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At least 163 records · Page 9

Mechanistic modeling of in vitro transcription incorporating effects of magnesium pyrophosphate crystallization

The in vitro transcription (IVT) reaction used in the production of messenger RNA vaccines and therapies remains poorly quantitatively understood. Mechanistic modeling of IVT could inform reaction design, scale-up, and control. In this work, we develop a mechanistic model of IVT to include nucleation and growth of magnesium pyrophosphate crystals and subsequent agglomeration of crystals and DNA. To help generalize this model to different constructs, a novel quantitative description is included for the rate of transcription as a function of target sequence length, DNA concentration, and T7 RNA polymerase concentration. The model explains previously unexplained trends in IVT data and quantitatively predicts the effect of adding the pyrophosphatase enzyme to the reaction system. The model is validated on additional literature data showing an ability to predict transcription rates as a function of RNA sequence length.

59 BASIC BIOLOGICAL SCIENCES↗

BATMODS-lite [SWR-25-108]

Battery Analysis and Training Models for Optimization and Design Studies (BATMODS) is a Python package with an API for pre-built battery models. The original purpose of the package was to quickly generate synthetic data for machine learning models to train with. However, the models are generally useful for any battery simulations or analysis. BATMODS-lite includes the following: 1) A library and API for pre-built battery models 2) Kinetic/transport properties for common battery materials

Randall, Corey [National Laboratory of the Rockies↗

MatCal Users Guide: Release 1.3.0

Any continuum mechanics model will require three components: (1) a discretized geometry of the boundary value problem being studied, (2) the partial differential equations to be solved, and (3) the initial conditions and boundary conditions for the problem. To describe material behavior in these computational models, material models contribute to (2) the underlying equations and, occasionally, to (3) the initial conditions for the simulation. These material models can exhibit a mathematical form that is empirically based, based on first principles, or developed from both empirical observations and known physics. In general, these models are meant to represent a class of materials with well understood behavior. As a result, material models have parameters that must be tuned or calibrated so that the model response matches characterization data available for the specific material it is intended to represent when used to simulate a specific system. For simple models, such as isotropic, linear elastic materials in solid mechanics, this calibration process can be a simple analytical calculation directly extracting the parameters from experimental measurements. For complex models that have many inputs and require many characterization datasets to adequately identify the material behavior, the model calibration process can require an inverse problem approach where an optimization is performed to tune the model parameters to the available data.

36 MATERIALS SCIENCE↗

An Integrated Hydroclimatic Assessment of Future Reservoir and Hydropower Operations in the U.S.

The engineering of rivers by dams is a formative feature of human-nature systems and the interconnectivity of water, energy, and the climate. Sufficient and broad-based representations of dams in large-scale hydrological models prove essential to mapping their extensive regulation of river flow and biogeochemistry and gauging climate-linked provisions, including freshwater supply and hydropower. We present an integrated modeling framework to investigate future streamflow and hydropower generation in the Contiguous U.S. (1990–2075), leveraging an ensemble of six downscaled and bias-corrected General Circulation Models (GCMs) from the high-end SSP585 scenario of the CMIP6. To achieve this, we develop a reservoir operations and parameterization scheme for 1,384 dams in a high-resolution river network, including simulated hydropower generation for 326 dams. For the GCM ensemble mean, we simulate a widespread increase in regulated streamflow into the late-century (11% annual and 17% in winter for the dam median) with region-specific changes in summer streamflow that feature prominent declines in the Northwest (−7%). Mediation by reservoirs is shown to dampen intra-annual streamflow changes, delivering additional summer releases that partially mitigate declining flows. Total hydropower generation is projected to increase modestly (+3%), with boosted generation in the winter (+9%) and spring (+5%) offsetting declined summer generation (−3.4%), suggesting strong adaptation potential for hydropower in the future energy portfolio. Further analysis reveals that the choice of GCM, particularly in western regions, has significant bearing on projected streamflow and hydropower changes.

