxicity to the respiratory tract was investigated evaluating sixteen OECD reference NMs (TiO{sub 2}, ZnO, CeO{sub 2}, SiO{sub 2}, Ag, multi-walled carbon nanotubes (MWCNTs)). Upon 24-hour test substance exposure, the PCLuS system was able to detect early events of NM toxicity: total protein, reduction in mitochondrial activity, caspase-3/-7 activation, glutathione depletion/increase, cytokine induction, and histopathological evaluation. Ion shedding NMS (ZnO and Ag) induced severe tissue destruction detected by the loss of total protein. Two anatase TiO{sub 2} NMs, CeO{sub 2} NMs, and two MWCNT caused significant (determined by trend analysis) cytotoxicity in the WST-1 assay. At non-cytotoxic concentrations, different TiO{sub 2} NMs and one MWCNT increased GSH levels, presumably a defense response to reactive oxygen species, and these substances further induced a variety of cytokines. One of the SiO{sub 2} NMs increased caspase-3/-7 activities at non-cytotoxic levels, and one rutile TiO{sub 2} only induced cytokines. Investigating these effects is, however, not sufficient to predict apical effects found in vivo. Reproducibility of test substance measurements was not fully satisfactory, especially in the GSH and cytokine assays. Effects were frequently observed in negative controls pointing to tissue slice vulnerability even though prepared and handled with utmost care. Comparisons of the effects observed in the PCLuS to in vivo effects reveal some concordances for the metal oxide NMs, but less so for the MWCNT. The highest effective dosages, however, exceeded those reported for rat short-term inhalation studies. To become applicable for NM testing, the PCLuS system requires test protocol optimization. - Highlights: • 16 OECD reference nanomaterials were tested in rat precision-cut lung slices. • Nanomaterial cytotoxicity, apoptose, oxidative stress, and inflammation were detected. • Investigating these early effects is not sufficient to predict in vivo outcome. • Reproducibility was not fully satisfactory in the glutathione and cytokine assays. • Further work is required to adjust effective dosages in vitro to in vivo doses.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Fresh-slice multicolour X-ray free-electron lasers

X-ray free-electron lasers (XFELs) provide femtosecond X-ray pulses with a narrow energy bandwidth and unprecedented brightness. Ultrafast physical and chemical dynamics, initiated with a site-specific X-ray pulse, can be explored using XFELs with a second ultrashort X-ray probe pulse. However, existing double-pulse schemes are complicated, difficult to customize or provide only low-intensity pulses. Here we present the novel fresh-slice technique for multicolour pulse production, wherein different temporal slices of an electron bunch lase to saturation in separate undulator sections. This method combines electron bunch tailoring from a passive wakefield device with trajectory control to provide multicolour pulses. The fresh-slice scheme outperforms existing techniques at soft X-ray wavelengths. It produces femtosecond pulses with a power of tens of gigawatts and flexible colour separation. The pulse delay can be varied from temporal overlap to almost one picosecond. As a result, we also demonstrate the first three-colour XFEL and variably polarized two-colour pulses.

43 PARTICLE ACCELERATORS↗

DOE OSTI2013

Improved sliced velocity map imaging apparatus optimized for H photofragments

Time-sliced velocity map imaging (SVMI), a high-resolution method for measuring kinetic energy distributions of products in scattering and photodissociation reactions, is challenging to implement for atomic hydrogen products. We describe an ion optics design aimed at achieving SVMI of H fragments in a broad range of kinetic energies (KE), from a fraction of an electronvolt to a few electronvolts. In order to enable consistently thin slicing for any imaged KE range, an additional electrostatic lens is introduced in the drift region for radial magnification control without affecting temporal stretching of the ion cloud. Time slices of {approx}5 ns out of a cloud stretched to Greater-Than-Or-Slanted-Equal-To 50 ns are used. An accelerator region with variable dimensions (using multiple electrodes) is employed for better optimization of radial and temporal space focusing characteristics at each magnification level. The implemented system was successfully tested by recording images of H fragments from the photodissociation of HBr, H{sub 2}S, and the CH{sub 2}OH radical, with kinetic energies ranging from <0.4 eV to >3 eV. It demonstrated KE resolution Less-Than-Or-Equivalent-To 1%-2%, similar to that obtained in traditional velocity map imaging followed by reconstruction, and to KE resolution achieved previously in SVMI of heavier products. We expect it to perform just as well up to at least 6 eV of kinetic energy. The tests showed that numerical simulations of the electric fields and ion trajectories in the system, used for optimization of the design and operating parameters, provide an accurate and reliable description of all aspects of system performance. This offers the advantage of selecting the best operating conditions in each measurement without the need for additional calibration experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Multi-slice electron ptychographic tomography for three-dimensional phase-contrast microscopy beyond the depth of focus limits

