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At least 739 records · Page 41

Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes

Motivation: Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As `omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results: We propose a workflow (`Omics to Reactive Transport – ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBASE and PFLOTRAN. Live, interactive models, which incorporate the results from this narrative into a PFLOTRAN simulation, are available (without login) at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/.

Rubinstein, Rebecca L↗

Landscape-scale Characterization of Arctic Tundra Vegetation Composition, Structure, and Function with a Multi-sensor Unoccupied Aerial System: Supporting Data.

Airborne remote sensing data collected using the Brookhaven National Laboratory's (BNL) heavy-lift unoccupied aerial system (UAS) octocopter platform, the Osprey, operated by the Terrestrial Ecosystem Science and Technology (TEST) group (https://www.bnl.gov/testgroup). This package includes data from three flights flown over the NGEE-Arctic Council, Kougarok and Teller sites in July, 2018. The Osprey is a multi-sensor UAS platform that simultaneously measures very high spatial resolution optical red/green/blue (RGB) and thermal infrared (TIR) surface 'skin' temperature imagery, as well as surface reflectance at 1 nm intervals in the visible to near-infrared spectral range 350 - 1000 nm measured at regular intervals along each flight path. Derived image products include ortho-mosaiced RGB and TIR images, an RGB-based digital surface model (DSM) using the structure from motion (SfM) technique, digital terrain model (DTM), and a canopy height model (CHM). In addition, a VNIR surface reflectance file is provided for the trigger locations collected during each flight campaign. Ancillary aircraft data, flight mission parameters, and general flight conditions provided by the onboard flight and data collection computers are also included. Unprocessed and processed data products are included in this package (processing levels 0-3). Data and metadata are provided as text (*.txt, *.json, *.kml, *hdr, *.enp), tabular (*.dat, *.csv, *.waypoint, ENVI format (no extension)), point cloud (*.laz) and image (*.jpg, *.tif, *png) formats. This metadata document contains flight campaign, instrument and file metadata, along with a description of data processing levels, data products and file naming scheme.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), 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↗

Active motion of multiphase oil droplets: emergent dynamics of squirmers with evolving internal structure

Synthetic soft matter systems, when driven beyond equilibrium by active processes, offer the potential to achieve dynamical states and functions of a complexity found in living matter. Emulsions offer the basis of a simple yet versatile system for identification of the physicochemical principles underlying active soft matter, but how multiple internal phases within emulsion droplets (e.g., Janus morphologies) organize to impact emergent dynamics is not understood. Here, we create multiphase oil droplets with ultralow interfacial tensions but distinct viscosities, and drive them into motion in aqueous micellar solutions. Preferential solubilization of select components of the oil both drives the droplet motion and yields a progression of internal phase morphological states with distinct symmetries. In this work, we find the active droplets to exhibit five dynamical states during morphogenesis. By quantifying microscopic flow fields, we show that it is possible to map the diverse droplet behaviors to squirmer models of spherical microswimmers in Stokes flow, thus showing that multiphase droplets offer the basis of a versatile platform with which to study and engineer the hydrodynamics of microswimmers.

36 MATERIALS SCIENCE↗

Enhanced Planar Antenna Efficiency Through Magnetic Thin-Films

This work proposes to use magnetic material as the substrate of planar antennas to overcome the platform effect caused by the conducting ground plane. The upper bound of the radiation efficiency of an electric-current-driven low-profile antenna is theoretically derived, which is inversely proportional to the Gilbert damping factor of the magnetic material. Meanwhile, the improvement of radiation due to the use of magnetic material is demonstrated by a three-dimensional (3D) multiphysics and multiscale time-domain model. The simulation results match the theoretical derivation, showing 25% radiation efficiency from a planar antenna backed by a FeGaB thin film with 2.56 m thickness. Furthermore, for conductive ferromagnetic materials, it is shown that the eddy current loss can be well suppressed by laminating the thin film into multiple layers. Here, the radiation efficiency of the modeled antenna with a conductive ferromagnetic substrate is improved from 2.2% to 11.8% by dividing the substrate into 10 layers, with a ferromagnetic material fill factor of 93%.

