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At least 1,009 records · Page 56

Stop Codon Reassignment in the Wild

Since the discovery of the genetic code and protein translation mechanisms (1), a limited number of variations of the standard assignment between unique base triplets (codons) and their encoded amino acids and translational stop signals have been found in bacteria and phages (2-3). Given the apparent ubiquity of the canonical genetic code, the design of genomically recoded organisms with non-canonical codes has been suggested as a means to prevent horizontal gene transfer between laboratory and environmental organisms (4). It is also predicted that genomically recoded organisms are immune to infection by viruses, under the assumption that phages and their hosts must share a common genetic code (5). This paradigm is supported by the observation of increased resistance of genomically recoded bacteria to phages with a canonical code (4). Despite these assumptions and accompanying lines of evidence, it remains unclear whether differential and non-canonical codon usage represents an absolute barrier to phage infection and genetic exchange between organisms. Our knowledge of the diversity of genetic codes and their use by viruses and their hosts is primarily derived from the analysis of cultivated organisms. Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages (6). These initial findings suggest that large scale systematic studies of uncultivated microorganisms and viruses may reveal the extent and modes of divergence from the canonical genetic code operating in nature. To explore alternative genetic codes, we carried out a systematic analysis of stop codon reassignments from the canonical TAG amber, TGA opal, and TAA ochre codons in assembled metagenomes from environmental and host-associated samples, single-cell genomes of uncultivated bacteria and archaea, and a collection of phage sequences

09 BIOMASS FUELS↗

Foundations of plasma standards

Abstract The field of low-temperature plasmas (LTPs) excels by virtue of its broad intellectual diversity, interdisciplinarity and range of applications. This great diversity also challenges researchers in communicating the outcomes of their investigations, as common practices and expectations for reporting vary widely in the many disciplines that either fall under the LTP umbrella or interact closely with LTP topics. These challenges encompass comparing measurements made in different laboratories, exchanging and sharing computer models, enabling reproducibility in experiments and computations using traceable and transparent methods and data, establishing metrics for reliability, and in translating fundamental findings to practice. In this paper, we address these challenges from the perspective of LTP standards for measurements, diagnostics, computations, reporting and plasma sources. This discussion on standards, or recommended best practices, and in some cases suggestions for standards or best practices, has the goal of improving communication, reproducibility and transparency within the LTP field and fields allied with LTPs. This discussion also acknowledges that standards and best practices, either recommended or at some point enforced, are ultimately a matter of judgment. These standards and recommended practices should not limit innovation nor prevent research breakthroughs from having real-time impact. Ultimately, the goal of our research community is to advance the entire LTP field and the many applications it touches through a shared set of expectations.

data and reaction mechanisms↗

Initial Alloy 709 constitutive models for use with the ASME design by inelastic analysis and EPP+SMT design methods

This report details a preliminary inelastic constitutive model describing the behavior of Alloy 709. This model will serve two purposes: (1) integration into Nonmandatory Appendix HBB-Z of the ASME Boiler & Pressure Vessel Code Section III, Division 5 and (2) extrapolating cyclic test data to difficult to measure conditions for formulating improved creep-fatigue design methods. For both applications, the model must accurately capture the material behavior across a wide range of temperatures and a variety of test conditions, both monotonic and cyclic. For this purpose we adopt a universal model form under consideration to standardize the description of high temperature constitutive models in the ASME Code. This report briefly restates that model form and how we calibrate the model against the test data, summarizes the test database, and validates the final, trained model by comparison to the experimental tests.

36 MATERIALS SCIENCE↗

Mandating better buildings: a global review of building codes and prospects for improvement in the United States

This paper provides a global overview of the design, implementation, and evolution of building energy codes. Reflecting alternative policy goals, building energy codes differ significantly across the United States, the European Union, and China. This review uncovers numerous innovative practices including greenhouse gas emissions caps per square meter of building space, energy performance certificates with retrofit recommendations, and inclusion of renewable energy to achieve “nearly zero-energy buildings”. These innovations motivated an assessment of an aggressive commercial building code applied to all US states, requiring both new construction and buildings with major modifications to comply with the latest version of the ASHRAE 90.1 Standards. Using the National Energy Modeling System (NEMS), we estimate that by 2035, such building codes in the United States could reduce energy for space heating, cooling, water heating and lighting in commercial buildings by 16%, 15%, 20% and 5%, respectively. Impacts on different fuels and building types, energy rates and bills as well as pollution emission reductions are also examined.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Update on ASME AG-1 and Revision of the DOE Nuclear Air Cleaning Handbook - 20536

