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802 records · Page 45

Thinking Bayesian for plasma physicists

Bayesian statistics offers a powerful technique for plasma physicists to infer knowledge from the heterogeneous data types encountered. To explain this power, a simple example, Gaussian Process Regression, and the application of Bayesian statistics to inverse problems are explained. The likelihood is the key distribution because it contains the data model, or theoretic predictions, of the desired quantities. By using prior knowledge, the distribution of the inferred quantities of interest based on the data given can be inferred. Because it is a distribution of inferred quantities given the data and not a single prediction, uncertainty quantification is a natural consequence of Bayesian statistics. The benefits of machine learning in developing surrogate models for solving inverse problems are discussed, as well as progress in quantitatively understanding the errors that such a model introduces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Striving to translate shale physics across ten orders of magnitude: What have we learned?

Shales will play an important role in the successful transition of energy from fossil-based resources to renewables in the coming decades. Aside from being a significant source of low-carbon intensity fuels, like natural gas, they also serve as geologic seals of subsurface formations that may be used to isolate nuclear waste, sequester CO 2 , or store intermittent energy (e.g., solar hydrogen). Despite their importance, shales pose significant engineering and environmental challenges due to their nanoporous structure and extreme heterogeneity that spans at least ~10 orders of magnitude in spatial scale. Two challenges inhibit a system-level understanding: (1) the physics of fluid flow and phase behavior in shales are poorly understood due to the dominant molecular interactions between minerals and fluids under confinement, and (2) the apparent lack of scale separation that prevents a reliable (closed) description of the physics at any single scale of observation. In this review, we focus on the latter issue and discuss scale translation, which in its broadest sense is transforming data or simulations from one spatiotemporal scale to another. While effective scale translation is not exclusive to shales, but all geologic porous media, the need for it is especially acute in shales given their high degree of heterogeneity. Classical theories like homogenization, while indispensable, fail when scales are not separated. Other methods, like numerical upscaling, scale-translate in only one direction: small to large, but not the reverse, called downscaling. However, the confluence of advances in three areas are bringing challenging problems such as shales within reach: increased computational power and scalable algorithms; high-resolution imaging and multi-modal data acquisition; and machine learning to process massive amounts of data. While these advances equip geoscientists with a wide array of experimental and computational tools, no individual tool can probe the entire gamut of heterogeneity in shales. Their effective use, therefore, requires an ability to bridge between various data types obtained at different scales. The aim of this review is to present a coherent account of computational and experimental methods that may be used to achieve just that, i.e., to perform scale translation. We provide a broader definition of scale translation, one that transcends classical homogenization and upscaling methods, but is consistent with them and accommodates notions like downscaling and data translation. After a brief introduction to homogenization, we review hybrid methods, numerical upscaling and its recent extensions, multiscale computing, high-resolution imaging, and machine learning. We place particular emphasis on multiscale computing and propose an algorithmic framework to bridge between the pore (micro) and Darcy (macro) scales. Throughout the paper, we draw comparisons between the various methods and highlight their (often hidden) similarities, differences, benefits, and pitfalls. We finally conclude with two case studies on shales that exemplify some of the methods presented.

58 GEOSCIENCES↗

Missing data in multi-omics integration: Recent advances through artificial intelligence

Biological systems function through complex interactions between various ‘omics (biomolecules), and a more complete understanding of these systems is only possible through an integrated, multi-omic perspective. This has presented the need for the development of integration approaches that are able to capture the complex, often non-linear, interactions that define these biological systems and are adapted to the challenges of combining the heterogenous data across ‘omic views. A principal challenge to multi-omic integration is missing data because all biomolecules are not measured in all samples. Due to either cost, instrument sensitivity, or other experimental factors, data for a biological sample may be missing for one or more ‘omic techologies. Recent methodological developments in artificial intelligence and statistical learning have greatly facilitated the analyses of multi-omics data, however many of these techniques assume access to completely observed data. A subset of these methods incorporate mechanisms for handling partially observed samples, and these methods are the focus of this review. We describe recently developed approaches, noting their primary use cases and highlighting each method's approach to handling missing data. We additionally provide an overview of the more traditional missing data workflows and their limitations; and we discuss potential avenues for further developments as well as how the missing data issue and its current solutions may generalize beyond the multi-omics context.

