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At least 487 records · Page 27

Comparison of numerical predictions with CO{sub 2} pipeline release datasets of relevance to carbon capture and storage applications

Predicting the correct multi-phase fluid flow behaviour during the discharge process in the near-field of sonic CO{sub 2} jets is of particular importance in assessing the risks associated with transport aspects of carbon capture and storage schemes, given the very different hazard profiles of CO{sub 2} in the gaseous and solid states. In this paper, we apply our state-of-the-art mathematical model implemented in an efficient computational method to available data. Compared to previous applications, an improved equation of state is used. We also compare to all the available data, rather than just subsets as previously, and demonstrate both the improved performance of the fluid flow model and the variation between the available datasets. The condensed phase fraction at the vent, puncture or rupture release point is revealed to be of key importance in understanding the near-field dispersion of sonic CO{sub 2}.

54 ENVIRONMENTAL SCIENCES↗

Corrosion Evaluation of CoCrFeMnNi High-Entropy Alloys (HEAs) for Corrosion Protection of Natural Gas Transmission Pipelines

High-entropy alloys (HEAs), are multicomponent alloys composed of at least five elements with compositions of 5-35 atomic % for each element. These alloys are being investigated for corrosion protection of natural gas transmission pipelines by studying their behavior under aqueous acidic conditions. Electrochemical and immersion experiments were carried out in 3.5 weight % NaCl solution at pH 4 and 40°C. Oxygen was purged out from the solution by using CO2 as stripping gas. The electrochemical experiments included potentiodynamic and electrochemical impedance spectroscopy tests, used to calculate corrosion rates. Potentiodynamic polarization curves, including cyclic voltammograms, were used to explain active, active-passive, and passive regions of these alloys and susceptibility to localized corrosion. Surface characterization of the corroded samples were performed using scanning electron microscopy (SEM) and x-ray diffraction (XRD). The results of the immersion and electrochemical testing indicate that some of the HEAs have better corrosion performance than commercial alloys UNS N10276, UNS K03014, and UNS 31600.

03 NATURAL GAS↗

A Detection Pipeline for Galactic Binaries in LISA Data

The Galaxy is suspected to contain hundreds of millions of binary white dwarf systems, a large fraction of which will have sufficiently small orbital period to emit gravitational radiation in band for space-based gravitational wave detectors such as the Laser Interferometer Space Antenna (LISA). LISA's main science goal is the detection of cosmological events (supermassive black hole mergers) etc.) however the gravitational signal from the galaxy will be the dominant contribution to the data - including instrumental noise - over approximately two decades in frequency. The catalogue of detectable binary systems will serve as an unparalleled means of studying the Galaxy. Furthermore, to maximize the scientific return from the mission, the data must be "cleansed" of the galactic foreground. We will present an algorithm that can accurately resolve and subtract greater than or equal to 10000 of these sources from simulated data supplied by the Mock LISA Data Challenge Task Force. Using the time evolution of the gravitational wave frequency, we will reconstruct the position of the recovered binaries and show how LISA will sample the entire compact binary population in the Galaxy.

Littenberg, Tyson B.↗

Dark Energy Survey Year 1 Results: Cosmological Constraints from Cosmic Shear

Here, we use 26 million galaxies from the Dark Energy Survey (DES) Year 1 shape catalogs over 1321 deg 2 of the sky to produce the most significant measurement of cosmic shear in a galaxy survey to date. We constrain cosmological parameters in both the flat CDM and wCDM models, while also varying the neutrino mass density. These results are shown to be robust using two independent shape catalogs, two independent photo- z calibration methods, and two independent analysis pipelines in a blind analysis. We find a 3% fractional uncertainty on σ 8 ( Ω m =0.3)0.5 = 0.789$+0.024\atop{0.026}$ at 68% CL, which is a factor of three improvement over the fractional constraining power of our DES Science Verification results and a factor 1.5 tighter than the previous state-of-the-art cosmic shear results. In wCDM, we find a 5% fractional uncertainty on 8( m=0:3)0:5 = 0.789$+0.036\atop{0.038}$ and a dark energy equation-of-state w = -0.82$+0.26\atop{-0.48}$. Though we find results that are consistent with previous cosmic shear constraints in 8 – m, we nevertheless see no evidence for disagreement of our weak lensing data with data from the CMB. Finally, we find no evidence preferring a wCDM model allowing w≠ -1. Finally, we expect further significant improvements with subsequent years of DES data, which will more than triple the sky coverage of our shape catalogs and double the effective integrated exposure time per galaxy.