The American Society of Mechanical Engineers AG-1 Code on Nuclear Air and Gas Treatment is updated every two years. This paper provides an overview of issues being discussed within AG-1 committee meetings and revisions that will be included in the next version of the code. Additional information is provided on issues being discussed ranging from media velocity limits, control of airflow using actual versus and standard cubic feet per minute. Navigation and identification of applicable high-efficiency particulate air (HEPA) filter code sections can be confusing for those unfamiliar with AG-1. A general reorganization of filtration code sections clarifies geometry, flow, and performance envelopes for nuclear grade HEPA filters. The initial step consists of establishment of Section FN covering qualification of conventional, ceramic, metal, and high strength fibrous glass media. Future filter sections are currently expected to be characterized by geometry and flow direction (axial vs. radial). The Department of Energy's (DOE) Nuclear Air Cleaning Handbook (NACH) is also undergoing revision. An update on the status of that effort, along with issues and changes being considered. The original charter of the AG-1 Code was specific to commercial nuclear power plants, and to safety-related air cleaning systems. This has evolved over the years to include normal non-safety ventilation systems and process gas systems. Corollary guidance for DOE facilities has been available in several editions of the Nuclear Air Cleaning Handbook, starting with ORNL-NSIC 65. The latest edition of the Handbook, 2003, is undergoing revision and modifications. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

SCALE 6.2 Lattice Physics Performance Assessment

The US Nuclear Regulatory Commission relies on the lattice physics analysis capabilities of the SCALE code system to perform confirmatory licensing analyses. Either SCALE lattice physics code—TRITON/NEWT or Polaris—can be used to generate cross section data used by the PARCS nodal core simulator for full-core neutronics calculations. This report presents an assessment of the accuracy of SCALE lattice physics codes for preparation of lattice physics data that are used to support simulator codes such as the NRC’s PARCS, for UO 2 -mixed oxide (MOX)/Zr fueled light water reactor (LWR) analyses. Due to the nature of lattice physics calculations, critical reactor experiment benchmarks cannot be modeled in explicit detail in a lattice physics code. However, this limitation does not mean that these measurement data are not usable for lattice physics studies. Therefore, either geometry approximations or axial buckling must be implemented to determine the critical water height. These modeling limitations have led to development of a three-phase assessment strategy. In the first phase, selected critical experiment benchmarks are modeled using the SCALE 3D continuous-energy (CE) Monte Carlo (MC) code KENO, which is the most rigorous neutron transport method available in SCALE, with no approximations in the spatial, angle, or energy treatments. Biases and statistical uncertainties in quantities of interest such as k eff and pin power distributions are determined by comparing CE KENO results to experimental data. This first phase in the accuracy assessment is to demonstrate and establish the use of CE KENO as a reference solution for the second phase. In the second phase, 14 numerical test suites are used to compare SCALE lattice physics calculations with CE KENO as a reference solution. In the third phase, SCALE lattice physics depletion calculations are performed, and the spent fuel isotopic results are compared with available radiochemical assay measurements. Isotopic measurement comparisons provide quantitative assessment of isotopic density distribution predictions with the depletion models in SCALE lattice physics codes. This report documents results for all test suites. The assessment was performed using standard production techniques unless otherwise noted. Both TRITON/NEWT and Polaris exhibited acceptable accuracy for most test cases. For the few test cases in which acceptable accuracy criteria were not met, further code and data development are planned. The computer codes used in this assessment are as follows: SCALE 6.2 rev19189 (pre-release of 6.2.1) was used for CE KENO, TRITON/NEWT and Polaris (PWR only) calculations; SCALE 6.2.2 was used for Polaris calculations to address several updates in support of support boiling water reactor (BWR) lattice geometries. For this work, there is no difference between SCALE 6.2.1 and SCALE 6.2.2 beyond the inclusion of the Polaris BWR analysis capability; The ENDF/B-VII.1 continuous energy and 252 group libraries deployed in SCALE 6.2 were generated with AMPX 6.2 that is distributed with SCALE.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Assessment of the MAMMOTH and PRONGHORN Pebble Bed Reactor Modeling Capabilities for the HTR-PM Design