13 HYDRO ENERGY↗

PhysBERT: A text embedding model for physics scientific literature

The specialized language and complex concepts in physics pose significant challenges for information extraction through Natural Language Processing (NLP). Central to effective NLP applications is the text embedding model, which converts text into dense vector representations for efficient information retrieval and semantic analysis. In this work, we introduce PhysBERT, the first physics-specific text embedding model. Pre-trained on a curated corpus of 1.2 × 106 arXiv physics papers and fine-tuned with supervised data, PhysBERT outperforms leading general-purpose models on physics-specific tasks, including the effectiveness in fine-tuning for specific physics subdomains.

Hellert, Thorsten (ORCID:0000000227970926)↗

Carbon storage cost modeling for the offshore Gulf of Mexico

Groundbreaking for geologic carbon storage (GCS) projects in the offshore Gulf of Mexico is imminent, and there is great interest in utilizing this region for GCS projects. Offshore saline reservoirs provide a significant and accessible resource for GCS. However, conducting GCS in the offshore environment will pose distinct challenges pertaining to site selection, operations, infrastructure use, and monitoring compared to operating onshore that ultimately affect technoeconomic assessment of offshore GCS projects. Carbon storage and transport costs are critical to project developers looking to deploy carbon storage in the offshore environment. We present CO2_S_COM_Offshore, a model developed by the National Energy Technology Laboratory (NETL) as a screening-level offshore saline GCS cost modeling tool. Based on NETL’s widely used CO2_S_COM cost model for onshore saline CS, CO2_S_COM_Offshore enables technoeconomic analysis of GCS in offshore areas. This model comprehensively incorporates multiple facets of offshore GCS projects, from regional evaluation and site selection to permitting, transport, operations, monitoring, site closure, and decommissioning. In general, the model can explore the cost implications for potential offshore GCS project(s) by enabling the user to change several project operational and financial attribute configurations. Key inputs include offshore storage formation options, CO2 injection rate and duration, infrastructure types, monitoring intensity, project financing, and post-injection site care duration. Supporting cost algorithms within CO2_S_COM_Offshore were compiled utilizing S&P Global’ s QUE$TORTM cost estimation software alongside a variety of open-source scientific literature. In addition to reviewing key model components, we discuss several sensitivity analyses, input variabilities, and results on analysis of break-even CO2 price required by a project based on different regulation/policy and operational scenarios for the offshore Gulf of Mexico. These results indicate the value of modeling offshore GCS specifically, and the potential of offshore GCS within a decarbonization value chain. Presented at the 41st USAEE/IAEE North American Conference, 3-6 November 2024, Baton Rouge, LA, United States.

Mark-Moser, Mackenzie K.↗

First-Principles Cost Analysis of Advanced High-Temperature Nuclear Plants

Due to the vast number of recent nuclear reactor innovations, particularly those pertaining to generation IV reactor types like high-temperature gas cooled reactors (HTGRs) and sodium-cooled fast reactors (SFRs), and the newer deployment strategies envisioned, such as use of small modular reactors (SMRs) or even microreactors, reliable, detailed, and complete costs of these nuclear innovations are needed in wide availability. The types of models that generally achieve these objectives are those incorporating the fundamental nature of the real-world systems they aspire to predict, such as first-principles models. Furthermore, first principles models typically offer predictiveness that is not attained by most other types of individual-models. However, detailed, first-principles cost modeling of nuclear reactors and entire nuclear plants is relatively limited. To address this limitation in the availability of detailed, predictive models based on fundamentals, we recently developed a range of cost models, mostly based on first-principles methodologies, to project full lifecycle costs (LCCs) of nuclear power plants (NPPs) based on multiple parallel SM-HTG-pebble bed reactors (PBRs) and SM-SFRs.

Prosser, Jacob H. [Strategic Analysis, Inc., Arlin↗

First-Principles Cost Analysis of Advanced High-Temperature Nuclear Plants

Due to the vast number of recent nuclear reactor innovations, particularly those pertaining to generation IV reactor types like high-temperature gas cooled reactors (HTGRs) and sodium-cooled fast reactors (SFRs), and the newer deployment strategies envisioned, such as use of small modular reactors (SMRs) or even microreactors, reliable, detailed, and complete costs of these nuclear innovations are needed in wide availability. The types of models that generally achieve these objectives are those incorporating the fundamental nature of the real-world systems they aspire to predict, such as first-principles models. Furthermore, first principles models typically offer predictiveness that is not attained by most other types of individual-models. However, detailed, first-principles cost modeling of nuclear reactors and entire nuclear plants is relatively limited. To address this limitation in the availability of detailed, predictive models based on fundamentals, we recently developed a range of cost models, mostly based on first-principles methodologies, to project full lifecycle costs (LCCs) of nuclear power plants (NPPs) based on multiple parallel SM-HTG-pebble bed reactors (PBRs) and SM-SFRs.

