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DOE OSTI2022

The DREAM Endstation at the Linac Coherent Light Source

Free-electron lasers (FEL), with their ultrashort pulses, ultrahigh intensities, and high repetition rates at short wavelength, have provided new approaches to Atomic and Molecular Optical Science. One such approach is following the birth of a photo electron to observe ion dynamics on an ultrafast timescale. Such an approach presents the opportunity to decipher the photon-initiated structural dynamics of an isolated atomic and molecular species. It is a fundamental step towards understanding single- and non-linear multi-photon processes and coherent electron dynamics in atoms and molecules, ultimately leading to coherent control following FEL research breakthroughs in pulse shaping and polarization control. A key aspect for exploring photoinduced quantum phenomena is visualizing the collective motion of electrons and nuclei in a single reaction process, as dynamics in atoms/ions proceed at femtosecond (10 –15 s) timescales while electronic dynamics take place in the attosecond timescale (10 –18 s). Here, we report on the design of a Dynamic Reaction Microscope (DREAM) endstation located at the second interaction point of the Time-Resolved Molecular and Optical (TMO) instrument at the Linac Coherent Light Source (LCLS) capable of following the photon–matter interactions by detecting ions and electrons in coincidence. The DREAM endstation takes advantage of the pulse properties and high repetition rate of LCLS-II to perform gas-phase soft X-ray experiments in a wide spectrum of scientific domains. With its design ability to detect multi-ions and electrons in coincidence while operating in step with the high repetition rate of LCLS-II, the DREAM endstation takes advantage of the inherent momentum conservation of reaction product ions with participating electrons to reconstruct the original X-ray photon–matter interactions. In this report, we outline in detail the design of the DREAM endstation and its functionality, with scientific opportunities enabled by this state-of-the-art instrument.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Interaction of Soil pH and Mineralogy Controls Soil Organic Matter Persistence through Changes in the Composition and Amount of Microbial Necromass

Microbial necromass–mineral associations are key to long-term soil organic matter (SOM) persistence. However, how soil pH and mineralogy interact to regulate SOM stability remains poorly understood. Here, we used artificial soils to test how three clay minerals (bentonite, kaolinite, and goethite), adjusted to four pH levels (5–8), affect microbial activity (respiration), microbial physiology (carbon use efficiency, CUE), microbial-derived residue material (necromass), and the formation and stability of mineral-associated organic matter (MAOM). Artificial soils were inoculated with a rhizosphere-derived microbial community cultured under the same pH conditions and on two representative simulated exudate types (organic acids and carbohydrates) and incubated for 6 weeks. In two complementary experiments, we added necromass from known microbial taxa to the same minerals across pH levels to isolate the role of necromass chemistry and loading. We found that soil pH shaped MAOM chemistry by altering microbial activity and necromass composition. In interaction with mineral type, pH also controlled MAOM thermal stability. Higher necromass loading weakened mineral-organic bonding, reducing MAOM stability, consistent with zonal mineral–organic interaction models. Our results demonstrate that microbial activity, rather than carbon use efficiency, better predicts MAOM formation and that pH-dependent necromass composition and loading govern MAOM persistence. These findings advance mechanistic understanding of SOM stabilization and have implications for predicting soil carbon dynamics under shifting environmental conditions.

carbon use efficiency↗

DOE OSTI2024

Metabolic complexity drives divergence in microbial communities

Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here, in this work, we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Planting a Lyman alpha forest on ABACUSSUMMIT

