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At least 631 records · Page 35

Assessing impacts of PBL and surface layer schemes in simulating the surface–atmosphere interactions and precipitation over the tropical ocean using observations from AMIE/DYNAMO

Accuracy of turbulence parameterization in representing Planetary Boundary Layer (PBL) processes in climate models is critical for predicting the initiation and development of clouds, air quality issues, and underlying surface-atmosphere-cloud interactions. In this study, we 1) evaluate WRF model-simulated spatial patterns of precipitation and surface fluxes, as well as vertical profiles of potential temperature, humidity, moist static energy and moisture tendency terms as simulated by WRF at various spatial resolutions and with PBL, surface layer and shallow convection schemes against measurements, 2) identify model biases by examining the moisture tendency terms contributed by PBL and convection processes through nudging experiments, and 3) evaluate the dependence of modeled surface latent heat (LH) fluxes onPBL and surface layer schemes over the tropical ocean. The results show that PBL and surface parameterizations have surprisingly large impacts on precipitation, convection initiation and surface moisture fluxes over tropical oceans. All of the parameterizations tested tend to overpredict moisture in PBL and free atmosphere, and consequently result in larger moist static energy and precipitation. Moisture nudging tends to suppress the initiation of convection and reduces the excess precipitation. The reduction in precipitation bias in turn reduces the surface wind and LH flux biases, which suggests that the model drifts at least partly because of a positive feedback between precipitation and surface fluxes. The updated shallow convection scheme KF-CuP tends to suppress the initiation and development of deep convection, consequently decreasing precipitation. The Eta surface layer scheme predicts more reasonable LH fluxes and the LH-Wind Speed relationship than the MM5 scheme, especially when coupled with the MYJ scheme. By examining various parameterization schemes in WRF, we identify sources of biases and weaknesses of current PBL, surface layer and shallow convection schemes in reproducing PBL processes, the initiation of convection and intra-seasonal variability of precipitation.

54 ENVIRONMENTAL SCIENCES↗

Physics and Dynamics Coupling Across Scales in the Next Generation CESM: Meeting the Challenge of High-Resolution (Final Report)

This project examines physics/dynamics coupling, that is, exchange of meteorological profiles and tendencies between an atmospheric model’s dynamical core and its various physics parameterizations. Most model physics parameterizations seek to represent processes that occur on scales smaller than the smallest scale resolved by the dynamical core. As a consequence a key conceptual aspect of parameterizations is an assumption about the subgrid variability of quantities such as temperature, humidity or vertical wind. Most existing parameterizations of processes such as turbulence, convection, cloud, and gravity wave drag make relatively ad hoc assumptions about this variability and are forced to introduce empirical parameters, i.e., “tuning knobs” to obtain realistic simulations. These knobs make systematic dependences on model grid size difficult to quantify.

54 ENVIRONMENTAL SCIENCES↗

Final Technical Report for "Reducing tropical precipitation biases in CESM"

In state-of-the-art climate models, each cloud type is treated using its own separate cloud parameterization and its own separate microphysics parameterization. This use of separate schemes for separate cloud regimes is undesirable because it is theoretically unfounded, it hampers interpretation of results, and it leads to the temptation to overtune parameters. In this grant, we have created a climate model that contains a unified cloud parameterization (“CLUBB”) and a unified microphysics parameterization (“MG2”). In this model, all cloud types --- including marine stratocumulus, shallow cumulus, and deep cumulus --- are represented with a single equation set. This model improves the representation of convection in the Tropics. The model has been compared with ARM observations. The chief benefit of the project is to provide a climate model that is based on a more theoretically rigorous formulation.

54 ENVIRONMENTAL SCIENCES↗

CMDV (CM)4 Project - University of Washington contribution. Final report

The original goal of this project was to diagnose and improve CLUBB, the turbulence and cloud fraction parameterization used in DOE’s E3SM model. For this purpose, we planned to use large-eddy simulation (LES) and ARM observations from the NE Pacific Ocean and the SGP site, in coordination with ARM’s LASSO program. It was determined that for these cloud regimes, many of the turbulent ‘moment closures’ which underlie CLUBB’s mathematical formulation are inconsistent with LES, which is an appropriate benchmark for testing this. The research assistant found that these closures could be more accurately formulated using machine learning using the LES as a training dataset. However the resulting parameterization proved to quickly drift away from physical plausibility. A novel machine-learning based boundary layer parameterization called MARBLE based on matching the time evolution of a parameterized cloud-topped boundary layer to reanalysis was then developed and published.

