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At least 181 records · Page 10

The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels

Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology.

09 BIOMASS FUELS↗

The Energy Exascale Earth System Model Version 3: 1. Overview of the Atmospheric Component

This paper describes the atmospheric component of the US Department of Energy's Energy Exascale Earth System Model (E3SM) version 3. Significant updates have been made to the atmospheric physics compared to earlier versions. Specifically, interactive gas chemistry has been implemented, along with improved representations of aerosols and dust emissions. A new stratiform cloud microphysics scheme more physically treats ice processes and aerosol‐cloud interactions. The deep convection parameterization has been largely improved with sophisticated microphysics for convective clouds, making model convection sensitive to large‐scale dynamics, and incorporating the dynamical and physical effects of organized mesoscale convection. Improvements in aerosol wet removal processes and parameter re‐tuning of key aerosol and cloud processes have improved model aerosol radiative forcing. The model's vertical resolution has increased from 72 to 80 layers with the extra eight layers added in the lower stratosphere to better simulate the Quasi‐Biennial Oscillation. These improvements have enhanced E3SM's capability to couple aerosol, chemistry, and biogeochemistry and reduced some long‐standing biases in simulating tropical variability. Compared to its predecessors, the model shows a much stronger signal for the Madden‐Julian Oscillation, Kelvin waves, mixed Rossby‐gravity waves, and eastward inertia‐gravity waves. Aerosol radiative forcing has been considerably reduced and is now better aligned with community best estimates, leading to significantly improved skill in simulating historical temperature records. Its simulated mean‐state climate is largely comparable to E3SMv2, but with some notable degradation in shortwave cloud radiative effect, precipitable water, and surface wind stress, which will be addressed in future updates.

54 ENVIRONMENTAL SCIENCES↗

Leveraging Open-Source Tools for Collaborative Macro-energy System Modeling Efforts

The authors are founding team members of a new effort to develop an Open Energy Outlook for the United States. The effort aims to apply best practices of policy-focused energy system modeling, ensure transparency, build a networked community, and work toward a common purpose: examining possible US energy system futures to inform energy and climate policy efforts. Individual author biographies can be found on the project website: https://openenergyoutlook.org/.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Distribution System Model Calibration for GMLC 3.3.3 "Incipient Failure Identification for Common Grid Asset Classes" - Project Summary

Distribution system model calibration is a key enabling task for incipient failure identification within the distribution system. This report summarizes the work and publications by Sandia National Laboratories on the GMLC project titled “Incipient Failure Identification for Common Grid Asset Classes”. This project was a joint effort between Sandia National Laboratories, Lawrence Livermore National Laboratory, National Energy Technology Laboratory, and Oak Ridge National Laboratory. The included work covers distribution system topology identification, transformer groupings, phase identification, regulator and tap position estimation, and the open-source release and implementation of the developed algorithms.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Electrical Submersible Pumps: A System Modeling Approach for Power Quality Analysis With Variable Frequency Drives

This article proposes a high-level engineering guide to develop an integrated system model for power quality analysis in electrical submersible pump (ESP) applications with variable frequency drives (VFDs). Such analyses are troublesome in the industry due to the complexity of these systems. In this article, simple steps to perform system integration analyses of such arrangements, including torsional analysis, are developed. A simplified VFD-ESP model suitable for coupled electrical and mechanical analysis in steady state is proposed in all their configurations of practical interest. Such a model can be easily implemented in common simulation software, significantly reducing engineering efforts for implementation and analysis. The focus of the proposed model is the prediction of ESP failures that might result from a poor power quality caused by VFDs. Analytical expressions of different types of harmonics in these systems, as well as their accurate locations in the frequency domain, including their interharmonics and common-mode harmonics, are derived for this purpose. Further, the effectiveness of the proposed model is verified through offline and real-time hybrid simulation results. Finally, a comparison between simulation results obtained using the proposed model and measurements collected on a down-scale laboratory prototype is carried out to demonstrate the accuracy of the suggested modeling approach.

