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At least 145 records · Page 8

De novo design of small beta barrel proteins

Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy–based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.

59 BASIC BIOLOGICAL SCIENCES↗

RELAP5-3D Capabilities for High-Temperature Gas-Cooled Reactor Analysis

RELAP5-3D is the premier systems thermal-hydraulic code in the world. The code has been used significantly for high-temperature gas-cooled reactor (HTGR) analyses over the last 10 years, but there has not been a comprehensive summary of RELAP5-3D capabilities and methods for HTGR modeling. In this paper, we provide a guide for how novice users can build models for prismatic HTGRs. This guide includes best practices for developing heat structures and setting up radiation and conduction heat transfer. We also provide a summary of relevant validation studies. These studies are divided into three categories: separate effects tests, integral effects tests, and nuclear reactor studies. We present a comprehensive review of RELAP5-3D HTGR applications for reactor modeling over the last 10 years. These applications include work for the Modular High-Temperature Gas-Cooled Reactor benchmark, design activities for a prismatic HTGR as part of the U.S. Department of Energy’s Advanced Demonstration and Test Reactor Options Study, and studies performed to design gas-cooled microreactors. Following the comprehensive literature review, we present a gap analysis highlighting capabilities of RELAP5-3D that are available and missing for a complete analysis of HTGR thermal hydraulics. We also discuss the limitations of existing code capabilities and potential improvements that could improve analyses. Current research efforts have yet to fully validate RELAP5-3D for a prismatic HTGR analysis; however, some of this is attributable to confounding factors in the available experimental data as opposed to code capabilities. In conclusion, this paper presents the most comprehensive review to date on RELAP5-3D capabilities, limitations, and applications for HTGR analysis.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

Scalable Object Store v. 1.0.0

SOS is software that stores data values in a set of structured flat files. The data is organized in the files based upon functions specified by the user in order to enable fast insertion and retrieval of data.

Tucker, Thomas↗

GBCGE Subsurface Database Explorer and APIs

This submission defines a DOI for the Great Basin Center for Geothermal Energy's (GBCGE) Subsurface Database Explorer web application and underlying data services, and acknowledges the INGENIOUS project as a major source of funding for data compilation and quality assurance. The GBCGE Subsurface Database Explorer is an interactive web mapping application that provides public access to the GBCGE Subsurface Database, and its collection of datasets pertinent to geothermal exploration, oil and gas exploration, critical mineral exploration, and other subsurface characterization for the Great Basin Region, western US. This is a living database, and will be continuously updated with new data and datasets as funding and motivations allow. The underlying database views that populate the web application are on an automated refresh schedule. Data sources and acknowledgements: We thank our partners with the Nevada Division of Minerals (NDOM), the Southern Methodist University (SMU), and Great Basin State Geological Surveys for their active efforts in data curation, schema design, and quality assurance. We also thank contributors among the USGS, Oregon Institute of Technology, State Divisions of Water Resources, State Divisions of Oil, Gas, and Minerals, and State Geological Surveys for open data availability and direct contributions made under the National Geothermal Data System (NGDS).