Electron ptychography is a powerful computational method for atomic-resolution imaging with high contrast for weakly and strongly scattering elements. Modern algorithms coupled with fast and efficient detectors allow imaging specimens with tens of nanometers thicknesses with sub-0.5 Ångstrom lateral resolution. However, the axial resolution in these approaches is currently limited to a few nanometers, limiting their ability to solve novel atomic structures ab initio. Here, we experimentally demonstrate multi-slice ptychographic electron tomography, which allows atomic resolution three-dimensional phase-contrast imaging in a volume surpassing the depth of field limits. We reconstruct tilt-series 4D-STEM measurements of a $\mathrm{Co_3O_4}$ nanocube, yielding 2 Å axial and 0.7 Å transverse resolution in a reconstructed volume of $\mathrm{(18.2\,nm)^3}$. Our results demonstrate a 13.5-fold improvement in axial resolution compared to multi-slice ptychography while retaining the atomic lateral resolution and the capability to image volumes beyond the depth of field limit. Multi-slice ptychographic electron tomography significantly expands the volume of materials accessible using high-resolution electron microscopy. We discuss further experimental and algorithmic improvements necessary to also resolve single weakly scattering atoms in 3D.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Structure Slicing: Extending Logical Regions with Fields, In: SC '14: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis

Applications on modern supercomputers are increasingly limited by the cost of data movement, but mainstream programming systems have few abstractions for describing the structure of a program's data. Consequently, the burden of managing data movement, placement, and layout currently falls primarily upon the programmer. To address this problem we previously proposed a data model based on logical regions and described Legion, a programming system incorporating logical regions. In this paper, we present structure slicing, which incorporates fields into the logical region data model. We show that structure slicing enables Legion to automatically infer task parallelism from field non-interference, decouple the specification of data usage from layout, and reduce the overall amount of data moved. We demonstrate that structure slicing enables both strong and weak scaling of three Legion applications including S3D, a production combustion simulation that uses logical regions with thousands of fields, with speedups of up to 3.68X over a vectorized CPU-only Fortran implementation and 1.88X over an independently hand-tuned OpenACC code.

Computer Science↗

DOE OSTI2013

The effect of head size/shape, miscentering, and bowtie filter on peak patient tissue doses from modern brain perfusion 256-slice CT: How can we minimize the risk for deterministic effects?

Purpose: To determine patient-specific absorbed peak doses to skin, eye lens, brain parenchyma, and cranial red bone marrow (RBM) of adult individuals subjected to low-dose brain perfusion CT studies on a 256-slice CT scanner, and investigate the effect of patient head size/shape, head position during the examination and bowtie filter used on peak tissue doses. Methods: The peak doses to eye lens, skin, brain, and RBM were measured in 106 individual-specific adult head phantoms subjected to the standard low-dose brain perfusion CT on a 256-slice CT scanner using a novel Monte Carlo simulation software dedicated for patient CT dosimetry. Peak tissue doses were compared to corresponding thresholds for induction of cataract, erythema, cerebrovascular disease, and depression of hematopoiesis, respectively. The effects of patient head size/shape, head position during acquisition and bowtie filter used on resulting peak patient tissue doses were investigated. The effect of eye-lens position in the scanned head region was also investigated. The effect of miscentering and use of narrow bowtie filter on image quality was assessed. Results: The mean peak doses to eye lens, skin, brain, and RBM were found to be 124, 120, 95, and 163 mGy, respectively. The effect of patient head size and shape on peak tissue doses was found to be minimal since maximum differences were less than 7%. Patient head miscentering and bowtie filter selection were found to have a considerable effect on peak tissue doses. The peak eye-lens dose saving achieved by elevating head by 4 cm with respect to isocenter and using a narrow wedge filter was found to approach 50%. When the eye lies outside of the primarily irradiated head region, the dose to eye lens was found to drop to less than 20% of the corresponding dose measured when the eye lens was located in the middle of the x-ray beam. Positioning head phantom off-isocenter by 4 cm and employing a narrow wedge filter results in a moderate reduction of signal-to-noise ratio mainly to the peripheral region of the phantom. Conclusions: Despite typical peak doses to skin, eye lens, brain, and RBM from the standard low-dose brain perfusion 256-slice CT protocol are well below the corresponding thresholds for the induction of erythema, cataract, cerebrovascular disease, and depression of hematopoiesis, respectively, every effort should be made toward optimization of the procedure and minimization of dose received by these tissues. The current study provides evidence that the use of the narrower bowtie filter available may considerably reduce peak absorbed dose to all above radiosensitive tissues with minimal deterioration in image quality. Considerable reduction in peak eye-lens dose may also be achieved by positioning patient head center a few centimeters above isocenter during the exposure.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