54 ENVIRONMENTAL SCIENCES↗

Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model

Computational strain-design prediction accuracy has been the focus for many recent efforts through the selective integration of kinetic information into metabolic models. In general, kinetic model prediction quality is determined by the range and scope of genetic and/or environmental perturbations used during parameterization. Here, we apply the k-OptForce procedure on a kinetic model of E. coli core metabolism constructed using the Ensemble Modeling (EM) method and parameterized using multiple mutant strains data under aerobic respiration with glucose as the carbon source. Minimal interventions are identified that improve succinate yield under both aerobic and anaerobic conditions to test the fidelity of model predictions under both genetic and environmental perturbations. Under aerobic condition, k-OptForce identifies interventions that match existing experimental strategies while pointing at a number of unexplored flux re-directions such as routing glyoxylate flux through the glycerate metabolism to improve succinate yield. Many of the identified interventions rely on the kinetic descriptions that would not be discoverable by a purely stoichiometric description. In contrast, under fermentative (anaerobic) condition, k-OptForce fails to identify key interventions including up-regulation of anaplerotic reactions and elimination of competitive fermentative products. This is due to the fact that the pathways activated under anaerobic condition were not properly parameterized as only aerobic flux data were used in the model construction. This study shed light on the importance of condition-specific model parameterization and provides insight on how to augment kinetic models so as to correctly respond to multiple environmental perturbations.

59 BASIC BIOLOGICAL SCIENCES↗

Towards Unifying the Planetary Boundary Layer and Shallow Convection in CAM5 with the Eddy-Diffusivity/Mass-Flux Approach

The modular structure of the boundary layer and convection parameterizations in atmospheric models have long been affecting the numerical representation of subgrid-scale motions and their mutual interactions. A promising alternative, the eddy-diffusivity/mass-flux approach (EDMF), has the potential for unifying the existing formulations into a consistent scheme and improving some of the long-standing issues. This study documents a step towards developing such a unified approach by implementing a stochastic multi-plume EDMF scheme into the Community Atmosphere Model (Version 5.0). Its performance in single-column mode is evaluated against the control parameterization and large-eddy simulation (LES) for two benchmark cases: marine and continental shallow convection. Overall, the results for the two parameterizations agree well with each other and with LES in terms of mean profiles of moist conserved variables and their vertical fluxes, as well as the updraft properties. However, systematic differences between the two schemes, especially for transient continental convection, are also documented. Using EDMF helps improve some of the parameterized features of shallow convection. In particular, for the highest tested vertical resolution, the EDMF cloud base and top heights and the vertical fluxes of energy and water are remarkably close to LES.

54 ENVIRONMENTAL SCIENCES↗

Toward more realistic projections of soil carbon dynamics by Earth system models

Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system modeling in the future IPCC and other assessments. To achieve this goal, we suggest that (1) model structures should reflect real-world processes, (2) parameters should be calibrated to match model outputs with observations, and (3) external forcing variables should accurately prescribe the environmental conditions that soils experience. First, most soil C cycle models simulate C input from litter production and C release through decomposition. The latter process has traditionally been represented by first-order decay functions, regulated primarily by temperature, moisture, litter quality, and soil texture. While this formulation well captures macroscopic soil organic C (SOC) dynamics, better understanding is needed of their underlying mechanisms as related to microbial processes, depth-dependent environmental controls, and other processes that strongly affect soil C dynamics. Second, incomplete use of observations in model parameterization is a major cause of bias in soil C projections from ESMs. Optimal parameter calibration with both pool-and flux-based data sets through data assimilation is among the highest priorities for near-term research to reduce biases among ESMs. Third, external variables are represented inconsistently among ESMs, leading to differences in modeled soil C dynamics. Furthermore, we recommend the implementation of traceability analyses to identify how external variables and model parameterizations influence SOC dynamics in different ESMs. Overall, projections of the terrestrial C sink can be substantially improved when reliable data sets are available to select the most representative model structure, constrain parameters, and prescribe forcing fields.

