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DOE OSTI2023

Technical descriptions of the experimental dynamical downscaling simulations over North America by the CAM–MPAS variable-resolution model

Abstract. Comprehensive assessment of climate datasets is important for communicating model projections and associated uncertainties to stakeholders. Uncertainties can arise not only from assumptions and biases within the model but also from external factors such as computational constraint and data processing. To understand sources of uncertainties in global variable-resolution (VR) dynamical downscaling, we produced a regional climate dataset using the Model for Prediction Across Scales (MPAS; dynamical core version 4.0) coupled to the Community Atmosphere Model (CAM; version 5.4), which we refer to as CAM–MPAS hereafter. This document provides technical details of the model configuration, simulations, computational requirements, post-processing, and data archive of the experimental CAM–MPAS downscaling data. The CAM–MPAS model is configured with VR meshes featuring higher resolutions over North America as well as quasi-uniform-resolution meshes across the globe. The dataset includes multiple uniform- (240 and 120 km) and variable-resolution (50–200, 25–100, and 12–46 km) simulations for both the present-day (1990–2010) and future (2080–2100) periods, closely following the protocol of the North American Coordinated Regional Climate Downscaling Experiment. A deviation from the protocol is the pseudo-warming experiment for the future period, using the ocean boundary conditions produced by adding the sea surface temperature and sea-ice changes from the low-resolution version of the Max Planck Institute Earth System Model (MPI-ESM-LR) in the Coupled Model Intercomparison Project Phase 5 to the present-day ocean state from a reanalysis product. Some unique aspects of global VR models are evaluated to provide background knowledge to data users and to explore good practices for modelers who use VR models for regional downscaling. In the coarse-resolution domain, strong resolution sensitivity of the hydrological cycles exists over the tropics but does not appear to affect the midlatitude circulations in the Northern Hemisphere, including the downscaling target of North America. The pseudo-warming experiment leads to similar responses of large-scale circulations to the imposed radiative and boundary forcings in the CAM–MPAS and MPI-ESM-LR models, but their climatological states in the historical period differ over various regions, including North America. Such differences are carried to the future period, suggesting the importance of the base state climatology. Within the refined domain, precipitation statistics improve with higher resolutions, and such statistical inference is verified to be negligibly influenced by horizontal remapping during post-processing. Limited (≈50 % slower) throughput of the current code is found on a recent many-core/wide-vector high-performance computing system, which limits the lengths of the 12–46 km simulations and indirectly affects sampling uncertainty. Our experience shows that global and technical aspects of the VR downscaling framework require further investigations to reduce uncertainties for regional climate projection.

58 GEOSCIENCES↗

DOE OSTI2024

Impact of ITCZ width on global climate: ITCZ-MIP

Abstract. The width of the Inter-Tropical Convergence Zone (ITCZ) affects tropical rainfall, Earth's albedo, large-scale circulation, and climate sensitivity. To better understand the ITCZ width and its effects on global climate, we present a protocol to force changes in ITCZ width in climate models. Starting from an aquaplanet configuration with a slab ocean, adding surface heat fluxes in the deep tropics forces the ITCZ to narrow, and subtracting them causes it to widen. The protocol successfully generates changes in ITCZ width in all four climate models used in this study. ITCZ width in each model responds linearly to forcing magnitude and sign. Comparing across the four climate models, a response to varying ITCZ width that is remarkably consistent among models is the ITCZ strength, which is greater the narrower the ITCZ. On the other hand, the effect of varying ITCZ width on climate sensitivity is divergent among our four models, varying even in sign. Results from this pilot study highlight the connections between surface fluxes, ITCZ width, and the wider climate. A comprehensive model intercomparison project (MIP) has the potential to advance understanding of both the physical processes shaping ITCZ width and its influence on remote atmospheric circulations and global climate.

Geology↗

DOE OSTI2021

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗

DOE OSTI2024

Impact of storage and extraction methods on peat soil microbiomes

Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modifiedPowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations.

Science & Technology - Other Topics↗

DOE OSTI2020

An effective survey method for studying volant species activity and behavior at tall structures

