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At least 37 records · Page 2

Reviews and syntheses: Four decades of modeling methane cycling in terrestrial ecosystems

Abstract. Over the past 4 decades, a number of numerical models have been developed to quantify the magnitude, investigate the spatial and temporal variations, and understand the underlying mechanisms and environmental controls of methane (CH4) fluxes within terrestrial ecosystems. These CH4 models are also used for integrating multi-scale CH4 data, such as laboratory-based incubation and molecular analysis, field observational experiments, remote sensing, and aircraft-based measurements across a variety of terrestrial ecosystems. Here we summarize 40 terrestrial CH4 models to characterize their strengths and weaknesses and to suggest a roadmap for future model improvement and application. Our key findings are that (1) the focus of CH4 models has shifted from theoretical to site- and regional-level applications over the past 4 decades, (2) large discrepancies exist among models in terms of representing CH4 processes and their environmental controls, and (3) significant data–model and model–model mismatches are partially attributed to different representations of landscape characterization and inundation dynamics. Three areas for future improvements and applications of terrestrial CH4 models are that (1) CH4 models should more explicitly represent the mechanisms underlying land–atmosphere CH4 exchange, with an emphasis on improving and validating individual CH4 processes over depth and horizontal space, (2) models should be developed that are capable of simulating CH4 emissions across highly heterogeneous spatial and temporal scales, particularly hot moments and hotspots, and (3) efforts should be invested to develop model benchmarking frameworks that can easily be used for model improvement, evaluation, and integration with data from molecular to global scales. These improvements in CH4 models would be beneficial for the Earth system models and further simulation of climate–carbon cycle feedbacks.

54 ENVIRONMENTAL SCIENCES↗

A combinatorially complete epistatic fitness landscape in an enzyme active site

Protein engineering often targets binding pockets or active sites which are enriched in epistasis—nonadditive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a nonnative environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

biocatalysis↗

Efficient sampling of free energy landscapes with functions in Sobolev spaces

Molecular simulations of biological and physical phenomena generally involve sampling complicated, rough energy landscapes characterized by multiple local minima. In this work, we introduce a new family of methods for advanced sampling that draw inspiration from functional representations used in machine learning and approximation theory. As shown here, such representations are particularly well suited for learning free energies using artificial neural networks. As a system evolves through phase space, the proposed methods gradually build a model for the free energy as a function of one or more collective variables, from both the frequency of visits to distinct states and generalized force estimates corresponding to such states. Implementation of the methods is relatively simple and, more importantly, for the representative examples considered in this work, they provide computational efficiency gains of up to several orders of magnitude over other widely used simulation techniques.

Approximation theory↗

Local lattice distortions and the structural instabilities in bcc Nb–Ta–Ti–Hf high-entropy alloys: An ab initio computational study

Local lattice distortions (LLD) and structural stability of body-centered cubic (bcc) Nb–Ta–Ti–Hf high-entropy alloys (HEAs) are studied as functions of composition employing ab initio density-functional theory calculations, with specific focus on the role of the relative concentrations of group IV (Ti and Hf) versus group V (Nb and Ta) elements. Calculated results are presented as a function of composition x in Nb x Ta 0.25 Ti (0.75-x)/2 Hf (0.75-x)/2 alloys, for elastic moduli, phonon spectral functions, LLD and structural energy differences for the bcc and competing hexagonal close-packed (hcp) and ω phases. The results highlight the important role of group V elements and LLD in stabilizing the bcc structure. They further reveal how composition x can be tuned to alter both the magnitude of the LLD and structural energy differences. Specifically, the magnitude of the structural energy differences, and elastic and dynamic stability of the bcc phase, are enhanced with increasing x, while the LLD increase in magnitude as this concentration is decreased. The results also show evidence of correlated LLD at lower values of x, reflecting local structural distortions towards the ω phase, but not hcp. The degree of ω-collapse is nevertheless partial i.e., transformation towards this phase is not observed to be complete due to the presence of Ta and Nb. At lower values of x we further find an energy landscape characterized by multiple, nearly degenerate local energy minima for different values of the LLD.