54 ENVIRONMENTAL SCIENCES↗

Intercomparison of methods of coupling between convection and large-scale circulation: 2. Comparison over nonuniform surface conditions

As part of an international intercomparison project, the weak temperature gradient (WTG) and damped gravity wave (DGW) methods are used to parameterize large-scale dynamics in a set of cloud-resolving models (CRMs) and single column models (SCMs). The WTG or DGW method is implemented using a configuration that couples a model to a reference state defined with profiles obtained from the same model in radiative-convective equilibrium. We investigated the sensitivity of each model to changes in SST, given a fixed reference state. We performed a systematic comparison of the WTG and DGW methods in different models, and a systematic comparison of the behavior of those models using the WTG method and the DGW method. The sensitivity to the SST depends on both the large-scale parameterization method and the choice of the cloud model. In general, SCMs display a wider range of behaviors than CRMs. All CRMs using either the WTG or DGW method show an increase of precipitation with SST, while SCMs show sensitivities which are not always monotonic. CRMs using either the WTG or DGW method show a similar relationship between mean precipitation rate and column-relative humidity, while SCMs exhibit a much wider range of behaviors. DGW simulations produce large-scale velocity profiles which are smoother and less top-heavy compared to those produced by the WTG simulations. Lastly, these large-scale parameterization methods provide a useful tool to identify the impact of parameterization differences on model behavior in the presence of two-way feedback between convection and the large-scale circulation.

54 ENVIRONMENTAL SCIENCES↗

Dependence of radiation belt simulations to assumed radial diffusion rates tested for two empirical models of radial transport

Radial diffusion is one of the dominant physical mechanisms that drives acceleration and loss of the radiation belt electrons, which makes it very important for nowcasting and forecasting space weather models. In this paper, we investigate the sensitivity of the two parameterizations of the radial diffusion of Brautigam and Albert (2000) and Ozeke et al. (2014) on long-term radiation belt modeling using the Versatile Electron Radiation Belt (VERB). Following Brautigam and Albert (2000) and Ozeke et al. (2014), we first perform 1-D radial diffusion simulations. Comparison of the simulation results with observations shows that the difference between simulations with either radial diffusion parameterization is small. To take into account effects of local acceleration and loss, we perform 3-D simulations, including pitch angle, energy, and mixed diffusion. We found that the results of 3-D simulations are even less sensitive to the choice of parameterization of radial diffusion rates than the results of 1-D simulations at various energies (from 0.59 to 1.80 MeV). This result demonstrates that the inclusion of local acceleration and pitch angle diffusion can provide a negative feedback effect, such that the result is largely indistinguishable simulations conducted with different radial diffusion parameterizations. Finally, we also perform a number of sensitivity tests by multiplying radial diffusion rates by constant factors and show that such an approach leads to unrealistic predictions of radiation belt dynamics.

54 ENVIRONMENTAL SCIENCES↗

Mesoscale to microscale wind farm flow modeling and evaluation

The increasing size of wind turbines, with rotors already spanning more than 150 m diameter and hub heights above 100 m, requires proper modeling of the atmospheric boundary layer (ABL) from the surface to the free atmosphere. Furthermore, large wind farm arrays create their own boundary layer structure with unique physics. This poses significant challenges to traditional wind engineering models that rely on surface-layer theories and engineering wind farm models to simulate the flow in and around wind farms. However, adopting an ABL approach offers the opportunity to better integrate wind farm design tools and meteorological models. The challenge is how to build the bridge between atmospheric and wind engineering model communities and how to establish a comprehensive evaluation process that identifies relevant physical phenomena for wind energy applications with modeling and experimental requirements. A framework for model verification, validation, and uncertainty quantification is established to guide this process by a systematic evaluation of the modeling system at increasing levels of complexity. In terms of atmospheric physics, ‘building the bridge’ means developing models for the so-called ‘terra incognita,’ a term used to designate the turbulent scales that transition from mesoscale to microscale. This range of scales within atmospheric research deals with the transition from parameterized to resolved turbulence and the improvement of surface boundary-layer parameterizations. The coupling of meteorological and wind engineering flow models and the definition of a formal model evaluation methodology, is a strong area of research for the next generation of wind conditions assessment and wind farm and wind turbine design tools. Some fundamental challenges are identified in order to direct future research in this area.

