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DOE OSTI2021

Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes

Host-associated microbial communities (microbiomes) play critical roles in human, animal, and plant health and development. However, interactions between the host, members of the microbiome, and invading pathogens are in most cases still poorly understood. Such interactions are multidimensional and can alter the taxonomic composition and/or the functional metabolic activities of the microbiome in response to disease or treatment conditions. For example, after 2 days of antibiotic treatment, the mouse gut microbiome is altered and more susceptible to invasion by the pathogen Clostridioides difficile. Studies of these multidimensional interactions have been fueled by the ability to use high-throughput sequencing of phylogenetic marker genes to profile microbial community composition and shotgun metagenomics to profile functional potential. However, many protein-coding genes predicted from metagenomes are not necessarily expressed under a given condition, and thus, it is difficult to assess the activities and functional interactions in microbial communities based on DNA sequencing data alone. The physiological and pathological processes expressed in these communities under specific conditions are better reflected by the abundances of transcripts or proteins. In this Pearl, we provide a brief introduction to metaproteomics, which is a tool for the large-scale analysis of proteins in microbiomes that allows researchers to address a diversity of questions related to functions and interactions in microbiomes. The term “metaproteomics” was first used in 2004 for “the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time”, and since then, a large array of metaproteomics approaches have been developed. Our objective in this Pearl is to highlight what we feel are 5 essential elements to be considered for a metaproteomics research campaign and to introduce nonexpert readers to the topic without going into too much technical detail.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Radiation measurements at ICOS ecosystem stations

Solar radiation is a prime driver of energy and carbon fluxes in natural ecosystems. Radiation measurements are essential for interpreting ecosystem scale greenhouse gases and energy fluxes as well as many other observations performed at ecosystem stations of the Integrated Carbon Observation System (ICOS). Here, we describe and explain the relevance of the radiation variables that are monitored continuously at ICOS ecosystem stations and define recommendations to perform these measurements with consistent and comparable accuracy. The measurement methodology and instruments are described including detailed technical specifications. Guidelines for instrumental set up as well as for operation, maintenance and data collection are defined considering both ICOS scientific objectives and practical operational constraints. For measurements of short-wave (solar) and long wave (infrared) radiation components, requirements for the ICOS network are based on available well-defined state-of-the art standards (World Meteorological Organization, International Organization for Standardization). For photosynthetically active radiation measurements, some basic instrumental requirements are based on the performance of commercially available sensors. Since site specific conditions and practical constraints at individual ICOS ecosystem stations may hamper the applicability of standard requirements, we recommend that ICOS develops mid-term coordinated actions to assess the effective level of uncertainties in radiation measurements at the network scale.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2013

Advanced Energy Retrofit Guide: Practical Ways to Improve Energy Performance; Grocery Stores (Revised) [Book]

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2012

Route-Specific Passage Proportions and Survival Rates for Fish Passing through John Day Dam, The Dalles Dam, and Bonneville Dam in 2010 and 2011

This report fulfills a request of the U.S. Army Engineer District, Portland, Oregon, to produce an interim report of estimates of route-specific fish passage proportions and survival rates for lower Columbia River dams in 2010 and 2011. The estimates are needed to update the Compass Model for the Columbia River Treaty and the new Biological Opinion before detail technical reports are published in late 2012. This report tabulates route-specific fish-passage proportions and survival rates for steelhead and Chinook salmon smolts passing through various sampled routes at John Day Dam, The Dalles Dam, and Bonneville Dam in 2010 and 2011. Results were compiled from analyses of data acquired in spring 2010 and 2011 studies that were specifically designed to estimate dam-passage and forebay-to-tailrace survival rates, travel time metrics, and spill passage efficiency, as stipulated by the 2008 Federal Columbia River Power System Biological Opinion and the Columbia Basin Fish Accords. The study designs allowed for estimation of route-specific fish passage proportions and survival rates as well as estimation of forebay-passage survival, all of which are summarized herein.

