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DOE OSTI2022

Future changes in extreme precipitation over the San Francisco Bay Area: Dependence on atmospheric river and extratropical cyclone events

Extreme precipitation poses a major challenge for local governments, including the City and County of San Francisco, California, as flooding can damage and destroy infrastructure and property. As the climate continues to warm, reliable future precipitation projections are needed to provide the best possible information to decision makers. However, future changes in the magnitude of extreme precipitation are uncertain, as current state-of-the-art global climate models are typically run at relatively coarse horizontal resolutions that require the use of convective parameterization and have difficulty simulating observed extreme rainfall rates. Here, we performed ensembles of convection-permitting regional climate model simulations to investigate how five historically impactful extreme precipitation events over the San Francisco Bay Area could change if similar events occurred in future climates. We found that changes in storm-total precipitation depend strongly on storm type. Precipitation associated with an atmospheric river (AR) accompanied by an extratropical cyclone (ETC) is projected to increase at a rate exceeding (by up to 1.5 times) the theoretical Clausius Clapeyron scaling of 6–7% per °C warming. On the other hand, future precipitation changes are weak or negative for events characterized by an AR only, despite increases in precipitable water and integrated vapor transport that are similar to those of the co-occurring AR and ETC events. The differences in the sign of future precipitation change between AR-only events and co-occurring AR and ETC events is instead linked with changes in mid-tropospheric vertical velocity. Given that the majority of observed ARs are associated with an ETC, this research has important implications for future precipitation impacts over the Bay Area, as it indicates that storm-total precipitation associated with the most common type of storm event may increase by up to 26–37% in 2100 relative to historical.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Roles for Countercharge in the Voltage Sensor Domain of Ion Channels

Voltage-gated ion channels share a common structure typified by peripheral, voltage sensor domains. Their S4 segments respond to alteration in membrane potential with translocation coupled to ion permeation through a central pore domain. The mechanisms of gating in these channels have been intensely studied using pioneering methods such as measurement of charge displacement across a membrane, sequencing of genes coding for voltage-gated ion channels, and the development of all-atom molecular dynamics simulations using structural information from prokaryotic and eukaryotic channel proteins. One aspect of this work has been the description of the role of conserved negative countercharges in S1, S2, and S3 transmembrane segments to promote sequential salt-bridge formation with positively charged residues in S4 segments. These interactions facilitate S4 translocation through the lipid bilayer. In this review, we describe functional and computational work investigating the role of these countercharges in S4 translocation, voltage sensor domain hydration, and in diseases resulting from countercharge mutations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Characterization of nonlinear ultrasonic waves behavior while interacting with poor interlayer bonds in large-scale additive manufactured materials

Over the past decades, researchers have developed several nonlinear ultrasonic techniques for quality control of materials commonly used in different applications. Owing to the superior sensitivity of nonlinear ultrasound waves to small defects such as micro-cracks, their applicability in different nondestructive testing (NDT) problems has been investigated in numerous studies. These studies utilize frequency domain analysis to detect the generation of higher harmonics because of the formation of defects in the inspected medium. Frequency domain analysis based on the Fourier transform is a significant approach used in linear systems; however, it may not perform adequately on nonlinear systems. Hence, studies on nonlinear dynamics and physics consider analyzing systems' behavior in the phase-space domain. In contrast to the frequency domain analysis, which can result in information loss, analysis in the phase-space domain retains all the information regarding a system's states. Here, we investigate the nonlinearities induced by poor interlayer bonding in polymer-based additive manufactured parts in the phase-space domain. It is convenient to characterize the nonlinearity in the phase-space domain because it provides a geometrical representation of a system's states. Two types of low quality interlayer bond are considered. The first type is simulated artificially while the second type is manufactured by reducing the bond quality during the printing process. The analysis verified that the received ultrasonic signals exhibit classical nonlinear behavior in the phase-space domain while interacting with simulated poor interlayer bonds. In addition, the results showed that the behavior of ultrasonic waves is amplitude-dependent and evolves into models that have not been previously reported. Furthermore, Largest Lyapunov Exponent (LLE) is used to quantify the behavior of nonlinear ultrasonic waves while interacting with poor interlayer bonds. Using LLE, it was observed that the divergence rate of the phase-space trajectories depends on the amplitude of the excitation. This observation quantitatively proves that nonlinear behavior of ultrasound while interacting with poor interlayer bonds can be amplitude-dependent. The results of both simulated and inherent poor interlayer bond cases showed that LLE can be used as a reliable quantitative damage-sensitive feature to detect and potentially characterize weak bonds, which are difficult to detect using conventional approaches. Additionally, the reported results in the phase-space domain provide a basis for proposing a new mathematical model for ultrasonic waves interacting with poor interlayer bonds.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Data and scripts associated with a manuscript investigating impacts of solid phase extraction on freshwater organic matter optical signatures and mass spectrometry pairing

