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At least 325 records · Page 18

Substitution Models of Protein Evolution with Selection on Enzymatic Activity

Abstract Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme–substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.

Ferreiro, David↗

2005 Washoe County Travel Characteristics Study

The primary objective of the 2005 Washoe County Travel Characteristics Study was to document travel behavior data characteristics of regional households in Washoe County, Nevada, in order to update the regional transportation model. The household travel survey, which was conducted from October through November, was one of several surveys conducted in the fall of 2005 for the Regional Transportation Commission (RTC) of Washoe County, with the other surveys focusing on documenting transit usage, visitor travel behavior, and external travel through the region. The data collected were drawn from 1,174 households within the RTC planning area and contain information about 2,679 household members, 2,138 vehicles, and 11,077 unlinked trips. The household travel survey entailed the collection of activity and travel information for all household members regardless of age during a specific 24-hour period. The survey relied on the willingness of regional households to 1) provide demographic information about their household, its members, and its vehicles and 2) have all household members record all travel and activity for a specific 24-hour period, including address information for all locations visited, trip purpose, mode, and travel times.

1Hz data↗

U-Surf: a global 1 km spatially continuous urban surface property dataset for kilometer-scale urban-resolving Earth system modeling

High-resolution urban climate modeling has faced substantial challenges due to the absence of a globally consistent, spatially continuous, and accurate dataset to represent the spatial heterogeneity of urban surfaces and their biophysical properties. This deficiency has long obstructed the development of urban-resolving Earth system models (ESMs) and ultra-high-resolution urban climate modeling, over large domains. Here, we present U-Surf, a first-of-its-kind 1 km resolution present-day (circa 2020) global continuous urban surface parameter dataset. Using the urban canopy model (UCM) in the Community Earth System Model as a base model for satisfying dataset requirements, U-Surf leverages the latest advances in remote sensing, machine learning, and cloud computing to provide the most relevant urban surface biophysical parameters, including radiative, morphological, and thermal properties, for UCMs at the facet and canopy level. Generated using a systematically unified workflow, U-Surf ensures internal consistency among key parameters, making it the first globally coherent urban canopy surface dataset. U-Surf significantly improves the representation of the urban land heterogeneity both within and across cities globally; provides essential, high-fidelity surface biophysical constraints to urban-resolving ESMs; enables detailed city-to-city comparisons across the globe; and supports next-generation kilometer-resolution Earth system modeling across scales. U-Surf parameters can be easily converted or adapted to various types of UCMs, such as those embedded in weather and regional climate models, as well as air quality models. The fundamental urban surface constraints provided by U-Surf can also be used as features for machine learning models and can have other broad-scale applications for socioeconomic, public health, and urban planning contexts. We expect U-Surf to advance the research frontier of urban system science, climate-sensitive urban design, and coupled human–Earth systems in the future. The dataset is publicly available at https://doi.org/10.5281/zenodo.11247598 (Cheng et al., 2024).

Cheng, Yifan [Univ. of Illinois at Urbana-Champaig↗

Host-region parameters for an adjustable model for crustal earthquakes to facilitate the implementation of the backbone approach to building ground-motion logic trees in probabilistic seismic hazard analysis

The backbone approach to constructing a ground-motion logic tree for probabilistic seismic hazard analysis (PSHA) can address shortcomings in the traditional approach of populating the branches with multiple existing, or potentially modified, ground-motion models (GMMs) by rendering more transparent the relationship between branch weights and the resulting distribution of predicted accelerations. To capture epistemic uncertainty in a tractable manner, there are benefits in building the logic tree through the application of successive adjustments for differences in source, path, and site characteristics between the host region of the selected backbone GMM and the target region for which the PSHA is being conducted. The implementation of this approach is facilitated by selecting a backbone GMM that is amenable to such host-to-target adjustments for individual source, path, and site characteristics. The NGA-West2 GMM of Chiou and Youngs (CY14) has been identified as a highly adaptable model for crustal seismicity that is well suited to such adjustments. Rather than using generic source, path, and site characteristics assumed appropriate for the host region, the final suite of adjusted GMMs for the target region will be better constrained if the host-region parameters are defined specifically on the basis of their compatibility with the CY14 backbone GMM. To this end, making use of a recently developed crustal shear-wave velocity profile consistent with CY14, we present an inversion of the model to estimate the key source and path parameters, namely the stress parameter and the anelastic attenuation. With these outputs, the effort in constructing a ground-motion logic tree for any PSHA dealing with crustal seismicity can be focused primarily on the estimation of the target-region characteristics and their associated uncertainties. The inversion procedure can also be adapted for any application in which different constraints might be relevant.