97 MATHEMATICS AND COMPUTING↗

Data-driven materials research enabled by natural language processing and information extraction

Given the emergence of data science and machine learning throughout all aspects of society, but particularly in the scientific domain, there is increased importance placed on obtaining data. Data in materials science are particularly heterogeneous, based on the significant range in materials classes that are explored and the variety of materials properties that are of interest. This leads to data that range many orders of magnitude, and these data may manifest as numerical text or image-based information, which requires quantitative interpretation. The ability to automatically consume and codify the scientific literature across domains - enabled by techniques adapted from the field of natural language processing - therefore has immense potential to unlock and generate the rich datasets necessary for data science and machine learning. This review focuses on the progress and practices of natural language processing and text mining of materials science literature and highlights opportunities for extracting additional information beyond text contained in figures and tables in articles. Here, we discuss and provide examples for several reasons for the pursuit of natural language processing for materials, including data compilation, hypothesis development, and understanding the trends within and across fields. Current and emerging natural language processing methods along with their applications to materials science are detailed. We, then, discuss natural language processing and data challenges within the materials science domain where future directions may prove valuable.

36 MATERIALS SCIENCE↗

Satellite solar-induced chlorophyll fluorescence and near-infrared reflectance capture complementary aspects of dryland vegetation productivity dynamics

Mounting evidence indicates dryland ecosystems play an important role in driving the interannual variability and trend of the terrestrial carbon sink. Nevertheless, our understanding of the seasonal dynamics of dryland ecosystem carbon uptake through photosynthesis [gross primary productivity (GPP)] remains relatively limited due in part to the limited availability of long-term data and unique challenges associated with satellite remote sensing across dryland ecosystems. Here, we comprehensively evaluated longstanding and emerging satellite vegetation proxies in their ability to capture seasonal dryland GPP dynamics. Specifically, we evaluated: 1) reflectance-based proxies normalized difference vegetation index (NDVI), soil adjusted vegetation index (SAVI), near infrared reflectance index (NIR v ), and kernel NDVI (kNDVI) from the MODerate resolution Imaging Spectroradiometer (MODIS); and 2) newly available physiologically-based proxy solar-induced chlorophyll fluorescence (SIF) from the TROPOspheric Monitoring Instrument (TROPOMI). As a performance benchmark, we used GPP estimates from a robust network of 21 western United States eddy covariance tower sites that span representative gradients in dryland ecosystem climate and functional composition. We found that NIR v and SIF were the best performing GPP proxies and captured complementary aspects of seasonal GPP dynamics across dryland ecosystem types. NIR v offered better performance than the other proxies across relatively low-productivity, sparsely non-evergreen vegetated sites (R 2 = 0.59 ± 0.13); whereas SIF best captured seasonal dynamics across relatively high-productivity sites, including evergreen-dominated sites (R 2 = 0.74 ± 0.07). Notably, across grass-dominated sites, all reflectance-based proxies (NDVI, SAVI, NIRv and kNDVI) showed significant seasonal bias (hysteresis) that strengthened with the total fraction of woody vegetation cover, likely due to seasonal patterns in woody vegetation reflectance that are unrelated to or decoupled from GPP. In conclusion, future efforts to fully integrate the complementary strengths of NIR v and SIF could significantly improve our understanding and representation of dryland GPP dynamics in satellite-based models.

54 ENVIRONMENTAL SCIENCES↗

Configuration Space Integration for Adsorbate Partition Functions: The Effect of Anharmonicity on the Thermophysical Properties of CO–Pt(111) and CH 3 OH–Cu(111)

A method for computing anharmonic thermophysical properties for adsorbates on metal surfaces has been extended to include libration, or frustrated rotation. Classical phase space integration is used with Monte Carlo sampling of the configuration space to obtain the partition function of CO on Pt(111) and CH 3 OH on Cu(111). A minima-preserving neural network potential energy surrogate is used within the integration routines. Direct state counting using discrete variable representation is used to benchmark the results. We find that the phase space integration approach is in excellent agreement with the direct state counting results. Comparison with standard models such as the harmonic oscillator indicates that anharmonicity contributes significantly to the thermodynamic properties of CH 3 OH on Cu(111). We find that there is also a considerable difference between the harmonic oscillator and phase space integration for CO on Pt(111), although the discrepancy can largely be attributed to the presence of multiple binding sites within the unit cell. We demonstrate that a multisite harmonic oscillator model might be sufficient for CO-Pt(111). A more thorough description of the potential energy surface, which can be achieved with phase space integration, is necessary for weakly bound adsorbates such as CH 3 OH. In conclusion, the thermophysical properties were used to calculate free energies of adsorption on the respective metals, and subsequently the equilibrium constants and Langmuir isotherms in relevant temperature ranges. The results show that the choice of model to obtain partition functions greatly affects the resulting surface coverages in kinetic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamic, Adaptive, Systems and Materials: Complex, Simple and Emergent Behaviors

