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At least 667 records · Page 37

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DOE OSTI2022

Assessment of human nuclear and mitochondrial DNA qPCR assays for quantification accuracy utilizing NIST SRM 2372a

In forensic DNA casework, a highly accurate real-time quantitative polymerase chain reaction (qPCR) assay is recommended per the Scientific Working Group on DNA Analysis Methods (SWGDAM) (SWGDAM Validation Guidelines for DNA Analysis Methods [1]) to determine whether a DNA sample is of sufficient quantity and robust quality to move forward with downstream short tandem repeats (STR) or sequencing analyses. Most of these assays rely on a standard curve, referred to herein and traditionally as absolute qPCR, in which an unknown is compared, relative to that curve. However, one fundamental issue with absolute qPCR is the quantifiable concentration of commercial assay standards can vary depending on (1) origin, i.e., whether from a cell line or a human subject, (2) supplier, (3) lot number, (4) shipping method, etc. In 2018, the National Institute for Standards and Technology (NIST) released a human DNA standard reference material for evaluating qPCR quantification standards, Standard Reference Material (SRM) 2372a, Romsos et al. (2018) [2] which contains three well-characterized human genomic DNA samples: Component A) a single male1 donor, Component B) a single female 1 donor, and Component C) a 1:3 male 2 :female 2 donor, each with certification data for nDNA and informational mitochondrial DNA(mtDNA)/nuclear DNA (nDNA) ratio data. The SRM 2372a was used to assess four qPCR assays: (1) Quantifiler Trio (Thermo Fisher Scientific, Waltham, MA) for nDNA quantification, (2) NovaQUANT (EMD Millipore Corporation, San Diego, CA) for nDNA and mtDNA quantification, (3) a custom duplex mtDNA assay, and (4) a custom triplex mtDNA assay. Additionally, extracts from eighteen (18) skeletal remains were tested with the latter three assays for concordance of DNA concentration and with assays (2) and (3), for the degradation state. Our assessment revealed that an accurate, efficient, and reproducible qPCR assay is dependent on (1) the quality and reliability of the DNA standard, (2) the qPCR chemistry, and (3) the specific primers, and probes (if applicable), used in an assay. Finally, our findings indicate qPCR assays may not always quantify as expected and that performance of each lot should be verified using a well-characterized DNA standard such as the NIST SRM 2372a and adjusted if warranted.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Experimental and numerical investigation of proppant embedment and conductivity reduction within a fracture in the Caney Shale, Southern Oklahoma, USA

The current worldwide energy supply is insufficient to meet the rising demand. As a result, the energy prices are expected to keep soaring despite the recent increases in a variety of renewable energy resources. Although not renewable, shale oil and gas — “unconventional” hydrocarbon resources are relatively clean forms of energy resources, which still hold a vast share of the energy market. For many oil and gas companies, meeting profitable production goals from shale reservoirs is sometimes challenging, due to the loss of fracture conductivity and premature declines in the production. In this paper we investigate the stress-dependent changes in the hydraulic conductivity of proppant-filled fractures and mechanical fracture–proppant interactions in Caney Shale, a calcareous, organic-rich mudrock, through laboratory experiments and numerical modeling. American Petroleum Institute (API) fracture conductivity tests were conducted using 2% KCl on five locations within the Caney Shale that consisted of selecting three brittle (reservoir) zones and two ductile zones. Confining pressures ranged from 1,000 psi to 12,000 psi at 210 °F. Conductivity, permeability as well as embedment were measured during the test. Also, an additional, laboratory in-situ visualization test was conducted to examine the detailed proppant-shale matrix interaction under elevated stress (3,920 psi effective stress) and temperature (252 °F), with a synthetic reservoir fluid. Our experimental results have confirmed that improved fracture conductivity is attributed to proppant size, and that the increase in porosity of the proppant pack, closure pressure changes and the reduction in fracture conductivity are a function of many factors such as fracture closure stress.