42 ENGINEERING↗

Reaction kinetics during early hydration of calcined phyllosilicates in clinker-free model systems

Investigations of nearly pure, calcined phyllosilicates (“meta-phyllosilicates”) in clinker-free model systems were performed in presence and absence of sulfate. Calorimetric investigations show a pronounced reaction during the early reaction period only for metakaolin. Quantitative in situ X-ray diffraction reveals calcium silicate hydrate formation in the systems with metakaolin and metaillite, but not in those with metamuscovite. Ettringite crystallizes in all systems containing sulfate, where only the metakaolin system reaches the maximum ettringite content possible. The amount of aluminum ions released from 2:1 meta-phyllosilicates seems to be insufficient to reach the maximum content. Differences in portlandite dissolution and bound water indicate adsorption effects of calcium or calcium – sulfate ion pair complexes on surfaces of the calcined clay particles. Thus, the chemical as well as the physical influence of the meta-phyllosilicates must be considered to predict the reaction kinetics of calcined clays during early hydration.

36 MATERIALS SCIENCE↗

Distribution System Model Calibration Algorithms

SAND2021-15065 O This release contains Python code for two distribution system model calibration algorithms as well as some sample data and documentation for the algorithms and code. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Blakely, Logan↗

Systematic and objective evaluation of Earth system models: PCMDI Metrics Package (PMP) version 3

Systematic, routine, and comprehensive evaluation of Earth system models (ESMs) facilitates benchmarking improvement across model generations and identifying the strengths and weaknesses of different model configurations. By gauging the consistency between models and observations, this endeavor is becoming increasingly necessary to objectively synthesize the thousands of simulations contributed to the Coupled Model Intercomparison Project (CMIP) to date. The Program for Climate Model Diagnosis and Intercomparison (PCMDI) Metrics Package (PMP) is an open-source Python software package that provides quick-look objective comparisons of ESMs with one another and with observations. The comparisons include metrics of large- to global-scale climatologies, tropical inter-annual and intra-seasonal variability modes such as the El Niño–Southern Oscillation (ENSO) and Madden–Julian Oscillation (MJO), extratropical modes of variability, regional monsoons, cloud radiative feedbacks, and high-frequency characteristics of simulated precipitation, including its extremes. The PMP comparison results are produced using all model simulations contributed to CMIP6 and earlier CMIP phases. An important objective of the PMP is to document the performance of ESMs participating in the recent phases of CMIP, together with providing version-controlled information for all datasets, software packages, and analysis codes being used in the evaluation process. Among other purposes, this also enables modeling groups to assess performance changes during the ESM development cycle in the context of the error distribution of the multi-model ensemble. Quantitative model evaluation provided by the PMP can assist modelers in their development priorities. In this paper, we provide an overview of the PMP, including its latest capabilities, and discuss its future direction.

54 ENVIRONMENTAL SCIENCES↗

High-Resolution WRF-Based Downscaling of Earth System Model Projections for Energy Applications across CONUS

Evaluating energy resources under future scenarios requires meteorological information that adequately resolves regional-scale variability and is suitable for regional energy system studies. Although Earth system model (ESM) outputs provide essential large-scale context, their coarse resolution and inherent biases limit direct use in energy system applications. This work presents a high-resolution dynamical downscaling framework using the Weather Research and Forecasting (WRF) model to generate energy-relevant regional fields for future scenarios over the contiguous United States (CONUS). The framework first identifies an optimal WRF configuration through sensitivity experiments, then evaluates raw and bias-corrected ESM initial and boundary conditions, with soil moisture and soil temperature bias correction implemented as an integral component of the bias-corrected ESM atmospheric forcing prior to WRF dynamical downscaling to improve land-atmosphere interactions. Simulations performed at 4-km resolution show that uncorrected ESM forcing leads to systematically dry and cold soil states, which propagate into elevated near-surface air temperature and solar irradiance biases, particularly during summer for the period 2000-2014. Incorporating bias-corrected atmospheric forcing together with soil state bias correction substantially reduces these errors and improves the representation of surface energy processes in WRF simulations. The results highlight the importance of bias-aware initialization strategies in high-resolution dynamical downscaling for future energy system analysis and planning.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Enhancing Biopreparedness through a Model System to Understand the Molecular Mechanisms that Lead to Pathogenesis and Disease Transmission: NW-BRaVE