13 HYDRO ENERGY↗

DOE OSTI2012

Analytic solutions of an unclassified artifact

This report provides the technical detail for analytic solutions for the inner and outer profiles of the unclassified CMM Test Artifact (LANL Part Number 157Y-700373, 5/03/2001) in terms of radius and polar angle. Furthermore, analytic solutions are derived for the legacy Sheffield measurement hardware, also in terms of radius and polar angle, using part coordinates, i.e., relative to the analytic profile solutions obtained. The purpose of this work is to determine the exact solution for the “cosine correction” term inherent to measurement with the Sheffield hardware. The cosine correction is required in order to interpret the actual measurements taken by the hardware in terms of an actual part definition, or “knot-point spline definition,” that typically accompanies a component drawing. Specifically, there are two portions of the problem: first an analytic solution must be obtained for any point on the part, e.g., given the radii and the straight lines that define the part, it is required to find an exact solution for the inner and outer profile for any arbitrary polar angle. Next, the problem of the inspection of this part must be solved, i.e., given an arbitrary sphere (representing the inspection hardware) that comes in contact with the part (inner and outer profiles) at any arbitrary polar angle, it is required to determine the exact location of that intersection. This is trivial for the case of concentric circles. In the present case, however, the spherical portion of the profiles is offset from the defined center of the part, making the analysis nontrivial. Here, a simultaneous solution of the part profiles and the sphere was obtained.

42 ENGINEERING↗

DOE OSTI2012

PORFLOW Modeling Supporting The H-Tank Farm Performance Assessment

Numerical simulations of groundwater flow and contaminant transport in the vadose and saturated zones have been conducted using the PORFLOW code in support of an overall Performance Assessment (PA) of the H-Tank Farm. This report provides technical detail on selected aspects of PORFLOW model development and describes the structure of the associated electronic files. The PORFLOW models for the H-Tank Farm PA, Rev. 1 were updated with grout, solubility, and inventory changes. The aquifer model was refined. In addition, a set of flow sensitivity runs were performed to allow flow to be varied in the related probabilistic GoldSim models. The final PORFLOW concentration values are used as input into a GoldSim dose calculator.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2012

Summary of Carbon Storage Project Public Information Meeting and Open House

The Kentucky Geological Survey (KGS) completed a second phase of carbon dioxide (CO 2 ) injection and seismic imaging in the Knox Group, a Cambrian Ordovician dolomite and sandstone sequence in September 2010. This work completed 2 years of activity at the KGS No. 1 Marvin Blan well in Hancock County, Kentucky. The well was drilled in 2009 by a consortium of State and industry partners (Kentucky Consortium for Carbon Storage). An initial phase of CO 2 injection occurred immediately after completion of the well in 2009. The second phase of injection and seismic work was completed in September 2010 as part of a U.S. DOE funded project, after which the Blan well was plugged and abandoned. Following completion of research at the Blan well, a final public meeting and open house was held in Hancock County on October 28, 2010. This meeting followed one public meeting held prior to drilling of the well, and two on site visits during drilling (one for news media, and one for school teachers). The goal of the final public meeting was to present the results of the project to the public, answer questions, and address any concerns. Despite diligent efforts to publicize the final meeting, it was poorly attended by the general public. Several local county officials and members of the news media attended, but only one person from the general public showed up. We attribute the lack of interest in the results of the project to several factors. First, the project went as planned, with no problems or incidents that affected the local residents. The fact that KGS fulfilled the promises it made at the beginning of the project satisfied residents, and they felt no need to attend the meeting. Second, Hancock County is largely rural, and the technical details of carbon sequestration were not of interest to many people. The county officials attending were an exception; they clearly realized the importance of the project in future economic development for the county.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2013

Digital Full-Scope Simulation of a Conventional Nuclear Power Plant Control Room, Phase 2: Installation of a Reconfigurable Simulator to Support Nuclear Plant Sustainability