79 ASTRONOMY AND ASTROPHYSICS↗

Influence of Rare Earth Ce Additions on Microstructure and Mechanical Properties of Experimental Pipeline Steels

Herein, the effect of Ce additions ranging from 57 to 263 ppm is evaluated for an experimental pipeline steel. Compared to the Ce-free steel, progressive Ce additions result in a slightly refined microstructure, significantly improve transverse impact properties, and slightly increase strength. All these observations can be attributed to the gradual transformation of Mn sulfide and Mn–Si–Al oxide inclusions to Ce-containing oxide/sulfides. In particular, the inclusions consist exclusively of sub-5 μm spherical Ce 2 O 2 S particles upon near-stoichiometric additions of Ce, considering the oxygen and sulfur impurity level of the steel. In conclusion, the results suggest that Ce is a potentially promising alloying addition for next-generation pipeline steels by replacing overtly deleterious inclusions with potentially beneficial ones.

36 MATERIALS SCIENCE↗

Advanced genomics identifies growth effectors for proteotoxic ER stress recovery in Arabidopsis thaliana

Abstract Adverse environmental and pathophysiological situations can overwhelm the biosynthetic capacity of the endoplasmic reticulum (ER), igniting a potentially lethal condition known as ER stress. ER stress hampers growth and triggers a conserved cytoprotective signaling cascade, the unfolded protein response (UPR) for ER homeostasis. As ER stress subsides, growth is resumed. Despite the pivotal role of the UPR in growth restoration, the underlying mechanisms for growth resumption are yet unknown. To discover these, we undertook a genomics approach in the model plant species Arabidopsis thaliana and mined the gene reprogramming roles of the UPR modulators, basic leucine zipper28 (bZIP28) and bZIP60, in ER stress resolution. Through a network modeling and experimental validation, we identified key genes downstream of the UPR bZIP-transcription factors (bZIP-TFs), and demonstrated their functional roles. Our analyses have set up a critical pipeline for functional gene discovery in ER stress resolution with broad applicability across multicellular eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗

Building a custom high-throughput platform at the Joint Genome Institute for DNA construct design and assembly—present and future challenges

Abstract The rapid design and assembly of synthetic DNA constructs have become a crucial component of biological engineering projects via iterative design–build–test–learn cycles. In this perspective, we provide an overview of the workflows used to generate the thousands of constructs and libraries produced each year at the U.S. Department of Energy Joint Genome Institute. Particular attention is paid to describing pipelines, tools used, types of scientific projects enabled by the platform and challenges faced in further scaling output.

36 MATERIALS SCIENCE↗

Sci-Thur PM - Colourful Interactions: Highlights 04: A Fast Quantitative MRI Acquisition and Processing Pipeline for Radiation Treatment Planning and Simulation