This assessment explores the current analysis methodologies of various external and MOOSE-based tools available at the Idaho National Laboratory to model pebble bed reactor multiphysics phenomena. The study involves three MOOSE-based, coupled codes: 1) MAMMOTH for reactor physics, 2) Rattlesnake for neutron transport and 3) Pronghorn for thermal fluids and strongly coupled conjugate heat transfer. These advanced tools are being developed under DOE-NE’s Nuclear Energy Advanced Modeling and Simulation program (NEAMS). They currently contain a collection of advanced modeling capabilities that allow high-fidelity simulations of advanced reactor concepts including gas and fluoride-salt cooled pebble bed reactors. Software development of these tools follows NQA-1 standards ensuring software quality that many of the currently deployed legacy codes lack. In this work, the MAMMOTH Pronghorn tools are compared to the legacy codes PEBBED-THERMIX-KONVEK. The external codes in use are LAMMPS for pebble mechanics and Serpent for cross section preparation. The coupling under MOOSE enables significant flexibility for modern engineering tools since MOOSE applications can be seamlessly coupled with various levels of resolution. This report focuses on low-resolution (r-z) and midresolution (3-D) homogenized geometries. The high-resolution Pebble Tracking Transport solution is not pursued herein and is postponed to future work. The results from this assessment show that the new MOOSE-based tools compare well with the results from legacy tools (r-z) and produce reasonable accuracy limited by the methods in the legacy tools. In the 3-D studies, the PJFNK-SPH methodology available in MAMMOTH allows the reproduction of Monte Carlo results with a transport-corrected diffusion solution. This has implications for the coupled solutions since without the SPH correction the temperature coefficient of reactivity is under-predicted and leads to lower temperature feedback and a significantly higher eigenvalue showing a difference of 2000 pcm.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Parallelization of a Proxy Transport App Using ComputeCPP and SYCL

This document details the attempts to parallelize a multi-group Monte Carlo proxy app using SYCL and the ComputeCPP Community Edition compiler. SYCL is a standard set by the Khronos Group and is described as a, “cross-platform abstraction layer that builds on the underlying concepts, portability and efficiency of OpenCL that enables code for heterogeneous processors to be written in a “single-source” style using completely standard C++.” ComputeCpp Community Edition (CE) is a heterogeneous parallel programming platform that provides a conformant implementation of the SYCL™ 1.2.1 Khronos specification. ComputeCPP provides a compiler and an SDK containing a build system to improve the usability of the compiler. The supported OpenCL 1.2 platforms for ComputeCpp are AMD® and Intel®, with experimental support for PTX which is used on Nvidia graphics cards as well as experimental support for ARM chips. All testing reported in this document was done on the Darwin computer cluster using an Nvidia GTX Titan X graphics card. Since ComputeCPP does not support using this card with OpenCL, ComputeCPP’s experimental PTX64 bit-code generation was used to generate device code.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Comparison of German and American fabrication standards for transportation and storage containments of high level radioactive material type B packages - 15055

As the competent authority for the evaluation of German radioactive material (RAM) transport and storage packages, BAM (the German Federal Institute for Materials Research and Testing) has evaluated various international cask manufacturers regarding compliance with the German Type B(U) licensing requirements. The US NRC has recommended paragraphs in the ASME Boiler and Pressure Vessel (B and PV) Code, Section III, Division 3, as the measure to quantify the safety requirements of the US regulations regarding fabrication of RAM transportation and storage containments. The objective of this study is to compare the fabrication criteria of the German Dangerous Goods Procedural Rules (BAM-GGR) and the German Institute for Standardization (DIN) with the US quantitative measures for fabrication of RAM package containment vessels. This comparison will cover major similarities and differences between the requirements of the German standards and the ASME Code requirements for Type B package containment fabrication QC (quality control). While the material most often used for German RAM containment applications is ductile cast iron (DCI), in the US forged austenitic stainless steel is typically used. This study focuses on fabrication QC measures required to ensure reproducible and acceptable properties for DCI containments. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Indoor air quality in new and renovated low-income apartments with mechanical ventilation and natural gas cooking in California