42 ENGINEERING↗

Final Technical Report for DE-SC0022206

This project developed foundational genetic, genomic, and epigenetic tools for anaerobic fungi (Neocallimastigomycota), a group of microorganisms with exceptional natural abilities to deconstruct lignocellulosic biomass. Efficient biomass deconstruction remains a major barrier to economical production of renewable fuels, chemicals, and materials from agricultural and forestry residues. The project sought to enable mechanistic studies and future engineering of anaerobic fungi by improving genomic resources, establishing methods for gene expression, and investigating epigenetic regulation of biomass-degrading pathways. Major accomplishments included generation of the first chromosome-scale genome assemblies for multiple anaerobic fungal species, providing publicly available genomic resources that support both engineering and fundamental biological research. The project established the first reproducible system for heterologous gene expression in anaerobic fungi and identified genomic features and mobile genetic elements that may support future development of stable transformation technologies. In parallel, the project demonstrated direct conversion of untreated lignocellulosic biomass into fuels and specialty chemicals through a fungal-yeast bioprocess and identified anaerobic fungal enzymes with utility for metabolic engineering. The research also revealed that epigenetic regulation plays an important role in controlling fungal gene expression and enzyme production, identifying potential strategies for enhancing biomass degradation. Collectively, this work established anaerobic fungi as a tractable emerging platform for bioenergy and biomanufacturing research, generated valuable public resources, trained the next generation of researchers, and advanced DOE-BER goals related to predictive biology, sustainable bioprocessing, and the circular bioeconomy.

Solomon, Kevin [University of Delaware] (ORCID:000↗

Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models

Microbiomes are vital to human health, agriculture, and protecting the environment. Predicting behavior of self-assembled or synthetic microbiomes, however, remains a challenge. In this work, we used unicellular and guild-based metabolic models to investigate production of medium-chain fatty acids by a mixed microbial community that is fed multiple organic substrates. Modeling results provided insights into metabolic pathways of three medium-chain fatty acid-producing guilds and identified potential strategies to increase production of medium-chain fatty acids. This work demonstrates the role of metabolic models in augmenting multi-omic studies to gain greater insights into microbiome behavior.

59 BASIC BIOLOGICAL SCIENCES↗

Remote Monitoring and Diagnostics of Pitch-Bearing Defects in an MW-Scale Wind Turbine Using Pitch Symmetrical-Component Analysis

Recently, multiple wind turbine failure databases have reviewed that the pitch system is one of the subassemblies with the highest failure rates and largest contributors to the overall downtime. Therefore, there has been an increasing interest to provide remote health monitoring for wind turbine pitch system. While most of the research articles are discussing pitch actuation system (hydraulic or electric actuator) faults only, there is very limited research on pitch-bearing-defect detection. This article provides a remote and hardware-free solution to monitor multiaxis pitch-bearing health condition called pitch symmetrical-component analysis. It leverages readily available low-resolution (100 Hz) electrical measurements, mechanical measurements, and control signals from the existing pitch control platform, and innovatively applies symmetrical-component analysis in multiphase ac system to multiaxis pitch control system and introduces multiaxis pitch-bearing degradation trending curves. This hardware-free solution can be directly applied to the existing wind turbines and successfully give the wind farm operator an early warning before multiaxis pitch bearing fails. It has been proved to be accurate, low cost, and has minimum impacts on turbine normal operation, and has been validated by field data from several North America MW-scale wind farms. This approach turns out to be the first hardware-free (no additional hardware needed) method to remotely monitor and diagnose multiaxis wind turbine pitch-bearing condition.

17 WIND ENERGY↗

A stable 15-member bacterial SynCom promotes Brachypodium growth under drought stress

Introduction: Rhizosphere microbiomes are known to drive soil nutrient cycling and influence plant fitness during adverse environmental conditions. Field-derived robust Synthetic Communities (SynComs) of microbes mimicking the diversity of rhizosphere microbiomes can greatly advance a deeper understanding of such processes. However, assembling stable, genetically tractable, reproducible, and scalable SynComs remains challenging. Methods: Here, we present a systematic approach using a combination of network analysis and cultivation-guided methods to construct a 15-member SynCom from the rhizobiome of Brachypodium distachyon. This SynCom incorporates diverse strains from five bacterial phyla. Genomic analysis of the individual strains was performed to reveal encoded plant growth-promoting traits, including genes for the synthesis of osmoprotectants (trehalose and betaine) and Na+/K+ transporters, and some predicted traits were validated by laboratory phenotypic assays. Results: The SynCom demonstrates strong stability both in vitro and in planta. Most strains encoded multiple plant growth-promoting functions, and several of these were confirmed experimentally. The presence of osmoprotectant and ion transporter genes likely contributed to the observed resilience of Brachypodium to drought stress, where plants amended with the SynCom recovered better than those without. We further observed preferential colonization of SynCom strains around root tips under stress, likely due to active interactions between plant root metabolites and bacteria. Discussion: Our results demonstrate that trait-informed construction of synthetic communities can yield stable, functionally diverse consortia that enhance plant resilience under drought. Preferential colonization near root tips points to active, localized plant-microbe signaling as a component of stress-responsive recruitment. This stable SynCom provides a scalable platform for probing mechanisms of plant-microbe interaction and for developing microbiome-based strategies to improve soil and crop performance in variable environments.