The full-shape correlations of the Lyman alpha (Ly$α$) forest contain a wealth of cosmological information through the Alcock Paczynski effect. However, these measurements are challenging to model without robustly testing and verifying the theoretical framework used for analyzing them. Here, we leverage the accuracy and volume of the $N$-body simulation suite ABACUSSUMMIT to generate high-resolution Ly$α$ skewers and quasi-stellar object (QSO) catalogs. One of the main goals of our mocks is to aid in the full-shape Ly$α$ analysis planned by the Dark Energy Spectroscopic Instrument (DESI) team. We provide optical depth skewers for six of the fiducial cosmology base-resolution simulations ($L$ box = 2 $h$ -1 Gpc, $N$ = 6912 3 ) at $z$ = 2.5. We adopt a simple recipe based on the Fluctuating Gunn-Peterson Approximation (FGPA) for constructing these skewers from the matter density in an $N$-body simulation and calibrate it against the 1D and 3D Ly$α$ power spectra extracted from the hydrodynamical simulation IllustrisTNG (TNG; $L$ box = 205 $h$ -1 Mpc, $N$ = 2500 3 ). As an important application, we study the non-linear broadening of the baryon acoustic oscillation (BAO) peak and show the cross-correlation between DESI-like QSOs and our Ly$α$ forest skewers. We find differences on small scales between the Kaiser approximation prediction and our mock measurements of the Ly$α$×QSO cross-correlation, which would be important to account for in upcoming analyses. The ABACUSSUMMIT Ly$α$ forest mocks open up the possibility for improved modelling of cross correlations between Ly$α$ and cosmic microwave background (CMB) lensing and Ly$α$ and QSOs, and for forecasts of the 3-point Ly$α$ correlation function. Furthermore, our catalogues and skewers are publicly available on Globus via the National Energy Research Scientific Computing Center (NERSC) (full link under Data Availability).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Computational fluid dynamics modeling and analysis of silica nanoparticle synthesis in a flame spray pyrolysis reactor

Flame Spray Pyrolysis (FSP) is a method for large-scale production of nanoparticles and nanoscale powders employed in a wide range of industrial applications. Particle size and morphology are complex functions of the physicochemical phenomena occurring in the FSP reactor. An extensive study of FSP-related phenomena can be utilized to develop effective strategies for achieving desired particle size/morphology and scaling up the overall yield of an FSP system. In this work, a computational fluid dynamics (CFD) model of an FSP reactor is developed to simulate the coupling of key phenomena involved in the particle synthesis process: liquid spray breakup and evaporation, mixing, combustion, and particle formation/growth of silica nanoparticles. Herein, the particle sizes and their distributions from the CFD simulations are validated against experimental data. Subsequently, the simulations are utilized to investigate the impact of process parameters on the resultant flame dynamics and particle growth. Firstly, the CFD results show that the particle sizes are strongly correlated with the precursor concentration in the solvent. At lower precursor concentrations, the spread of the distribution is relatively insensitive to the value of the concentration. At higher concentrations, the spread is higher as the collision probability between particles is higher. Secondly, increasing the pilot flow rate increases the length of the pilot flames impacting the local ignition location of the spray flame. Lastly, it is shown that the dispersion gas flow rate strongly influences the spray flame shape. This shape can be used for control of particle growth as it helps determine the regions of high temperature and the residence time of the particles in the high temperature region enabling the design and process optimization of the FSP reactor.

42 ENGINEERING↗

DOE OSTI2021

Thermal and Mechanical Energy Performance Analysis of Closed-loop Systems in Hot-Dry-Rock and Hot-Wet-Rock Reservoirs

To understand the potential and limitations for recovering thermal and mechanical energy from closed-loop geothermal systems a collaborative study is underway that will investigate an array of system configurations, working fluids, geothermal reservoir characteristics, operational periods, and heat transfer enhancements. Closed-loop geothermal systems are distinguished from hydrothermal or enhanced geothermal systems (EGS) in that the working fluid only circulates through drilled boreholes. Principal objectives of this study are to determine upper limits for thermal and mechanical energy recovery and optimal operational and configuration parameters for each scenario. Teams of scientists and engineers are applying a suite of numerical simulation and analytical tools to model the heat recovery from closed-loop geothermal systems, and then optimizing operational and configuration parameters to maximize the thermal and mechanical energy recovery. Results from the suite of numerical simulators and analytical tools, such as outlet and inlet states and temperature profiles in the geothermal reservoir over time are intercompared to increase confidence in the analysis. This paper documents the study findings for closed-loop systems in hot-dry-rock and hot-wet-rock reservoirs, where water is the working fluid. The characteristics of the hot-dry-rock reservoir were based on the U.S. Department of Energy’s Utah Frontier Observatory for Research in Geothermal Energy (FORGE) site, near Milford Utah. Two objective functions are defined to optimize the operational and configuration parameters of the system, one each for the recovery of mechanical and thermal energy over the period of operation. For both objective functions, a surface plant thermal to mechanical energy conversion factor and an energy drilling cost is required. In keeping with the study objectives the surface plant conversion factor is determined from a second-law of thermodynamics analysis of a generic binary plant, and drilling costs are based on those from the Utah FORGE site and current national electrical costs.

