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At least 1,315 records · Page 73

Three Decades of Wetland Methane Surface Flux Modeling by Earth System Models–Advances, Applications, and Challenges

Earth System Models (ESMs) simulate the exchange of mass and energy between the land surface and the atmosphere, with a key focus on modeling natural greenhouse gas feedbacks. Methane is the second most important greenhouse gas after carbon dioxide. There are growing concerns over the rapidly increasing methane concentration in the atmosphere, underscoring the need for accurate global modeling of its emissions using ESMs. Of the multitude of sources of methane globally, wetlands are the largest natural emitters for methane, leading to significant efforts targeting their representation in ESMs with a special focus on their methane emissions. In this review, we first provide a historical overview of including wetland–methane components in ESMs and how methane modeling approaches have evolved over time. Second, we discuss recent modeling advancements that show promise for improvements in methane emissions predictions, namely the coupling of surface and atmospheric modules of ESMs, the representation of microtopography and transport mechanisms, the resolution of microbial processes at different spatial–temporal scales, and the improved mapping of wetland area extent across the different wetland types. Third, we shed light on the different challenges hindering accurate estimations of wetland–methane emissions, as shown by the consistent discrepancy between bottom–up and top–down models' predictions. Finally, we emphasize that more detailed representation of biogeochemistry and dynamic hydrology while resolving the within–wetland vegetation heterogeneity should improve model predictions, especially when coupled with expanding ground–based measurement networks and high–resolution remote sensing mapping of methane–relevant variables, such as water elevation, water table depth, and methane concentration.

54 ENVIRONMENTAL SCIENCES↗

Nutrient Dynamics in a Coupled Terrestrial Biosphere and Land Model (ELM-FATES-CNP)

We present a representation of nitrogen and phosphorus cycling in the Functionally Assembled Terrestrial Ecosystem Simulator, a demographic vegetation model within the Energy Exascale Earth System land model. This representation is modular, and designed to allow testing of multiple hypothetical approaches for carbon-nutrient coupling in plants. Novel model hypotheses introduced in this work include, (a) the controls on plant acquisition of aqueous mineralized nutrients in the soil and (b) fairly straight forward methods of allocating nutrients to specific plant organs and their losses through live plant turnover as well as litter fluxes generated through plant mortality. This combines the new with pre-existing hypotheses (such as nitrogen fixation and soil decomposition) into a system that can accommodate plant-soil dynamics for a large number of size- and functional-type-resolved plant cohorts within a time-since-disturbance-resolved ecosystem. Root uptake of nutrients is governed by fine root biomass, and plants vary in their fine root biomass allocation in order to balance carbon and nutrient limitations to growth. We test the sensitivity of the model to a wide range of parameter variations and structural representations, and in the context of observations at Barro Colorado Island, Panama. A key model prediction is that plants in the high-light-availability canopy positions allocate more carbon to fine roots than plants in low-light understory environments, given the widely different carbon versus nutrient constraints of these two niches within a given ecosystem. This model provides a basis for exploring carbon-nutrient coupling with vegetation demography within Earth system models.

54 ENVIRONMENTAL SCIENCES↗

The GFDL Variable-Resolution Global Chemistry-Climate Model for Research at the Nexus of US Climate and Air Quality Extremes

We present a variable-resolution global chemistry-climate model (AM4VR) developed at NOAA's Geophysical Fluid Dynamics Laboratory (GFDL) for research at the nexus of US climate and air quality extremes. AM4VR has a horizontal resolution of 13 km over the US, allowing it to resolve urban-to-rural chemical regimes, mesoscale convective systems, and land-surface heterogeneity. With the resolution gradually reducing to 100 km over the Indian Ocean, we achieve multi-decadal simulations driven by observed sea surface temperatures at 50% of the computational cost for a 25-km uniform-resolution grid. In contrast with GFDL's AM4.1 contributing to the sixth Coupled Model Intercomparison Project at 100 km resolution, AM4VR features much improved US climate mean patterns and variability. In particular, AM4VR shows improved representation of: precipitation seasonal-to-diurnal cycles and extremes, notably reducing the central US dry-and-warm bias; western US snowpack and summer drought, with implications for wildfires; and the North American monsoon, affecting dust storms. AM4VR exhibits excellent representation of winter precipitation, summer drought, and air pollution meteorology in California with complex terrain, enabling skillful prediction of both extreme summer ozone pollution and winter haze events in the Central Valley. AM4VR also provides vast improvements in the process-level representations of biogenic volatile organic compound emissions, interactive dust emissions from land, and removal of air pollutants by terrestrial ecosystems. We highlight the value of increased model resolution in representing climate–air quality interactions through land-biosphere feedbacks. AM4VR offers a novel opportunity to study global dimensions to US air quality, especially the role of Earth system feedbacks in a changing climate.