This data package is associated with the publication “Investigating the impacts of solid phase extraction on dissolved organic matter optical signatures and the pairing with high-resolution mass spectrometry data in a freshwater system” submitted to “Limnology and Oceanography: Methods.” This data is an extension of the River Corridor and Watershed Biogeochemistry SFA’s Spatial Study 2021 (https://doi.org/10.15485/1898914). Other associated data and field metadata can be found at the link provided. The goal of this manuscript is to assess the impact of solid phase extraction (SPE) on the ability to pair ultra-high resolution mass spectrometry data collected from SPE extracts with optical properties collected on ambient stream samples. Forty-seven samples collected from within the Yakima River Basin, Washington were analyzed dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC), absorbance, and fluorescence. Samples were subsequently concentrated with SPE and reanalyzed for each measurement. The extraction efficiency for the DOC and common optical indices were calculated. In addition, SPE samples were subject to ultra-high resolution mass spectrometry and compared with the ambient and SPE generated optical data. Finally, in addition to this cross-platform inter-comparison, we further performed and intra-comparison among the high-resolution mass spectrometry data to determine the impact of sample preparation on the interpretability of results. Here, the SPE samples were prepared at 40 milligrams per liter (mg/L) based on the known DOC extraction efficiency of the samples (ranging from ~30 to ~75%) compared to the common practice of assuming the DOC extraction efficiency of freshwater samples at 60%. This data package folder consists of one main data folder with one subfolder (Data_Input). The main data folder contains (1) readme; (2) data dictionary (dd); (3) file-level metadata (flmd); (4) final data summary output from processing script; and (5) the processing script. The R-markdown processing script (SPE_Manuscript_Rmarkdown_Data_Package.rmd) contains all code needed to reproduce manuscript statistics and figures (with the exception of that stated below). The Data_Input folder has two subfolders: (1) FTICR and (2) Optics. Additionally, the Data_Input folder contains dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data (SPS_NPOC_Summary.csv) and relevant supporting Solid Phase Extraction Volume information (SPS_SPE_Volumes.csv). Methods information for the optical and FTICR data is embedded in the header rows of SPS_EEMs_Methods.csv and SPS_FTICR_Methods.csv, respectively. In addition, the data dictionary (SPS_SPE_dd.csv), file level metadata (SPS_SPE_flmd.csv), and methods codes (SPS_SPE_Methods_codes.csv) are provided. The FTICR subfolder contains all raw FTICR data as well as instructions for processing. In addition, post processed FTICR molecular information (Processed_FTICRMS_Mol.csv) and sample data (Processed_FTICRMS_Data.csv) is provided that can be directly read into R with the associated R-markdown file. The Optics subfolder contains all Absorbance and Fluorescence Spectra. Fluorescence spectra have been blank corrected, inner filter corrected, and undergone scatter removal. In addition, this folder contains Matlab code used to make a portion of Figure 1 within the manuscript, derive various spectral parameters used within the manuscript, and used for parallel factor analysis (PARAFAC) modeling. Spectral indices (SPS_SpectralIndices.csv) and PARAFAC outputs (SPS_PARAFAC_Model_Loadings.csv and SPS_PARAFAC_Sample_Scores.csv) are directly read into the associated R-markdown file. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected some of these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