The effects of anthropogenic modification of air space on wildlife, particularly volant species, is not fully understood. Thus, it is essential to understand wildlife-interactions with tall structures to implement effective mitigation strategies. Yet, we are currently lacking standard protocols for visual surveys of wildlife behavior at such heights. Our study sought to determine an effective, repeatable method using readily available night vision and thermal technology to survey wildlife at tall structures. Using bats as the taxonomic group of interest, we (1) created a key to identify bats and their behavior, (2) compared the effectiveness of 2 different technologies, and (3) assessed optimal equipment placement to visually capture bat activity and behavior in proximity to wind turbine towers. For the latter, we tested thermal cameras at four distances from the base of the tower. The results of our study revealed that thermal cameras captured ∼34% more flying animals than night vision at a 2 m distance. However, due to the heat signature of the turbine towers themselves, it was challenging to identify behaviors and interactions that occurred in close proximity to the towers. In contrast, it was difficult to identify bats approaching the towers using night vision, yet we were able to clearly observe interactions with the towers themselves. With regards to equipment placement, we visually captured more bats with the thermal cameras placed 2 m from the tower base compared to farther distances. From our findings, we recommend that when using either thermal or night vision technology at tall structures, they be placed 2 m from the base to effectively observe interactions along the length of these structures. In addition, we further recommend that consideration be given to the use of these two technology types together to effectively conduct such surveys. If these survey techniques are incorporated into standard protocols, future surveys at a variety of tall structures are likely to become comparable and repeatable, thereby more effectively informing any mitigation strategies that may be required.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Metabolite, Protein, and Lipid Extraction (MPLEx): a method that simultaneously inactivates Middle East respiratory syndrome coronavirus and allows analysis of multiple host cell components following infection

Mass spectrometry (MS)-based, integrated proteomics, metabolomics, and lipidomics (collectively, multi-omics) studies provide a very detailed snap shot of virus-induced changes to the host following infection and can lead to the identification of novel prophylactic and therapeutic targets for preventing or lessening disease severity. Multi-omics studies with Middle East respiratory syndrome coronavirus (MERS-CoV) are challenging as the requirements of Biosafety Level 3 containment limit the numbers of samples that can be safely managed. To address these issues, the multi-omics sample preparation technique MPLEx (metabolite, protein, and lipid extraction) was developed to partition a single sample into three distinct parts (metabolites, proteins and lipids) for multi-omics analysis, while simultaneously inactivating MERS-CoV by solubilizing and disrupting the viral envelope and denaturing viral proteins. Here we describe the MPLEx protocol, highlight the step of inactivation, and describe the details of downstream processing, instrumental analysis of studies with Middle East respiratory syndrome coronavirus (MERS-CoV) are challenging as the requirements of Biosafety Level 3 containment limit the numbers of samples that can be safely managed. To address these issues, the multi-omics sample preparation technique MPLEx (metabolite, protein, and lipid extraction) was developed to partition a single sample into three distinct parts (metabolites, proteins and lipids) for multi-omics analysis, while simultaneously inactivating MERS-CoV by solubilizing and disrupting the viral envelope and denaturing viral proteins. Here we describe the MPLEx protocol, highlight the step of inactivation, and describe the details of downstream processing, instrumental analysis of the three separate analytes and their subsequent informatics pipelines.

Nicora, Carrie D.↗

DOE OSTI2020

Remote Hardware-in-the-Loop Approach for Microgrid Controller Evaluation

Utilities have been installing microgrids because of the increased resilience and reliability advantages they may provide to the distribution system. A microgrid controller is a critical component in microgrids. It is of great benefit to derisk the installation of microgrid controllers before field deployment. Hardware-in-the-loop (HIL) testing is used by controller developers and utilities to evaluate the controllers under stressful conditions. In this work, a microgrid control function developed by the Synchrophasor Grid Monitoring and Automation (SyGMA) laboratory at the University of California, San Diego is tested in a remote HIL (RHIL) setup. The digital real-time simulation of the detailed microgrid system was operated at the National Renewable Energy Laboratory's Energy Systems Integration Facility. Under such RHIL setup, successful controller operation is contingent on understanding and characterizing the communications channel and in particular network latencies. The novelty of this paper is the proposed use of a RHIL setup that leverages existing power system communications protocols to evaluate the controller in conjunction with the simulation capabilities of a remote facility. The work presented here will provide the complete setup of the HIL evaluation platform, the details of the communications protocols used by the setup for data transfer between the two organizations, test cases developed to evaluate the controller, and the results from the experiments.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Methods and materials for determination of distribution coefficients for separation materials

Methods and materials for determining the affinity of separation materials for targeted species are described. A composite separation medium is described that combines a separation material such as an ion exchange material or a sorbent with an SERS substrate. Methods and materials can be utilized to determine the distribution coefficient of a species for a separation material after running a single separation protocol followed by examination of the separation material of the protocol according to SERS. Disclosed methods can be utilized to determine the affinity of existing separation materials for targeted species as well as to determine the affinity of newly engineered separation materials to characterize species.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Characterizing intracellular proteomes for microbes: An experimental approach using label-free protein quantitation

Genomic and transcriptomic studies generate a rich source of molecular information; however, neither a static genome nor the presence of a messenger RNA provides the most direct insight into the functional state of a microbial cell at any given time. Rather, it is the ensemble of proteins (i.e., proteome) that is the primary workhorse for most biological processes that are concurrent and coordinately active in a living cell. Currently, mass-spectrometry-based (MS) technologies provide unprecedented information into the composition of the proteome, shedding light on the numerous complex biological processes actively shaping observed phenotypes. Herein, we detail a protocol for the exploration of intracellular proteomes through the large-scale, unbiased identification of proteins and their relative abundances using liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS). In general, this protocol is applicable to both microbial and eukaryotic systems.