17 WIND ENERGY↗

Diagnosis of the Marine Low Cloud Simulation in the NCAR Community Earth System Model (CESM) and the NCEP Global Forecast System (GFS)-Modular Ocean Model v4 (MOM4) coupled model

We present a diagnostic analysis of the marine low cloud climatology simulated by two state-of-the-art coupled atmosphere-ocean models: the NCAR Community Earth System Model (CESM) and the NCEP Global Forecasting System (GFS). In both models, the shallow convection and boundary layer turbulence parameterizations have been recently updated: both models now use a mass-flux scheme for the parameterization of shallow convection, and a turbulence parameterization capable of handling Stratocumulus (Sc)-topped Planetary Boundary Layers (PBLs). For shallow convection, both models employ a convective trigger function based on the concept of convective inhibition and both include explicit convective overshooting/penetrative entrainment formulation. For Sc-topped PBL, both models treat explicitly turbulence mixing and cloud-top entrainment driven by cloud-top radiative cooling. Our focus is on the climatological transition from Sc to shallow Cumulus (Cu)-topped PBL in the subtropical eastern oceans. We show that in the CESM the coastal Sc-topped PBLs in the subtropical Eastern Pacific are well-simulated but the climatological transition from Sc to shallow Cu is too abrupt and happens too close to the coast. By contrast, in the GFS coupled simulation the coastal Sc amount and PBL depth are severely underestimated while the transition from Sc to shallow Cu is ³delayed² and offshore Sc cover is too extensive in the subtropical Eastern Pacific. We discuss the possible connections between such differences in the simulations and differences in the parameterizations of shallow convection and boundary layer turbulence in the two models.

Xiao, Heng↗

Carbon and energy fluxes in cropland ecosystems: a model-data comparison

Croplands are extremely productive ecosystems that contribute to land–atmosphere exchange of carbon, energy, and water during their short growing seasons. We evaluated and compared net ecosystem exchange (NEE), latent heat flux (LE), and sensible heat flux (H) simulated by a suite of ecosystem models at five agricultural eddy covariance flux tower sites in the central United States as part of the North American Carbon Program Site Synthesis project. Most of the models overestimated H and underestimated LE during the growing season, leading to overall higher Bowen ratios compared to the observations. Most models systematically under predicted NEE, especially at rain-fed sites. Certain crop-specific models that were developed considering the high productivity and associated physiological changes in specific crops better predicted the NEE and LE at both rain-fed and irrigated sites. Models with specific parameterization for different crops better simulated the inter-annual variability of NEE for maize-soybean rotation compared to those models with a single generic crop type. Stratification according to basic model formulation and phenological methodology did not explain significant variation in model performance across these sites and crops. The under prediction of NEE and LE and over prediction of H by most of the models suggests that models developed and parameterized for natural ecosystems cannot accurately predict the more robust physiology of highly bred and intensively managed crop ecosystems. When coupled in Earth System Models, it is likely that the excessive physiological stress simulated in many land surface component models leads to overestimation of temperature and atmospheric boundary layer depth, and underestimation of humidity and CO 2 seasonal uptake over agricultural regions.

54 ENVIRONMENTAL SCIENCES↗

Effects of downscaled high-resolution meteorological data on the PSCF identification of emission sources