The CYBER security – Competency Health and Maturity Progression (CYBER-CHAMP) model: Extending the National Initiative for Cybersecurity Education (NICE) Framework Across Organizational Security

Problem Statement: There is a pervasive talent deficit in the cybersecurity industry that prevents employers from being able to fill their open positions efficiently. A holistic approach to security is required to ensure organizations have adequate prevention and response capabilities in case of a cyberattack. Specifically, industrial control systems (ICS’s) and their operational technology (OT) components have become a constant target for cyberattacks. Research Questions: It is proposed that the NICE Framework should be extended in the following areas: 1) Include guidance regarding the job roles and competencies for both IT and OT professionals. 2) Offer step-by-step solutions, based on the work role mappings from the NICE Framework, to increase cybersecurity through employee training and education. 3) Provide a streamlined, lifecycle approach to building a cybersecurity program. Contribution: The CYBER security – Competency Health and Maturity Progression (CYBER-CHAMP©) model provides a customized solution for businesses to understand their education gaps in organizational security and target areas for improvement. Rationale: The Framework for Improving Critical Infrastructure Cybersecurity v1.1 addresses ICS but does not offer a measurement of cybersecurity maturity or clear methods to ascertain an organization’s current risk profile. In Phases 1 and 5 of the model, measurements are provided to help an organization build their current and target risk profiles. The NICE framework provides a structure for planning an IT cybersecurity workforce, but the OT aspects of cybersecurity are only briefly discussed. The model uses Phases 2-3 to examine the competencies of an organization’s workforce, which includes both IT and OT roles. Current frameworks do not offer next steps to increase an organization’s cybersecurity. During Phase 4, employees’ roles are mapped to training, education, and/or certifications from common vendors. Investigative Approach: The model provides measurements and metrics for both an organization’s status and continual improvement. This improvement methodology includes guidance for creating an overall strategic plan for security improvement via products designed to increase an organization’s operational readiness through workforce competency health. Lessons Learned: Depending on who was participating, there were contradicting answers given in Phase 1 due to different security cultures in the organization. This revelation has influenced the steps listed in the User’s Guide, where Phase 1’s first recommended step is to assemble a team that champions the facilitation and implementation of the model in the organization. During Phase 2, the discovery was made that organizations may be missing roles that are necessary to perform critical cybersecurity functions. By understanding the functional roles and competencies needed, they can contract or hire cybersecurity help to fill these gaps. Implications: Using the model, organizations can discuss quantitative measures for improvement as a business case for advancing their security program. Future research can validate and extend the present theory and model to a variety of environments. It is of interest to investigate additional security roles and knowledge domains that are used to build standardized cybersecurity curriculum.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Stabilizing a strongly nonlinear structure through shaker dynamics in fixed frequency voltage control tests

Bifurcations are commonly encountered during force controlled swept and stepped sine testing of nonlinear structures, which generally leads to the so-called jump-down or jump-up phenomena between stable solutions. There are various experimental closed-loop control algorithms, such as control-based continuation and phase-locked loop, to stabilize dynamical systems through these bifurcations, but they generally rely on specialized control algorithms that are not readily available with many commercial data acquisition software packages. A recent method was developed to experimentally apply sequential continuation using the shaker voltage that can be readily deployed using commercially available software. By utilizing the stabilizing effects of electrodynamic shakers and the force dropout phenomena in fixed frequency voltage control sine tests, this approach has been demonstrated to stabilize the unstable branch of a nonlinear system with three branches, allowing for three multivalued solutions to be identified within a specific frequency bandwidth near resonance. Recent testing on a strongly nonlinear system with vibro-impact nonlinearity has revealed jumping behavior when performing sequential continuation along the voltage parameter, like the jump phenomena seen during more traditional force controlled swept and stepped sine testing. Here, this paper investigates the stabilizing effects of an electrodynamic shaker on strongly nonlinear structures in fixed frequency voltage control tests using both numerical and experimental methods. The harmonic balance method is applied to the coupled shaker-structure system with an electromechanical model to simulate the fixed voltage control tests and predict the stabilization for different parameters of the model. The simulated results are leveraged to inform the design of a set of experiments to demonstrate the stabilization characteristics on a fixture-pylon assembly with a vibro-impact nonlinearity. Through numerical simulation and experimental testing on two different strongly nonlinear systems, the various parameters that influence the stability of the coupled shaker-structure are revealed to better understand the performance of fixed frequency voltage control tests.