This program has been funded by DoE/BES for twenty years. It has moved into and out of various subjects as it has developed, but it has retained its focus on complexity and complex systems. The project has evolved in the following way: Self-Assembly and Biomimetic Self-Assembly: All self-assembling systems depend upon a minimum of two types of interaction: a repulsion and an attraction. For the familiar molecular systems, attractive interactions are typically hydrogen bonds and electrostatic interactions. Repulsive interactions include steric effects, hydrophobic effects (in biological systems), and charge-charge repulsion. We have expanded this repertoire to include surface interactions, magnetic interactions, and others. I list these systems in the order in which we have explored them: i) A key emphasis in current work is in understanding how the movement of ions in a magnetic field (the Lorentz effect) interacts with catalytic systems. We have demonstrated that an acceleration in rate of reduction of CO 2 to CO can be accomplished by applying an external magnetic field. This acceleration is largely due to the application of the Lorentz effect on mass transport at the catalyst’s surface. ii) We have also extensively explored the influence of electrostatics, as exhibited in self-assembling systems, by tribocharging. iii) Another key system involves surface tension effects; examples include interactions between heavy particles floating at a liquid-air interface, and interacting by changes in surface area; interactions of bubbles and bubble rafts, behaviors of bubble trains in microfluidic networks, and behaviors of microorganisms in constraining environments. iv) This work has intentionally de-emphasized biological systems; but it does include some work on protein-ligand interactions and interactions among microorganisms. v) We have also explored applications of some of these effects, these explorations include bubble rafts as diffraction gratings, exploration of the structures that can be obtained by tribocharging and uses of these structures in exploring nucleation and melting of crystals. vi) Although not a major focus of this work, several other topics have emerged and offer opportunities for future work. These include the behavior of bubble trains and bubble rafts in microfluidic systems. A particularly interesting example is the formation of bubble trains that repeat in the alteration of large and small bubbles according to rules we do not presently understand, but are uniquely large-period oscillating systems. These systems offer a new route into understanding the instabilities of the type represented by oscillations. vii) We have also begun exploratory projects on magnetic levitation (especially to determine molecular density), and information storage (in molecules). Magnetic Levitation: Self-assembling and biomimetic systems require both attraction and repulsion. We have used electrostatics (tribocharging), interfacial free-energies (surface tension and related forces) and others. Potential uses include reconfigurable diffraction gratings and liquid lenses; exploration of mechanisms in tribocharging; tunneling in EGaIn junctions; and bubble trains (especially in micro-fluidic systems). Examples of systems representing these topics is included in the following papers: Complexity: Disks rotating at a water-air interface; Benard-Marangoni effects; Vortex-Crystals from spinning magnetic disks (Marangoni effects); EGaIn Electrode to study quantum tunneling; Self-Assembly of electrostatically-charged metallic spheres (electrets); Dynamically reconfigurable lens; Using computational designs of ligands for enzymes; Electrostatic self-assembly by tribocharging; Monodisperse bubble trains in microchannel systems; Inverted dripping faucet; Flames; Printing of micro-organisms to regenerate the “ink” of printing device; Using micro-organisms to move loads (“microoxen”); Motion of bacterial swarms near surfaces; Making monodisperse particles in microfluidic systems; Coding/decoding of information stored in droplet trains in microfluidic networks; Magnetic levitation; and Information storage. i) Tribocharging. The change in focus of this work on electrets from the fundamentals of charging to applications of these materials in studying self-assembly using electrostatic interactions. ii) Bubbles in Microchannels. The realization that systems of bubbles in microchannels represented a major opportunity to study complexity in a very tractable system, and the development of a semi-quantitative theory of this subject. iii) Flames. The growth of “flames” remains an exploratory subject for the research, although their currently relatively little active work involving it ongoing. iv) Systems with Microorganisms. The removal of work in biological systems from this project. Based on work supported in this program, we now have a significant project on the development of microfluidic tools for studying C. elegans (a nematode), but this work was not appropriate for a program focused on complexity, and we developed separate support for it. (It is, however, an example of successful seeding of a new area by BES.) The work on electrets has gone through a period in which a part of the program was the subject of a MURI; the focus of this work was to develop materials that did not charge electrostatically on friction or contact. The MURI is now over, and the work on dynamic self-assembly (supported by BES) is the major focus. “Flames” has also enjoyed synergistic support, in terms of a project supported by DARPA on flame suppression (in the absence of extinguishing agents, using acoustic and electrostatic interactions). This work was helpful in understanding some of the basics of flames, but is entirely distinct from the BES focus in complexity. A growing interest is in the Lorentz effect. The Lorentz effect is the force exerted on charged particles (electrons, ions, charged molecules) when they move through a perpendicular magnetic field. The Lorentz effect is almost ubiquitous in modern technology: examples of applications include electric motors, dynamos, cathode ray tubes, many batteries, and most systems that control electrical currents with magnetic forces. We have begun to explore the Lorentz effect in electrochemical systems and heterogeneous catalytic systems involving charged organic species and inorganic ions. This work is still at an early stage, but initial studies that Lorentz effects can be large when ions move through magnetic fields, or magnetic fields move in the presence of ions.