The Potential Source Contribution Function (PSCF) model has been successfully used for identifying regions of emission source at a long distance in this study, the PSCF model relies on backward trajectories calculated by the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model. In this study, we investigated the impacts of grid resolution and Planetary Boundary Layer (PBL) parameterization (e.g., turbulent transport of pollutants) on the PSCF analysis. The Mellor-Yamada-Janjic (MYJ) and Yonsei University (YUS) parameterization schemes were selected to model the turbulent transport in the PBL within the Weather Research and Forecasting (WRF version 3.6) model. Two separate domain grid sizes (83 and 27 km) were chosen in the WRF downscaling in generating the wind data for driving the HYSPLIT calculation. The effects of grid size and PBL parameterization are important in incorporating the influ- ence of regional and local meteorological processes such as jet streaks, blocking patterns, Rossby waves, and terrain-induced convection on the transport of pollutants by a wind trajectory. We found high resolution PSCF did discover and locate source areas more precisely than that with lower resolution meteorological inputs. The lack of anticipated improvement could also be because a PBL scheme chosen to produce the WRF data was only a local parameterization and unable to faithfully duplicate the real atmosphere on a global scale. The MYJ scheme was able to replicate PSCF source identification by those using the Reanalysis and discover additional source areas that was not identified by the Reanalysis data. In conclusion, a potential benefit for using high-resolution wind data in the PSCF modeling is that it could discover new source location in addition to those identified by using the Reanalysis data input.

54 ENVIRONMENTAL SCIENCES↗

CFD-DEM Modeling of Autothermal Pyrolysis of Corn Stover with a Coupled Particle- and Reactor-Scale Framework

Autothermal operation of fast pyrolysis is an efficient process-intensification technique wherein exothermic oxidation reactions are used to overcome the heat-transfer bottleneck of conventional pyrolysis. The development of accurate, reliable modeling toolsets is imperative to generating a deeper understanding of biomass autothermal pyrolysis systems to support scale-up and industrial deployment. This modeling effort describes the development of single-particle and reactor models which incorporate detailed reaction schemes and simultaneous exothermic oxidation reactions. The particle-scale model was parameterized for corn stover feedstock with particle morphology, density, ash content, and biopolymer composition, all of which impact the emergent conversion characteristics during pyrolysis. Results were then used to parameterize a reactor-scale autothermal pyrolysis model, which was developed using a coarse-grained computational fluid dynamic-discrete element method. The simulation results compared well with experimental results, with the predicted bio-oil, light gas, and biochar yield within 3.0 wt% of the experimental yields. Further analyses were performed to test the influence of equivalence ratio, biomass injection position, and particle size distribution on autothermal pyrolysis. The analysis of the physio-chemical properties of the fluid and solid phase inside the reactor and at the reactor outlet help reveal important process interactions of autothermal pyrolysis.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗

Computation at a coordinate singularity

Coordinate singularities are sometimes encountered in computational problems. An important example involves global atmospheric models used for climate and weather prediction. Classical spherical coordinates can be used to parameterize the manifold – that is, generate a grid for the computational spherical shell domain. This particular parameterization offers significant benefits such as orthogonality and exact representation of curvature and connection (Christoffel) coefficients. But it also exhibits two polar singularities and at or near these points typical continuity/integral constraints on dependent fields and their derivatives are generally inadequate and lead to poor model performance and erroneous results. Other parameterizations have been developed that eliminate polar singularities, but problems of weaker singularities and enhanced grid noise compared to spherical coordinates (away from the poles) persist. Here, in this study reparameterization invariance of geometric objects (scalars, vectors and the forms generated by their covariant derivatives) is utilized to generate asymptotic forms for dependent fields of interest valid in the neighborhood of a pole. The central concept is that such objects cannot be altered by the metric structure of a parameterization. The new boundary conditions enforce symmetries that are required for transformations of geometric objects. They are implemented in an implicit polar filter of a structured grid, nonhydrostatic global atmospheric model that is simulating idealized Held–Suarez flows. A series of test simulations using different configurations of the asymptotic boundary conditions are made, along with control simulations that use the default model numerics with no absorber, at three different grid sizes. Typically the test simulations are ~ 20% faster in wall clock time than the control—resulting from a decrease in noise at the poles in all cases. In the control simulations adverse numerical effects from the polar singularity are observed to increase with grid resolution. In contrast, test simulations demonstrate robust polar behavior independent of grid resolution.