Stafford, Peter J.↗

Simulation of a High-Confinement Tidal Energy Array (Abstract)

When the projected area of a current turbine array occupies a substantial fraction of a tidal or river channel cross-sectional area, the confinement associated with the channel boundaries substantially increases turbine efficiency. This effect can be exploited to substantially reduce the levelized cost of energy for current turbine arrays. However, the presence of such an array will affect inflow velocity, water depth, and circulation in the surrounding area. This has implications for array performance and environmental impacts. This project combines existing numerical modeling capability from PNNL with an understanding of confined array performance from UW. The work will 1) Simulate tidal currents and water surface elevation in a regional circulation model that includes the Knik Arm site at appropriate resolution; 2) Incorporate a varying thrust coefficient into this model that reflects the outcomes of tidal hydrodynamic simulations of confined turbine arrays; 3) Use the model to determine the effects of array operation on water levels and inflow conditions as a function of different blockage ratios and control strategies; and 4) Identify the “far field” environmental implications of operating an array of this type. UW will use the outputs from this model to evaluate the implications of “feedback effects” and variable inflow conditions on levelized cost of energy estimates for a confinement exploiting array of cross-flow turbines.

16 TIDAL AND WAVE POWER↗

Statistical emulation of a perturbed basal melt ensemble of an ice sheet model to better quantify Antarctic sea level rise uncertainties

Abstract. Antarctic ice shelves are vulnerable to warming ocean temperatures, and some have already begun thinning in response to increased basal melt rates. Sea level is therefore expected to rise due to Antarctic contributions, but uncertainties in its amount and timing remain largely unquantified. In particular, there is substantial uncertainty in future basal melt rates arising from multi-model differences in thermal forcing and how melt rates depend on that thermal forcing. To facilitate uncertainty quantification in sea level rise projections, we build, validate, and demonstrate projections from a computationally efficient statistical emulator of a high-resolution (4 km) Antarctic ice sheet model, the Community Ice Sheet Model version 2.1. The emulator is trained to a large (500-member) ensemble of 200-year-long 4 km resolution transient ice sheet simulations, whereby regional basal melt rates are perturbed by idealized (yet physically informed) trajectories. The main advantage of our emulation approach is that by sampling a wide range of possible basal melt trajectories, the emulator can be used to (1) produce probabilistic sea level rise projections over much larger Monte Carlo ensembles than are possible by direct numerical simulation alone, thereby providing better statistical characterization of uncertainties, and (2) predict the simulated ice sheet response under differing assumptions about basal melt characteristics as new oceanographic studies are published, without having to run additional numerical ice sheet simulations. As a proof of concept, we propagate uncertainties about future basal melt rate trajectories, derived from regional ocean models, to generate probabilistic sea level rise estimates for 100 and 200 years into the future.