36 MATERIALS SCIENCE↗

How initial conditions-, structural-, and parameter-based model uncertainty interact and influence predictions in permafrost ecosystems: Modeling Archive

This dataset contains model output and input data, as well as source code examples for the Terrestrial Ecosystem Model with the Dynamic Vegetation Model and Dynamic Organic Soil (DVM-DOS-TEM) for the field sites Imnavait creek and the Bonanza creek Long Term Ecological Research Network (LTER). The data covers simulations from the last glacial maximum (LGM) until 2100 for a selection of paleo scenarios, setting the mean temperature of the LGM up to 10°C lower than pre-industrial conditions. The model structure was modulated to represent various model versions, and this dataset contains the relevant changes in the source code. The raw output data, the processed statistical data, the setup and processing scripts as well as parameter value distribution files from a parameter sensitivity analysis are included as well. Model outputs include active layer depth, organic soil carbon, soil layer depths, gross primary productivity (GPP) with and without nitrogen limitation, net primary productivity (NPP), soil liquid water content, heterotrophic, maintenance, and growth respiration, soil temperature, and vegetation carbon (*.nc files). The Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) project is a research effort to reduce uncertainty in the Department of Energy’s Energy Exascale Earth System Model (E3SM) by developing a predictive understanding of Arctic tundra ecosystems underlain by permafrost and to quantify feedbacks from the Arctic tundra to the Earth system. NGEE Arctic is supported by the Department of Energy's Office of Biological and Environmental Research.Over Phases 1–3, observations made by the NGEE Arctic team across a gradient of permafrost landscapes in Arctic Alaska improved the representation of tundra processes in the land surface component of E3SM (the E3SM Land Model, ELM). Model improvements emphasized unique aspects of permafrost environments and explored reductions in model complexity while retaining predictive power. The Arctic-informed ELM developed by NGEE Arctic has been used to make novel predictions on processes ranging from permafrost thaw to soil biogeochemical cycling to Earth system feedbacks associated with the unique characteristics of tundra plants. In Phase 4, the NGEE Arctic team is evaluating our new predictive understanding under novel conditions across the Arctic domain. In collaboration with partners at long-term pan-Arctic research sites we are examining whether an Arctic-informed ELM can faithfully simulate interactions among surface and subsurface processes at site, regional, and pan-Arctic scales. In turn, we are using variety of tools to dynamically extend and evaluate ELM inference, with an emphasis on data synthesis and pan-Arctic model evaluation, reintegration of code with an evolving E3SM, scaling across heterogeneous Arctic landscapes, and the appropriate representation of the impacts of increasingly frequent Arctic disturbances.

54 ENVIRONMENTAL SCIENCES↗

Applying Improved Optical Recognition with Machine Learning on Sorting Cu Impurities in Steel Scrap