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2020

Analysis of thermal response of new diagnostic probe in TCV

Thermal response of the new multi-purpose diagnostic probe inside the TCV (Tokamak à Configuration Variable) tokamak is studied. The New Probe Head (NPH) was constructed at the University of Innsbruck and developed in collaboration with various European laboratories within EUROfusion program. The NPH can be used in different MST devices by applying corresponding adapters. Its design, followed by the prototype, has to go through a number of tests (numerical and experimental), before it can be used in the tokamak environment, where it has to withstand repeated exposure to the Scrape-Off-Layer (SOL) plasma. Presented numerical analyses of the NPH thermal response inside the TCV tokamak are performed by the Jožef Stefan Institute.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Cybersecurity Vulnerability Mitigation Framework through Empirical Paradigm: Enhanced Prioritized Gap Analysis

Existing cybersecurity vulnerability assessment tools were designed based on the policies and standards defined by organizations such as the U.S. Department of Energy and the National Institute of Standards and Technology (NIST). Frameworks such as the cybersecurity capability maturity model (C2M2) and the NIST Cybersecurity Framework (CSF) are often used by the critical infrastructure owners and operators to determine the cybersecurity maturity of their facility. Although these frameworks are exceptional at performing qualitative cybersecurity analysis and identifying vulnerabilities, they do not provide a means to perform prioritized mitigation of those vulnerabilities in order to achieve a desired cybersecurity maturity. To address that challenge, we developed a framework and software application called the cybersecurity vulnerability mitigation framework through empirical paradigm (CyFEr). This paper presents the detailed architecture of CyFEr’s enhanced prioritized gap analysis (EPGA) methodology and its application to CSF. The efficacy of the presented framework is demonstrated by comparing against existing similar models and testing against the cyber injects from a real-world cyber-attack that targeted industrial control systems (ICS) in critical infrastructures.

Gourisetti, Sri Nikhil G.↗

DOE OSTI2024

Extreme-scale workflows: A perspective from the JLESC international community

The Joint Laboratory for Extreme-Scale Computing (JLESC) focuses on software challenges in high-performance computing systems to meet the needs of today’s science campaigns, which often require large resources, consist of multiple tasks, and generate vast amounts of data. In this context, extreme-scale workflows have been the key factor in enabling scientific discoveries by helping scientists automate the dependencies and data exchanges between workflow tasks, instead of managing those manually. Here, in this paper, we present representative extreme-scale workflows and feature workflow systems developed by JLESC participating institutions. We present lessons learned while developing these tools, alongside with the open challenges and future research directions in the field of extreme-scale workflows.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

MITgcm-AD v2: Open source tangent linear and adjoint modeling framework for the oceans and atmosphere enabled by the Automatic Differentiation tool Tapenade

The Massachusetts Institute of Technology General Circulation Model (MITgcm) is widely used by the climate science community to simulate planetary atmosphere and ocean circulations. A defining feature of the MITgcm is that it has been developed to be compatible with an algorithmic differentiation (AD) tool, TAF, enabling the generation of tangent-linear and adjoint models. These provide gradient information which enables dynamics-based sensitivity and attribution studies, state and parameter estimation, and rigorous uncertainty quantification. Importantly, gradient information is essential for computing comprehensive sensitivities and performing efficient large-scale data assimilation, ensuring that observations collected from satellites and in-situ measuring instruments can be effectively used to optimize a large uncertain control space. As a result, the MITgcm forms the dynamical core of a key data assimilation product employed by the physical oceanography research community: Estimating the Circulation and Climate of the Ocean (ECCO) state estimate. Although MITgcm and ECCO are used extensively within the research community, the AD tool TAF is proprietary and hence inaccessible to a large proportion of these users. The new version 2 (MITgcm-AD v2) framework introduced here is based on the source-to-source AD tool Tapenade, which has recently been open-sourced. Another feature of Tapenade is that it stores required variables by default (instead of recomputing them) which simplifies the implementation of efficient, AD-compatible code. The framework has been integrated with the MITgcm model’s main branch and is now freely available.