54 ENVIRONMENTAL SCIENCES↗

Evaluating Cloud Properties at Scott Base: Comparing Ceilometer Observations With ERA5, JRA55, and MERRA2 Reanalyses Using an Instrument Simulator

This study compares CL51 ceilometer observations made at Scott Base, Antarctica, with statistics from the ERA5, JRA55, and MERRA2 reanalyses. To enhance the comparison we use a lidar instrument simulator to derive cloud statistics from the reanalyses which account for instrumental factors. The cloud occurrence in the three reanalyses is slightly overestimated above 3 km, but displays a larger underestimation below 3 km relative to observations. Unlike previous studies, we see no relationship between relative humidity and cloud occurrence biases, suggesting that the cloud biases do not result from the representation of moisture. We also show that the seasonal variation of cloud occurrence and cloud fraction, defined as the vertically integrated cloud occurrence, are small in both the observations and the reanalyses. We also examine the quality of the cloud representation for a set of weather states derived from ERA5 surface winds. The variability associated with grouping cloud occurrence based on weather state is much larger than the seasonal variation, highlighting weather state is a strong control of cloud occurrence. All the reanalyses continue to display underestimates below 3 km and overestimates above 3 km for each weather state. But the variability in ERA5 statistics matches the changes in the observations better than the other reanalyses. We also use a machine learning scheme to estimate the quantity of supercooled liquid water cloud from the ceilometer observations. Ceilometer low-level supercooled liquid water cloud occurrences are considerably larger than values derived from the reanalyses, further highlighting the poor representation of low-level clouds in the reanalyses.

54 ENVIRONMENTAL SCIENCES↗

Enhanced Convective Microphysics Scheme and Its Impacts on Mean Climate in E3SM

Abstract To improve the representation of microphysical processes in convective clouds and their interaction with aerosol and stratiform clouds, a two‐moment convective microphysics parameterization (CMP) scheme developed by Song and Zhang (2011, https://doi.org/10.1029/2010jd014833 ) is upgraded and implemented in E3SM. The new developments include: (a) implementing a parameterization for graupel to enhance the representation of ice‐phase microphysical processes; (b) representing the impact of spatial inhomogeneity of cloud droplets in cumulus ensembles on autoconversion and accretion processes to improve the representation of warm‐rain microphysical processes; (c) implementing a comprehensive Bergeron process parameterization to better represent mixed‐phase microphysical processes; and (d) representing the interactions between ice‐phase microphysics and cloud thermodynamics. Simulations show that the cloud microphysical properties simulated by the CMP are generally in good agreement with observations. It reasonably simulates the changes in droplets effective radius related to precipitation formation in convective clouds, as identified from satellite observations. It also successfully simulates the contrast in these processes between maritime and continental clouds, demonstrating its capability to simulate the impact of aerosols on convection. Analyses of the impact of CMP on climate mean state simulation demonstrate that the CMP slightly improves the simulations of precipitation, cloud macrophysical properties, longwave cloud radiative forcing, zonal wind, and temperature. However, a degradation in shortwave cloud radiative forcing occurs.

GCM↗

Importance of Spatially Continuous Urban Surface Properties in Urban‐Resolving Earth System Modeling

Accurate representation of urban properties and processes at higher resolutions in global modeling systems is essential for advancing our ability to capture the complexities of urban systems and informing effective resilience strategies. However, the prescription of coarse global-scale urban properties in most state-of-the-art Earth system models (ESMs) is limiting their potential for capturing urban signals as they advance toward kilometer-scale simulation capabilities. To bridge this gap in inadequate urban property representation and to advance urban-resolving Earth system modeling, this work integrates the newly-developed global 1 km-resolution facet-level urban surface property data set, U-Surf, into the land component of Community Earth System Model (CESM)—Community Terrestrial System Model (CTSM). The land-only CTSM simulations are validated against satellite measurements, ground-based urban weather stations, flux tower observations, and reanalysis data. Results demonstrate that the enhanced urban properties allow improved simulations of urban meteorology and surface energy fluxes compared to the default coarse-resolution categorical urban canopy parameters. Spatial scaling analysis reveals regime-dependent information loss during resolution aggregation, as well as substantial scale-dependent variations in urban surface energy flux representation. Furthermore, these findings have critical implications for coupled Earth system modeling when including the effect of land-atmosphere interaction. This work establishes a foundation for future urban-resolving kilometer-scale ESM development, which will enable systematic intra- and inter-city comparisons that inform urban adaptation strategies across diverse global urban environments.