The U.S. Department of Energy’s Light Water Reactor Sustainability program has developed a control room simulator in support of control room modernization at nuclear power plants in the U.S. This report highlights the recent completion of this reconfigurable, full-scale, full-scope control room simulator buildout at the Idaho National Laboratory. The simulator is fully reconfigurable, meaning it supports multiple plant models developed by different simulator vendors. The simulator is full-scale, using glasstop virtual panels to display the analog control boards found at current plants. The present installation features 15 glasstop panels, uniquely achieving a complete control room representation. The simulator is also full-scope, meaning it uses the same plant models used for training simulators at actual plants. Unlike in the plant training simulators, the deployment on glasstop panels allows a high degree of customization of the panels, allowing the simulator to be used for research on the design of new digital control systems for control room modernization. This report includes separate sections discussing the glasstop panels, their layout to mimic control rooms at actual plants, technical details on creating a multi-plant and multi-vendor reconfigurable simulator, and current efforts to support control room modernization at U.S. utilities. The glasstop simulator provides an ideal testbed for prototyping and validating new control room concepts. Equally importantly, it is helping create a standardized and vetted human factors engineering process that can be used across the nuclear industry to ensure control room upgrades maintain and even improve current reliability and safety.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2013

High Performance Cathodes for Li-Air Batteries

The overall objective of this project was to develop and fabricate a multifunctional cathode with high activities in acidic electrolytes for the oxygen reduction and evolution reactions for Li-air batteries. It should enable the development of Li-air batteries that operate on hybrid electrolytes, with acidic catholytes in particular. The use of hybrid electrolytes eliminates the problems of lithium reaction with water and of lithium oxide deposition in the cathode with sole organic electrolytes. The use of acid electrolytes can eliminate carbonate formation inside the cathode, making air breathing Li-air batteries viable. The tasks of the project were focused on developing hierarchical cathode structures and bifunctional catalysts. Development and testing of a prototype hybrid Li-air battery were also conducted. We succeeded in developing a hierarchical cathode structure and an effective bifunctional catalyst. We accomplished integrating the cathode with existing anode technologies and made a pouch prototype Li-air battery using sulfuric acid as catholyte. The battery cathodes contain a nanoscale multilayer structure made with carbon nanotubes and nanofibers. The structure was demonstrated to improve battery performance substantially. The bifunctional catalyst developed contains a conductive oxide support with ultra-low loading of platinum and iridium oxides. The work performed in this project has been documented in seven peer reviewed journal publications, five conference presentations, and filing of two U.S. patents. Technical details have been documented in the quarterly reports to DOE during the course of the project.

25 ENERGY STORAGE↗

DOE OSTI2012

A Soft-Switching Inverter for High-Temperature Advanced Hybrid Electric Vehicle Traction Motor Drives

The state-of-the-art hybrid electric vehicles (HEVs) require the inverter cooling system to have a separate loop to avoid power semiconductor junction over temperatures because the engine coolant temperature of 105°C does not allow for much temperature rise in silicon devices. The proposed work is to develop an advanced soft-switching inverter that will eliminate the device switching loss and cut down the power loss so that the inverter can operate at high-temperature conditions while operating at high switching frequencies with small current ripple in low inductance based permanent magnet motors. The proposed tasks also include high-temperature packaging and thermal modeling and simulation to ensure the packaged module can operate at the desired temperature. The developed module will be integrated with the motor and vehicle controller for dynamometer and in-vehicle testing to prove its superiority. This report will describe the detailed technical design of the soft-switching inverters and their test results. The experiments were conducted both in module level for the module conduction and switching characteristics and in inverter level for its efficiency under inductive and dynamometer load conditions. The performance will be compared with the DOE original specification.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2013

Fluoride Salt-Cooled High-Temperature Reactor Technology Development and Demonstration Roadmap