97 MATHEMATICS AND COMPUTING↗

Projected Changes in Temperature and Precipitation Over the United States, Central America, and the Caribbean in CMIP6 GCMs

The Coupled Model Intercomparison Project Phase 6 (CMIP6) dataset is used to examine projected changes in temperature and precipitation over the United States (U.S.), Central America and the Caribbean. The changes are computed using an ensemble of 31 models for three future time slices (2021–2040, 2041–2060, and 2080–2099) relative to the reference period (1995–2014) under three Shared Socioeconomic Pathways (SSPs; SSP1-2.6, SSP2-4.5, and SSP5-8.5). The CMIP6 ensemble reproduces the observed annual cycle and distribution of mean annual temperature and precipitation with biases between – 0.93 and 1.27 °C and – 37.90 to 58.45%, respectively, for most of the region. However, modeled precipitation is too large over the western and Midwestern U.S. during winter and spring and over the North American monsoon region in summer, while too small over southern Central America. Temperature is projected to increase over the entire domain under all three SSPs, by as much as 6 °C under SSP5-8.5, and with more pronounced increases in the northern latitudes over the regions that receive snow in the present climate. Annual precipitation projections for the end of the twenty-first century have more uncertainty, as expected, and exhibit a meridional dipole-like pattern, with precipitation increasing by 10–30% over much of the U.S. and decreasing by 10–40% over Central America and the Caribbean, especially over the monsoon region. Seasonally, precipitation over the eastern and central subregions is projected to increase during winter and spring and decrease during summer and autumn. Over the monsoon region and Central America, precipitation is projected to decrease in all seasons except autumn. The analysis was repeated on a subset of 9 models with the best performance in the reference period; however, no significant difference was found, suggesting that model bias is not strongly influencing the projections.

54 ENVIRONMENTAL SCIENCES↗

VERA User's Guide for Ex-core Applications

The Virtual Environment for Reactor Applications, or VERA, allows users to set up models to calculate time-dependent and fully coupled solutions for ex-core quantities of interest such as vessel and coupon fluence, and detector responses for multiple statepoints and cycles. MPACT and COBRA-TF together perform in-core transport calculations with temperature feedback while Shift performs the fluence and detector response calculations in the ex-core region. The in-core region is modeled using VERA’s native input format and the ex-core region is defined using Shift’s general geometry package, also known as Omnibus General Geometry. Fixed source ex-core calculations with Shift can be run in forward mode without advanced variance reduction (VR) methods, or with Consistent Adjoint Driven Importance Sampling (CADIS), which is an automated VR method. This document serves as a guide for setting up inputs, running ex-core calculations and post-processing the results.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

MARS-Q modeling of kink-peeling instabilities in DIII-D QH-mode plasma

In quiescent H-mode (QH-mode) regime, edge harmonic oscillations (EHOs) are believed to provide necessary radial transport to prevent occurrence of large edge localized modes. A systematic modeling study is performed here on the low- n EHOs in a DIII-D QH-mode plasma (Chen et al 2016 Nucl. Fusion 56 076011), by utilizing the MARS-Q code (Liu et al 2013 Phys. Plasmas 20 042503). Both the n = 1 and n = 2 instabilities are found to be strongly localized near the plasma edge, exhibiting the edge-peeling characteristics. The DIII-D resistive wall is found to have minor effects on these instabilities. The plasma resistivity is found to strongly modify the mode growth rate. Assuming the Spitzer model for the plasma resistivity, the computed mode growth rate scales as S sup>-1/3 with S being the Lundquist number. Toroidal flow of the plasma slightly stabilizes these edge localized kink-peeling modes. Drift kinetic effects all have a destabilization effect on these modes. Non-perturbative magneto-hydrodynamic-kinetic hybrid computations find that the drift kinetic effects associated with thermal particle species push the peak location of the eigenmode radially inward but still in the pedestal region. The modeled plasma temperature and density fluctuations in the plasma edge region, as well as the poloidal magnetic field perturbations along both the low and high field sides of the plasma surface, are in good agreement with experimental measurements. Finally, the quasi-linear initial value simulations find a strong non-linear interplay between the kink-peeling instability and the toroidal flow near the plasma edge. The combined effect of the damping of the flow amplitude and change of the edge flow shear is found to be the stabilizing factor for the kink-peeling mode, leading to the mode saturation and thus EHOs.