36 MATERIALS SCIENCE↗

Change detection and classification of land cover in multispectral satellite imagery using clustering of sparse approximations (CoSA) over learned feature dictionaries

Neuromimetic machine vision and pattern recognition algorithms are of great interest for landscape characterization and change detection in satellite imagery in support of global climate change science and modeling. We present results from an ongoing effort to extend machine vision methods to the environmental sciences, using adaptive sparse signal processing combined with machine learning. A Hebbian learning rule is used to build multispectral, multiresolution dictionaries from regional satellite normalized band difference index data. Land cover labels are automatically generated via our CoSA algorithm: Clustering of Sparse Approximations, using a clustering distance metric that combines spectral and spatial textural characteristics to help separate geologic, vegetative, and hydrologie features. We demonstrate our method on example Worldview-2 satellite images of an Arctic region, and use CoSA labels to detect seasonal surface changes. In conclusion, our results suggest that neuroscience-based models are a promising approach to practical pattern recognition and change detection problems in remote sensing.

97 MATHEMATICS AND COMPUTING↗

Predicting Climate Feedbacks and Impacts in the Terrestrial Arctic: w14_terraarctic progress report

Regarding the Arctic Terrestrial Simulator (ATS), previous work solved integrated hydrology (coupled surface/subsurface flow) on multiple polygons, and surface flow over larger domains to guide landscape characterization. Solved thermal hydrology with freeze/thaw dynamics in three dimensions. Ongoing efforts apply state of the art thermal hydrology model to complex topography, and include mesh deformation processes.

54 ENVIRONMENTAL SCIENCES↗

Thermal Infrared Remote Sensing for Analysis of Landscape Ecological Processes: Current Insights and Trends

NASA or NOAA Earth-observing satellites are not the only space-based TIR platforms. The European Space Agency (ESA), the Chinese, and other countries have in orbit or plan to launch TIR remote sensing systems. Satellite remote sensing provides an excellent opportunity to study land-atmosphere energy exchanges at the regional scale. A predominant application of TIR data has been in inferring evaporation, evapotranspiration (ET), and soil moisture. In addition to using TIR data for ET and soil moisture analysis over vegetated surfaces, there is also a need for using these data for assessment of drought conditions. The concept of ecological thermodynamics provides a quantification of surface energy fluxes for landscape characterization in relation to the overall amount of energy input and output from specific land cover types.

Quattrochi, Dale A.↗

Characterization of Forested Landscapes From Remotely Sensed Data Using Fractals and Spatial Autocorrelation

The characterization of forested areas is frequently required in resource management practice. Passive remotely sensed data, which are much more accessible and cost effective than are active data, have rarely, if ever, been used to characterize forest structure directly, but rather they usually focus on the estimation of indirect measurement of biomass or canopy coverage. In this study, some spatial analysis techniques are presented that might be employed with Landsat TM data to analyze forest structure characteristics. A case study is presented wherein fractal dimensions, along with a simple spatial autocorrelation technique (Moran s I), were related to stand density parameters of the Oakmulgee National Forest located in the southeastern United States (Alabama). The results of the case study presented herein have shown that as the percentage of smaller diameter trees becomes greater, and particularly if it exceeds 50%, then the canopy image obtained from Landsat TM data becomes sufficiently homogeneous so that the spatial indices reach their lower limits and thus are no longer determinative. It also appears, at least for the Oakmulgee forest, that the relationships between the spatial indices and forest class percentages within the boundaries can reasonably be considered linear. The linear relationship is much more pronounced in the sawtimber and saplings cases than in samples dominated by medium sized trees (poletimber). In addition, it also appears that, at least for the Oakmulgee forest, the relationships between the spatial indices and forest species groups (Hardwood and Softwood) percentages can reasonably be considered linear. The linear relationship is more pronounced in the forest species groups cases than in the forest classes cases. These results appear to indicate that both fractal dimensions and spatial autocorrelation indices hold promise as means of estimating forest stand characteristics from remotely sensed images. However, additional work is needed to confirm that the boundaries identified for Oakmulgee forest and the linear nature of the relationship between image complexity indices and forest characteristics are generally evident in other forests. In addition, the effects of other parameters such ,as topographic relief and image distortion due to sun angle and cloud cover, for example, need to be examined.