MRI-only Radiation Treatment Planning (RTP) is becoming increasingly popular because of a simplified work-flow, and less inconvenience to the patient who avoids multiple scans. The advantages of MRI-based RTP over traditional CT-based RTP lie in its superior soft-tissue contrast, and absence of ionizing radiation dose. The lack of electron-density information in MRI can be addressed by automatic tissue classification. To distinguish bone from air, which both appear dark in MRI, an ultra-short echo time (UTE) pulse sequence may be used. Quantitative MRI parametric maps can provide improved tissue segmentation/classification and better sensitivity in monitoring disease progression and treatment outcome than standard weighted images. Superior tumor contrast can be achieved on pure T{sub 1} images compared to conventional T{sub 1}-weighted images acquired in the same scan duration and voxel resolution. In this study, we have developed a robust and fast quantitative MRI acquisition and post-processing work-flow that integrates these latest advances into the MRI-based RTP of brain lesions. Using 3D multi-echo FLASH images at two different optimized flip angles (both acquired in under 9 min, and 1mm isotropic resolution), parametric maps of T{sub 1}, proton-density (M{sub 0}), and T{sub 2}{sup *} are obtained with high contrast-to-noise ratio, and negligible geometrical distortions, water-fat shifts and susceptibility effects. An additional 3D UTE MRI dataset is acquired (in under 4 min) and post-processed to classify tissues for dose simulation. The pipeline was tested on four healthy volunteers and a clinical trial on brain cancer patients is underway.

60 APPLIED LIFE SCIENCES↗

Data for "Efficient Mutagenesis and Genotyping of Maize Inbreds Using Biolistics, Multiplex CRISPR/Cas9 Editing, and Indel-Selective PCR"

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

gene editing↗

Increasing throughput of multiplexed electrical bus in pipe-lined architecture

Techniques are disclosed for increasing the throughput of a multiplexed electrical bus by exploiting available pipeline stages of a computer or other system. For example, a method for increasing a throughput of an electrical bus that connects at least two devices in a system comprises introducing at least one signal hold stage in a signal-receiving one of the two devices, such that a maximum frequency at which the two devices are operated is not limited by a number of cycles of an operating frequency of the electrical bus needed for a signal to propagate from a signal-transmitting one of the two devices to the signal-receiving one of the two devices. Preferably, the signal hold stage introduced in the signal-receiving one of the two devices is a pipeline stage re-allocated from the signal-transmitting one of the two devices.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Adaptive Performance-Constrained in Situ Visualization of Atmospheic Simulations

While many parallel visualization tools now provide in situ visualization capabilities, the trend has been to feed such tools with large amounts of unprocessed output data and let them render everything at the highest possible resolution. This leads to an increased run time of simulations that still have to complete within a fixed-length job allocation. In this paper, we tackle the challenge of enabling in situ visualization under performance constraints. Our approach shuffles data across processes according to its content and filters out part of it in order to feed a visualization pipeline with only a reorganized subset of the data produced by the simulation. Our framework leverages fast, generic evaluation procedures to score blocks of data, using information theory, statistics, and linear algebra. It monitors its own performance and adapts dynamically to achieve appropriate visual fidelity within predefined performance constraints. Experiments on the Blue Waters supercomputer with the CM1 simulation show that our approach enables a 5 speedup with respect to the initial visualization pipeline and is able to meet performance constraints.

54 ENVIRONMENTAL SCIENCES↗

Ramdb: The NASA Raman Spectral Database (version 1.00).