Abraham, Paul↗

DOE OSTI2020

GeoRePORT Case Study Examples: Reporting Using the Geothermal Resource Portfolio Optimization and Reporting Technique (GeoRePORT)

The Geothermal Research Portfolio Optimization & Reporting Technique (GeoRePORT) was developed with funding from the United States Department of Energy's Geothermal Technologies Office (GTO) to assist in identifying and pursuing long-term investment strategies through the development of a resource reporting protocol. GeoRePORT provides scientists and non-scientists a comprehensive and quantitative means of reporting: (1) features intrinsic to geothermal sites (project grade) and, (2) maturity of the development (project readiness). Because geothermal feasibility is not determined by any single factor (e.g. temperature, permeability, permitting), a site's project grade and readiness are evaluated on twelve independent attributes pertaining to geological, technical, or socio-economic feasibility. In this paper, we present case studies illustrating how GeoRePORT can be used to compare geological, technical, and socio-economic attributes between geothermal systems. The consistent and objective assessment protocols used in GeoRePORT allow for comparison of project attributes across unique locations and geological settings. GeoRePORT case studies outline the geological, socio-economic and technical features of four individual geothermal sites: Coso, Chena, Dixie Valley, and White Sands Missile Range. The case studies presented herein illustrate the usefulness of GeoRePORT in evaluating project risk/return, identifying gaps in reported data, evaluating R&D impact, and gathering insights on successes/failures as applicable to future projects.

40 EE - Geothermal Technologies Office (EE-4G)↗

DOE OSTI2020

One step removed shadow network

A system and method includes an operational network that communicates with an external network by opening a first transmission protocol socket. A data diode coupled to the operational network and a gateway enables the one-way transfer of all information received from the external network and transmitted by the operational network to the gateway such that no information travels from the gateway to the operational network or the external network. The gateway opens a second transmission protocol socket by mapping a sequence number to an acknowledgement number and increasing that mapped acknowledgement number by a value of one. A transmitter then transmits the acknowledgment to a remote network or a gateway.

Park, Brent K.↗

DOE OSTI2021

Emergency Voltage Regulation in Power Systems via Ripple-Type Control: Preprint

With increasing penetration of volatile renewable generation and cyber-physical disruptions, ensuring safe operation of bulk power systems has become unprecedentedly challenging. Since communication and computational costs restrict centralized system dispatch to be called upon every few minutes; and purely local schemes are shown to be insufficient, distributed controls have been advocated for handling unanticipated system conditions in real time. However, the applicability of distributed control schemes is fundamentally limited by their need for widespread communication and model cognizance. In this con-text, we put forth a hybrid low-communication saturation-driven protocol for the coordination of control agents that are distributed over a physical system and are allowed to communicate with peers over a ‘hotline’ communication network. Under this protocol, when agents observe a constraint violation based on local measurements, they respond locally until their control resources saturate, in which case they send a beacon for assistance to peer agents. The scheme ensures that minor violations are efficiently mitigated via fast local controls, while severe violations may be handled by a collaboration of a relatively small set of agents. We evaluate the performance of this scheme via extensive numerical tests on the IEEE 14-bus test feeder, where agents act upon noisy measurements under diverse scenarios of random load variations and severe low/high voltage events.

distributed control↗

DOE OSTI2021

Ripple-Type Control for Enhancing Resilience of Networked Physical Systems: Preprint

Distributed control agents have been advocated as an effective means for improving the resiliency of our physical in-frastructures under unexpected events. While purely local control has been shown to be insufficient, centralized optimal resource allocation approaches can be slow. In this context, we put forth a hybrid low-communication saturation-driven protocol for the coordination of control agents that are distributed over a physicalsystem and are allowed to communicate with peers over a 'hot-line' communication network. According to this protocol, agents act upon on local readings unless their control resources have been depleted, in which case they send a beacon for assistance to peer agents. Our ripple-type scheme triggers communication locally only for the agents with saturated resources, and is proved to converge. Moreover, under a monotonicity assumption on the underlying physical law coupling control outputs to inputs, the devised control is proved to converge to a configuration satisfying safe operational constraints. The assumption is shown to hold for voltage control in electric power systems and pressure control in water distribution networks. Numerical tests on both networks corroborate the efficacy of the novel scheme.

distributed control↗

DOE OSTI2021

Introducing the GeoRePORT Resource Size Tool: Reporting on Geothermal Resource Size Estimations Using the Geothermal Resource Portfolio Optimization and Reporting Technique (GeoRePORT): Preprint