Adjoints↗

DOE OSTI2020

Review of the first charged-particle transport coefficient comparison workshop

We present the results of the first Charged-Particle Transport Coefficient Code Comparison Workshop, which was held in Albuquerque, NM October 4–6, 2016. In this first workshop, scientists from eight institutions and four countries gathered to compare calculations of transport coefficients including thermal and electrical conduction, electron–ion coupling, inter-ion diffusion, ion viscosity, and charged particle stopping powers. In this paper, we give general background on Coulomb coupling and computational expense, review where some transport coefficients appear in hydrodynamic equations, and present the submitted data. Large variations are found when either the relevant Coulomb coupling parameter is large or computational expense causes difficulties. Understanding the general accuracy and uncertainty associated with such transport coefficients is important for quantifying errors in hydrodynamic simulations of inertial confinement fusion and high-energy density experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Phase-selection algorithms to minimize cost and imbalance in U.S. synthetic distribution systems

Not Available

Postigo, Fernando↗

DOE OSTI2025

Benchmarking CO₂ storage simulations: Results from the 11 th Society of Petroleum Engineers Comparative Solution Project

The 11 th Society of Petroleum Engineers Comparative Solution Project (shortened SPE11 herein) benchmarked simulation tools for geological carbon dioxide (CO 2 ) storage. A total of 45 groups from leading research institutions and industry across the globe signed up to participate, with 18 ultimately contributing valid results that were included in the comparative study reported here. This paper summarizes the SPE11 results. A comprehensive introduction and qualitative discussion of the submitted data are provided, together with an overview of online resources for accessing the full depth of data. A global metric for analyzing the relative distance between submissions is proposed and used to conduct a quantitative analysis of the submissions. This analysis attempts to statistically resolve the key aspects influencing the variability between submissions. The study shows that the major qualitative variation between the submitted results is related to thermal effects, dissolution-driven convective mixing, and resolution of facies discontinuities. Moreover, a strong dependence on grid resolution is observed across all three versions of the SPE11. However, our quantitative analysis suggests that the observed variations are predominantly influenced by factors not documented in the technical responses provided by the participants. We therefore identify that unreported variations due to human choices within the process of setting up, conducting, and reporting on the simulations underlying each SPE11 submission are at least as impactful as the computational choices reported.

Nordbotten, Jan M. [Univ. of Bergen (Norway); Norw↗

DOE OSTI2022

The development of natural gas and hydrogen pipeline capital cost estimating equations

Natural gas pipeline cost data collected by the Oil and Gas Journal (O&GJ) for interstate pipelines constructed from 1980 through 2017 were used to develop capital cost estimating equations that are a function of pipeline diameter, length, and U.S. region. Equations were developed for material, labor, miscellaneous, and right-of-way costs, the four cost components in the O&GJ data, for six different regions of the United States (U.S.). Each equation is a function of pipeline diameter and length. Adjustment mechanisms were then developed for converting the natural gas pipeline equations into equations for estimating the costs of hydrogen pipelines. These adjustments were based in part on an analysis completed by the National Institute for Standards and Technology (NIST). Here the results of this work were used to update cost models in the Hydrogen Delivery Scenario Analysis Model (HDSAM), developed by Argonne National Laboratory for the U.S. Department of Energy’s Hydrogen Program. Our analysis shows a wide range of pipeline cost across different U.S. regions, especially with respect to labor and right-of-way costs. The developed cost formulas for hydrogen pipelines are both important and timely as hydrogen is being considered as a zero-carbon energy carrier with the potential to decarbonize all energy sectors, and the cost of hydrogen transportation is essential for techno-economic analysis of its potential use in these sectors.

03 NATURAL GAS↗

DOE OSTI2021

Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track

Blockchain distributed ledger technology is just starting to be adopted in genomics and healthcare applications. Despite its increased prevalence in biomedical research applications, skepticism regarding the practicality of blockchain technology for real-world problems is still strong and there are few implementations beyond proof-of-concept. We focus on benchmarking blockchain strategies applied to distributed methods for sharing records of gene-drug interactions. We expect this type of sharing will expedite personalized medicine. We generated gene-drug interaction test datasets using the Clinical Pharmacogenetics Implementation Consortium (CPIC) resource. We developed three blockchain-based methods to share patient records on gene-drug interactions: Query Index, Index Everything, and Dual-Scenario Indexing. We achieved a runtime of about 60 s for importing 4,000 gene-drug interaction records from four sites, and about 0.5 s for a data retrieval query. Our results demonstrated that it is feasible to leverage blockchain as a new platform to share data among institutions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

A verification study of fatigue-based methods in API RP 1183 for estimating fatigue life of pipeline dents