This work presents pollutant concentrations and performance data for code-required mechanical ventilation equipment in 23 low-income apartments at 4 properties constructed or renovated 2013-2017. All apartments had natural gas cooking burners. Occupants pledged to not use windows for ventilation during the study but several did. Measured airflows of range hoods and bathroom exhaust fans were lower than product specifications. Only eight apartments operationally met all ventilation code requirements. Pollutants measured over one week in each apartment included time-resolved fine particulate matter (PM 2.5 ), nitrogen dioxide (NO 2 ), formaldehyde and carbon dioxide (CO 2 ) and time-integrated formaldehyde, NO 2 and nitrogen oxides (NO X ). Compared to a recent study of California houses with code-compliant ventilation, apartments were smaller, had fewer occupants, higher densities, and higher mechanical ventilation rates. Mean PM 2.5 , formaldehyde, NO 2 , and CO 2 were 7.7 µg/m 3 , 14.1 ppb, 18.8 ppb, and 741 ppm in apartments; these are 4% lower, 25% lower, 165% higher, and 18% higher compared to houses with similar cooking frequency. Four apartments had weekly PM 2.5 above the California annual outdoor standard of 12 µg/m 3 and also discrete days above the World Health Organization 24-h guideline of 25 µg/m 3 . Two apartments had weekly NO 2 above the California annual outdoor standard of 30 ppb.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Baseline Evaluation of Eddy Current Testing for PWSCC Susceptible Materials

This technical letter report (TLR) summarizes technical efforts focused on assessments of eddy current testing (ET) examinations using various mockups for obtaining baseline surface and subsurface conditions on materials susceptible to primary water stress corrosion cracking (PWSCC). The scope of this work included nondestructive evaluation characterization of weld surfaces on mockups that were identified for application of various surface peening approaches. All of the work reported here was conducted prior to planned peening of these surfaces to evaluate pre-peening conditions, and subsequently compare the baseline ET results with post-peening conditions. The overall objective of this work was to demonstrate the effectiveness of employing ET for detecting near/sub-surface defects on mockups in support of peening assessments for surface stress improvement and mitigation of PWSCC in these materials. The U.S. Nuclear Regulatory Commission has communicated their expectations to industry for eddy current inspections of peened, inlayed, and onlayed dissimilar metal welds and is interested in better understanding detection performance and sensitivity of ET techniques to support the development of a technical foundation for detection and sizing limits, effective ET qualification requirements, alternate inspections or programs for evaluating PWSCC mitigation processes, and development of ET acceptance standards that can be referenced in the appropriate American Society of Mechanical Engineers Section XI Code Case (N-770-X). This TLR provides a technical discussion focused on the ET data obtained, the analysis, and conclusions drawn from surface examinations of various plate standards and actual components extracted from cancelled nuclear power plants.

36 MATERIALS SCIENCE↗

MPACT Standard Input User s Manual, Version 2.2.0

The MPACT (Michigan PArallel Charactistics based Transport) code is designed to perform high-fidelity light water reactor (LWR) analysis using whole-core pin-resolved neutron transport calculations on modern parallel-computing hardware. The code consists of several libraries which provide the functionality necessary to solve steady-state eigenvalue problems. Several transport capabilities are available within MPACT including both 2-D and 3-D Method of Characteristics (MOC). A three-dimensional whole core solution based on the 2D-1D solution method provides the capability for full core depletion calculations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

RealGasBrine v1.0 option of TOUGH+ v1.5

RealGasBrine v1.0 is a numerical code that for the simulation of the behavior of gas-bearing porous and/fractured geologic media. It is an option of TOUGH+ v1.5 [Moridis, 2014], a successor to the TOUGH2 [Pruess et al., 1999; 2012] family of codes for multi-component, multiphase fluid and heat flow developed at the Lawrence Berkeley National Laboratory. RealGasBrine v1.0 needs the TOUGH+ v1.5 core code in order to compile and execute. It is written in standard FORTRAN 95/2003, and can be run on any computational platform (workstation, PC, Macintosh) for which such compilers are available. RealGasBrine v1.0 describes the non-isothermal two- (for pure water) or three-phase (for brine) flow of an aqueous phase and a real gas mixture in a gas-bearing medium, with a particular focus in ultra-tight (such as tight-sand and shale gas) systems. Up to 12 individual real gases can be tracked, and salt can precipitate as solid halite. The capabilities of the code include coupled flow and thermal effects, real gas behavior, Darcy and non-Darcy flow, several isotherm options of gas sorption onto the grains of the porous media, complex fracture descriptions, gas solubility into water, and geomechanical effects on flow properties. RealGasBrine v1.0 allows the study of flow and transport of fluids and heat over a wide range of time frames and spatial scales not only in gas reservoirs, but also in any problem involving the flow of gases in geologic media, including the geologic storage of greenhouse gas mixtures, the behavior of geothermal reservoirs with multi-component condensable (H2O and CO2) and non-condensable gas mixtures, the transport of water and released H2 in nuclear waste storage applications, etc.