Closed-loop geothermal systems, hot-dry-rock, hot-↗

DOE OSTI2024

Ecosystem Water‐Saving Timescale Varies Spatially With Typical Drydown Length

Abstract Stomatal optimization theory is a commonly used framework for modeling how plants regulate transpiration in response to the environment. Most stomatal optimization models assume that plants instantaneously optimize a reward function such as carbon gain. However, plants are expected to optimize over longer timescales given the rapid environmental variability they encounter. There are currently no observational constraints on these timescales. Here, a new stomatal model is developed and is used to analyze the timescales over which stomatal closure is optimized. The proposed model assumes plants maximize carbon gain subject to the constraint that they cannot draw down soil moisture below a critical value. The reward is integrated over time, after being weighted by a discount factor that represents the timescale ( τ ) that a plant considers when optimizing stomatal conductance to save water. The model is simple enough to be analytically solvable, which allows the value of τ to be inferred from observations of stomatal behavior under known environmental conditions. The model is fitted to eddy covariance data in a range of ecosystems, finding the value of τ that best predicts the dynamics of evapotranspiration at each site. Across 82 sites, the climate metrics with the strongest correlation to τ are measures of the average number of dry days between rainfall events. Values of τ are similar in magnitude to the longest such dry period encountered in an average year. The results here shed light on which climate characteristics shape spatial variations in ecosystem‐level water use strategy.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Depth-dependent links between microbial taxa and nitrous oxide emissions in a long-term cotton cropping system employing soil health practices

Long-term management practices can shape soil microbial communities in ways that influence nitrogen (N) dynamics and nitrous oxide (N 2 O) emissions. We leverage a 41-year continuous cotton cropping experiment with contrasting tillage, cover cropping, and N fertilization regimes to investigate how these long-term strategies influence soil microbial communities and their associations with N 2 O fluxes during the cotton growing season. Using 16S rRNA gene metabarcoding, we assessed microbial composition in surface and subsurface soils and evaluated its relationship with temporal N 2 O emissions. Among the management practices, N fertilization – a known driver of N 2 O emissions – had the strongest effect on microbial community composition and was linked to a greater number of taxa correlated to N 2 O emissions, particularly in surface soils. Soil pH emerged as a key variable influencing microbial structure across depth and was negatively associated with both N 2 O emissions and microbial composition in the surface layers of fertilized soils. In total, 57 archaeal/bacterial taxa were correlated with N 2 O fluxes, but only seven were shared across depths, suggesting distinct microbial contributors in surface and subsurface soils. Several of these taxa have been previously reported to be associated with N and C cycling processes such as nitrate respiration or carbon turnover, indicating functional context to their correlation with N 2 O fluxes. Temporal shifts in the abundance of key taxa aligned with seasonal peaks in N 2 O emissions, notably in early and late August, and were most pronounced under conventional tillage, hairy vetch cover cropping, and N fertilization. While 16S-based associations cannot confirm functional gene presence or activity, these findings demonstrate that long-term fertilization and associated soil acidification are dominant drivers of microbial shifts linked to N 2 O emissions and highlight the importance of accounting for depth-specific and seasonal microbial dynamics when evaluating management impacts on greenhouse gas emissions.