Prosser, Jacob H. [Strategic Analysis, Inc., Arlin↗

Global Corn Heat Stress: Mean and SD of Degree Days Above 29°C based on NEX-GDDP-CMIP6 Climate Projections

Description This global dataset provides the estimated mean and standard deviation (SD) of corn heat stress (degree days above 29°C) for a set of climate models in NEX-GDDP-CMIP6 at 0.25-degree resolution. The NEX-GDDP-CMIP6 dataset is comprised of global downscaled climate scenarios derived from the General Circulation Model (GCM) runs conducted under the Coupled Model Intercomparison Project Phase 6 (CMIP6). The current dataset includes: Long-Term Average Degree Days Above 29°C- Historical Long-Term Average Degree Days Above 29°C- SSP245 Long-Term Standard Deviation of Degree Days Above 29°C- Historical Long-Term Standard Deviation of Degree Days Above 29°C- SSP245 The mean and SD are calculated over 1985-2014 for the historical period and over 2035-2064 for future projections. A full description of methods, including growing season, daily temperature distribution, and statistical coefficients, can be found in Haqiqi (2024). The source climate data are obtained from https://ds.nccs.nasa.gov/thredds2/catalog/catalog.html and are described in Thrasher et al (2022). The codes used to create this dataset are available at https://github.com/ihaqiqi/dd29c_nex_cmip6. Acknowledgments This work was supported by the US Department of Energy, Office of Science, Biological and Environmental Research Program, Earth and Environmental Systems Modeling, MultiSector Dynamics under Cooperative Agreement DE-SC0022141. The data processing, computation, and storage were completed on Purdue Anvil supercomputer and cyberinfrastructure supported by the National Science Foundation HDR award # 2118329: "NSF Institute for Geospatial Understanding through an Integrative Discovery Environment (I-GUIDE)". References Haqiqi. I. (2024). Trade can buffer climate-induced risks and volatilities in crop supply. Environmental Research: Food Systems. https://doi.org/10.1088/2976-601X/ad7d12 Thrasher, B., Wang, W., Michaelis, A., Melton, F., Lee, T., & Nemani, R. (2022). NASA global daily downscaled projections, CMIP6. Scientific Data, 9(1), 262. https://doi.org/10.1038/s41597-022-01393-4

Climate Change↗

Intelligent Manufacturing Support: Specialized LLMs for Composite Material Processing and Equipment Operation

Engineering educational curriculum and standards cover many material and manufacturing options. However, engineers and designers are often unfamiliar with certain composite materials or manufacturing techniques. Large language models (LLMs) could potentially bridge the gap. Their capacity to store and retrieve data from large databases provides them with a breadth of knowledge across disciplines. However, their generalized knowledge base can lack targeted, industry-specific knowledge. To this end, we present two LLM-based applications based on the GPT-4 architecture: (1) The Composites Guide: a system that provides expert knowledge on composites material and connects users with research and industry professionals who can provide additional support and (2) The Equipment Assistant: a system that provides guidance for manufacturing tool operation and material characterization. By combining the knowledge of general AI models with industry-specific knowledge, both applications are intended to provide more meaningful information for engineers. In this paper, we discuss the development of the applications and evaluate it through a benchmark and two informal user studies. The benchmark analysis uses the Rouge and Bertscore metrics to evaluate our models’ performance against GPT-4o. The results show that GPT-4o and the proposed models perform similarly or better on the ROUGE and BERTScore metrics. The two user studies supplement this quantitative evaluation by asking experts to provide qualitative and open-ended feedback about our model’s performance on a set of domain-specific questions. The results of both studies highlight a potential for more detailed and specific responses with the Composites Guide and the Equipment Assistant.