42 ENGINEERING↗

DOE OSTI2022

Beyond carbon flux partitioning: Carbon allocation and nonstructural carbon dynamics inferred from continuous fluxes

Carbon (C) allocation and nonstructural carbon (NSC) dynamics play essential roles in plant growth and survival under stress and disturbance. However, quantitative understanding of these processes remains limited. Here, in this work, we propose a framework where we connect commonly measured carbon cycle components (eddy covariance fluxes of canopy CO 2 exchange, soil CO 2 efflux, and allometry-based biomass and net primary production) by a simple mass balance model to derive ecosystem-level NSC dynamics (NSC i ), C translocation (dC i ), and the biomass production efficiency (BPE i ) in above- and belowground plant (i = agp and bgp) compartments. We applied this framework to two long-term monitored loblolly pine (Pinus taeda) plantations of different ages in North Carolina and characterized the variations of NSC and allocation in years under normal and drought conditions. The results indicated that the young stand did not have net NSC flux at the annual scale, whereas the mature stand stored a near-constant proportion of new assimilates as NSC every year under normal conditions, which was comparable in magnitude to new structural growth. Roots consumed NSC in drought and stored a significant amount of NSC post drought. The above- and belowground dC i and BPE i varied more from year to year in the young stand and approached a relatively stable pattern in the mature stand. The belowground BPE bgp differed the most between the young and mature stands and was most responsive to drought. With the internal C dynamics quantified, this framework may also improve biomass production estimation, which reveals the variations resulting from droughts. Overall, these quantified ecosystem-scale dynamics were consistent with existing evidence from tree-based manipulative experiments and measurements and demonstrated that combining the continuous fluxes as proposed here can provide additional information about plant internal C dynamics. Given that it is based on broadly available flux data, the proposed framework is promising to improve the allocation algorithms in ecosystem C cycle models and offers new insights into observed variability in soil–plant–climate interactions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Orientation-Dependent Nanomechanical Behavior of Pentaerythritol Tetranitrate as Probed by Multiple Nanoindentation Tip Geometries

Nanoindentation can be leveraged to aid in the high fidelity modeling of dislocation mediated plasticity in pentaerythritol tetranitrate (PETN), an anisotropic energetic molecular crystal. Moreover, nanoindentation tip parameters such as tip geometry, size, and degree of acuity can be utilized to target anisotropic behavior. In this work, nanoindentation was conducted across a range of orientations on the (110) face of PETN to characterize resultant yield behavior, mechanical property measurements, and resultant slip behavior and fracture initiation. Three different indentation tips were utilized: a 3-sided pyramidal Berkovich tip, a 4-sided high aspect ratio Knoop tip, and a 90° conical tip. Ultimately, indenter tip radius was documented to impact yield behavior, whereas tip geometry affected larger scale processes such as slip, and tip acuity was the dominating factor that led to fracture. The axisymmetric conical tip, serving as a baseline, showed the least amount of variation in mechanical property measurements but also the largest distribution of maximum shear stress at which initial yielding occurred. Its high degree of acuity, however, was more prone to induce fracture at higher loads. The Knoop tip was shown to be suitable for average measurements, but also for elucidation of certain anisotropic features. A distinctly higher perceived hardness at 45° was measured with the Knoop tip, indicating less dislocation motion in that direction also observed in this work via scanning probe microscopy. Lastly, the commonly used Berkovich tip was a good compromise whereby it provided a representative volume element describing the average behavior of the material. These results can be utilized to target desired anisotropic behavior in a wider range of molecular crystals, as well as to inform theoretical considerations for dislocation mediated plasticity in PETN.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

High-throughput screening tools facilitate calculation of a combined exposure-bioactivity index for chemicals with endocrine activity