16S rRNA gene sequencing↗

DOE OSTI2022

A Subspace-Inclusive Sampling Method for the Computational Design of Compositionally Graded Alloys

Abstract Compositionally graded alloys, a subclass of functionally graded materials (FGMs), utilize localized variations in composition with a single metal part to achieve higher performance than traditional single material parts. In previous work [Kirk, T., Galvan, E., Malak, R., and Arroyave, R., 2018, “Computational Design of Gradient Paths in Additively Manufactured Functionally Graded Materials,” J. Mech. Des., 140, p. 111410. 10.1115/1.4040816], the authors presented a computational design methodology that avoids common issues which limit a gradient alloy’s feasibility, such as deleterious phases, and optimizes for performance objectives. However, the previous methodology only samples the interior of a composition space, meaning designed gradients must include all elements in the space throughout the gradient. Because even small amounts of additional alloying elements can introduce new deleterious phases, this characteristic often neglects potentially simpler solutions to otherwise unsolvable problems and, consequently, discourages the addition of new elements to the state space. The present work improves upon the previous methodology by introducing a sampling method that includes subspaces with fewer elements in the design search. The new method samples within an artificially expanded form of the state space and projects samples outside the true region to the nearest true subspace. This method is evaluated first by observing the sample distribution in each subspace of a 3D, 4D, and 5D state space. Next, a parametric study in a synthetic 3D problem compares the performance of the new sampling scheme to the previous methodology. Lastly, the updated methodology is applied to design a gradient from stainless steel to equiatomic NiTi that has practical uses such as embedded shape memory actuation and for which the previous methodology fails to find a feasible path.

Engineering↗

DOE OSTI2022

Hardness Prediction by Incorporating Heat Transfer and Molten Pool Fluid Flow in a Multi-pass, Multi-layer Weld for Onsite Repair of Grade 91 steel

Introduction: In the current fleet of fossil-fired power plants, creep strength enhanced ferritic steels (CSEF) are used to sustain the harsh service conditions. Enhanced properties of Grade 91 steel result from tempered martensite with a fine distribution of MX and M23C6 carbides. Grade 91 steel is subjected to onsite welding repair to remedy their degradation due to extreme service condition. Knowledge of weld repairability of these steels, such as as-welded hardness distribution, is essential to establishing sound repair procedures. Experimental trial and error tests can consume a lot of time as many welding variables need to be studied. For numerical modelling, most of the multi-pass multi-layer models are based on finite element method, which are limited to solve the heat conduction equation and ignore convective heat transfer due to melt flow. Moreover, the mesh has to be pre-built based on a known or assumed weld cross-section geometry. These finite element based models thus have limited predictive capability as defects are not considered and nugget size are pre-assumed. This research aims at developing a thermal and microstructure evolution model incorporating molten pool dynamics in a multi-pass multi-layer material deposition to predict the as-welded hardness distribution. Technical Approach: All the thermal, physical, and metallurgical properties of Grade 91 as a function of temperature are collected from the literature and inputted into the thermo-fluid model based on Flow-3D, a computational fluid dynamics software. A multi-pass, multi-layer material deposition is simulated where the melting of filler wire into the molten pool is directly considered based on the volume of fluid (VOF) method. The flow behaviour of the molten pool is used to understand the formation of deposition geometry and defects. The temperature profiles during the multi-pass, multi-layer welding are calculated. The results computed using the new model are compared against the experimental data of fusion zone geometry and thermal cycles. Hardness prediction in the heat-affected zone (HAZ) are made using Johnson-Mehl-Avrami (JMA) equation for solid-state phase transformation kinetics. The JMA parameters are extracted from the experimental data available in the literature. For comparison, a standard finite element heat conduction model is also developed to predict the thermal cycles and hardness distribution in the multi-pass, multi-layer weld. Expected Result: Results obtained using the molten pool dynamic simulation versus the finite element heat conduction model are compared. Specifically, the effects of convective heat transfer on the accuracy of the calculated thermal history, bead shape and size, and HAZ hardness distribution are examined.