Given that, in most instances, minimal sample preparation is required and due to its contactless instrument design, Raman spectroscopy is one of the most versatile vibrational spectroscopic techniques for the chemical analysis of environmental and biological specimens. The diversity of applications of Raman spectroscopy ranges anywhere from art [1] to planetary science missions [2]. The advancement in the use of Raman spectroscopy in Solar System missions, notably in post-mission sample return analysis, requires a spectral library holding the broad range of specimens that could be found in Solar System sources. For this purpose, we have initiated the development of a Raman spectral database (Ramdb) at NASA Ames Research Center. Currently, the database includes experimental and theoretical Raman spectra of PAHs [3, 4], as well as laboratory Raman spectra of amino acids, carbon allotropes, minerals, and analogs relevance to Earth Sciences [5], Exobiology [6], Planetary [7], and Astrochemistry [8] to name just a few examples. Ramdb can be found on the web at www.astrochemistry.org/ramdb, where raw and processed Raman spectra can be downloaded in CSV format. The laboratory Raman spectra are measured using a laser Raman spectrometer (JASCO NRS-5500-532QRI). The Raman instrument is equipped with three excitation lasers, with wavelengths of 405, 532, and 785 nm. A clean silicon substrate is used as the internal standard for wavenumber calibration. Powdered samples were prepared (microscopic >10 um, grounded microscopic < 10 um) on glass slides. Some raw data exhibited a background signal arising as a combination of laser-induced fluorescence from the sample. To correct this background, we developed a Python pipeline that uses open-source Python libraries. Ramdb provides both raw and processed (using Python pipeline) data, which includes tabulated Raman shift transitions and other measurement details. The theoretical Raman band positions of PAHs (pyrene monomers and tetramer clusters) were computed using density functional theory (DFT) with the help of the Gaussian 16 suite of programs [9]. In the near future, Ramdb will serve as a repository of Raman spectral data from Laboratory Astrophysics and Planetary Science experiments involving the irradiation of organic compounds under simulated space and planetary conditions. In addition, online and offline tools will be developed for utilising the database for comparison to the user’s sample.

N Punnakayathil↗

Intro to HPC Bootcamp: Engaging New Communities Through Energy Justice Projects

The U.S. Department of Energy (DOE) is a long-standing leader in research and development of high-performance computing (HPC) in the pursuit of science. However, we face daunting challenges in fostering a robust and diverse HPC workforce. Basic HPC is not typically taught at early stages of students' academic careers, and the capacity and knowledge of HPC at many institutions are limited. Even so, such topics are prerequisites for advanced training programs, internships, graduate school, and ultimately for careers in HPC. To help address this challenge, as part of the DOE Exascale Computing Project's Broadening Participation Initiative, we recently launched the Introduction to HPC Training and Workforce Pipeline Program to provide accessible introductory material on HPC, scalable AI, and analytics. We describe the Intro to HPC Bootcamp, an immersive program designed to engage students from underrepresented groups as they learn foundational HPC skills. Here, the program takes a novel approach to HPC training by turning the traditional curriculum upside down. Instead of focusing on technology and its applications, the bootcamp focuses on energy justice to motivate the training of HPC skills through project-based pedagogy and real-life science stories. Additionally, the bootcamp prepares students for internships and future careers at DOE labs. The first bootcamp, hosted by the advanced computing facilities at Argonne, Lawrence Berkeley, and Oak Ridge National Labs and organized by Sustainable Horizons Institute, took place in August 2023.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Optimal high-throughput virtual screening pipeline for efficient selection of redox-active organic materials

As global interest in renewable energy continues to increase, there has been a pressing need for developing novel energy storage devices based on organic electrode materials that can overcome the shortcomings of the current lithium-ion batteries. One critical challenge for this quest is to find materials whose redox potential (RP) meets specific design targets. In this study, we propose a computational framework for addressing this challenge through the effective design and optimal operation of a high-throughput virtual screening (HTVS) pipeline that enables rapid screening of organic materials that satisfy the desired criteria. Starting from a high-fidelity model for estimating the RP of a given material, we show how a set of surrogate models with different accuracy and complexity may be designed to construct a highly accurate and efficient HTVS pipeline. We demonstrate that the proposed HTVS pipeline construction and operation strategies substantially enhance the overall screening throughput.