High-throughput and computational tools provide a new opportunity to calculate combined bioactivity of exposure to diverse chemicals acting through a common mechanism. We used high throughput in vitro bioactivity data and exposure predictions from the U.S. EPA’s Toxicity and Exposure Forecaster (ToxCast and ExpoCast) to estimate combined estrogen receptor (ER) agonist activity of non-pharmaceutical chemical exposures for the general U.S. population. High-throughput toxicokinetic (HTTK) data provide conversion factors that relate bioactive concentrations measured in vitro (µM), to predicted population geometric mean exposure rates (mg/kg/day). These data were available for 22 chemicals with ER agonist activity and were estimated for other ER bioactive chemicals based on the geometric mean of HTTK values across chemicals. For each chemical, ER bioactivity across ToxCast assays was compared to predicted population geometric mean exposure at different levels of in vitro potency and model certainty. Dose additivity was assumed in calculating a Combined Exposure-Bioactivity Index (CEBI), the sum of exposure/bioactivity ratios. Combined estrogen bioactivity was also calculated in terms of the percent maximum bioactivity of chemical mixtures in human plasma using a concentration-addition model. Estimated CEBIs vary greatly depending on assumptions used for exposure and bioactivity. In general, CEBI values were <1 when using median of the estimated general population chemical intake rates, while CEBI were ≥1 when using the upper 95th confidence bound for those same intake rates for all chemicals. Concentration-addition model predictions of mixture bioactivity yield comparable results. Based on current in vitro bioactivity data, HTTK methods, and exposure models, combined exposure scenarios sufficient to influence estrogen bioactivity in the general population cannot be ruled out. Future improvements in screening methods and computational models could reduce uncertainty and better inform the potential combined effects of estrogenic chemicals.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Holocene paleoclimate change in the western US: The importance of chronology in discerning patterns and drivers

We report sediment in lakes and meadows forms a powerful archive that can be used to reconstruct environmental change through time. Reconstructions of lake level, of chemical, biological, and hydrological conditions, and of surrounding vegetation provide detailed information about past climate conditions, both locally and regionally. Indeed, most of our current knowledge of centennial- to millennial-scale climate variability in the arid western United States, where information about past hydroclimate is particularly important, comes from such sediment-based reconstructions. The pressing need for robust, precise predictions of future conditions is a significant motivation for paleoclimate science, and current research questions frequently require Holocene reconstructions to be resolved at sub-centennial timescales. Increasingly, regional syntheses seek to identify synoptic-scale patterns similar to those defined from modern observations (seasonal, interannual, multi-decadal, etc.) or to compare with the output of climate model simulations. However, the age control on existing records, especially those more than about 20 years old, is often sufficient only for millennial-scale interpretation. Here we assess the age control for 84 published and unpublished records from lakes and meadows in the Great Basin, California, and desert southwest, and use Bayesian modeling to evaluate the 95% uncertainty ranges for the 42 best-dated records. In the Late Holocene, about half of the 42 records have <400-year mean uncertainty ranges; however, high-precision age control is especially critical for young records, used to develop an accurate understanding of a proxy’s response to known climate variations. In the Middle Holocene, records vary from 400 to >800-year mean uncertainty and records of the Early Holocene have 600- to >1400-year mean uncertainty ranges. We find that the largest control on modeled uncertainties is dating density, with at least 2 dates/kyr being optimal and suggest obtaining “range-finder” dates at the onset of a study to better predict the total number of dates needed for an adequate age model. Such a density avoids a commonly observed phenomenon of significant peaks in uncertainty arising in gaps between age control points. Analysis of the uncertainties associated with proxy shifts reveal that more than half are >400 years. Although such large uncertainties currently prevent sub-centennial interpretations in most cases, increased dating density, strategic use of limited funds (including budgeting for a 2 date/kyr minimum at the proposal stage), construction of age-depth models with Bayesian methods, and critical evaluation of chronological uncertainty will shed light on past climate variability at finer timescales, enhancing our understanding of global and regional drivers of western U.S. climate.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

RF-Net 2: fast inference of virus reassortment and hybridization networks

Abstract Motivation A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method called RF-Net for accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens. Results Here, we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, called Fast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. In addition, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical IAV evolutionary analyses. Availability and implementation RF-Net 2 is available at https://github.com/flu-crew/rf-net-2. Supplementary information Supplementary data are available at Bioinformatics online.