The science of biopreparedness to counter biological threats hinges on understanding the fundamental principles and molecular mechanisms that lead to pathogenesis and disease transmission. Our vision to address this challenge is to create a powerful and user-friendly platform to elucidate the fundamental principles of how molecular interactions drive pathogen-host relationships and host shifts. We will enable groundbreaking discoveries by integrating a wide range of structural, genomics, proteomics, and other advanced omics measurements, along with evolutionary and artificial intelligence predictions. To make sure the system is applicable to real-world problems, we will develop it in the context of a tractable model system, the small, abundant, and accessible photosynthetic cyanobacteria and their constantly co-adapting viral pathogens, cyanophages. This model will maintain the system’s applicability to real-world problems and techniques, but the overall focus will be on elucidating general principles of detecting, assessing, and surveilling molecular interaction, adaptation, and coevolution that are system agnostic and therefore extensible to other viral-host interactions. Our overall objectives are to (1) identify the molecular complexes that comprise the cyanobacteria redox macromolecular subsystem and how they dynamically change with bacteriophage infection in situ, using cryo-electron tomography; (2) profile regulatory changes during infection using proteomics, multiomics, and experimental validation, and integrate the data with in situ structures; (3) use genomics and metagenomics to determine environmental and population factors across time scales that impact the interactions between marine cyanobacteria and their cyanophage parasites, predicting the evolutionary origins of in situ structural and functional interactions, convergence and coevolution; and (4) develop a data integration and transformation platform that facilitates the integration of in situ, proteomic, and evolutionary measurements of molecular interactions to surveil diverse hosts and parasites in various environmental contexts. These objectives address Focus Area 2 Reveal Molecular Interactions Across Biological Scales for Design of Targeted Interventions. Our powerful and user-friendly platform will enhance connections between the often-siloed fields of structure, molecular phenotype, and evolutionary genomics that are key to biopreparedness, but in need of integration (Figure 1). We will build an integrated navigation tool to facilitate the effective use of globally distributed experimental data for integrated analysis and predictive modeling. The project will develop, implement, and test a platform to assess host-pathogen molecular interactions, adaptation to hosts and host shifts, and coevolution between hosts and pathogens, successfully impacting the research community by revolutionizing abilities to study any host-pathogen interaction, encourage diverse community contributions, and gain fundamental insights into how proteins adapt to new contexts. This ability will be critical for designing early interventions to address future threats. We will build surveillance training capability, aiming for a fair and equitable response to future pandemics and biothreats.

59 BASIC BIOLOGICAL SCIENCES↗

PCMDI - An Earth System Model Evaluation Project Lawrence Livermore National Laboratory Annual Report

This annual report describes the activities of PCMDI – An Earth System Model Evaluation Project for the period November 1, 2019 – June 30, 2020. PCMDI is a project at Lawrence Livermore National Laboratory that is funded by the Climate and Environmental Sciences Division (CESD) of the Department of Energy. PCMDI is funded by two efforts within CESD: The Regional and Global Model Analysis program area (Dr. Renu Joseph, program manager) and the Atmospheric Systems Research program (Dr. Shaima Nasiri and Jeffrey Stehr, program managers). As instructed by Drs. Joseph, Nasiri, and Stehr, we provide an annual report addressing sections 4 (Progress and Plans) and 5 (Staffing and Budget Summary) of the SFA Program Management and Performance Reporting Criteria.