Al-Hamdan, Mohammad Z.↗

Mapping ecoregions under climate change: a case study from the biological ‘crossroads’ of three continents, Turkey

Context: Besides climate change vulnerability, most ecosystems are under threat from a history of improper land-use and conservation policies, yet there is little existing long-term ecological research infrastructure in Turkey. In regions with no ecological networks across large landscapes, ecoregion concept offers opportunities for characterizing the landscape under changing climate.Objectives: Aim is to develop contemporary and future quantitative ecoregions for Turkey based on climate model outputs, to identify climate change-sensitive areas of biodiversity and conservation significance, and to provide a framework for a comprehensive ecological observatory network design.Methods: Using Multivariate Spatio-Temporal Clustering and climate data contemporary and projected future distributions of Turkey’s ecoregions are delineated at several division levels.Results: Turkey’s contemporary ecoregions generally show a northward shift by the end of this century and the lengthening of the growing season across the country, especially eastward and northward. The increase in growing season length, along with the shift in precipitation seasonality and increasing growing season precipitation, shape future conditions within the climate change-sensitive areas. Apart from transboundary ecological and socioeconomic significance, these potentially vulnerable ecosystems also constitute the majority of Turkey’s biodiversity hotspots.Conclusions: Our study marks the first ‘ecoregionalization’ study for Turkey based on both contemporary and future climate scenarios. For countries like Turkey, where large-scale ecological networks have not been established, using such quantitative methodology for delineation of optimal ecoclimatic regions, and for mapping environments at risk from climate change provides an invaluable perspective for conservation planning strategies, and a framework for a comprehensive ecological observatory network design.

54 ENVIRONMENTAL SCIENCES↗

Permafrost Landscape History Shapes Fluvial Chemistry, Ecosystem Carbon Balance, and Potential Trajectories of Future Change

Intensifying permafrost thaw alters carbon cycling by mobilizing large amounts of terrestrial substrate into aquatic ecosystems. Yet, few studies have measured aquatic carbon fluxes and constrained drivers of ecosystem carbon balance across heterogeneous Arctic landscapes. Here, we characterized hydrochemical and landscape controls on fluvial carbon cycling, quantified fluvial carbon fluxes, and estimated fluvial contributions to ecosystem carbon balance across 33 watersheds in four ecoregions in the continuous permafrost zone of the western Canadian Arctic: unglaciated uplands, ice-rich moraine, and organic-rich lowlands and till plains. Major ions, stable isotopes, and carbon speciation and fluxes revealed patterns in carbon cycling across ecoregions defined by terrain relief and accumulation of organics. In previously unglaciated mountainous watersheds, bicarbonate dominated carbon export (70% of total) due to chemical weathering of bedrock. In lowland watersheds, where soil organic carbon stores were largest, lateral transport of dissolved organic carbon (50%) and efflux of biotic CO 2 (25%) dominated. In watersheds affected by thaw-induced mass wasting, erosion of ice-rich tills enhanced chemical weathering and increased particulate carbon fluxes by two orders of magnitude. From an ecosystem carbon balance perspective, fluvial carbon export in watersheds not affected by thaw-induced wasting was, on average, equivalent to 6–16% of estimated net ecosystem exchange (NEE). Finally, in watersheds affected by thaw-induced wasting, fluvial carbon export approached 60% of NEE. Because future intensification of thermokarst activity will amplify fluvial carbon export, determining the fate of carbon across diverse northern landscapes is a priority for constraining trajectories of permafrost region ecosystem carbon balance.

54 ENVIRONMENTAL SCIENCES↗

Remote Sensing Characterization of the Urban Landscape for Improvement of Air Quality Modeling