Pipeline dents are mechanical damage caused by a third party in buried pipelines during construction or maintenance repair. Dents are recognized as a leading cause of pipeline failures for both liquid and gas transmission lines, and their assessment and management are critical to pipeline integrity. To meet the industry need, American Institute of Petroleum (API) in 2020 published a recommended practice (RP) 1183 – Assessment and Management of Pipeline Dents. This API code provides the pipeline industry “standard methods” for evaluating severity and fatigue life of pipeline dents with a single peak. This paper performed an initial verification study of fatigue-based methods prescribed in API RP 1183 for estimating fatigue life of pipeline dents. A brief review was first given to the dent fatigue-based methods, including three dent screening methods for estimating dent fatigue life in Sections 7.4.1, 7.4.2, and 7.4.3 of API 1183 and one dent assessment method for predicting fatigue life in Section 8.3.4. In order to verify these fatigue life prediction methods, a set of “standard examples” of dents provided in Annexes A.1 to A.5 of API RP 1183 were utilized in this study to calculate fatigue life, to determine restraint condition, and to evaluate both screening and assessment methods for single-peak dents. Through detailed calculations and comparisons, this study confirmed some specifications of API RP 1183, but also found some self-inconsistences and errors existing in this new API code. Furthermore, this includes the self-inconsistences between three screening methods and the self-inconsistence between the screening and assessment methods. On this basis, recommendations were made on how the operators should use API RP 1183, and what actions API should take to improve this code.

42 ENGINEERING↗

DOE OSTI2022

DECOVALEX-2019: An international collaboration for advancing the understanding and modeling of coupled thermo-hydro-mechanical-chemical (THMC) processes in geological systems

The DECOVALEX Project is an international research collaboration for advancing the understanding and modeling of coupled thermo-hydro-mechanical-chemical (THMC) processes in geological systems. DECOVALEX stands for “DEvelopment of COupled Models and VALidation against EXperiments”. The creation of this international initiative, now running for almost 30 years, was motivated by the recognition that prediction of these coupled effects is an essential part of the performance and safety assessment of geologic disposal systems for radioactive waste and spent nuclear fuel, and also for a range of other sub-surface engineering activities. DECOVALEX emphasizes joint analysis and comparative modeling of state-of-the-art field and laboratory experiments, across a range of host rock options and repository designs. Participating research teams are from radioactive waste management organizations, national research institutes, regulatory agencies, universities, and consulting groups, providing a wide range of perspectives and solutions to these complex problems. The most recent phase of the DECOVALEX Project, here referred to as DECOVALEX-2019, started in 2016 and ended in 2019. Modeling teams from 13 international partner organizations participated in the comparative evaluation of seven modeling tasks involving complex field and/or laboratory experiments. Furthermore, this Virtual Special Issue on DECOVALEX-2019 provides an in-depth overview of these collaborative research efforts and how these have advanced the state-of-the-art of understanding and modeling coupled THMC processes.

58 GEOSCIENCES↗

DOE OSTI2021

Spinal Cord Dose Tolerance to Stereotactic Body Radiation Therapy

Spinal cord tolerance data for stereotactic body radiation therapy (SBRT) were extracted from published reports, reviewed, and modelled. For de novo SBRT delivered in 1 to 5 fractions, the following spinal cord point maximum doses (D{sub max}) are estimated to be associated with a 1% to 5% risk of radiation myelopathy (RM): 12.4 to 14.0 Gy in 1 fraction, 17.0 Gy in 2 fractions, 20.3 Gy in 3 fractions, 23.0 Gy in 4 fractions, and 25.3 Gy in 5 fractions. For reirradiation SBRT delivered in 1 to 5 fractions, reported factors associated with a lower risk of RM include cumulative thecal sac equivalent dose in 2 Gy fractions with an alpha/beta of 2 (EQD2{sub 2}) D{sub max} ≤70 Gy; SBRT thecal sac EQD2{sub 2} D{sub max} ≤25 Gy, thecal sac SBRT EQD2{sub 2} D{sub max} to cumulative EQD2{sub 2} D{sub max} ratio ≤0.5, and a minimum time interval to reirradiation of ≥5 months. Larger studies containing complete institutional cohorts with dosimetric data of patients treated with spine SBRT, with and without RM, are required to refine RM risk estimates.