Markin, Alexey (ORCID:0000000332809050)↗

DOE OSTI2021

Long-run Marginal CO2 Emission Rates Workbooks for 2020 Standard Scenarios Cambium Data

This dataset has been superseded by a new set of workbooks that can be found here: https://data.nlr.gov/submissions/183 These workbooks contain modeled estimates of long-run marginal CO2 emission rates (LRMER) for the contiguous United States. The LRMER is an estimate of the rate of emissions that would be either induced or avoided by a long-term (i.e., more than several years) change in electrical demand. It incorporates both the projected changes to the electric grid, as well as the potential for an incremental change in electrical demand to influence the structural evolution of the grid (i.e., the building and retiring of capital assets, such as generators and transmission lines). It is therefore distinct from the more-commonly-known short-run marginal, which treats grid assets as fixed. In addition to year-over-year data, the Levelized LRMER worksheet within each workbook is set up to produce a levelized long-run marginal emission rate based on user-provided inputs. These levelized LRMER values are intended for analysts to use when estimating the emissions induced (or avoided) by a long-term change in end-use electricity demand. Three future scenarios are provided in separate workbooks: A Mid-case (i.e., business-as-usual), and two scenarios with relatively higher or lower renewable energy costs. For more details on these scenarios, see the Standard Scenarios 2020 Report ( https://www.nlr.gov/docs/fy21osti/77442.pdf ). For more data underlying each scenario, see the Standard Scenarios 2020 project (Cambium data) at https://cambium.nlr.gov/ . This data was produced as part of the Cambium project. For more details about the methodology, see the Cambium Documentation: Version 2020 ( https://www.nlr.gov/docs/fy21osti/78239.pdf ). This data is planned to be updated annually. Information on the latest versions can be found at https://www.nlr.gov/analysis/cambium.html .

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Long-run Marginal Emission Rates for Electricity - Workbooks for 2021 Cambium Data

These workbooks contain modeled estimates of long-run marginal emission rates (LRMER) for the contiguous United States. The LRMER is an estimate of the rate of emissions that would be either induced or avoided by a long-term (i.e., more than several years) change in electrical demand. It incorporates both the projected changes to the electric grid, as well as the potential for an incremental change in electrical demand to influence the structural evolution of the grid (i.e., the building and retiring of capital assets, such as generators and transmission lines). It is therefore distinct from the more-commonly-known short-run marginal, which treats grid assets as fixed. The Levelized LRMER worksheet within each workbook is set up to produce a levelized long-run marginal emission rate based on user-provided inputs. These levelized LRMER values are intended for analysts to use when estimating the emissions induced (or avoided) by a long-term change in end-use electricity demand. There are two workbooks that supply the data at two different geographic resolutions: states and GEA regions (20 regions that are similar to, but not exactly the same as, the US EPA's eGRID regions). For more data underlying these emissions factors, see the Cambium 2021 project at https://cambium.nrel.gov/. For more details on the inputs into the scenarios available in the workbooks, see the Standard Scenarios 2021 Report (https://www.nrel.gov/docs/fy22osti/80641.pdf). This data was produced as part of the Cambium project. For more details about the methodology, see the Cambium Documentation: Version 2021 (https://www.nrel.gov/docs/fy22osti/81611.pdf). This data is planned to be updated annually. Information on the latest versions can be found at https://www.nrel.gov/analysis/cambium.html.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Height Above Nearest Drainage (HAND) and Hydraulic Property Table for CONUS