54 ENVIRONMENTAL SCIENCES↗

Global-Scale Convergence Obscures Inconsistencies in Soil Carbon Change Predicted by Earth System Models

Soil carbon (C) responses to environmental change represent a major source of uncertainty in the global C cycle. Feedbacks between soil C stocks and climate drivers could impact atmospheric CO 2 levels, further altering the climate. Here, we assessed the reliability of Earth system model (ESM) predictions of soil C change using the Coupled Model Intercomparison Project phases 5 and 6 (CMIP5 and CMIP6). ESMs predicted global soil C gains under the high emission scenario, with soils taking up 43.9 Pg (95% CI: 9.2–78.5 Pg) C on average during the 21st century. The variation in global soil C change declined significantly from CMIP5 (with average of 48.4 Pg [95% CI: 2.0–94.9 Pg] C) to CMIP6 models (with average of 39.3 Pg [95% CI: 23.9–54.7 Pg] C). For some models, a small C increase in all biomes contributed to this convergence. For other models, offsetting responses between cold and warm biomes contributed to convergence. Although soil C predictions appeared to converge in CMIP6, the dominant processes driving soil C change at global or biome scales differed among models and in many cases between earlier and later versions of the same model. Random Forest models, for soil carbon dynamics, accounted for more than 63% variation of the global soil C change predicted by CMIP5 ESMs, but only 36% for CMIP6 models. Although most CMIP6 models apparently agree on increased soil C storage during the 21st century, this consensus obscures substantial model disagreement on the mechanisms underlying soil C response, calling into question the reliability of model predictions.

54 ENVIRONMENTAL SCIENCES↗

Overestimated natural biological nitrogen fixation translates to an exaggerated CO 2 fertilization effect in Earth system models

CO 2 fertilization of the terrestrial biosphere is limited by nitrogen. Biological nitrogen fixation (BNF) is the dominant natural nitrogen source to the terrestrial biosphere and can alleviate nitrogen limitation but is poorly constrained in Earth system models (ESMs). Here, in this study, we compare terrestrial BNF from an ensemble of ESMs of the 6th Coupled Model Intercomparison Project to a new global synthesis of observations across natural and agricultural biomes. We find that compared to observations, ESMs underestimate agricultural BNF but overestimate natural BNF in the present day by over 50%. Natural BNF is overestimated in the most productive ecosystems that contribute most to the terrestrial carbon sink (forests and grasslands). ESMs with different BNF representations yield a range of BNF responses to CO 2 enrichment. Some ESMs with phenomenological representations of BNF predict a natural BNF increase in response to a doubling of CO 2 that aligns with a meta-analysis of CO 2 enrichment experiments (31% increase) but fail to account for the substantial carbon cost of BNF. In contrast, ESMs with mechanistic representations of BNF account for its carbon cost as well as its regulation by nitrogen limitation but overestimate the BNF response to a doubling of CO 2 (135% increase). Overall, all current BNF representations in ESMs fall short of fully capturing its response to rising atmospheric CO 2 . Finally, we find a positive correlation between modeled present-day natural BNF and the CO 2 fertilization effect across ESMs, suggesting that overestimated natural BNF translates to an exaggerated CO 2 fertilization effect of approximately 11% in ESMs.

Biological nitrogen fixation↗

The June 2012 North American Derecho: A Testbed for Evaluating Regional and Global Climate Modeling Systems at Cloud‐Resolving Scales