Physics↗

Mesoscale Convective Systems in DYAMOND Global Convection‐Permitting Simulations

Abstract This study examines the deep convection populations and mesoscale convective systems (MCSs) simulated in the DYAMOND (DYnamics of the atmospheric general circulation modeled on non‐hydrostatic domains) winter project. A storm tracking algorithm is applied to six DYAMOND simulations and a global high‐resolution satellite cloud and precipitation data set for comparison. The simulated frequencies of tropical deep convection and organized convective systems vary widely among models and regions, although robust MCSs are generally underestimated. The diurnal cycles of MCS initiation and mature stages are well simulated, but the amplitudes are exaggerated over land. Most models capture the observed MCS lifetime, cloud shield area, rainfall volume and movement speed. However, cloud‐top height and convective rainfall intensity are consistently overestimated, and stratiform rainfall area and amount are consistently underestimated. Possible causes for the model differences compared to observations and implications for future model developments are discussed.

58 GEOSCIENCES↗

Climate Change Impacts on the South American Monsoon System and Its Surface–Atmosphere Processes Through RegCM4 CORDEX-CORE Projections

Here, we evaluate projected changes in surface water and energy balances and surface–atmosphere coupling in the South American Monsoon System (SAMS) for the end of the century (2080–2099). The analyses are based on two ensemble datasets, which follow Representative Concentration Pathway 8.5 in the future period, and cover four subdomains (Northern and Southern—NAMZ and SAMZ—Amazon, La Plata Basin—LPB, and Southern Southeast Brazil—SSB). One ensemble consists of three Global Climate Models (HadGEM2-ES, MPI-ESM-MR and NorESM1-M), while the other consists of their dynamically downscaled version at 25 km horizontal grid spacing using Regional Climate Model version 4 (RegCM4). As both ensembles are able in reproducing the annual cycle of the components of the surface water and energy balances in the present climate, they can be used in the study of future climate. During the wet season (November–March), both ensembles project a decrease in precipitation over NAMZ and SAMZ (an exception is RegCM4 that projects a slight increase in SAMZ), and an increase across the LPB and SSB. These changes do not cause retreat or expansion of the monsoon area over the continent, which is similar to the present climate (1995–2014). For the wet season, the ensembles are in line with the presence of a strong surface–atmosphere coupling in LPB and SSB, weak coupling in SAMZ and very weak coupling in NAMZ. For future climate, the coupling is even weaker in NAMZ, which may be a driver for the negative changes in precipitation. For the other subdomains, while the ensembles project similar signals of precipitation changes, they disagree with the surface-atmosphere coupling highlighting the uncertainties in future climate.

54 ENVIRONMENTAL SCIENCES↗

Performance of Fire Danger Indices and Their Utility in Predicting Future Wildfire Danger Over the Conterminous United States

Abstract Predicting current and future wildfire frequency and size is central to wildfire control and management. Multiple fire danger indices (FDIs) that incorporate weather and fuel conditions have been developed and utilized to support wildfire predictions and risk assessment. However, the scale‐dependent performance of individual FDIs remains poorly understood, which leads to large uncertainty in the estimated fire sizes under climate change. Here, we calculate four commonly used FDIs over the conterminous United States using high‐resolution (4 km) climate and fuel data sets for the 1984–2019 period. The relationships of these four FDIs to the observed wildfire sizes show that higher values of FDIs correlate to larger total fire sizes; this correlation is more robust at larger spatial scales. Sensitivity analysis indicates that the daily minimum relative humidity and precipitation are the most important drivers of the annual mean fire danger. In the instances of extreme fire danger, wind speed becomes a critical factor and should be considered in the calculation of the FDI. To assess the impact of climate change on future fire size, we calculate the present‐day and end‐of‐century FDIs using the 12 km regional climate model simulations. The four FDIs generally predict consistent changes in future fire potential, suggesting an overall higher fire potential in conjunction with a prolonged wildfire season in future climate. Regionally, the four FDIs also reveal similar seasonal patterns as the enhancement arises mostly in spring and summer over the southwest US while in summer and fall over the northern and eastern US.