Cheng, Yifan [University of Illinois Urbana-Champa↗

Predicting orientation-dependent plastic susceptibility from static structure in amorphous solids via deep learning

It has been a long-standing materials science challenge to establish structure-property relations in amorphous solids. Here we introduce a rotationally non-invariant local structure representation that enables different predictions for different loading orientations, which is found essential for high-fidelity prediction of the propensity for stress-driven shear transformations. This novel structure representation, when combined with convolutional neural network (CNN), a powerful deep learning algorithm, leads to unprecedented accuracy for identifying atoms with high propensity for shear transformations (i.e., plastic susceptibility), solely from the static structure in both two- and three-dimensional model glasses. The data-driven models trained on samples at one composition and a given processing history are found transferrable to glass samples with different processing histories or at different compositions in the same alloy system. Our analysis of the new structure representation also provides valuable insight into key atomic packing features that influence the local mechanical response and its anisotropy in glasses.

36 MATERIALS SCIENCE↗

The need to operationalize climate modelling

We report climate models have changed the world. Starting out as simple globally averaged representations of vertical energy exchanges in the atmosphere in the 1950s, today’s climate models are highly complex numerical representations of the Earth system based on the fundamental laws of physics. Their development has largely been driven by scientific curiosity, with the many approximate virtual representations of Earth available today enabling the interrogation of the past and present climate system and the development of an understanding of the influence of human activity on its future. It is this understanding that underpins the climate mitigation targets enshrined in the Paris Agreement to limit global mean temperature increases.

54 ENVIRONMENTAL SCIENCES↗

An open source knowledge graph ecosystem for the life sciences

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoint resources and abstraction algorithms), and benchmarks (e.g., prebuilt KGs). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 different large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Enabling deeper learning on big data for materials informatics applications

Abstract The application of machine learning (ML) techniques in materials science has attracted significant attention in recent years, due to their impressive ability to efficiently extract data-driven linkages from various input materials representations to their output properties. While the application of traditional ML techniques has become quite ubiquitous, there have been limited applications of more advanced deep learning (DL) techniques, primarily because big materials datasets are relatively rare. Given the demonstrated potential and advantages of DL and the increasing availability of big materials datasets, it is attractive to go for deeper neural networks in a bid to boost model performance, but in reality, it leads to performance degradation due to the vanishing gradient problem. In this paper, we address the question of how to enable deeper learning for cases where big materials data is available. Here, we present a general deep learning framework based on Individual Residual learning (IRNet) composed of very deep neural networks that can work with any vector-based materials representation as input to build accurate property prediction models. We find that the proposed IRNet models can not only successfully alleviate the vanishing gradient problem and enable deeper learning, but also lead to significantly (up to 47%) better model accuracy as compared to plain deep neural networks and traditional ML techniques for a given input materials representation in the presence of big data.

36 MATERIALS SCIENCE↗

Counting generations in birth and death processes with competing Erlang and exponential waiting times

Lymphocyte populations, stimulated in vitro or in vivo, grow as cells divide. Stochastic models are appropriate because some cells undergo multiple rounds of division, some die, and others of the same type in the same conditions do not divide at all. If individual cells behave independently, then each cell can be imagined as sampling from a probability density of times to division and death. The exponential density is the most mathematically and computationally convenient choice. It has the advantage of satisfying the memoryless property, consistent with a Markov process, but it overestimates the probability of short division times. With the aim of preserving the advantages of a Markovian framework while improving the representation of experimentally-observed division times, we consider a multi-stage model of cellular division and death. We use Erlang-distributed (or, more generally, phase-type distributed) times to division, and exponentially distributed times to death. We classify cells into generations, using the rule that the daughters of cells in generation n are in generation n + 1. In some circumstances, our representation is equivalent to established models of lymphocyte dynamics. We find the growth rate of the cell population by calculating the proportions of cells by stage and generation. The exponent describing the late-time cell population growth, and the criterion for extinction of the population, differs from what would be expected if N steps with rate λ were equivalent to a single step of rate λ/N. We link with a published experimental dataset, where cell counts were reported after T cells were transferred to lymphopenic mice, using Approximate Bayesian Computation. In the comparison, the death rate is assumed to be proportional to the generation and the Erlang time to division for generation 0 is allowed to differ from that of subsequent generations. The multi-stage representation is preferred to a simple exponential in posterior distributions, and the mean time to first division is estimated to be longer than the mean time to subsequent divisions.