Fluoride salt-cooled High-temperature Reactors (FHRs) are an emerging reactor class with potentially advantageous performance characteristics, and fully passive safety. This roadmap describes the principal remaining FHR technology challenges and the development path needed to address the challenges. This roadmap also provides an integrated overview of the current status of the broad set of technologies necessary to design, evaluate, license, construct, operate, and maintain FHRs. First-generation FHRs will not require any technology breakthroughs, but do require significant concept development, system integration, and technology maturation. FHRs are currently entering early phase engineering development. As such, this roadmap is not as technically detailed or specific as would be the case for a more mature reactor class. The higher cost of fuel and coolant, the lack of an approved licensing framework, the lack of qualified, salt-compatible structural materials, and the potential for tritium release into the environment are the most obvious issues that remain to be resolved.

Holcomb, David Eugene↗

DOE OSTI2013

Advanced Energy Retrofit Guide: Practical Ways to Improve Energy Performance, K-12 Schools (Book)

The U.S. Department of Energy developed the Advanced Energy Retrofit Guides (AERGs) to provide specific methodologies, information, and guidance to help energy managers and other stakeholders plan and execute energy efficiency improvements. Detailed technical discussion is fairly limited. Instead, we emphasize actionable information, practical methodologies, diverse case studies, and unbiased evaluations of the most promising retrofit energy efficiency measures for each building type. A series of AERGs is under development, addressing key segments of the commercial building stock. K-12 schools were selected as one of the highest priority building sectors, because schools affect the lives of most Americans. They also represent approximately 8% of the energy use and 10% of the floor area in commercial buildings nationwide. U.S. K-12 school districts spend more than $8 billion each year on energy - more than they spend on computers and textbooks combined. Most occupy older buildings that often have poor operational performance - more than 30% of schools were built before 1960. The average age of a school is about 42 years - which is nearly the expected serviceable lifespan of the building. K-12 schools offer unique opportunities for deep, cost-effective energy efficiency improvements, and this guide provides convenient and practical guidance for exploiting these opportunities in the context of public, private, and parochial schools.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2013

HPCG Benchmark Technical Specification

The High Performance Conjugate Gradient (HPCG) benchmark [cite SNL, UTK reports] is a tool for ranking computer systems based on a simple additive Schwarz, symmetric Gauss-Seidel preconditioned conjugate gradient solver. HPCG is similar to the High Performance Linpack (HPL), or Top 500, benchmark [1] in its purpose, but HPCG is intended to better represent how today’s applications perform. In this paper we describe the technical details of HPCG: how it is designed and implemented, what code transformations are permitted and how to interpret and report results.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Secure Storage Architectures