The urban landscape is inherently complex and this complexity is not adequately captured in air quality models, particularly the Community Multiscale Air Quality (CMAQ) model that is used to assess whether urban areas are in attainment of EPA air quality standards, primarily for ground level ozone. This inadequacy of the CMAQ model to sufficiently respond to the heterogeneous nature of the urban landscape can impact how well the model predicts ozone pollutant levels over metropolitan areas and ultimately, whether cities exceed EPA ozone air quality standards. We are exploring the utility of high-resolution remote sensing data and urban growth projections as improved inputs to the meteorology component of the CMAQ model focusing on the Atlanta, Georgia metropolitan area as a case study. These growth projections include "business as usual" and "smart growth" scenarios out to 2030. The growth projections illustrate the effects of employing urban heat island mitigation strategies, such as increasing tree canopy and albedo across the Atlanta metro area, in moderating ground-level ozone and air temperature, compared to "business as usual" simulations in which heat island mitigation strategies are not applied. The National Land Cover Dataset at 30m resolution is being used as the land use/land cover input and aggregated to the 4km scale for the MM5 mesoscale meteorological model and the (CMAQ) modeling schemes. Use of these data has been found to better characterize low densityhburban development as compared with USGS 1 km land use/land cover data that have traditionally been used in modeling. Air quality prediction for fiture scenarios to 2030 is being facilitated by land use projections using a spatial growth model. Land use projections were developed using the 2030 Regional Transportation Plan developed by the Atlanta Regional Commission, the regional planning agency for the area. This allows the state Environmental Protection agency to evaluate how these transportation plans will affect fbture air quality.

Quattrochi, Dale A.↗

Characterization of the biofilm landscape of Bacillus subtilis by spatial microproteomics

Bulk proteomics has been demonstrated to differentiate subpopulations within bacterial colonies, yet advanced analyses by mass spectrometry imaging (MSI) hold even greater promise for the future. This technology can enable high-throughput spatial phenotyping that can reshape biological discovery by providing visualization of components of various biomolecular mechanisms. With high mass resolving power and high spatial resolution analyses being routine, we can confidently enable intact protein imaging directly from samples with minimal preparation. Pairing those analyses with bulk experimental libraries can provide high confidence in annotations of post-translational modifications (PTMs) and truncations. Revealing PTM localization within the samples unlocks a direct window into unknown biology at the microscale. However, top-down proteomics (TDP) is not commonplace for microbial species, largely due to challenges in identifying detected peptides and proteins; considering the theoretical proteome of even the well-studied model bacterium Bacillus subtilis was only partially mapped recently. With little still known about the form and function of many of these proteins – let alone proteoforms, where PTMs and truncations of the same protein may possess unique physiological roles – there is a wealth of work to be done. Here we jointly apply TDP and MSI to describe the microscale spatial proteomic landscape within B. subtilis and further demonstrate the feasibility of detecting differentiated subpopulations through proteoforms across the biofilm landscape.

bacterial biofilms↗

Energy Landscape, and Structural and Spectroscopic Characterization of Diazirine and Its Cyclic Isomers

Identifying new nitrogenated hydrocarbon molecules in the interstellar medium (ISM) is challenging due to the lack of comprehensive spectroscopic data from experiments. In this computational work, we focus on investigating the structures, relative energies, spectroscopic constants, and energy landscape of the cyclic isomers of diazirine (c-CH2N2) using ab initio quantum chemical methods. Density functional theory (DFT) methods and coupled cluster theory with singles and doubles including perturbative triples [CCSD(T)] and CCSD(T) with the explicitly correlated F12 b correction [CCSD(T)-F12b] were employed for this purpose along with large correlation consistent cc-pVTZ, cc-pVQZ, and cc-pV5Z basis sets. Harmonic vibrational frequencies, infrared vibrational intensities, rotational constants, and dipole moments are reported. An harmonic vibrational fundamentals along with centrifugal distortion constants, and vibration-rotation interaction constants are also reported for all the cyclic isomers. The energies computed with the CCSD(T) and CCSD(T)-F12b methods were extrapolated to the one-particle complete basis set (CBS) limit following a three-point formula. At the CCSD(T)-F12b/CBS level of theory the 3,3H-diazirine (c-CH2N2) is the lowest energy cyclic isomer followed by 1,3H-diazirine, (E)-1,2H-Diazirine, and (Z)-1,2H-diazirine which are 20.1, 47.8, and 51.3kcal mol-1above the 3,3H-Diazirine, respectively. Accurate structures and spectroscopic constants that are reported here could be useful for future identification of these cyclic nitrogenated organic molecules in the interstellar medium or circumstellar disks.