Modeling, Grade 91 steel, Multi-pass multi-layer d↗

DOE OSTI2022

Influence of living grass Roots and endophytic fungal hyphae on soil hydraulic properties

Soil hydraulic properties are often estimated based on laboratory data or pedotransfer functions dependent on soil physical properties, which often do not consider potential impacts of soil roots or fungal hyphae. Here, we first review current knowledge of how these soil biotic components affect hydraulic properties, then we conducted laboratory experiments to specifically test if the presence of roots and mycorrhizal fungi had a significant effect on the hydraulic properties of two soils with contrasting textures: Flint sand and Hamblen silt loam. Soil cores were seeded with (Panicum virgatum) and grown in a greenhouse over three separate growth periods. The endophytic fungus Serendipita indica was injected as liquid inoculant into designated mycorrhizal cores. Saturated hydraulic conductivity (K sat ) measurements were made with a constant head permeameter, and soil water retention curves were obtained by the evaporation method, supplemented at the dry end for Hamblen silt loam with water activity meter data. Retention curve parameters were obtained by fitting the van Genuchten equation to the resulting measurements. Mean root volume ratios were higher in the mycorrhizal inoculated treatment than in the uninoculated treatment for both soils. For Flint sand, analysis of variance revealed that K sat was reduced by the presence of roots as compared to bare soil. This was likely due to roots clogging soil pores. Results also indicated the presence of roots changed the shape of the water retention curve for Flint sand by increasing water content at saturation and by reducing the slope of the curve. These changes suggested roots created additional porosity and broadened the pore-size distribution. The presence of mycorrhizal fungi accentuated the root effects. The influence of roots and mycorrhizal fungi on hydraulic properties was less obvious for the Hamblen silt loam, as none of the treatments differed from each other at p < 0.05. The results highlight the necessity to consider the impact of root and fungal structures on models of soil hydraulic properties.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Robust ab initio predictions for dimensionless ratios of 𝐸⁢2 and radius observables. II. Estimation of 𝐸⁢2 transition strengths by calibration to the charge radius

Converged results for 𝐸⁢2 observables are notoriously challenging to obtain in ab initio no-core configuration interaction approaches. Matrix elements of the 𝐸⁢2 operator are sensitive to the large-distance tails of the nuclear wave function, which converge slowly in an oscillator basis expansion. Similar convergence challenges beset ab initio prediction of the nuclear charge radius. However, we exploit systematic correlations between the calculated 𝐸⁢2 and radius observables to yield meaningful predictions for relations among these observables. In particular, we examine ab initio predictions for dimensionless ratios of the form 𝐵⁡(𝐸⁢2)/(𝑒 2 ⁢𝑟 4 ) for nuclei throughout the 𝑝 shell. Finally, meaningful predictions for 𝐸⁢2 transition strengths may then be made by calibrating to the ground-state charge radius if experimentally known.

ab initio calculations↗

DOE OSTI2022

Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated by Starships, a newly discovered group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds of Starship-like regions across every major class of filamentous Ascomycetes, including 28 distinct Starships that range from 27 to 393 kb and last shared a common ancestor ca. 400 Ma. Using new long-read assemblies of the plant pathogen Macrophomina phaseolina, we characterize four additional Starships whose activities contribute to standing variation in genome structure and content. One of these elements, Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggesting Voyager’s activity underlies an ecological trade-off. We propose that Starships are eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first dedicated agents of active gene transfer in eukaryotes. Our results suggest that Starships have shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Competition between roughness and strength for scale-dependent surfaces