Kapoor, Gunnika [Oak Ridge National Laboratory (OR↗

The Modeled Seasonal Cycles of Surface N 2 O Fluxes and Atmospheric N 2 O

Nitrous oxide (N 2 O) is a greenhouse gas and stratospheric ozone-depleting substance with large and growing anthropogenic emissions. Previous studies identified the influx of N 2 O-depleted air from the stratosphere to partly cause the seasonality in tropospheric N 2 O (aN 2 O), but other contributions remain unclear. Here, we combine surface fluxes from eight land and four ocean models from phase 2 of the Nitrogen/N 2 O Model Intercomparison Project with tropospheric transport modeling to simulate aN 2 O at eight remote air sampling sites for modern and pre-industrial periods. Models show general agreement on the seasonal phasing of zonal-average N 2 O fluxes for most sites, but seasonal peak-to-peak amplitudes differ several-fold across models. The modeled seasonal amplitude of surface aN 2 O ranges from 0.25 to 0.80 ppb (interquartile ranges 21%–52% of median) for land, 0.14–0.25 ppb (17%–68%) for ocean, and 0.28–0.77 ppb (23%–52%) for combined flux contributions. The observed seasonal amplitude ranges from 0.34 to 1.08 ppb for these sites. The stratospheric contributions to aN 2 O, inferred by the difference between the surface-troposphere model and observations, show 16%–126% larger amplitudes and minima delayed by ~1 month compared to Northern Hemisphere site observations. Land fluxes and their seasonal amplitude have increased since the pre-industrial era and are projected to grow further under anthropogenic activities. Our results demonstrate the increasing importance of land fluxes for aN 2 O seasonality. Considering the large model spread, in situ aN 2 O observations and atmospheric transport-chemistry models will provide opportunities for constraining terrestrial and oceanic biosphere models, critical for projecting carbon-nitrogen cycles under ongoing global warming.

54 ENVIRONMENTAL SCIENCES↗

Machine Learning Models for Mapping Groundwater Pollution Risk: Advancing Water Security and Sustainable Development Goals in Georgia, USA

The widespread use of pesticides, such as atrazine and malathion, in agricultural systems raises significant concerns regarding the contamination of groundwater, which serves as a critical resource for drinking water. This study applies machine learning techniques to predict the concentrations of atrazine and malathion in groundwater across Georgia, USA, using 2019 data. A Random Forest classifier was employed to integrate various environmental and demographic factors, including pesticide application rates, precipitation, lithology, and population density, to predict pesticide contamination in groundwater. The models demonstrated high training accuracies of 100% and moderate average testing accuracy of 55% for atrazine and 60% for malathion across five iterations. The low test accuracy of the model, ranging from 50% to 75%, is likely due to overfitting, which can be attributed to the small dataset size and the complex nature of pesticide-contamination patterns, making it challenging for the model to generalize to unseen data. Feature importance analysis revealed that average pesticide usage emerged as the most influential factor for atrazine, while aquifer lithology and precipitation played crucial roles in both models. These results provide valuable insights into the dynamics of pesticide contamination, highlighting areas at greater risk of contamination. The findings underscore the importance of integrating environmental, geological, and agricultural variables for more effective groundwater management and sustainable agricultural practices, contributing to the protection of water resources and public health.

54 ENVIRONMENTAL SCIENCES↗

Divergent carbon use efficiency-growth rate tradeoff in popular biological growth models

Carbon use efficiency (CUE) is an important trait emerging from processes regulating biological growth. CUE can be computed either based on the growth of structural biomass or total biomass divided by substrate uptake rate. Nonequilibrium thermodynamics and observations suggest that, for an exponentially growing population of cells, structural biomass CUE should first increase, then peak, and finally decrease with specific growth rate; meanwhile, total biomass CUE increases asymptotically with specific growth rate. We compared predictions from six popular models that are often used for plant and microbial growth in existing ecosystem models. We found that, for an exponentially growing population of biological cells, (1) the source-driven Pirt and Compromise models predict that structural biomass CUE increase asymptotically with growth rate; (2) the apparent sink-driven modified Droop model predicts that structural biomass CUE decreases with growth rate; and (3) the sink-driven variable internal storage model and two dynamic energy budget models predict that structural biomass CUE first increases, then peaks, and finally decreases with growth rate. Moreover, the modified Droop model predicts that total biomass CUE is constant with growth rate, while all other five models predict that total biomass CUE increases with growth rate asymptotically. For non-exponential biological growth, we show that there is no static relationship between total biomass CUE or structural biomass CUE with respect to either growth rate or temperature. Therefore, we contend that biological growth models should explicitly represent interactions between substrate acquisition, substate transformation, and maintenance respiration to better capture observed CUE dynamics, and the sink-driven model should be preferred for general ecosystem biogeochemistry modeling.