Yadav, Archana↗

A Multiphysics Multiscale Simulation Platform for Damage, Environmental Degradation, and Life Prediction of CMCs in Extreme Environments

This project successfully developed a multiphysics, multiscale computational framework to enhance the design and development of CMCs, with a focus on modeling highly nonlinear, time-dependent damage mechanisms and material degradation under extreme conditions, such as those experienced in turbine service environments. The project made significant advances in improving our understanding of progressive damage, oxidative degradation, and time-dependent inelastic deformation in CMCs, with particular attention to the role of uncertainties in predictions. Key outcomes include the integration of advanced material characterization, uncertainty quantification, and multiphysics constitutive models to predict the behavior of CMCs over their service life. A novel multiscale methodology was employed, which integrated microscale constituent behaviors with structural-scale responses, enabling the manufacturing defects in the microstructure that are prone to damage nucleation. Through the development of DL algorithms, the project advanced the prediction of damage initiation and crack propagation, taking into account the defect morphology and statistical variations across multiple scales. The framework was rigorously validated using thermomechanical experiments, which tested CMCs under various mechanical loadings at elevated temperatures, further enhancing the model's predictive capability. Overall, the research outcomes have provided a more accurate, reliable method for predicting CMC component life, significantly advancing material design, and improving component reliability in extreme environments. This work has strong implications for the optimization of turbine components and other high-performance applications where CMCs are used.

03 NATURAL GAS↗

High-Throughput Microfluidics Platform for Intracellular Delivery and Sampling of Biomolecules from Live Cells

Nondestructive cell membrane permeabilization systems enable the intracellular delivery of exogenous biomolecules for cell engineering tasks as well as the temporal sampling of cytosolic contents from live cells for the analysis of dynamic processes. Here, in this paper, we report a microwell array format live-cell analysis device (LCAD) that can perform localized-electroporation induced membrane permeabilization, for cellular delivery or sampling, and directly interfaces with surface-based biosensors for analyzing the extracted contents. We demonstrate the capabilities of the LCAD via an automated high-throughput workflow for multimodal analysis of live-cell dynamics, consisting of quantitative measurements of enzyme activity using self-assembled monolayers for MALDI mass spectrometry (SAMDI) and deep-learning enhanced imaging and analysis. By combining a fabrication protocol that enables robust assembly and operation of multilayer devices with embedded gold electrodes and an automated imaging workflow, we successfully deliver functional molecules (plasmid and siRNA) into live cells at multiple time-points and track their effect on gene expression and cell morphology temporally. Furthermore, we report sampling performance enhancements, achieving saturation levels of protein tyrosine phosphatase activity measured from as few as 60 cells, and demonstrate control over the amount of sampled contents by optimization of electroporation parameters using a lumped model. Lastly, we investigate the implications of cell morphology on electroporation-induced sampling of fluorescent molecules using a deep-learning enhanced image analysis workflow.

59 BASIC BIOLOGICAL SCIENCES↗

Synthesis of Tunable SnS-TaS 2 Nanoscale Superlattices

Nanoscale superlattices represent a compelling platform for designed materials as the specific identity and spatial arrangement of constituent layers can lead to tunable properties. A number of kinetically stabilized, nonepitaxial superlattices with almost limitless structural tunability have been reported in telluride and selenide chemistries but have not yet been extended to sulfides. Here, we present SnS-TaS 2 nanoscale superlattices with tunable layer architecture. Layered amorphous precursors are prepared as thin films programmed to mimic the targeted superlattice; subsequent low temperature annealing activates self-assembly into crystalline nanocomposites. We investigate structure and composition of superlattices comprised of monolayers of TaS 2 and 3–7 monolayers of SnS per repeating unit. Furthermore, a graded precursor preparation approach is introduced, allowing stabilization of superlattices with multiple stacking sequences in a single preparation. Controlled synthesis of the architecture of nanoscale superlattices is a critical path toward tuning their exotic properties and enabling integration with electronic, optical, or quantum devices.