15 GEOTHERMAL ENERGY↗

Residential Building Energy Efficiency Field Studies: Low-Rise Multifamily

In recent years, the U.S. Department of Energy (DOE) has conducted a series of research studies to validate energy efficient building technologies in the field. Much of the work has focused on single-family construction, and some has also addressed commercial energy codes. The work detailed in this DOE-funded study (EE0007616) focuses on low-rise multifamily buildings (three stories or fewer above grade) in various regions of the United States, and reports on how state-level building codes are being implemented, both in terms of observed characteristics and also in terms of estimated energy impacts. Nearly 100 buildings across four states—Illinois, Minnesota, Oregon, and Washington—were sampled, which represent a range of climate types from mild temperature to very cold continental. Both common entry and outdoor entry buildings were included, and a parallel research project evaluated envelope air tightness and current still-evolving air tightness testing methods. Finally, a set of structured interviews of building designers and other relevant professionals was carried to out to gain more insight into this market. To the greatest extent possible, the methodology developed under the project for low-rise multifamily buildings mirrored the approach established by Pacific Northwest National Laboratory (PNNL) for single-family residential buildings (https://www.energy.gov/eere/buildings/downloads/residential-building-energy-code-field-study). This included the general approach to sampling, recruitment, and data collection, as well as data analysis and presentation. The range of permitting dates for the sites encompassed two energy code cycles in most regions. All states in the study had adopted a variation of the International Energy Conservation Code (IECC) for the structure of their state code. The low-rise multifamily occupancy presents a hybrid building type: most of the building’s conditioned floor area was covered by the residential chapter of the code while portions of the building (such as corridors and common spaces) fell under the commercial code chapter. The key items assessed in this work were: Building Shell—exterior wall insulation, ceiling insulation, foundation insulation, windows. Common Areas—HVAC and lighting. Living Units—lighting, ventilation. A few items were not assessed in detail, given their relative paucity in this occupancy type; these included duct leakage, pipe insulation, and hot water circulation controls. Building characteristics were collected via a combination of architectural, mechanical, electrical, and plumbing plan reviews and field inspections, and entered into a spreadsheet-based tool that was later queried to build a database. Data went through quality control both upon arrival and via a later semi-automated review and assurance process. Most of the data are presented graphically so that the reader can quickly assess compliance with the applicable energy codes (both by state and by code year). As a final step, EnergyPlus™ simulations were created for all buildings in the study to estimate both the as-found energy use intensity (EUI) and the energy and CO 2 that could be saved if features that were found to not meet code minimums were brought up to code. The savings estimates were tabulated for each of the four states in the study. The research team found that the single-family approach was largely applicable to low-rise multifamily buildings. This applies to both the data collection and the prototype EUI analysis. Most of the occupied space is living units and falls under residential energy codes, and many characteristics use similar envelope construction and relatively straightforward mechanical systems and lighting. One of the most challenging aspects of this work was to build an effective spreadsheet-based data collection instrument that could allow efficient collection of both building plan and field data. The research team is of the view that other methods could be equally effective if the work is done carefully with diligent quality control. The primary findings for the work center around the thermal envelope and mechanical systems and lighting at the sites: For thermal envelope components, the majority of buildings met or were better than the prescriptive code.This suggests that building designers and builders are aware of code requirements. In some cases, surveyed buildings were designed to qualify for energy efficiency certification programs. These buildings made up at least 20% of sampled buildings in each state. Almost all buildings met mechanical system efficiency requirements (for both living units and common areas). In some cases, sites employed systems that were considerably more efficient than required by the applicable energy code. Dwelling units had a majority of high-efficacy lighting, often in excess of the state’s residential code requirements. While high-efficacy fixtures were also typical in common areas (corridors and stairwells), lighting power densities (LPDs) in these areas were sometimes higher than levels dictated by the applicable part of the state commercial energy code. The simulation models run on a series of low-rise multifamily prototypes, informed by a composite of the field data collected, calculated annual EUIs of between 20 and 50 kBtu/ft2-yr, with the range representing the effects of both building characteristics and building location (climate zone). A detailed process (based on simulations of prototype buildings) was used to estimate the amount of avoided energy use that would occur if 100% adherence to energy codes were attained. The results indicated modest savings are attainable for items such as window thermal performance and common area lighting. The result is overall only a modest potential for additional energy savings, averaging about 10% of EUI.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Cambium Documentation: Version 2020

This is the documentation for the 2020 version of Cambium. Cambium is a tool that assembles structured data sets of simulated hourly cost and operational data for modeled futures of the U.S. electric sector with metrics designed to be useful for long-term decision-making. In this documentation, we define the metrics reported in Cambium databases and document the Cambium-specific methods for calculating those metrics.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Natural Systems Data Package for the Active Trenches of the Low-Level Burial Grounds, Hanford Site, Washington

This document summarizes the available information regarding the natural system (vadose zone and saturated zone) at the active trenches of the 200 West Area and 200 East Area Low-Level Burial Grounds (LLBGs). This information is relevant for developing the natural system fate and transport model for the update of the active trenches performance assessment. This document presents a description of the major features, events, and processes of the natural system at the active trenches of the 200 West Area and 200 East Area LLBGs that involves the geologic features or framework, and the vadose zone and groundwater flow and transport system. The description of the geologic features includes the following items: geologic setting, major structural features, major hydrostratigraphic units, and geologic framework. The discussion concerning vadose zone flow and transport at the active trenches of the 200 West Area and 200 East Area LLBGs includes the following topics: vadose zone features, events, and processes relevant to the development of the vadose zone conceptual model; hydrogeologic units and conditions; factors affecting moisture movement; and flow and transport properties of major units. The discussion concerning the groundwater flow and transport system in the vicinity of the active trenches of the 200 West Area and 200 East Area LLBGs includes the following topics: saturated zone features, events, and processes relevant to the saturated zone conceptual model; hydrogeologic units; groundwater flow conditions; and flow and transport properties.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Cambium Documentation: Version 2021