Rocks famously have scale-dependent strength, yet the actual dependence is notoriously hard to measure or incorporate into any theoretical framework. Natural rough surfaces present an opportunity to solve the problem. Surfaces sliding in shear evolve as protrusions collide. These asperities can deform or break, thus creating a new surface shape. In particular, natural surfaces have roughness at all scales as well as scale-dependent strength. Based on a scaling analysis, we have previously suggested that the scale-dependent aspect ratio of steady-state surfaces should be proportional to the scale-dependent shear strain at yield. If true, scale-dependent strength could easily be inferred from natural surfaces. Thus, moving beyond the scaling argument to a rigorous treatment of scale-dependent strength for multiscale rough surfaces in shear is important. However, analytic frameworks for analyzing multiscale problems are challenging, as conventional continuum mechanics typically involves a single value for a material property across scales. Here, in this work, we build on the formalism of Persson (2001) that presents a method to compute contact area for rough surfaces with a prescribed topographic spectrum using a stochastic differential equation. The Persson formalism allows for plastic yield under normal loading of otherwise elastic materials and leaves open the possibility of scale-dependent yield stress. In this study, we pursue this route to develop a theory and numerical results for the yielding of a rough, elastoplastic surface with scale-dependent yield stress. Here, we examine surfaces for which the power spectrum of the topography 𝐶 and yield stress 𝑌 follow power laws as a function of scale 𝜆, such that 𝐶∼𝜆 −𝑚 and 𝑌∼𝜆 −𝑛 , respectively. In this formal treatment of the problem, we focus on surfaces in contact and the resulting yield and do not impose shear. Numerical solutions show that the deviation from the elastic scaling solution is bounded as expected by the prior 1D heuristic scaling argument that anticipates the Hurst exponent as 1−𝑛. We also show that the plasticity is expected to erode the contacts if 𝑚 is lower than 𝑛−3, which corresponds to a Hurst exponent lower than 1−𝑛/2. This result is rigorously sound for 2D, i.e., realistic surfaces, and quantitatively different than the prior scaling argument. The theory now permits a correspondingly quantitative approach to interpreting natural surfaces.

elasticity↗

DOE OSTI2023

Finding simplicity: unsupervised discovery of features, patterns, and order parameters via shift-invariant variational autoencoders *

Abstract Recent advances in scanning tunneling and transmission electron microscopies (STM and STEM) have allowed routine generation of large volumes of imaging data containing information on the structure and functionality of materials. The experimental data sets contain signatures of long-range phenomena such as physical order parameter fields, polarization, and strain gradients in STEM, or standing electronic waves and carrier-mediated exchange interactions in STM, all superimposed onto scanning system distortions and gradual changes of contrast due to drift and/or mis-tilt effects. Correspondingly, while the human eye can readily identify certain patterns in the images such as lattice periodicities, repeating structural elements, or microstructures, their automatic extraction and classification are highly non-trivial and universal pathways to accomplish such analyses are absent. We pose that the most distinctive elements of the patterns observed in STM and (S)TEM images are similarity and (almost-) periodicity, behaviors stemming directly from the parsimony of elementary atomic structures, superimposed on the gradual changes reflective of order parameter distributions. However, the discovery of these elements via global Fourier methods is non-trivial due to variability and lack of ideal discrete translation symmetry. To address this problem, we explore the shift-invariant variational autoencoders (shift-VAEs) that allow disentangling characteristic repeating features in the images, their variations, and shifts that inevitably occur when randomly sampling the image space. Shift-VAEs balance the uncertainty in the position of the object of interest with the uncertainty in shape reconstruction. This approach is illustrated for model 1D data, and further extended to synthetic and experimental STM and STEM 2D data. We further introduce an approach for training shift-VAEs that allows finding the latent variables that comport to known physical behavior. In this specific case, the condition is that the latent variable maps should be smooth on the length scale of the atomic lattice (as expected for physical order parameters), but other conditions can be imposed. The opportunities and limitations of the shift VAE analysis for pattern discovery are elucidated.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

DeepPhenoMem V1.0: deep learning modelling of canopy greenness dynamics accounting for multi-variate meteorological memory effects on vegetation phenology