36 MATERIALS SCIENCE↗

Helium recovery system at IB3a

The increasing need for optimal and sustainable use of cryogenic resources to support Fermilab’s scientific mission has highlighted the necessity of improving the Laboratory’s helium management practices. An assessment of cryogenic test facilities identified the Technical Division’s Industrial Building 3a (IB3A) as a key site requiring upgrades to integrate a helium recovery system. The IB3A facility is essential for characterizing and testing superconductors, cables, and coils for various R&D projects, including the US High-Luminosity LHC Accelerator Upgrade Project (AUP), Mu2e, and other external collaborations. Currently, the facility relies on 500 L helium Dewars and vents the vaporized helium directly into the atmosphere, leading to significant helium loss. Given the non-renewable nature of helium, recovering and reusing this resource is critical for the sustainability of Fermilab’s operations. To address this challenge, a project has been initiated to connect IB3A to an existing helium purification station and refrigeration system located in another building via a dedicated pipeline pass over the roof of several buildings. This solution will enable the efficient capture of vented helium, its transfer to the purification station, and subsequent liquefaction for reuse in future operations. The project includes a detailed design phase, specifying the pipeline route, flow control mechanisms, and integration with the existing cryogenic infrastructure, followed by phased implementation and commissioning. By implementing this pipeline connection and upgrading IB3A, Fermilab aims to significantly reduce helium waste, lower operational costs, and align with its commitment to sustainability. This initiative provides a model for resource-efficient cryogenic operations and reinforces the Laboratory’s capacity to support its science mission for the long term.

Porwisiak, D. [Fermilab]↗

Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.

59 BASIC BIOLOGICAL SCIENCES↗

NASA Pilot-Engaged Expert Response Using IBM Watson Technology: Prototype Evaluation of Knowledge Retrieval System

NASA Langley Research Center and IBM have been investigating the use of IBM Watson technology in aerospace research and development. One application of Watson technology is the Pilot-Engaged Expert Response (PEER) use case. The PEER system is envisioned as an in-cockpit advisor that will act as a source of situationally-relevant information for pilots and other flight crew members to assist in decision making about real-time events and situations that arise in the course of aircraft operations. PEER will make available vast stores of knowledge and information quickly and directly, putting important informational resources where they are needed most. IBM has worked with NASA to develop an architecture and articulate a roadmap for the development of the PEER system. That vision is built around Watson Discovery Advisor (WDA) software solution, derived from IBM's Jeopardy!-winning automatic question answering system. PEER makes use of WDA's sophisticated question-answering capabilities as its core, adding important User Interface components and other customizations for the cockpit environment, including communication with flight systems and other external data sources. The development plan for PEER includes four development stages, with the current project constituting the first phase. In this project, a prototype instance of PEER was successfully adapted to the aviation domain, enabling users to ask questions about aviation topics and receive useful and accurate answers to these questions. Major tasks accomplished include the development of procedures for domain adaptation through automatic lexicon extraction from domain glossaries; generation of question-answer training data which was used to train the system; and assessment of the effectiveness of domain adaptation, which showed a dramatic improvement in the ability of the PEER system to answer domain-relevant questions. In addition, the vision for the PEER system was pushed forward by the articulation of a plan for the automatic enhancement of question-answering with contextual information. This initial phase focused on two main goals: 1) the targeted domain adaptation of the underlying WDA system to the aviation domain; and, 2) the design of the software systems needed to leverage flight-contextual data. Domain adaptation of the WDA system proceeds via three main activities: Domain data ingestion, lexical customization and model training. A textual corpus consisting of 1,147 individual documents with more than 7.5 million words of text was ingested into the system and this served as the basis of all further development. A domain lexicon of over 3,500 aviation-domain terms was semi-automatically generated from domain documents and used to train the system. In addition, a set of over 500 question-answer (QA) pairs relevant to the PEER use case was developed; these were used to train and assess the system. These important first steps established the basis for the PEER system. In addition, steps were taken towards the integration of the PEER system into the cockpit environment with the development of a functional design for the Contextual Data Augmentation (CDA) subsystem. This subsystem brings to bear contextual data to improve system responses. It has three main submodules: the Contextual Data Collection module, the Contextual Data Selection module, and the Contextual QA Augmentation module. These modules form a processing pipeline that addresses the problems associated with automatically integrating information from external resources into the knowledge-retrieval mechanism.

Machine learning↗