Cambium is a tool that assembles structured data sets of simulated hourly emission, cost, and operational data for modeled futures of the U.S. electric sector with metrics designed to be useful for long-term decision-making. It was built to expand the metrics reported in the National Renewable Energy Laboratory's (NREL's) Standard Scenarios - an annually released set of projections of how the U.S. electric sector could evolve across a suite of different potential futures, looking forward through 2050 (Cole et al. 2021) Information about Cambium and related publications can be found at https://nrel.gov/analysis/cambium.html, and the Cambium data sets for the Standard Scenarios can be viewed and downloaded at https://cambium.nrel.gov/. In this documentation, we define the metrics reported in Cambium databases (Section 4) and document the Cambium-specific methods for calculating those metrics (Section 5). As this document is intended to cover multiple Cambium data releases, we do not document specific scenarios here - for individual data releases, readers should look for an accompanying report that describes the assumptions and data that underlie that specific release. For Cambium databases that are built on NREL's Standard Scenarios, for example, reports describing the scenarios can be found on the Standard Scenarios web site (https://www.nrel.gov/analysis/standard-scenarios.html).

24 POWER TRANSMISSION AND DISTRIBUTION↗

Connecting the Radiative Influences of Aerosol upon the Mass Flux Profiles of Shallow Cumuli across the Southeast Atlantic Ocean Basin and its Boundaries (Final Report)

The Atlantic Ocean covers approximately 25% of Earth’s surface and the atmosphere above it is home to a complex array of clouds and aerosols that have important influences on regional and global weather and climate. These influences must be accurately depicted in short range, medium range, seasonal, and climate forecast models. Conditions over the tropical Atlantic are particularly complex due to continental scale plumes of dust from the Sahara Desert and smoke from agricultural burning in Africa that drift across the Atlantic Ocean basin toward the Americas. These plumes are often found meandering in the lower atmosphere above shallow tropical clouds that form above the ocean surface, presumably mingling with these clouds on occasion due to convective mixing processes. Elevated dust and smoke particles absorb incoming sunlight and substantially warm the marine atmosphere in the layer in which they are present. This warming may alter the thermal stability of the marine atmosphere and may throttle or enhance the development of clouds, change their internal structure and the rate at which they precipitate. Alternatively, it may isolate the lower atmosphere from drier layers above enabling water vapor to accumulate near the ocean surface potentially leading to the development of deeper convection. Our study was organized around the principal concept of determining the impact of African smoke and dust plumes upon cloud development at ASI and understanding how a popular shallow convection parameterization used in models responds to the presence of this aerosol. We analyzed observations collected during the US Department of Energy (DOE) Layered Atlantic Smoke Interactions with Clouds (LASIC) campaign using the Atmospheric Radiation Measurement Program’s Mobile Facility #1 (AMF-1), which was deployed to Ascension Island (ASI) in Southeastern Atlantic for a one-year period. Ascension Island is immediately downwind from an African source of these plumes, but far enough removed to enable the lower atmosphere to have reacted to their presence. A main goal of our study was to compute radiative heating rate profiles over Ascension Island and along the trajectory from the biomass burning regions along coastal Africa to Ascension Island. To compute the radiative heating rate due to aerosols and clouds, we employed observed profiles of temperature, humidity, and clouds from LASIC alongside aerosol optical properties from the Modern-era Retrospective analysis for Research and Applications Version 2 (MERRA-2), as input for the Rapid Radiation Transfer Model (RRTM). Radiative heating was also assessed across the southeast Atlantic Ocean using an ensemble of back trajectories from the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model. We were successful in this effort and the resulting publication is already being cited despite its relatively short lifetime in the literature. The second part of our study involved the process-level representation of the clouds observed over the Southeastern Atlantic in models. Our initial task, upon which the balance of this portion of the study depended, was to evaluate the representativeness of the clouds observed by AMF-1. What orographic influence did Ascension Island have on the measured cloud structure? We set out to answer this question by trying to separate observations that were clearly indicative of orographic forcing from those that were representative of open ocean. The siting of AMF-1, which was 340-m above sea-level on the slope of a steep escarpment, proved demonstrably problematic for cloud process measurements. Despite considerable effort using multiple approaches including artificial intelligence (AI), we were unable to successfully compensate for the orographic forcing present at the AMF-1 site on ASI and, hence, produce process-level summaries of the convective mass flux representative of open ocean over the Southeastern Atlantic. Even though the project has officially ended, we are making a final attempt using two new types of clustering algorithm (i.e., AI) on the recommendation of a former student, who is an expert in this area. Since we have only recently begun to test these new AI schemes, the recommendations from the second part of our project outlined below are based on our experience at the time of this report.