54 ENVIRONMENTAL SCIENCES↗

Systematic Benchmarking of Climate Models: Methodologies, Applications, and New Directions

As climate models become increasingly complex, there is a growing need to comprehensively and systematically assess model performance with respect to observations. Given the increasing number and diversity of climate model simulations in use, the community has moved beyond simple model intercomparison and toward developing methods capable of benchmarking a large number of simulations against a suite of climate metrics. Here, we present a detailed review of evaluation and benchmarking methods and approaches developed in the last decade, focusing primarily on scientific implications for Coupled Model Intercomparison Project (CMIP) simulations and CMIP6 results that contributed to the Intergovernmental Panel on Climate Change (IPCC) Sixth Assessment Report (AR6). Based on this review, we explain the resulting contemporary philosophy of model benchmarking, and provide clear distinctions and definitions of the terms model verification, process validation, evaluation, and benchmarking. While significant progress has been made in model development based on systematic evaluation and benchmarking efforts, some climate system biases still remain. The development of open‐source community software packages has played a fundamental role in identifying areas of significant model improvement and bias reduction. We review the key features of several software packages that have been commonly used over the past decade to evaluate and benchmark global and regional climate models. Additionally, we discuss best practices for the selection of evaluation and benchmarking metrics and for interpreting the obtained results, the importance of selecting suitable sources of reference data and accurate uncertainty quantification.

Environmental sciences↗

Key Drivers for Offshore Wind Deployment in the Western United States

The western coast of the United States has abundant natural resources, including wind, sun, and water. Despite strong ocean winds, offshore wind energy (OSW) in the Western United States is in the early stages of technology development due largely to the deep water off the coast, which requires floating platforms rather than fixed‐bottom turbines. Floating OSW increases the technical difficulty of installation and thus the cost relative to both fixed‐bottom OSW and land‐based turbines. OSW is a potential generation option to help meet increasing demand on the west coast of the United States because it likely has fewer land‐use conflicts than other technologies and complements sources in the existing electricity supply by providing energy during times of high system stress. This paper examines the possible drivers and barriers to OSW deployment on the West Coast using the National Laboratory of the Rockies' state‐of‐the‐art capacity expansion model and the Regional Energy Deployment System (ReEDS) model. We use ReEDS to explore a multitude of future scenarios looking at key drivers for OSW deployment, including variations on the cost of OSW, electricity demand growth, and the availability of competing technologies to examine the factors that may play a role in OSW growth. Assuming coastal state policies such as renewable portfolio and clean energy standards remain in place, we find that OSW can play a role in meeting electricity demand and provide energy during stressful grid conditions and find that deployment from the least‐cost investment model ranges from 7.6 to 38 GW by 2045.

17 WIND ENERGY↗

How May the Choice of Downscaling Techniques and Meteorological Reference Observations Affect Future Hydroclimate Projections?

Abstract We present an intercomparison of a suite of high‐resolution downscaled climate projections based on a six‐member General Circulation Model (GCM) ensemble from Coupled Models Intercomparison Project (CMIP6). The CMIP6 GCMs have been downscaled using dynamical and statistical downscaling techniques based on two meteorological reference observations over the conterminous United States. We use the regional climate model, RegCM4, for dynamical downscaling, double bias correction constructed analogs method for statistical downscaling, and Daymet and Livneh datasets as the reference observations for statistical training and bias‐correction. We evaluate the performances of downscaled data in both historical and future periods under the SSP585 scenario. While dynamical downscaling improves the simulation of some performance evaluation indices, it adds an extra bias in others, highlighting the need for statistical correction before its use in impact assessments. Downscaled datasets after bias‐correction compare exceptionally well with observations. However, the choice of downscaling techniques and the underlying reference observations influence the hydroclimate characteristics of downscaled data. For instance, the statistical downscaling generally preserves the GCMs climate change signal but overestimates the frequency of hot extremes. Similarly, simulated future changes are sensitive to the choice of reference observations, particularly for precipitation extremes that exhibit a higher projected increase in the ensembles trained and/or corrected by Daymet than Livneh. Overall, these results demonstrate that multiple factors, including downscaling techniques and reference observations, can substantially influence the outcome of downscaled climate projections and stress the need for a comprehensive understanding of such method‐based uncertainties.