Tang, Jinyun [Lawrence Berkeley National Laborator↗

Enhanced pedestal transport driven by edge collisionality on Alcator C-Mod and its role in regulating H-mode pedestal gradients

Experimental measurements of plasma and neutral profiles across the pedestal are used in conjunction with 2D edge modeling to examine pedestal stiffness in Alcator C-Mod H-mode plasmas. Enhanced D α experiments on Alcator C-Mod observed pedestal degradation and loss in confinement below a critical value of net power crossing the separatrix, P net = $P^{crit}_{net}$ ≈ 2.3 MW, in the absence of any external fueling. New analysis of ionization and particle flux profiles reveal saturation of the pedestal electron density, $n^{ped}_{e}$, despite continuous increases in ionization throughout the pedestal, inversely related to P net . A limi to the pedestal $\nabla$n e emerges as the particle flux, Γ D , continues to grow, implying increases in the effective particle diffusivity, D eff . This is well-correlated with the separatrix collisionality, $v^*_{sep}$ and a turbulence control parameter, α t , implying a possible transition in type of turbulence. The transition is well correlated with the experimentally observed value of $P^{crit}_{net}$. SOLPS-ITER modeling is performed for select discharges from the power scan, constrained with experimental electron and neutral densities, measured at the outer midpane. The modeling confirms general growth in D eff , consistent with experimental findings, and additionally suggests even larger growth in Χ e at the same $P^{crit}_{net}$.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Bias Correction and Statistical Downscaling of Future Solar Irradiance Projections Using the NSRDB

Assessing renewable energy resources under future climate scenarios has been highlighted to understand potential impacts of future climate change in renewable generation on the power sector. Climate model projection has been recognized by the renewable energy community as a useful data set to analyze the impacts of future climate change on renewable resources. However, future climate projections generated from general circulation models (GCMs) contain inherent biases that need to be corrected for accurate analysis of future projections of climate variables. In addition, the coarse spatiotemporal resolution of GCMs needs to be improved for regional climate studies. In this work, we develop statistical methods to downscale future projections of global horizontal irradiance (GHI) in a computationally efficient way. Our approach builds statistical downscaling models that correct bias of climate projection of GHI and downscale the future GHI projection from daily-scale to hourly-scale. The National Solar Radiation Database (NSRDB) is used to calibrate the statistical models and validate the downscaled GHI projections across the contiguous United State (CONUS). Preliminary results show that the statistical approach efficiently downscales climate projections of GHI with a nBIAS of 3%, nMAE of 34 % and nRMSE of 46% calculated against NSRDB for CONUS. This study describes the implemented methodology and initial results as well as future research to create high-resolution climate data sets for solar energy applications.

analytical models↗

How Frequent Will the Rarest Daily Rainfall Records of Hurricane Ida’s Remnants Be in the Future?