BiG-SLiCE 2 v1.0.0

BiG-SLiCE was originally an open source Python-based command line bioinformatics software that offers a highly scalable clustering analysis on biosynthetic gene clusters (BGC) data. It allows a simultaneous analysis of millions of BGCs, exceeding the capability of other existing tools (around one hundred thousands). As a tradeoff, the clustering accuracy is relatively lower and sometimes fall short in corner cases and specific BGC classes such as the RiPPs (Ribosomally-translated, Post-translationally modified Peptides). In BiG-SLiCE V2 (developed in LBNL), the clustering algorithm has been significantly improved to deliver a much accurate result even for RiPPs and other previous corner case classes. Moreover, the speed of the overall pipeline has been improved by 50-100%. Finally, additional features were implemented to support downstream analyses of BiG-SLiCE results, such as customized tabular (TSV/CSV) and columnar (Parquet) outputs.

Kautsar, Satria↗

DOE OSTI2021

Evaluation of “Tight Oil” Well Performance and Completion Practices in the Powder River Basin - “Time Slice” Analysis

The objective of this paper is to assess how well completion practices and well performance have evolved over time (“time slices”) in the tight sands and shales of the Powder River Basin (PRB). This information can provide a foundation for helping operators define more effective well completion practices and thus optimize well performance in an emerging “tight oil” basin. To start, the authors assembled a “database” containing well completion practices, production data, and geologic information for more than 800 horizontal (Hz) wells targeting three “tight oil” formations -- Turner, Frontier, and Mowry--placed on production in the past dozen years. To control for the impact of geologic and reservoir properties on well performance, the authors defined 12 geologically distinct areas (“partitions”) for the Turner, Frontier, and Mowry Shale in the Powder River Basin (4 partitions in each formation). This paper discusses the methodology for establishing “time slices” for each partition within each of the three “tight oil” formations, including (1) taking out, to the extent practical, the effects of geology by partitioning the three “tight oil” formations based on their geologic parameters; (2) using type curves and estimated ultimate recoveries (EURs) to establish a reliable measure of well performance; and (3) rigorously inspecting the production and well completion data to assure a quality dataset. Partition #2, a high thermal maturity area of the Frontier Sandstone in the western Powder River Basin, helps illustrate the results of the study. Using a dataset of 55 Hz wells, the study found that well performance has steadily improved, with oil EURs increasing from 180 MBbl in 2012-13 to 290 MBbl in 2018-19. Much of this improvement was due to the use of longer Hz laterals, increasing notably from 3,765 ft in 2012-13 to 10,260 ft in 2018-19. More intensive completion practices contributed, as well. For example, the number of frac stages more than doubled, from 17 to 35, and proppant concentrations increased from 1,060 lbs/ft to 1,320 lbs/ft. Finally, the data show diminishing returns to longer laterals and more intensive completion practices. For example, the key performance measure of oil EUR per 1,000 ft of lateral is decreasing. For 2012-13, Hz wells recovered 50 MBbl of oil per 1,000 ft of lateral while the more recent 2018-19 Hz wells only provide 30 MBbl of oil per 1,000 ft of lateral. Considerable insight can be gained by using “time slices” and geologic partitioning to better understand the relationship between changes in well drilling and completion practices and changes in well performance in emerging “tight oil” plays. The results from this study can also serve as a foundation for subsequent, more intense efforts involving data analytics for defining more optimum well completion practices targeting specified geologic settings and formations.