36 MATERIALS SCIENCE↗

Same-sided successive-shock HED instability experiments

Inertial confinement fusion (ICF) and high-energy density (HED) physics experiments experience complicated forcing for instability growth and mix due to the ubiquitous presence of multiple shocks interacting with perturbations on multiple material interfaces. One common driver of instability growth is successive shocks from the same direction. However, there is a severe lack of analytic work and modeling validation for same-sided successive shocks since they are extremely difficult to achieve with conventional (non-HED) drivers. Successive shocks access a large instability parameter space; idealized fluid theory [K. O. Mikaelian, Phys. Rev. A 31, 410 (1985)] predicts 15 different interface evolution scenarios for a sinusoidal perturbation. Growth becomes more complex for multi-mode, compressible HED systems. The Mshock campaign is the first experiment in any fluid regime to probe a wide portion of successive shock parameter space. This is enabled by our development of a hybrid direct/indirect drive platform capable of creating independently controllable successive shocks on the National Ignition Facility. These experiments have delivered the first data capable of rigorously challenging our models and their ability to accurately capture Richtmyer–Meshkov growth under successive shocks. Single-mode and two-mode experiments have successfully demonstrated the ability to access and control the various growth scenarios of the shocked interface, including re-inversion, freeze out, and continued growth. Simulations and theoretical modeling are shown to accurately capture the experimental observations in the linear growth phase, giving us confidence in our ICF/HED design codes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Tunable Atomic Layer Deposition into Ultra-High-Aspect-Ratio (>60000:1) Aerogel Monoliths Enabled by Transport Modeling

Atomic layer deposition (ALD) modification of ultra-high-aspect-ratio structures (>10,000:1) is a powerful platform with applications in catalysis, filtration, and energy conversion. However, the deposition of conformal and tunable ALD coatings at these aspect ratios remains challenging, resulting in empirical tradeoffs between precursor utilization and reaction time. Here, we demonstrate tunable control of the ALD infiltration depth into an aerogel monolith (AM) and develop a reaction-diffusion model to accurately describe the coating process. Specifically, we investigate the ALD exposure time and precursor dose needed to conformally coat a silica AM with pore sizes of ~20 nm, a monolith thickness of ~2.5 mm, and aspect ratios exceeding 60,000:1. We demonstrate complete infiltration into the AM, which is quantified by elemental mapping. A reaction-diffusion model is developed, which accounts for multiple doses and precursor depletion in the ALD chamber during an exposure step. The experimentally validated model enables the prediction and tuning of infiltration depth into a tortuous, high-aspect-ratio structure such as an AM, allowing for the synthesis of rationally designed material architectures. Additionally, the model allows for co-optimization of the total deposition time and percentage of unreacted precursor, which are important for the manufacturability and sustainability of ALD processing. Lastly, we demonstrate that ultra-thin ALD Al 2 O 3 coatings can be used to stabilize silica AMs against structural degradation under high-temperature annealing conditions (700-800 °C), by limiting changes in surface area and monolith volume. As a result, this improved high-temperature stability has implications for numerous aerogel applications, including catalysis and thermal insulation.

14 SOLAR ENERGY↗

Mapping Glacier Basal Sliding Applying Machine Learning

During the RESOLVE project (“High-resolution imaging in subsurface geophysics: development of a multi-instrument platform for interdisciplinary research”), continuous surface displacement and seismic array observations were obtained on Glacier d’Argentière in the French Alps for 35 days in May 2018. The data set is used to perform a detailed study of targeted processes within the highly dynamic cryospheric environment. In particular, the physical processes controlling glacial basal motion are poorly understood and remain challenging to observe directly. Especially in the Alpine region for temperate based glaciers where the ice rapidly responds to changing climatic conditions and thus, processes are strongly intermittent in time and heterogeneous in space. Spatially dense seismic and Global Positioning System (GPS) measurements are analyzed applying machine learning to gain insight into the processes controlling glacial motions of Glacier d’Argentière. Using multiple bandpass-filtered copies of the continuous seismic waveforms, we compute energy-based features, develop a matched field beamforming catalog and include meteorological observations. Features describing the data are analyzed with a gradient boosting decision tree model to directly estimate the GPS displacements from the seismic noise. We posit that features of the seismic noise provide direct access to the dominant parameters that drive displacement on the highly variable and unsteady surface of the glacier. The machine learning model infers daily fluctuations and longer term trends. The results show on-ice displacement rates are strongly modulated by activity at the base of the glacier. The techniques presented provide a new approach to study glacial basal sliding and discover its full complexity.