Energy Landscape↗

Characterization of River Networks: A GIS Approach and Its Applications

Abstract Fluvial geomorphology provides the basis for characterizing complex river networks and evaluating biophysical processes within watersheds. Understanding the spatial organization of morphological features, their influencing processes, and resultant geomorphic diversity in stream networks are important for efficient restoration, river health assessment, and improving our knowledge of the resilience of riverine landscapes. River characterization is a means to determine the biophysical character of river networks but many methods are fraught with pitfalls, such as the use of incorrect variables and limited acknowledgment of the hierarchical organization of rivers. In this paper, a top‐down geographic information system‐based approach for determining the physical typology of river networks is outlined. A suite of multivariate analyses are used to develop a nomenclature for functional process zones (FPZs) — large tracts of the river network with similar hydro‐geomorphological character. Applied to the Little Miami River, Ohio, six distinct FPZs emerged, which had a nonuniform distribution along the river network. Some FPZs repeated downstream; others were rare in terms of total length and number of FPZ segments. The physical structure of the Little Miami River network was analyzed using a series of community metrics. Application of this approach for river monitoring, establishing reference conditions, as well as management of threatened and endangered species and asset trading is highlighted.

Thoms, Martin↗

Unraveling the Effect of Conformational and Electronic Disorder in the Charge Transport Processes of Semiconducting Polymers

Charge transport in semiconducting polymers is inextricably linked to their microstructure, making the characterization of polymer morphology at all length-scales essential for understanding the factors that limit mobility in these materials. Indeed, charge transport depends both on the ability of polarons to delocalize at the approximately nanometer length-scale and navigate a complex energetic and morphological mesoscale landscape. While characterization of the mesoscale morphology of polymers is well-established, studies of the local chain packing and nanoscale disorder, which affect delocalization, can be significantly more difficult to carry out. Additionally, through infrared charge modulation spectroscopy and theoretical modeling, the effect of the local chain environment on polaron delocalization is directly measured and quantified. Using a series of polymers based on the model system, poly(3-hexylthiophene), the link between disorder and polaron localization is systematically explored. Polaron delocalization is correlated with known trends in mobility, revealing that while charge delocalization is always beneficial, the formation of tie-chains is necessary to reach the highest mobilities in semicrystalline polymers. The results provide direct evidence for the importance of both nanoscale (charge carrier delocalization) and mesoscale (tie-chains) orders, demonstrating the need to distinguish the key length-scale limiting charge transport in the design of new, high mobility polymers.

36 MATERIALS SCIENCE↗

A Look at the Truths and Misconceptions of the Variational Quantum Eigensolver and the Implications of Overparameterization

In this work, we investigate loss landscapes of the variational quantum eigensolver (VQE) by quantifying the number of local minima through empirical analyses. We focus on minimal models in chemistry and physics so that we can do a complete analysis using more computationally expensive tools. We employ Hessian eigenvalue calculations and the nudged elastic band algorithm to characterize these landscapes. Our results expand upon the existing literature by highlighting the optimization challenges faced by VQE. We find that, as the number of parameters in our ansatz increases, the number of basins increases while the corresponding loss function values converge toward the global minimum value. This observation implies that overparameterization may lead to an ``effective convexity'' in VQE loss landscapes, a phenomenon supported by theoretical and numerical work in classical machine learning.

quantum computing↗

Microtopographic characterization of ice-wedge polygon landscape in Utqiagvik (Barrow), Alaska: Troughs, rims, and centers derived from high-resolution (0.25 m) LiDAR data

The dataset represents microtopographic characterization of the ice-wedge polygon landscape in Barrow, Alaska, presented as Figure 3b in the publication by Gangodagamage et al. (2014). Three microtopographic features are delineated using 0.25 m high resolution digital elevation dataset derived from LiDAR (Light Detection and Ranging) available as PNG, TIF, and GEOJSON files as listed in the file-level metadata (CSV) file. User will need software or tools like a GIS viewer and Photo viewer to access the files. The troughs, rims, and centers are the three categories in this classification scheme. The polygon troughs are the surface expression of the ice-wedges that are in lower elevations than the interior polygon. The elevated shoulders of the polygon interior immediately adjacent to the polygon troughs are the polygon rims for the low center polygons. In case of high center polygons, these features are the topographic highs. In this classification scheme, both topographic highs and rims are considered as polygon rims. The interior part of the polygon just adjacent to the polygon rims are the polygon centers. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