02 PETROLEUM↗

DOE OSTI2019

Artifacts from manganese reduction in rock samples prepared by focused ion beam (FIB) slicing for X-ray microspectroscopy

The spatial distribution oftransition metal valence states is of broad interest in the microanalysis ofgeological and environmental samples. An example is rock varnish, a naturalmanganese (Mn)-rich rock coating, whose genesis mechanism remains a subjectof scientific debate. We conducted scanning transmission X-ray microscopywith near-edge X-ray absorption fine-structure spectroscopy (STXM-NEXAFS)measurements of the abundance and spatial distribution of different Mnoxidation states within the nano- to micrometer thick varnish crusts. Suchmicroanalytical measurements of thin and hard rock crusts require samplepreparation with minimal contamination risk. Focused ion beam (FIB) slicingwas used to obtain ~100–1000 nm thin wedge-shaped slices of thesamples for STXM, using standard parameters. Yet, while this preparationis suitable for investigating element distributions and structures in rocksamples, we observed artifactual modifications of the Mn oxidation states atthe surfaces of the FIB slices. Our results imply that the preparationcauses a reduction of Mn 4+ to Mn 2+ . We draw attention tothis issue, since FIB slicing, scanning electron microscopy (SEM) imaging,and other preparation and visualization techniques operating in thekilo-electron-volt range are well-established in geosciences, but researchersare often unaware of the potential for the reduction of Mn and possibly otherelements in the samples.

58 GEOSCIENCES↗

NASA NTRS1980

Method and apparatus for slicing crystals

The crystal slicing method is described as follows. A crystal is sliced in a plane parallel to flat, opposed parallel end faces of the crystal. The end faces of the crystal are gripped by a pair of opposed, perforated platens of a pair of vacuum chambers, one of which is translatable relative to the other. A blade cuts the crystal through the desired plane. A spring biases one of the vacuum chambers away from the other vacuum chamber while both of the faces are gripped by the vacuum chambers and the blade is cleaving the crystal. A sliced portion of the crystal gripped by one of the vacuum chambers is pulled away from the remainder of the crystal gripped by the second vacuum chamber when the crystal was cleaved by the blade through the plane.

Benedicto, J. S. J.↗

NASA NTRS1981

Economics of ingot slicing with an internal diameter saw for low-cost solar cells

Slicing of silicon ingots using diamond impregnated internal diameter blade saws has been a standard technology of the semiconductor industry. This paper describes work on improvements to this technology for 10 cm diameter ingot slicing. Ingot rotation, dynamic blade edge control with feedback, mechanized blade dressing and development of thinner blades are the approaches tried. A comparison of the results for wafering with and without ingot rotation is also made. A sensitivity analysis of the major cost elements in wafering is performed for 10 cm diameter ingot and extended to the 15 cm diameter ingot case. Various parameter values such as machine cost, feed rate and consumable materials cost are identified both for single and multiple ingot slicing.

Daud, T.↗

NASA NTRS1989

The luminosity function for the CfA redshift survey slices

The luminosity function for two complete slices of the extension of the CfA redshift survey is calculated. The nonparametric technique of Lynden-Bell (1971) and Turner (1979) is used to determine the shape for the luminosity function of the 12 deg slice of the redshift survey. The amplitude of the luminosity function is determined, taking large-scale inhomogeneities into account. The effects of the Malmquist bias on a magnitude-limited redshift survey are examined, showing that the random errors in the magnitudes for the 12 deg slice affect both the determination of the luminosity function and the spatial density constrast of large scale structures.

De Lapparent, Valerie↗

NASA NTRS1993

The theory of interface slicing

Interface slicing is a new tool which was developed to facilitate reuse-based software engineering, by addressing the following problems, needs, and issues: (1) size of systems incorporating reused modules; (2) knowledge requirements for program modification; (3) program understanding for reverse engineering; (4) module granularity and domain management; and (5) time and space complexity of conventional slicing. The definition of a form of static program analysis called interface slicing is addressed.