The purpose of this report is to clarify the challenges associated with storage for secure enclaves. The major focus areas for the report are: - review of relevant parallel filesystem technologies to identify assets and gaps; - review of filesystem isolation/protection mechanisms, to include native filesystem capabilities and auxiliary/layered techniques; - definition of storage architectures that can be used for customizable compute enclaves (i.e., clarification of use-cases that must be supported for shared storage scenarios); - investigate vendor products related to secure storage. This study provides technical details on the storage and filesystem used for HPC with particular attention on elements that contribute to creating secure storage. We outline the pieces for a a shared storage architecture that balances protection and performance by leveraging the isolation capabilities available in filesystems and virtualization technologies to maintain the integrity of the data. Key Points: There are a few existing and in-progress protection features in Lustre related to secure storage, which are discussed in (Chapter 3.1). These include authentication capabilities like GSSAPI/Kerberos and the in-progress work for GSSAPI/Host-keys. The GPFS filesystem provides native support for encryption, which is not directly available in Lustre. Additionally, GPFS includes authentication/authorization mechanisms for inter-cluster sharing of filesystems (Chapter 3.2). The limitations of key importance for secure storage/filesystems are: (i) restricting sub-tree mounts for parallel filesystem (which is not directly supported in Lustre or GPFS), and (ii) segregation of hosts on the storage network and practical complications with dynamic additions to the storage network, e.g., LNET. A challenge for VM based use cases will be to provide efficient IO forwarding of the parallel filessytem from the host to the guest (VM). There are promising options like para-virtualized filesystems to help with this issue, which are a particular instances of the more general challenge of efficient host/guest IO that is the focus of interfaces like virtio. A collection of bridging technologies have been identified in Chapter 4, which can be helpful to overcome the limitations and challenges of supporting efficient storage for secure enclaves. The synthesis of native filesystem security mechanisms and bridging technologies led to an isolation-centric storage architecture that is proposed in Chapter 5, which leverages isolation mechanisms from different layers to facilitate secure storage for an enclave. Recommendations: The following highlights recommendations from the investigations done thus far. - The Lustre filesystem offers excellent performance but does not support some security related features, e.g., encryption, that are included in GPFS. If encryption is of paramount importance, then GPFS may be a more suitable choice. - There are several possible Lustre related enhancements that may provide functionality of use for secure-enclaves. However, since these features are not currently integrated, the use of Lustre as a secure storage system may require more direct involvement (support). (*The network that connects the storage subsystem and users, e.g., Lustre s LNET.) - The use of OpenStack with GPFS will be more streamlined than with Lustre, as there are available drivers for GPFS. - The Manilla project offers Filesystem as a Service for OpenStack and is worth further investigation. Manilla has some support for GPFS. - The proposed Lustre enhancement of Dynamic-LNET should be further investigated to provide more dynamic changes to the storage network which could be used to isolate hosts and their tenants. - The Linux namespaces offer a good solution for creating efficient restrictions to shared HPC filesystems. However, we still need to conduct a thorough round of storage/filesystem benchmarks. - Vendor products should be more closely reviewed, possibly to include evaluation of performance/protection of select products. (Note, we are investigation the option of evaluating equipment from Seagate/Xyratex.) Outline: The remainder of this report is structured as follows: - Section 1: Describes the growing importance of secure storage architectures and highlights some challenges for HPC. - Section 2: Provides background information on HPC storage architectures, relevant supporting technologies for secure storage and details on OpenStack components related to storage. Note, that background material on HPC storage architectures in this chapter can be skipped if the reader is already familiar with Lustre and GPFS. - Section 3: A review of protection mechanisms in two HPC filesystems; details about available isolation, authentication/authorization and performance capabilities are discussed. - Section 4: Describe technologies that can be used to bridge gaps in HPC storage and filesystems to facilitate...

Aderholdt, Ferrol↗

DOE OSTI2015

Measure Guideline. Deep Energy Enclosure Retrofit for Interior Insulation of Masonry Walls

This Measure Guideline describes a deep energy enclosure retrofit solution for insulating mass masonry buildings from the interior. It describes the retrofit assembly, technical details, and installation sequence for retrofitting masonry walls. Interior insulation of masonry retrofits might adversely affect the durability of the wall. This guideline includes a review of decision criteria pertinent to retrofitting masonry walls from the interior and the possible risk of freeze-thaw damage.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2015

Measure Guideline: Deep Energy Enclosure Retrofit for Interior Insulation of Masonry Walls

This Measure Guideline describes a deep energy enclosure retrofit (DEER) solution for insulating mass masonry buildings from the interior. It describes the retrofit assembly, technical details, and installation sequence for retrofitting masonry walls. Interior insulation of masonry retrofits has the potential to adversely affect the durability of the wall; this document includes a review of decision criteria pertinent to retrofitting masonry walls from the interior and the possible risk of freeze-thaw damage.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2015

Efficient Probability of Failure Calculations for QMU using Computational Geometry (LDRD 13-0144 Final Report)

This SAND report summarizes our work on the Sandia National Laboratory LDRD project titled "Efficient Probability of Failure Calculations for QMU using Computational Geometry" which was project #165617 and proposal #13-0144. This report merely summarizes our work. Those interested in the technical details are encouraged to read the full published results, and contact the report authors for the status of the software and follow-on projects.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