The continental flood inundation mapping (CFIM) framework is a high-performance computing (HPC)-based computational framework for the Height Above Nearest Drainage (HAND)-based inundation mapping methodology. Using the 10m Digital Elevation Model (DEM) data produced by U.S. Geological Survey (USGS) 3DEP (the 3-D Elevation Program) and the NHDPlus hydrography dataset produced by USGS and the U.S. Environmental Protection Agency (EPA), a hydrological terrain raster called HAND is computed for HUC6 units in the conterminous U.S. (CONUS). The value of each raster cell in HAND is an approximation of the relative elevation between the cell and its nearest water stream. Derived from HAND, a hydraulic property table is established to calculate river geometry properties for each of the 2.7 million river reaches covered by NHDPlus (5.5 million kilometers in total length). This table is a lookup table for water depth given an input stream flow value. Such lookup is available between water depth 0m and 25m at 1-foot interval. The flood inundation map is then computed by using HAND and this lookup table based on the near real-time water forecast from the National Water Model (NWM) at the National Oceanic and Atmospheric Administration (NOAA). HAND and the Hydraulic Property Table version 0.2. is created to correspond to data updates in the USGS 1/3 arcsec DEM, the USGS National Hydrography Dataset, including its Water Boundary Dataset, and the NHDPlus medium resolution dataset. This dataset comprises 331 HUC6 units for CONUS (excluding the five great lakes units), each is a downloadable zip file. Version 0.1 was computed at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urban-Champaign in 2016 and is currently hosted at the Texas Advanced Computing Center (TACC). Please cite this data DOI and the following publications and data DOIs when you use HAND and the hydraulic property table: Liu, Yan Y., David R. Maidment, David G. Tarboton, Xing Zheng, and Shaowen Wang. 'A CyberGIS integration and computation framework for high-resolution continental-scale flood inundation mapping.' JAWRA Journal of the American Water Resources Association 54, no. 4 (2018): 770-784. DOI: 10.1111/1752-1688.12660 Zheng, Xing, David G. Tarboton, David R. Maidment, Yan Y. Liu, and Paola Passalacqua. 'River channel geometry and rating curve estimation using height above the nearest drainage.' JAWRA Journal of the American Water Resources Association 54, no. 4 (2018): 785-806. DOI: 10.1111/1752-1688.12661 Liu, Y. (2018). Height Above Nearest Drainage (HAND) for CONUS - v0.1, HydroShare, https://doi.org/10.4211/hs.69f7d237675c4c73938481904358c789 LICENSE FOR USE -- MAPS AND DATA DISCLAIMER This resource is shared under the Creative Commons Attribution CC BY, http://creativecommons.org/licenses/by/4.0/ MAPS AND DATA DISCLAIMER The Oak Ridge National Laboratory (ORNL) shall not be held liable for improper or incorrect use of the data described or information contained on this map or associated series of maps. The data and related map graphics are not legal, land survey or engineering documents and are not intended to be used as such. ORNL gives no warranty, express or implied, as to the accuracy, reliability, utility or completeness of this information. The user of these maps and data assumes all responsibility and risk for the use of the maps and data. ORNL disclaims all warranties, representations or endorsements either express or implied, with regard to the information contained in this map product, including, but not limited to, all implied warranties of merchantability, fitness for a particular purpose or non-infringement. This preliminary map product is for research and review purposes only. It is not intended to be used for emergency management operational or life safety decisions at the local or regional governmental level or by the general public. Users requiring information regarding hazardous conditions or meteorological conditions for specific geographic areas should consult directly with their city or county emergency management office.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Relating land surface, water table, and weathering fronts with a conceptual valve model for headwater catchments

Knowing little about how porosity and permeability are distributed at depth, we commonly develop models of groundwater by treating the subsurface as a homogeneous black box even though porosity and permeability vary with depth. One reason for this depth variation is that infiltrating meteoric water reacts with minerals to affect porosity in localized zones called reaction fronts. We are beginning to learn to map and model these fronts beneath headwater catchments and show how they are distributed. The subsurface landscapes defined by these fronts lie subparallel to the earth-air interface but with lower relief. They can be situated above, below, or at the water table. These subsurface landscapes of reaction are important because porosity developed from weathering can control subsurface water storage. In addition, porosity often changes at the weathering fronts, and when this affects permeability significantly, the front can act like a valve that re-orients water flowing through the subsurface. We explore controls on the positions of reaction fronts under headwater landscapes by accounting for the timescales of erosion, chemical equilibration, and solute transport. One strong control on the landscape of subsurface reaction is the land surface geometry, which is in turn a function of the erosion rate. In addition, the reaction fronts, like the water table, are strongly affected by the lithology and water infiltration rate. We hypothesize that relationships among the land surface, reaction fronts, and the water table are controlled by feedbacks that can push landscapes toward an “ideal hill”. In this steady state, reaction-front valves partition water volumes into shallow and deep flowpaths. Furthermore, these flows dissolve low- and high-solubility minerals, respectively, allowing their reaction fronts to advance at the erosion rate. This conceptualization could inform better models of subsurface porosity and permeability, replacing the black box.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Unifying principles for catalytic hydrotreating processes (Final Technical Report)