59 BASIC BIOLOGICAL SCIENCES↗

Improving deep learning model performance under parametric constraints for materials informatics applications

Abstract Modern machine learning (ML) and deep learning (DL) techniques using high-dimensional data representations have helped accelerate the materials discovery process by efficiently detecting hidden patterns in existing datasets and linking input representations to output properties for a better understanding of the scientific phenomenon. While a deep neural network comprised of fully connected layers has been widely used for materials property prediction, simply creating a deeper model with a large number of layers often faces with vanishing gradient problem, causing a degradation in the performance, thereby limiting usage. In this paper, we study and propose architectural principles to address the question of improving the performance of model training and inference under fixed parametric constraints. Here, we present a general deep-learning framework based on branched residual learning (BRNet) with fully connected layers that can work with any numerical vector-based representation as input to build accurate models to predict materials properties. We perform model training for materials properties using numerical vectors representing different composition-based attributes of the respective materials and compare the performance of the proposed models against traditional ML and existing DL architectures. We find that the proposed models are significantly more accurate than the ML/DL models for all data sizes by using different composition-based attributes as input. Further, branched learning requires fewer parameters and results in faster model training due to better convergence during the training phase than existing neural networks, thereby efficiently building accurate models for predicting materials properties.

36 MATERIALS SCIENCE↗

ZeoNet: 3D convolutional neural networks for predicting adsorption in nanoporous zeolites

Zeolites are one of the most widely used materials in the chemical industry due to their nanometer-sized pores that can adsorb and react upon molecules selectively. With hundreds of known framework topologies and hundreds of thousands of computationally predicted structures, the ability to rapidly predict zeolite performance allows researchers to prioritize their efforts on the most promising structures for a given application. Although the accuracy of forcefield-based atomistic simulations has advanced significantly in the past two decades, these simulations can be computationally expensive, especially for long-chain, complex molecules. Here, we present ZeoNet, a representation learning framework using convolutional neural networks (ConvNets) and 3D volumetric representations for predicting adsorption in zeolites. ZeoNet was trained on the task of predicting Henry's constants for adsorption, k H , of n-octadecane in more than 330 000 known and predicted zeolite materials. Employing a 3D grid based on the distances to solvent-accessible surfaces, a volumetric representation that can be generated efficiently, the best-performing ZeoNet achieved a correlation coefficient r 2 = 0.977 and a mean-squared error MSE = 3.8 in ln k H , which corresponds to an error of 9.3 kJ mol -1 in adsorption free energy. In comparison, a model based on hand-designed geometric features has values of r 2 = 0.783 and MSE = 35.7. ZeoNet is also relatively efficient and can process ≈8 structures per second on an Nvidia RTX 2080TI GPU, orders of magnitude faster than forcefield-based simulations. A systematic analysis was conducted to investigate how the choice of ConvNet architectures, the linear dimension (L) and spatial resolution (Δd) of the distance grids, batch size, optimizer, and learning rate impact the model performance. We found that ConvNets based on the ResNet architecture offer the best tradeoff between expressiveness and efficiency. The performance for all models reaches a plateau at L = 30–45 Å and depends less sensitively on grid resolution, with a small benefit around Δd = 0.30–0.45 Å. Finally, saliency maps were visualized to identify which regions of the materials contributed the most to model predictions. It was found, interestingly, that the predictions are driven primarily by the accessible pore volume rather than the region occupied by the framework atoms.

36 MATERIALS SCIENCE↗

Image-driven discriminative and generative machine learning algorithms for establishing microstructure–processing relationships

We investigate methods of microstructure representation for the purpose of predicting processing condition from microstructure image data. A binary alloy that is currently under development as a nuclear fuel was studied for the purpose of developing an improved machine learning approach to image recognition, characterization, and building predictive capabilities linking microstructure to processing conditions. Here, we test different microstructure representations and evaluate model performance based on classification accuracy. A classification accuracy of 95.8% was achieved fordistinguishing between micrographs corresponding to ten different thermo-mechanical material processing conditions.We find that our newly developed microstructure representation describes image data well, and the traditional approachof utilizing area fractions of different phases is insufficient for distinguishing between multiple classes using a relativelysmall, imbalanced original data set of 272 images. To explore the applicability of generative methods for supplementing such limited data sets, generative adversarial networks were trained to generate artificial microstructure images. Two different generative networks were trained and tested to assess performance. Challenges and best practices associated with applying machine learning to limited microstructure image data sets is also discussed. Our work has implications for quantitative microstructure analysis, and development of microstructure-processing relationships in limited data sets typical of metallurgical process design studies.