The Geothermal Resource Portfolio Optimization and Reporting Technique (GeoRePORT) was developed with funding from the U.S. Department of Energy Geothermal Technologies Office to assist in identifying and pursuing long-term investment strategies through the development of a resource reporting protocol. The assessment protocols used in GeoRePORT allow for comparison of project attributes across locations and geological settings to understand the feasibility of geothermal development. This work introduces the Resource Size Tool, a new feature within the GeoRePORT package that compiles two independent methods for estimating geothermal resource size in terms of energy capacity in MW. Energy production potential for twenty-three case studies was estimated with the Resource Size Tool in order to 1) generate a reasonable range of resource size estimates for a particular geothermal field; 2) illustrate the advantages and limitations of each methodology (such as data input requirements, estimate accuracy and precision, and the appropriate circumstances of use); and 3) test the ability of the resource size tool to provide useful and accurate information for geothermal stakeholders. The tool employs two methods widely used in the geothermal industry: (1) USGS Volumetric and (2) Power Density. Results from our case studies show general overlap between these two methods in terms of resource size estimates; however, they also reveal key differences between the two approaches that should be considered when using such estimates to drive development. First, the two methods rely on different input parameters and therefore one method may be more appropriate and/or accurate for a given project than the other. Second, the Power Density method was found to generate wider ranges of resource size predictions, more consistently aligning with actual power production of the field but with larger scales of error; whereas the USGS Volumetric method predicts narrower ranges but tends to overestimate when compared to current MW production. Future work will refine variables used in the methods with input data from other sections of GeoRePORT and modify uncertainty levels based on the particular datasets used for a given project.

geological↗

DOE OSTI2022

Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach

The unprecedented scientific achievements in combating the COVID-19 pandemic reflect a global response informed by unprecedented access to data. We now have the ability to rapidly generate a diversity of information on an emerging pathogen and, by using high-performance computing and a systems biology approach, we can mine this wealth of information to understand the complexities of viral pathogenesis and contagion like never before. These efforts will aid in the development of vaccines, antiviral medications, and inform policymakers and clinicians. Here we detail computational protocols developed as SARS-CoV-2 began to spread across the globe. They include pathogen detection, comparative structural proteomics, evolutionary adaptation analysis via network and artificial intelligence methodologies, and multiomic integration. These protocols constitute a core framework on which to build a systems-level infrastructure that can be quickly brought to bear on future pathogens before they evolve into pandemic proportions.

Teixeira Prates, Erica↗

DOE OSTI2022

Photovoltaic Module R&D Considerations for Soiling Mitigation

Photovoltaic (PV) modules work best in the sunniest environments. Unfortunately, often the sunniest places also have substantial amounts of airborne "dust" that deposits on the front surface of the modules and blocks the sunlight; reducing energy output. In fact, natural soiling has reduced the energy output of PV systems since the technology was first used, and viable mitigation strategies have remained elusive ever since. With the ever-increasing deployments around the world, especially in dusty environments, soiling is becoming a billion-dollar problem, worldwide. While substantial work has been done to examine and resolve some of the issues with PV soiling, often mitigation comes down to physically cleaning the modules. However, a more systematic evaluation of the different module properties correlations to soiling mitigation needs to be done. In many instances, the causal connections between module properties and soiling are simply not known. This lack of knowledge results in a substantial increase in time and effort to evaluate and qualify appropriate soiling mitigation protocols based on site specific issues and the intrinsic module properties that are typically not optimized for mitigating soiling in a given environment. Thus, module property protocols and/or standards are needed to more quickly help identify appropriate module and site-specific mitigation.

mitagation↗

DOE OSTI2022

Mapping entry invalidation

A memory access system may include a first memory address translator, a second memory address translator and a mapping entry invalidator. The first memory address translator translates a first virtual address in a first protocol of a memory access request to a second virtual address in a second protocol and tracks memory access request completions. The second memory address translator is to translate the second virtual address to a physical address of a memory. The mapping entry invalidator requests invalidation of a first mapping entry of the first mapping address translator requests invalidation of a second mapping entry of the second memory address translator corresponding to the first mapping entry following invalidation of the first mapping entry and based upon the tracked memory access request completions.

Walker, Shawn K.↗

DOE OSTI2022

Enhancing obfuscation of digital content through use of linear error correction codes

Technologies related to enhancing security of digital content are described. Linear error correction codes (LECCs) are employed for dual purposes: 1) to obfuscate digital content; and 2) to verify integrity of the digital content. A transmitter computing system obfuscates digital content based upon an obfuscation protocol, wherein the obfuscated digital content includes an LECC. A receiver computing system deobfuscates the digital content by performing the inverse of the obfuscation protocol.

Corral, Celestino A.↗