54 ENVIRONMENTAL SCIENCES↗

Benchmarking the PCMCI Causal Discovery Algorithm for Spatiotemporal Systems

Causal discovery algorithms construct hypothesized causal graphs that depict causal dependencies among variables in observational data. While powerful, the accuracy of these algorithms is highly sensitive to the underlying dynamics of the system in ways that have not been fully characterized in the literature. In this report, we benchmark the PCMCI causal discovery algorithm in its application to gridded spatiotemporal systems. Effectively computing grid-level causal graphs on large grids will enable analysis of the causal impacts of transient and mobile spatial phenomena in large systems, such as the Earth’s climate. We evaluate the performance of PCMCI with a set of structural causal models, using simulated spatial vector autoregressive processes in one- and two-dimensions. We develop computational and analytical tools for characterizing these processes and their associated causal graphs. Our findings suggest that direct application of PCMCI is not suitable for the analysis of dynamical spatiotemporal gridded systems, such as climatological data, without significant preprocessing and downscaling of the data. PCMCI requires unrealistic sample sizes to achieve acceptable performance on even modestly sized problems and suffers from a notable curse of dimensionality. This work suggests that, even under generous structural assumptions, significant additional algorithmic improvements are needed before causal discovery algorithms can be reliably applied to grid-level outputs of earth system models.

54 ENVIRONMENTAL SCIENCES↗

Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators

Alquimia v1.0 is a generic interface to geochemical solvers that facilitates development of multiphysics simulators by enabling code coupling, prototyping and benchmarking. The interface enforces the function arguments and their types for setting up, solving, serving up output data and carrying out other common auxiliary tasks while providing a set of structures for data transfer between the multiphysics code driving the simulation and the geochemical solver. Alquimia relies on a single-cell approach that permits operator splitting coupling and parallel computation. We describe the implementation in Alquimia of two widely used open-source codes that perform geochemical calculations: PFLOTRAN and CrunchFlow. We then exemplify its use for the implementation and simulation of reactive transport in porous media by two open-source flow and transport simulators: Amanzi and ParFlow. We also demonstrate its use for the simulation of coupled processes in novel multiphysics applications including the effect of multiphase flow on reaction rates at the pore scale with OpenFOAM, the role of complex biogeochemical processes in land surface models such as the E3SM Land Model (ELM) and the impact of surface–subsurface hydrological interactions on hydrogeochemical export from watersheds with the Advanced Terrestrial Simulator (ATS). These applications make it apparent that the availability of a well-defined yet flexible interface has the potential to improve the software development workflow, freeing up resources to focus on advances in process models and mechanistic understanding of coupled problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NEUTRINO EMISSION PROCESSES, STELLAR EVOLUTION AND SUPERNOVA. PART II.

When the internal temperature of a star exceeds 1 BK (109 °K) the evolution is very rapid. The time scale is around 3000 years. Energy dissipated by emission of neutrinos is several orders of magnitude higher than that by optical radiation. Neutrinos have exceedingly long mean free path (∼10(exp 20) gram/cm(exp 2)) and they will escape as soon as they are produced. The star will contract to release gravitational energy to make up the energy lost to neutrinos and the internal temperature will rise to comply with the virial theorem. It is possible in this fast evolutionary phase, to neglect optical radiations all together as compared with the neutrino radiation. A set of structural equations is thus obtained. The envelope is replaced by boundary conditions. A simple model is constructed to illustrate our approach.

Star↗

Nanosecond radar observations of the ocean surface from a stable platform

The measurement of ocean surface waves with a nanosecond radar pulse from a fixed platform at vertical incidence is discussed. By reducing the pulse width of radar until the pulse width resolves the vertical water wave structure, a set of radar returns is available to describe the ocean surface characteristics which differs from returns obtained by conventional radars. A block diagram of the radar and the principles of operation are presented.