58 GEOSCIENCES↗

Hofstadter states and re-entrant charge order in a semiconductor moiré lattice

The emergence of moiré materials with flat bands provides a platform to systematically investigate and precisely control correlated electronic phases. Here, we report local electronic compressibility measurements of a twisted WSe2/MoSe2 heterobilayer which reveal a rich phase diagram of interpenetrating Hofstadter states and electron solids. We show that this reflects the presence of both flat and dispersive moiré bands whose relative energies, and therefore occupations, are tuned by density and magnetic field. At low densities, competition between moiré bands leads to a transition from commensurate arrangements of singlets at doubly occupied sites to triplet configurations at high fields. Hofstadter states (i.e., Chern insulators) are generally favored at high densities as dispersive bands are populated, but are suppressed by an intervening region of reentrant charge-ordered states in which holes originating from multiple bands cooperatively crystallize. Our results reveal the key microscopic ingredients that favor distinct correlated ground states in semiconductor moiré systems, and they demonstrate an emergent lattice model system in which both interactions and band dispersion can be experimentally controlled.

36 MATERIALS SCIENCE↗

Toward three-dimensional DNA industrial nanorobots

Nanoscale industrial robots have potential as manufacturing platforms and are capable of automatically performing repetitive tasks to handle and produce nanomaterials with consistent precision and accuracy. We demonstrate a DNA industrial nanorobot that fabricates a three-dimensional (3D), optically active chiral structure from optically inactive parts. By making use of externally controlled temperature and ultraviolet (UV) light, our programmable robot, ~100 nanometers in size, grabs different parts, positions and aligns them so that they can be welded, releases the construct, and returns to its original configuration ready for its next operation. Our robot can also self-replicate its 3D structure and functions, surpassing single-step templating (restricted to two dimensions) by using folding to access the third dimension and more degrees of freedom. Our introduction of multiple-axis precise folding and positioning as a tool/technology for nanomanufacturing will open the door to more complex and useful nano- and microdevices.

Robotics↗

Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution

Although the use of ionic liquids (ILs) for the pretreatment of lignocellulosic biomass has been limited due to high costs, recent efforts to develop low-cost protic ILs show promise for achieving cost-effectiveness for biorefineries. However, an additional challenge remains in that ILs present in biomass hydrolysates are toxic to most microbial hosts, resulting in poor growth phenotypes. To address this issue, we applied an adaptive laboratory evolution (ALE) approach for tolerizing Pseudomonas putida KT2440, an industrially relevant bacterial host, to two low-cost ILs (triethanolammonium acetate [TEOH][OAc] and triethylammonium hydrogen sulfate [TEA][HS]). After continuous cultivations with gradually increased IL levels, we obtained evolved strains showing significant improvements in their growth performance under high concentrations of the ILs (maximum 4% [TEOH][OAc] and 8% [TEA][HS], in w/v) at which the wild-type strain cannot grow. Sequencing of evolved strains revealed multiple regions where mutations were associated with improved performance in minimal media conditions (relA, gacS, oprB/PP_1446, fleQ, tktA, and uvrY/PP_4100) and in IL-specific conditions (PP_5350, PP_4929/emrE, oprD, and PP_5324). We further validated the causality of the PP_5350 and emrE genes for improved IL tolerance via reverse engineering and transcriptomic analysis. Here, a common mutation in the PP_5350 gene, encoding a RpiR family transcriptional regulator, was shown to significantly upregulate the glyoxylate cycle for efficient acetate catabolism. In addition, it was suggested that the emrE gene encodes an efflux pump which can export [TEA][HS]. Finally, the cultivation of two of the best performing evolved strains with IL-treated biomass hydrolysates demonstrated their considerable potential to be used as platform strains. Taken as a whole, this work provides strains for utilization of IL-treated biomass and a mechanistic understanding that could be further leveraged to develop efficient microbial bioprocesses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