Annually, 20–55 million tons of electronic waste (e-waste) is produced worldwide (5% of all municipal solid waste). Although e-waste embodies only 2% of America’s municipal waste, it accounts for a significantly larger proportion of the heavy metals and flame retardants present in the waste stream. Currently, less than 20% of all e-waste is recycled in the United States because the heterogeneity of the feedstock limits the opportunity for reuse in high value products and processing of the waste itself is often too costly to justify handling. To address this concern, the aims of this study are: 1) to identify the major plastic and metal compositions within electronic shredder residue (ESR), 2) to formulate solvents and processing conditions to separate 90% of the plastics targeted from consumer shred ESR, and 3) to develop a process design model to estimate the cost and energy efficiency of the proposed solvent-based processing. In this study, a pre-sorted heterogeneous ESR feedstock (one where aluminum, magnetic components, and hazardous battery materials removed by an e-waste recycling facility) was used, with the major compositions of the ESR characterized. It was found that 25 wt.% of the feedstock was composed of plastics, 6 wt.% rubber, 27 wt.% printed circuit boards, 23% wire, and the remainder metals and capacitors. Within the plastic portion, polystyrene (PS, 40 wt.%), acrylonitrile butadiene styrene (ABS, 25 wt.%), and styrene-acrylonitrile (SAN, 9wt.%) were identified to compose the majority of the screened plastics using Fourier transform infrared spectroscopy (FTIR). Next, selective solvents were screened using Hansen Solubility Parameter Theory (HSP) for dissolving PS and ABS. The pre-screening results show that methylene chloride (dichloromethane, DCM) and tetrahydrofuran (THF) are capable of dissolving the most PS and ABS, while methanol (MeOH) and ethylene glycol (EG) are capable of precipitating the most PS and ABS. These solvents were subsequently used to recover polymers and remove. flame retardants within the ESR feedstock. By optimizing the dissolution time and the solvents used, the highest polymer dissolution yield (99 wt.%%) was achieved using DCM for 48 hr. Both pre-screened anti-solvents (MeOH and EG) showed the highest polymer precipitation yield (71 wt.%). In terms of flame retardant removal rate, EG was found to have a high phosphorus-containing flame retardant removal rate (up to 98%). Characterization shows that the proposed solvent-based processing can preserve a high molecular weight fraction of the polymers and effectively remove flame retardants. Cost analysis indicates that the amount of the solvent/anti-solvent recovered after the reaction would play a critical role in reducing the operating costs. The energy analysis shows that the proposed solvent-based processes can save up to 60% of the embodied energy used to manufacture plastics used in electronics (PS and ABS were used for calculations). The results from this project prove the potential of solvent-based processing to produce secondary materials (plastics and metals) from e-waste for cross-industry reuse.

36 MATERIALS SCIENCE↗

Tracking the phase changes in micelle-based NiGa nanocatalysts for methanol synthesis under activation and working conditions

The hydrogenation of CO 2 into high energy density fuels such as methanol, where the required H 2 is obtained from renewable sources, is of utmost importance for a sustainable society. In recent years, NiGa alloys have attracted attention as promising catalyst material systems for the hydrogenation of CO 2 into methanol at ambient pressures. They thus represent an energy-saving alternative to the Cu-based catalysts employed in today's catalytic industry that require high pressures for the CO 2 hydrogenation. However, the underlying reaction mechanisms for the NiGa system are still under debate. One of the challenges here is to unravel the evolution and coexistence of the different species in the heterogeneous NiGa catalyst system under activation and reaction conditions. To shed light on their evolution under activation in H 2 and their catalytic roles under CO 2 hydrogenation working conditions on well-defined Ni 3 Ga 1 and Ni 5 Ga 3 nanoparticle (NP) catalysts, we employed a multi-probe approach in this study. It included advanced machine learning-based analysis of operando X-ray absorption spectroscopy data combined with operando powder X-ray diffraction and near ambient pressure X-ray photoelectron spectroscopy measurements, as well as reactivity studies using bed-packed mass flow reactors. In addition, we employed atomic force microscopy and scanning transmission electron microscopy for structural characterization. Under H 2 activation at 1 bar total pressure, we concluded the formation of metallic Ni, starting for Ni 3 Ga 1 at 300 °C, and for Ni 5 Ga 3 at 400 °C. At higher temperatures, the formation of NiGa alloys follows. The α'-Ni 3 Ga 1 alloy phase is predominantly formed for the Ni 3 Ga 1 NPs, while the coexistence of α'-Ni 3 Ga 1 , δ-Ni 5 Ga 3 and Ga 2 O 3 phases is observed for the Ni 5 Ga 3 NPs after the H 2 activation. The formation of the Ga 2 O 3 phase also results in the presence of excess metallic Ni. Under CO 2 hydrogenation reaction conditions, Ga partially oxidizes again to form a Ga 2 O 3 -rich particle shell for both NP compositions, yet, to a larger extent for the Ni 3 Ga 1 NPs, which, in turn, feature a higher amount of excess Ni. We reveal that metallic Ni is responsible for the high selectivity of the Ni 3 Ga 1 NPs towards the production of methane in our catalytic tests. In contrast, the Ni 5 Ga 3 NPs display a strong selectivity toward methanol production (>92%), more than one order of magnitude higher than that for the Ni 3 Ga 1 NPs, which we ascribe to the presence of the δ-Ni 5 Ga 3 phase.

77 NANOSCIENCE AND NANOTECHNOLOGY↗