This project builds on the hypothesis that the hydrotreating processes for the removal of oxygen and sulfur are fundamentally similar at the atomic-scale and existing knowledge from the treatment of petroleum derived feedstock can be leveraged for the design of novel catalysts for the upgrade of bio-oil. We tested this hypothesis by comparing computed potential energy diagrams for hydrodesulfurization (HDS) of thiophene over MoS 2 with hydrodeoxygenation (HDO) of furan over MoO 3 and concluded that certain aspects, such as catalyst promotion with transition metals, are valid strategies for both reactions. On the other hand, we also noticed significant differences in the mechanism for hydrogen (H 2 ) activation, which requires sites with metallic character. While MoS 2 is known to have metallic edge states that can catalyze H 2 dissociation, this elementary step is prohibitively slow on defect-free oxides. Only in the presence of vacancies or by creating metal/oxide interfaces can efficient H 2 activation sites during HDO be formed. The need for bifunctional catalyst when it comes to efficient and selective HDO or dehydrogenation reactions was further corroborated in joint experimental and theoretical studies of the Guerbet reaction for the coupling of biomass derived oxygenates over PdCu alloys, nitrate reduction over In-promoted Pd nanoparticles, and ethylene dehydroaromatization over Ga-exchanged ZSM-5 zeolites. All of these catalytic systems have in common that catalytic sites with distinct functional requirements are needed to create a working catalyst. Detailed computational studies were carried out for HDO of m -cresol and phenol on Ru-modified TiO 2 surfaces, which allowed us to attribute catalytic activity to the metal/oxide interface. A surprising finding was that heterolytic cleavage of the H-H bond across the Ru/TiO 2 interface was critically important, despite lower barriers for homolytic H 2 activation on Ru metal. The explanation lies in the high barriers for hydrogen spillover from Ru to TiO 2 , which becomes unnecessary in the heterolytic activation pathway. Moreover, we also reported that proton transfer steps between metal and oxide sites are mediated by weakly adsorbed surface water. During attempts to develop and validate a kinetic Monte Carlo (kMC) model for HDO reactions at the Ru/TiO 2 interface, it became clear that lateral interactions are paramount to describe realistic surface chemistry and without these interactions, the reduction and hydroxylation behavior from our simulations was inconsistent with reported experiments. To assess the importance of lateral interactions in popular computational catalyst design strategies relying on the identification of reactivity descriptors, which can be used along with Brønsted–Evans–Polanyi (BEP) and scaling relations as input to a microkinetic model (MKM) to make predictions for activity or selectivity trends, we compared predicted trends with those obtained from descriptor-based kMC models. We critically evaluated the benefits of kMC over MKM in terms of trend predictions and computational cost when using only a small set of input parameters. After confirming that in the absence of lateral interactions the kMC and MKM approaches yield identical trends and mechanistic information, we observed substantial differences between the two kinetic models when lateral interactions were introduced. The mean-field implementation applies coverage corrections directly to the descriptors, causing an artificial overprediction of the activity of strongly binding metals. In contrast, the cluster expansion in kMC implementation can differentiate among the highly active metals but it is very sensitive to the set of included interaction parameters. Considering that computational screening relies on a minimal set of descriptors, for which MKM makes reasonable trend predictions at a ca. three orders of magnitude lower computational cost than kMC, we concluded that the MKM approach does provide an overall better entry point for computational catalyst design. Overall, this project has led to 11 peer-reviewed publications, and their scientific is impact is well illustrated by their combined 702 citations.

08 HYDROGEN↗