Abstract In this paper, we introduce a testbed for evaluating and comparing climate modeling systems at cloud resolving scales using hindcasts of the June 2012 North American derecho. To demonstrate its utility for model intercomparison, the testbed is applied to two models: the regionally‐refined Simple Cloud‐Resolving E3SM Atmosphere Model (SCREAM) at 6.5, 3.25 and 1.625 km grid spacing and the Weather Research and Forecasting (WRF) model with 3.2 and 1.6 km grid spacing. We find the simulation results to be highly sensitive to the initial conditions (ICs), initialization time, and model configurations, with ICs from the Rapid Refresh producing the best simulation. Significant improvement is identified in both models as horizontal grid spacing is refined. While a propagation delay of approximately 2 hr is found in both models, SCREAM at 1.625 km simulates the observed bow echo structure of the derecho well and predicts strong surface gusts that exceed 30 m/s. In comparison, WRF has difficulty producing surface wind over 25 m/s, with wind gusts in WRF 42%–46% lower than in SCREAM. However, WRF has a lower bias in simulating cloud top temperature and extent, but overestimates precipitation intensity. Both models reproduce the observed outgoing longwave radiation spatial patterns well (Pearson correlation >0.88), but, compared with NEXRAD observations, simulate generally larger areas of composite radar reflectivity >40 dBZ and underestimate the precipitating area by ∼47%.

2012 North American derecho↗

Mechanisms in Regulating the Quasi‐Biennial Oscillation in Exascale Earth System Model Version 2

Abstract The update to the deep convection parameterization in the energy exascale Earth system model version 2 (E3SMv2) makes the simulated quasi‐biennial oscillation (QBO) have a shorter period than without the update when other tunable parameters the same since the update makes convection more intense but less frequent while leaving the time‐mean convective heating tendency almost unchanged. Amplitudes of momentum fluxes of parameterized gravity waves (GWs) are intensified since they are determined by the square of convective heating tendency. In addition, stronger planetary waves are simulated in E3SMv2 with the convection scheme update, partially due to the tropospheric precipitation change. Furthermore, there is evidence that planetary waves are intensified in the stratosphere due to the dissipation of enhanced parameterized GWs. These factors are found to be responsible for modulating the QBO simulated in E3SMv2.

Li, Yuanpu [Climate and Global Dynamics Division U↗

Arctic Amplification in the Community Earth System Models (CESM1 and CESM2)

We compare the Arctic amplification (AA) produced by the two Community Earth System Models CESM1 and CESM2, members of the CEMIP5 (Coupled Models Intercomparison Project phase 5) and CEMIP6 collections, respectively. We find that the CESM1 model reproduces the recent high values of the AA deduced from the observed temperature much better than the CESM2. The correlation coefficient within the 1970–2012 time period between CESM1-simulated AA and the observed one is 0.47, while the CESM2 simulation leads to an anticorrelation of r = –0.53. Even the more successful model (CESM1) is not able to reproduce recent high AA values of 4–5. The main cause of this failure is the model’s overestimate of the rate of increase in the mean global temperature in years post 1990. When the CESM1 model’s simulated trend of the mean global temperature is replaced in the expression for the AA by the observed temperature trend, the correlation coefficient increases from 0.47 to 0.75. The CESM1 model is among the best north American models in AA simulation while the CESM2 model is among the least successful.

54 ENVIRONMENTAL SCIENCES↗

Modeling and control of nuclear–renewable integrated energy systems: Dynamic system model for green electricity and hydrogen production

The need for decarbonization and diversification of energy resources has led to the development of integrated energy systems (IESs), where multiple resources supply more than one energy sector. Here, one such IES with small modular nuclear reactors and renewables (wind and solar) as generating resources, catering to the demand of the electric grid while producing hydrogen for industries, is modeled in this paper. The physics-based component models are represented using the Modelica language and interconnected to form the IES. The control and coordination of the overall system are ensured by designing a suitable control architecture composed of individual subsystem-level controls and supervisory control. The dynamic performance and the load-following capability of the IES are evaluated, while satisfying the safe operational limits of the components. Different configurations and modes of IES operation are considered, where the adaptability of the control system in the presence of varying demands and renewable generations is validated. The simulation results indicate that hydrogen as a flexible load facilitates the supply of varying grid demand. Additionally, the renewables are also accommodated into the IES owing to the flexibility of the balance of plant associated with the nuclear reactors.

24 POWER TRANSMISSION AND DISTRIBUTION↗