ORNL Evaluation of Electrabel Safety Cases for Doel 3 / Tihange 2: Final Report

Oak Ridge National Laboratory (ORNL) performed a detailed technical review of the 2015 Electrabel (EBL) Safety Cases prepared for the Belgium reactor pressure vessels (RPVs) at Doel 3 and Tihange 2 (D3/T2). The Federal Agency for Nuclear Control (FANC) in Belgium commissioned ORNL to provide a thorough assessment of the existing safety margins against cracking of the RPVs due to the presence of almost laminar flaws found in each RPV. Initial efforts focused on surveying relevant literature that provided necessary background knowledge on the issues related to the quasilaminar flaws observed in D3/T2 reactors. Next, ORNL proceeded to develop an independent quantitative assessment of the entire flaw population in the two Belgian reactors according to the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code, Section XI, Appendix G, Fracture Toughness Criteria for Protection Against Failure, New York (1992 and 2004). That screening assessment of all EBL-characterized flaws in D3/T2 used ORNL tools, methodologies, and the ASME Code Case N-848, Alternative Characterization Rules for QuasiLaminar Flaws . Results and conclusions from the ORNL flaw acceptance assessments of D3/T2 were compared with those from the 2015 EBL Safety Cases. Specific findings of the ORNL evaluation of that part of the EBL structural integrity assessment focusing on stability of the flaw population subjected to primary design transients include the following: ORNL s analysis results were similar to those of EBL in that very few characterized flaws were found not compliant with the ASME (1992) acceptance criterion. ORNL s application of the more recent ASME Section XI (2004) produced only four noncompliant flaws, all due to LOCAs. The finding of a greater number of non-compliant flaws in the EBL screening assessment is due principally to a significantly more restrictive (conservative) criterion for flaw size acceptance used by EBL. ORNL s screening assessment results (obtained using an analysis methodology different from that of EBL) are interpreted herein as confirming the EBL screening results for D3/T2. ORNL s independent refined analysis demonstrated the EBL-characterized flaw 1660, which is non-compliant in the ORNL and EBL screening assessment, is rendered compliant when modeled as a more realistic individual quasi-laminar flaw using a 3-D XFEM analysis approach. ORNL s and EBL s refined analyses are in good agreement for the flaw 1660 close to the clad/base metal interface; ORNL is not persuaded that repeating this exercise for more than one non-compliant flaw is necessary to accept the EBL conclusions derived from the aggregate of EBL refined analysis results. ORNL General Conclusions Regarding the Structural Integrity Assessment (SIA) Conducted by EBL for D3/T2 Based on comparative evaluations of ORNL and EBL SIA analyses and on consideration of other results, ORNL is in agreement with the general conclusions reported by Electrabel in their RPV D3/T2 Technical Summary Note of April 14, 2015: More than 99 percent of flaws in D3/T2 meet the defined screening criterion, rendering them benign with respect to initiation in the event of a design transient. Refined analyses of non-compliant flaws from the screening assessment indicate that only 11 of the 16196 detected flaws have a critical reference-temperature material index (designated RTNDT) that implies the possibility of the initiation of cleavage fracture at some future time. For those 11 2 flaws, the calculated margin in RTNDT (a measure of acceptable embrittlement relative to end-ofservice-life conditions) is significant, being greater than 80 C. Fatigue crack growth is not a concern in the flaw-acceptability analyses. Primary stress re-evaluation confirms that the collapse pressure is more than 1.5 times the design pressure in the presence of defects detected in D3/T2. Sufficient conservatisms are built into the input data and into the different steps of the SIA; in some cases, those conservatisms are quantified and imply that additional margins exist in the SIA. Taken as a whole, the foregoing results and conclusions confirm the structural integrity of Doel 3 and Tihange 2 under all design transients with ample margin in the presence of the 16196 detected flaws.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