54 ENVIRONMENTAL SCIENCES↗

Exploring the Consistency of Water Scarcity Inferences between Large-Scale Hydrologic and Node-Based Water System Model Representations of the Upper Colorado River Basin

Water resources model development and simulation efforts have seen rapid growth in recent decades to aid evaluations and planning around water scarcity and allocation. Models are typically developed by two distinct communities: (1) large-scale hydrologic modelers emphasizing hydroclimatological processes, and (2) water systems modelers emphasizing environmental, infrastructural, and institutional features that shape water scarcity at the local basin level. This study assesses whether two representative models from these communities produce consistent insights when evaluating the water scarcity vulnerabilities in the Upper Colorado River Basin within the state of Colorado. Results showed that although the regional-scale model [model for scale adaptive river transport (MOSART)—water management (WM)] can capture the aggregate effect of all water operations in the basin, it underestimates the subbasin-scale variability in specific user’s vulnerabilities. The basin-scale water systems model [State of Colorado’s Stream Simulation Model (StateMod)] suggests a larger variance of scarcity across the basin’s water users due to its more detailed accounting of local water allocation infrastructure and institutional processes. This model intercomparison highlights potentially significant limitations of large-scale studies in seeking to evaluate water scarcity and actionable adaptation strategies, as well as ways in which basin-scale water systems model’s information can be used to better inform water allocation and shortage when used in tandem with larger-scale hydrological modeling studies.

54 ENVIRONMENTAL SCIENCES↗

Future projections of storm surge in Hurricane Katrina and sensitivity to meteorological forcing resolution

In this study, we investigated whether and how the storm surge induced by Hurricane Katrina could change if it occurs in a future warmer climate, and the sensitivity of the changes to atmospheric forcing resolution. Climate model simulations of Hurricane Katrina at 27 km, 4.5 km, and 3 km resolutions were used to drive storm surge simulations in historical and future climates using the ADvanced CIRCulation (ADCIRC) model. We found that peak surge height increased significantly in the future with all forcing resolutions. However, the future projection is 22% greater in the 3 km forcing, typical of regional climate models, compared to the 27 km forcing, typical of state-of-the-art global climate models. Additionally, the spatial extent of the future change is highly sensitive to forcing resolution, extending most broadly under the 27 km forcing. Furthermore, we found that storm surge duration decreases in the future with all forcing resolutions due to increasing TC translation speed and decreasing ocean lifetime. However, the future change in the surge duration is sensitive to the forcing resolution, decreasing by 31% in the 27 km forcing and 6% in the 3 km forcing.

54 ENVIRONMENTAL SCIENCES↗

An Analysis of High Opportunity Geothermal Leasing Areas on BLM and USFS Lands

This analysis, conducted by the National Renewable Energy Laboratory (NREL) with support from the U.S. Department of Energy (DOE) Geothermal Technologies Office (GTO), models potential geothermal deployment on BLM and USFS land for the years 2025, 2030, 2035, and 2050 under various scenarios using the Renewable Energy Potential (reV) model and the Regional Energy Deployment System (ReEDS) model. This report identifies potential future high opportunity geothermal leasing areas (i.e., Best, Middle, and Least identified opportunities) based on available data for geothermal resource potential, natural resource conflicts, and transmission access. In addition, this analysis considers the impacts of the Energy Policy Act of 2005's (EPAct 2005's) default competitive leasing provisions, specifically the impact this may have had on geothermal resource discovery outside of known geothermal resource areas.

15 GEOTHERMAL ENERGY↗