Abstract Gaining continued insights into the impact of global warming on the occurrence of hurricane-associated intense record downpours is essential for building climate resilient communities. This study investigates projected future changes in extreme rainfall over the Northeast United States, as represented by extreme daily amounts during Hurricane Ida in 2021. We used historical control simulations of Weather Research and Forecasting (WRF) Model generated from 40 years of weather events (1980–2014, 12 km) forced by the fifth generation European Centre for Medium-Range Weather Forecasts atmospheric reanalysis. These simulations are thermodynamically modified (2060–2100) via an imposed warming for the high-emission scenario of shared socioeconomic pathway (SSP585) from a range of general circulation models. Ground observations from the Global Historical Climatology Network (1950–2014) and WRF simulations (historical, 1980–2014, and future, 2060–2100) are integrated into a nonstationary generalized extreme value (GEV) framework to assess the frequency of Ida’s heaviest daily rain rates under the SSP585 scenario. Results show that Ida’s daily maximum rainfall recorded at different observation locations was higher than the single highest September daily maximum observed (1950–2014) for 5 out of 17 stations (∼30% of the stations). Ida-like extreme daily rain rates are projected to be, on average, more than 2 times more likely to occur at the end of the century in the simulations (with some regions as high as 5 times). This work demonstrates that integrating a high-resolution atmospheric model’s present-day and thermodynamically modified future simulations along with ground observations, within a nonstationary statistical framework, is crucial for understanding changing characteristics of extreme weather events. Significance Statement Daily scale extreme precipitation is expected to become more frequent and severe, as evidenced by observations and model simulations. While it is important to investigate how these intensifying heavy rainfall events affect current engineering standards, fewer studies have contextualized how warming impacts the most extreme rainfall from a single storm event relative to historical heavy downpours. In this study, we focused on the daily extreme rainfall associated with the extratropical transition of Hurricane Ida (2021), particularly over the northeastern United States—some of which exceeded the commonly used hydrologic design criteria for a 100-yr storm. Using a high-resolution atmospheric model simulation, we investigated how continued warming may influence the frequency of such daily rain rates. Under a high-emission scenario, these events are projected to become up to 5 times more likely at the end of the twenty-first century.

Dollan, Ishrat J↗

Hierarchical Testing of a Hybrid Machine Learning‐Physics Global Atmosphere Model

Machine learning (ML)-based models have demonstrated high skill and computational efficiency, often outperforming conventional physics-based models in weather and subseasonal predictions. While prior studies have assessed their fidelity in capturing synoptic-scale atmospheric dynamics, their performance across timescales and under out-of-distribution forcing, such as +3K or +4K uniform-warming forcings, and the sources of biases remain elusive, to establish the model's reliability for Earth science. Here, we design three sets of experiments targeting synoptic-scale phenomena, interannual variability, and out-of-distribution uniform-warming forcings. We evaluate the Neural General Circulation Model (NeuralGCM), a hybrid model integrating a dynamical core with ML-based component, against observations and physics-based Earth system models (ESMs). At the synoptic scale, NeuralGCM captures the evolution and propagation of extratropical cyclones with performance comparable to ESMs. At the interannual scale, when forced by El Niño-Southern Oscillation sea surface temperature (SST) anomalies, NeuralGCM successfully reproduces associated teleconnection patterns but exhibits deficiencies in capturing nonlinear response. Under out-of-distribution uniform-warming forcings, NeuralGCM simulates similar responses in global-average temperature and precipitation and reproduces large-scale tropospheric circulation features similar to those in ESMs. Notable weaknesses include overestimating the tracks and spatial extent of extratropical cyclones, biases in the teleconnected wave train triggered by tropical SST anomalies, and differences in upper-level warming and stratospheric circulation responses to SST warming compared to physics-based ESMs. The causes of these weaknesses were explored. Despite the noted weaknesses, NeuralGCM reproduces responses across experiments reasonably and performs comparably to ESMs. By integrating a dynamical core with ML, NeuralGCM shows potential for developing ML-based ESMs.

global warming↗

An asymptotic Grad–Shafranov equation for quasisymmetric stellarators

A first-order model is derived for quasisymmetric stellarators where the vacuum field due to coils is dominant, but plasma-current-induced terms are not negligible and can contribute to magnetic differential equations, with $\beta$ of the order of the ratio induced to vacuum fields. Under these assumptions, it is proven that the aspect ratio must be large and a simple expression can be obtained for the lowest-order vacuum field. The first-order correction, which involves both vacuum and current-driven fields, is governed by a Grad–Shafranov equation and the requirement that flux surfaces exist. These two equations are not always consistent, and so this model is generally overconstrained, but special solutions exist that satisfy both equations simultaneously. One family of such solutions is the set of first-order near-axis solutions. Thus, the first-order near-axis model is a subset of the model presented here. Several other solutions outside the scope of the near-axis model are also found. A case study comparing one such solution to a VMEC-generated solution shows good agreement.

Nikulsin, Nikita (ORCID:0000000318611777)↗