97 MATHEMATICS AND COMPUTING↗

Numerical simulation and analysis of the April 2013 Chicago floods

The weather event associated to record Chicago floods on April 2013 is investigated by using the Weather Research and Forecasting (WRF) model. Observations at Argonne National Laboratory and multi-sensor (weather radar and rain gauge) precipitation data from the National Weather Service were employed to evaluate the model’s performance. The WRF model captured the synoptic-scale atmospheric features well, but the simulated 24-h accumulated precipitation and short-period temporal evolution of precipitation over the heavy-rain region were less successful. To investigate the potential reasons for the model bias, four supplementary sensitivity experiments using various microphysics schemes and cumulus parameterizations were designed. Of the five tested parameterizations, the WRF Single-Moment 6-class (WSM6) graupel scheme and Kain-Fritsch (KF) cumulus parameterization outperformed the others, such as Grell-Dévényi (GD) cumulus parameterization, which underestimated the precipitation by 30–50% on a regional-average scale. Morrison microphysics and KF outperformed the others for the spatial patterns of 24-h accumulated precipitation. The spatial correlation between observation and Morrison-KF was 0.45, higher than those for other simulations. All of the simulations underestimated the precipitation over northeastern Illinois (especially at Argonne) during 0400–0800 UTC 18 April because of weak ascending motion or small moisture. In conclusion, all of the simulations except WSM6-GD also underestimated the precipitation during 1200–1600 UTC 18 April because of weak southerly flow.

54 ENVIRONMENTAL SCIENCES↗

Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale

The parameterization of kinetic models requires measurement of fluxes and/or metabolite levels for a base strain and a few genetic perturbations thereof. Unlike stoichiometric models that are mostly invariant to the specific strain, it remains unclear whether kinetic models constructed for different strains of the same species have similar or significantly different kinetic parameters. This important question underpins the applicability range and prediction limits of kinetic reconstructions. To this end, herein we parameterize two separate large-scale kinetic models using K-FIT with genome-wide coverage corresponding to two distinct strains of Saccharomyces cerevisiae: CEN.PK 113-7D strain (model k-sacce306-CENPK), and growth-deficient BY4741 (isogenic to S288c; model k-sacce306-BY4741). The metabolic network for each model contains 306 reactions, 230 metabolites, and 119 substrate-level regulatory interactions. The two models (for CEN.PK and BY4741) recapitulate, within one standard deviation, 77% and 75% of the fitted dataset fluxes, respectively, determined by 13 C metabolic flux analysis for wild-type and eight single-gene knockout mutants of each strain. Strain-specific kinetic parameterization results indicate that key enzymes in the TCA cycle, glycolysis, and arginine and proline metabolism drive the metabolic differences between these two strains of S. cerevisiae. Our results suggest that although kinetic models cannot be readily used across strains as stoichiometric models, they can capture species-specific information through the kinetic parameterization process.

59 BASIC BIOLOGICAL SCIENCES↗

Role of Troposphere-Convection-Land Coupling in the Southwestern Amazon Precipitation Bias of the Community Earth System Model version 1 (CESM1)

The Amazon forest plays an important role in the tropical circulation and global water and biogeochemical cycles. However, the common Amazon precipitation biases in global climate models undermine our ability to understand future changes in the Amazon and their global consequences. The Community Earth System Model exhibits a persistent wet season dry bias over the southwestern Amazon. The bias is also characterized by inaccurate diurnal timing and intensity of rainfall events. Analysis of a diverse set of simulations suggests that the bias originates from local processes. A known land model bias in the partitioning of surface energy fluxes is found not to contribute significantly to the rainfall bias. Key model processes are identified to be the low-level divergent circulation controlling horizontal moisture flow and the sensitivity of the modeled deep convection to the lower tropospheric moisture. The lower tropospheric moisture divergence dictates the spatiotemporal distributions of convective precipitation through parameterized entrainment mixing, which generally improves the rainfall diurnal cycle. However, it also limits convective precipitation over the areas with frequent and large-scale divergence in the lower troposphere. The southwestern Amazon is such an area, particularly in the late afternoon, although uncertainty exists in the low-level flow in the simulation and reanalyses. One way to sustain rainfall in the presence of low-level divergence is a convective trigger based on both the moisture and temperature changes by large-scale processes, which is shown to help in reducing the dry bias.

Sakaguchi, Koichi↗