36 MATERIALS SCIENCE↗

Stellarator optimization for good magnetic surfaces at the same time as quasisymmetry

A method is demonstrated to optimize a stellarator's geometry to eliminate magnetic islands and achieve other desired physics properties at the same time. For many physics quantities that have been used in stellarator optimization, including quasisymmetry, neoclassical transport, and magnetohydrodynamic stability, it is convenient to use a magnetic equilibrium representation that assures the existence of magnetic surfaces. However, this representation hides the possible presence of magnetic islands, which are typically undesirable. To include both surface-based objectives and island widths in a single optimization, two fixed-boundary equilibrium calculations are run at each iteration of the optimization: one that enforces the existence of magnetic surfaces (the Variational Moments Equilibrium Code) [S. P. Hirshman and J. C. Whitson, Phys. Fluids 26, 3553 (1983)] and one that does not (the Stepped Pressure Equilibrium Code) [Hudson et al., Phys. Plasmas 19, 112502 (2012)]. By penalizing the island residues in the objective function, the two magnetic field representations are brought into agreement during the optimization. Here, an example is presented in which, particularly on the surface where quasisymmetry was targeted, quasisymmetry is achieved more accurately than in previously published examples.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Discovering causal structure with reproducing-kernel Hilbert space ε -machines

We merge computational mechanics’ definition of causal states (predictively equivalent histories) with reproducing-kernel Hilbert space (RKHS) representation inference. The result is a widely applicable method that infers causal structure directly from observations of a system’s behaviors whether they are over discrete or continuous events or time. A structural representation—a finite- or infinite-state kernel ϵ-machine—is extracted by a reduced-dimension transform that gives an efficient representation of causal states and their topology. In this way, the system dynamics are represented by a stochastic (ordinary or partial) differential equation that acts on causal states. We introduce an algorithm to estimate the associated evolution operator. Paralleling the Fokker–Planck equation, it efficiently evolves causal-state distributions and makes predictions in the original data space via an RKHS functional mapping. We demonstrate these techniques, together with their predictive abilities, on discrete-time, discrete-value infinite Markov-order processes generated by finite-state hidden Markov models with (i) finite or (ii) uncountably infinite causal states and (iii) continuous-time, continuous-value processes generated by thermally driven chaotic flows. The method robustly estimates causal structure in the presence of varying external and measurement noise levels and for very high-dimensional data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Hybrid particle-spectral method for kinetic plasma simulations

A hybrid model for numerical solutions of the Vlasov–Poisson equations is presented, which blends spectral and particle approaches. The model splits the distribution function for plasma species into both spectral and particle representations in the velocity space to combine the advantages of each approach. The spectral representation leverages asymmetrically weighted Hermite basis, whereas the particle representation leverages the particle-in-cell method. Configuration phase space is decomposed with the Fourier method, which is well suited for periodic problems. We derive conservation equations for mass, momentum, and energy for the proposed combined method. It is shown that the coupling error between the two methods is absent in the semi-discrete setting (not taking into account time discretization). Finally, numerical test cases are presented simulating a weak electron beam interaction with plasma, leading to beam–plasma instability. The initially localized electron beam evolved into a highly non-equilibrium distribution function in the velocity space. A small growth rate and the resonance nature of instability make it difficult to obtain accurate solutions for purely particle methods due to noise, which falls as ∼1/Np with a number of particles. At the same time, purely spectral methods may require a large number of modes to capture the highly non-equilibrium state of the evolved beam. We show that the hybrid method is well suited for such problems: it reproduces the linear stage as well as nonlinear dynamics with sufficient accuracy using a highly non-equilibrium distribution function.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The accuracies of effective interactions in downfolding coupled-cluster approaches for small-dimensionality active spaces

Here, this paper evaluates the accuracy of the Hermitian form of the downfolding procedure using the double unitary coupled cluster (DUCC) ansatz on the benchmark systems of linear chains of hydrogen atoms, H6 and H8. The computational infrastructure employs the occupation-number-representation codes to construct the matrix representation of arbitrary second-quantized operators, allowing for the exact representation of exponentials of various operators. The tests demonstrate that external amplitudes from standard single-reference coupled cluster methods that sufficiently describe external (out-of-active-space) correlations reliably parameterize the Hermitian downfolded effective Hamiltonians in the DUCC formalism. The results show that this approach can overcome the problems associated with losing the variational character of corresponding energies in the corresponding SR-CC theories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