Beck, Jon↗

NASA NTRS2000

Tropospheric Ozone Profile Information Derived From "Cloud Slicing"

This study introduces a new approach to obtain ozone vertical profile information given coincident satellite measurements of both cloud-top pressure and above-cloud column ozone. This method is denoted "cloud slicing". In this study information of cloud-top pressure is derived from Geostationary Orbital Earth Satellite (GOES) infrared data, while above-cloud column ozone is obtained from the Earth Probe total ozone mapping spectrometer (TOMS) instrument. Several case examples are presented showing the feasibility of this technique as well as providing new geophysical results. Because the TOMS instrument measures backscattered UV radiation, it does detect ozone lying below dense water vapor clouds. This opaque property of TOMS can be used directly in conjunction with co-located cloud-top pressure data to derive ozone profile information in the troposphere. The cloud slicing method is an extension of the "Convective Cloud Differential" (CCD) method. In the CCD method, tropospheric column ozone (i.e., the total vertical column of ozone lying in the troposphere) is computed by taking total column ozone with low reflectivity (R less than 0.2) and subtracting from this a nearby measurement of above-cloud column ozone amount under conditions of high reflectivity (R greater than 0.9). (High reflectivity away from snow/ice conditions coincides with strong convection and tropopause-level clouds). The key element in determining tropospheric ozone profile information from the cloud slicing method is to have simultaneous and co-located measurements of both above-cloud column ozone and cloud-top pressure.

Ziemke, Jerald R.↗

NASA NTRS1987

Thermal dependence of neural activity in the hamster hippocampal slice preparation

1. Neural activity was recorded in an in vitro hamster hippocampal slice preparation while the temperature of the Ringer's solution bathing in the slice was controlled at selected levels. 2. The amplitude of the population spike (action potentials from a group of pyramidal cells) was measured as bath temperature was lowered from 35 degrees C to temperatures where a response could not be evoked. 3. Plots of population spike amplitude versus temperature have bell-shaped curves. The population spikes increased in amplitude as temperature was lowered from 35 degrees C, reached a peak amplitude between 25 and 20 degrees C, and then decreased until a response could not be evoked when temperature was further lowered. 4. These in vitro results obtained in the slice preparation are related to in vivo hippocampal studies. Results are interpreted as consistent with the proposal reviewed here that neural activity in the hippocampus plays a role at specific stages of entrance into and arousal from hibernation.

Non-NASA Center↗

NASA NTRS2010

Slice-Based Formal Specification Measures -- Mapping Coupling and Cohesion Measures to Formal Z

This paper demonstrates that existing slice-based measures can reasonably be mapped to the field of state-based specification languages. By making use of Z specifications this contribution renews the idea of slice-profiles and derives coupling and cohesion measures for them. The measures are then assessed by taking a critical look at their sensitiveness in respect to modifications on the specification source. The presented study shows that slice-based coupling and cohesion measures have the potential to be used as quality indicators for specifications as they reflect the changes in the structure of a specification as accustomed from their program-related pendants.

Bollin, Andreas↗

NASA NTRS2013

Software Method for Computed Tomography Cylinder Data Unwrapping, Re-slicing, and Analysis

A software method has been developed that is applicable for analyzing cylindrical and partially cylindrical objects inspected using computed tomography (CT). This method involves unwrapping and re-slicing data so that the CT data from the cylindrical object can be viewed as a series of 2D sheets (or flattened onion skins ) in addition to a series of top view slices and 3D volume rendering. The advantages of viewing the data in this fashion are as follows: (1) the use of standard and specialized image processing and analysis methods is facilitated having 2D array data versus a volume rendering; (2) accurate lateral dimensional analysis of flaws is possible in the unwrapped sheets versus volume rendering; (3) flaws in the part jump out at the inspector with the proper contrast expansion settings in the unwrapped sheets; and (4) it is much easier for the inspector to locate flaws in the unwrapped sheets versus top view slices for very thin cylinders. The method is fully automated and requires no input from the user except proper voxel dimension from the CT experiment and wall thickness of the part. The software is available in 32-bit and 64-bit versions, and can be used with binary data (8- and 16-bit) and BMP type CT image sets. The software has memory (RAM) and hard-drive based modes. The advantage of the (64-bit) RAM-based mode is speed (and is very practical for users of 64-bit Windows operating systems and computers having 16 GB or more RAM). The advantage of the hard-drive based analysis is one can work with essentially unlimited-sized data sets. Separate windows are spawned for the unwrapped/re-sliced data view and any image processing interactive capability. Individual unwrapped images and un -wrapped image series can be saved in common image formats. More information is available at http://www.grc.nasa.gov/WWW/OptInstr/ NDE_CT_CylinderUnwrapper.html.

Roth, Don J.↗