Moridis, GeorgeJ↗

User's Manual for the RealGasBrine v1.0 Option of TOUGH+ v1.5: A Code for the Simulation of System Behavior in Gas-Bearing Geologic Media

REALGASBRINE v1.0 is a numerical code that for the simulation of the behavior of gas-bearing porous and/fractured geologic media. It is an option of TOUGH+ v1.5 [Moridis, 2014], a successor to the TOUGH2 [Pruess et al., 1999] family of codes for multi-component, multiphase fluid and heat flow developed at the Lawrence Berkeley National Laboratory. REALGASBRINE v1.0 needs the TOUGH+ v1.5 core code in order to compile and execute. It is written in standard FORTRAN 95/2003, and can be run on any computational platform (workstation, PC, Macintosh) for which such compilers are available. REALGASBRINE v1.0 describes the non-isothermal two- (for pure water) or three-phase (for brine) flow of an aqueous phase and a real gas mixture in a gas-bearing medium, with a particular focus in ultra-tight (such as tight-sand and shale gas) systems. Up to 12 individual real gases can be tracked, and salt can precipitate as solid halite. The capabilities of the code include coupled flow and thermal effects, real gas behavior, Darcy and non-Darcy flow, several isotherm options of gas sorption onto the grains of the porous media, complex fracture descriptions, gas solubility into water, and geomechanical effects on flow properties. REALGASBRINE v1.0 allows the study of flow and transport of fluids and heat over a wide range of time frames and spatial scales not only in gas reservoirs, but also in any problem involving the flow of gases in geologic media, including the geologic storage of greenhouse gas mixtures, the behavior of geothermal reservoirs with multi-component condensable (H 2 O and CO 2 ) and non-condensable gas mixtures, the transport of water and released H 2 in nuclear waste storage applications, etc.

15 GEOTHERMAL ENERGY↗

Evolutionary instability of CUG-Leu in the genetic code of budding yeasts

The genetic code used in nuclear genes is almost universal, but here we report that it changed three times in parallel during the evolution of budding yeasts. All three changes were reassignments of the codon CUG, which is translated as serine (in 2 yeast clades), alanine (1 clade), or the ‘universal’ leucine (2 clades). The newly discovered Ser2 clade is in the final stages of a genetic code transition. Most species in this clade have genes for both a novel tRNA Ser (CAG) and an ancestral tRNA Leu (CAG) to read CUG, but only tRNA Ser (CAG) is used in standard growth conditions. The coexistence of these alloacceptor tRNA genes indicates that the genetic code transition occurred via an ambiguous translation phase. We propose that the three parallel reassignments of CUG were not driven by natural selection in favor of their effects on the proteome, but by selection to eliminate the ancestral tRNA Leu (CAG).

59 BASIC BIOLOGICAL SCIENCES↗

pnnl/openstudio-building-energy-standard-measures-gem

The OpenStudio Building Energy Standards Measure Repository is a comprehensive collection of innovative OpenStudio measures designed to facilitate energy code analysis. OpenStudio is a cutting-edge platform brings together physics-based building energy modeling (BEM), BEM process automation, and large-scale computing capabilities. Contains OpenStudio Standards Performance Rating Method Measure (IPID 32936) and OpenStudio Measure to Generate IPLV-specific Chiller Performance Curves for Chillers (IPID 32940)

Xu, Weili [PNNL]↗

Assessing the standard Molybdenum projector augmented wave VASP potentials

Density Functional Theory (DFT) based Equation of State (EOS) construction is a prominent part of Sandia’s capabilities to support engineering sciences. This capability is based on augmenting experimental data with information gained from computational investigations, especially in those parts of the phase space where experimental data is hard, dangerous, or expensive to obtain. A key part of the success of the Sandia approach is the fundamental science work supporting the computational capability. Not only does this work enhance the capability to perform highly accurate calculations but it also provides crucial insight into the limitations of the computational tools, providing high confidence in the results even where results cannot be, or have not yet been, validated by experimental data. This report concerns the key ingredient of projector augmented-wave (PAW) potentials for use in pseudo-potential computational codes. Using the tools discussed in SAND2012-7389 we assess the standard Vienna Ab-initio Simulation Package (VASP) PAWs for Molybdenum.

97 MATHEMATICS AND COMPUTING↗