Yaplee, B. S.↗

FGRAAL: Technical documentation

Implementation of FGRAAL, a FORTRAN-extended graph algorithmic language for the Univac 1108 is described. The report contains the description of the implemented data structures for sets, lists and graphs. It summarizes the changes made for the RALPH compiler to accommodate the special statements of FGRAAL; gives the calling sequences generated by the changed compiler; and describes the object time subroutine package.

Mesztenyi, C. K.↗

Shuttle avionics system

The avionics system of the Space Shuttle is designed in a fail operational/fail safe architecture. The guidance, navigation and control system is implemented, through the onboard Orbiter digital computers. Guidance, navigation and control sensors are triplex, while the flight control effectors are mechanized either in load sharing or quad structure. Two sets of basic flight instruments and controls are provided along with electronic interfaces to allow for multiple selection of input destination and display source selection. Communications, tracking and instrumentation subsystems are mechanized as a dual hardware design for key operational elements. The data processing system allows for quad, triplex, dual or single computer operation. The power distribution subsystem provides a triple bus system with appropriate tie elements. A functional description is given of the computer system, the data bus, the mass memory unit, the multiplexer/demultiplexer and the CRT display system.

Gardiner, R. A.↗

Interpretive computer simulator for the NASA Standard Spacecraft Computer-2 (NSSC-2)

An Interpretive Computer Simulator (ICS) for the NASA Standard Spacecraft Computer-II (NSSC-II) was developed as a code verification and testing tool for the Annular Suspension and Pointing System (ASPS) project. The simulator is written in the higher level language PASCAL and implented on the CDC CYBER series computer system. It is supported by a metal assembler, a linkage loader for the NSSC-II, and a utility library to meet the application requirements. The architectural design of the NSSC-II is that of an IBM System/360 (S/360) and supports all but four instructions of the S/360 standard instruction set. The structural design of the ICS is described with emphasis on the design differences between it and the NSSC-II hardware. The program flow is diagrammed, with the function of each procedure being defined; the instruction implementation is discussed in broad terms; and the instruction timings used in the ICS are listed. An example of the steps required to process an assembly level language program on the ICS is included. The example illustrates the control cards necessary to assemble, load, and execute assembly language code; the sample program to to be executed; the executable load module produced by the loader; and the resulting output produced by the ICS.

Smith, R. S.↗

Chaotic /strange/ and periodic behavior in instability saturation by the oscillating two-stream instability

The nonlinear Schroedinger equation with linear growth and damping is truncated to three waves. The resulting system of nonlinear ordinary differential equations describes the excitation of linearly damped waves by the oscillating two-stream instability driven by a linearly unstable pump wave. This system represents a simple model for the nonlinear saturation of a linearly unstable wave. The model is examined analytically and numerically as a function of the dimensionless parameters of the system. It is found that the model can exhibit a wealth of characteristic dynamical behavior including stationary equilibria, Hopf bifurcations to periodic orbits, period doubling bifurcations, chaotic solutions characteristic of a strange attractor, tangent bifurcations from chaotic to periodic solutions, transient chaos, and hysteresis. Many of these features are shown to be explainable on the basis of one-dimensional maps. In the case of chaotic solutions, evidence for the presence of a strange attractor is provided by demonstrating Cantor set-like structure (i.e., scale invariance) in the surface of section.

Russell, D. A.↗

Volcanoes and volcanic provinces - Martian western hemisphere

The recognition of some Martian landforms as volcanoes is based on their morphology and geologic setting. Other structures, however, may exhibit classic identifying features to a varying or a less degree; these may be only considered provisionally as having a volcanic origin. Regional geologic mapping of the western hemisphere of Mars from Viking images has revealed many more probable volcanoes and volcanotectonic features than were recognized on Mariner 9 pictures. These abundant volcanoes have been assigned to several distinct provinces on the basis of their areal distribution. Although the Olympus-Tharsis region remains as the principle center of volcanism on Mars, four other important provinces are now also recognized: the lowland plains, Tempe Terra plateau, southern highlands (in the Phaethontis and Thaumasia quadrangles), and a probable ignimbrite province, situated along the highland-lowland boundary in Amazonis Planitia. Volcanoes in any one province vary in morphlogy, size, and age, but volcanoes in each province tend to have common characteristics that distinguish that particular group.

Scott, D. H.↗