Abstract. Vegetation phenology plays a key role in controlling the seasonality of ecosystem processes that modulate carbon, water and energy fluxes between the biosphere and atmosphere. Accurate modelling of vegetation phenology in the interplay of Earth's surface and the atmosphere is thus crucial to understand how the coupled system will respond to and shape climatic changes. Phenology is controlled by meteorological conditions at different timescales: on the one hand, changes in key meteorological variables (temperature, water, radiation) can have immediate effects on the vegetation development; on the other hand, phenological changes can be driven by past environmental conditions, known as memory effects. However, the processes governing meteorological memory effects on phenology are not completely understood, resulting in their limited performance of vegetation phenology represented in land surface models. A deep learning model, specifically a long short-term memory network (LSTM), has the potential to capture and model the meteorological memory effects on vegetation phenology. Here, we apply the LSTM to model the vegetation phenology using meteorological drivers and high-temporal-resolution canopy greenness observations through digital repeat photography by the PhenoCam network. We compare a multiple linear regression model, a no-memory-effect LSTM model and a full-memory-effect LSTM model to predict the whole seasonal greenness trajectory and the corresponding phenological transition dates across 50 sites and 317 site years during 2009–2018, covering deciduous broadleaf forests, evergreen needleleaf forests and grasslands. Results show that the deep learning model outperforms the multiple linear regression model, and the full-memory-effect LSTM model performs better than the no-memory-effect model for all three plant function types (median R2 of 0.878, 0.957 and 0.955 for broadleaf forests, evergreen needleleaf forests and grasslands). We also find that the full-memory-effect LSTM model is capable of predicting the seasonal dynamic variations of canopy greenness and reproducing trends in shifting phenological transition dates. We also performed a sensitivity analysis of the full-memory-effect LSTM model to assess its plausibility, revealing its coherence with established knowledge of vegetation phenology sensitivity to meteorological conditions, particularly changes in temperature. Our study highlights that (1) multi-variate meteorological memory effects play a crucial role in vegetation phenology, and (2) deep learning opens up new avenues for improving the representation of vegetation phenological processes in land surface models via a hybrid modelling approach.

Geology↗

DOE OSTI2023

Unraveling Anisotropic and Pulsating Etching of ZnO Nanorods in Hydrochloric Acid via Correlative Electron Microscopy

Despite much technical progress achieved so far, the exact surface and shape evolution during wet chemical etching is less unraveled, especially in ionically bonded ceramics. Herein, by using in situ liquid cell transmission electron microscopy, a repeated two-stage anisotropic and pulsating periodic etching dynamic is discovered during the pencil shape evolution of a single crystal ZnO nanorod in aqueous hydrochloric acid. Specifically, the nanopencil tip shrinks at a slower rate along [0001̅] than that along the $\langle$101̅0$\rangle$ directions, resulting in a sharper ZnO pencil tip. Afterward, rapid tip dissolution happens due to accelerated etching rates along various crystal directions. Concurrently, the vicinal base region of the original nanopencil tip emerges as a new tip followed by the repeated sequence of tip shrinking and removal. The high-index surfaces, such as {101̅m} (m = 0, 1, 2, or 3) and {21̅1̅n} (n = 0, 1, 2, or 3), are found to preferentially expose in different ratios. Our 3D electron tomography, convergent beam electron diffraction, middle-angle bright-field STEM, and XPS results indicate the dissociative Cl – species were bound to the Zn-terminated tip surfaces. Furthermore, DFT calculation suggests the preferential Cl – passivation over the {101̅1} and (0001) surfaces of lower energy than others, leading to preferential surface exposures and the oscillatory variation of different facet etching rates. The boosted reactivity due to high-index nanoscale surface exposures is confirmed by comparatively enhanced chemical sensing and CO 2 hydrogenation activity. In conclusion, these findings provide an in-depth understanding of anisotropic wet chemical etching of ionic nanocrystals and offer a design strategy for advanced functional materials.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Sample shape and boundary dependence of measured transverse thermal properties

In spite of increased interest in thermal Hall measurements for the analysis of insulating quantum materials, there remains large uncertainty in such measurements due to contact misalignment. In this paper, we propose that sample geometry and uncertain boundary conditions provide an additional source of uncertainty in the measurement of $D_{xy}$ or $κ_{xy}$. By running simple simulations in an open source finite-element solver, we demonstrate that measured $D_{xy}$ can be changed by a non-negligible fraction in samples with similar width and length. This geometric corrective factor depends on the distinction between a uniform heat flow and constant temperature boundary couplings to a bath. Sample geometry and boundary conditions can be accounted for through simulation or by using rectangular samples to make thermal Hall measurements more reliable and reproducible. Finally, we detail a contactless optical method for measuring $D_{xy}$ based on an existing photothermal microscope technique. This method is insensitive to the longitudinal diffusivity pollution caused by contact misalignment.

36 MATERIALS SCIENCE↗