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At least 235 records · Page 13

Deep Learning Prediction of Interspecies Interactions from Self-organized Spatiotemporal Patterns of Co-evolving Organisms

Microorganisms colonizing natural habits such as soils co-evolve to form specific spatial patterns through interspecies interactions. These self-organized patterns are a key ecological phenotype, which provides critical information on their interaction mechanisms. However, conventional network inference techniques that analyze species population data in bulk have yet to be extended to account for such spatial heterogeneity. Here we proposed supervised deep learning as a new network inference tool for predicting interspecies interactions from spatiotemporal patterns of microbial evolution. Due to lack of biological imaging data that can be used for training deep learning networks, we used in silico data generated from high-fidelity agent-based models to determine model structure and parameters. Even though networks were trained under simple configurations where interaction coefficients are assumed to be spatially invariant, we demonstrated that the resulting model can be utilized to successfully predict spatial variation of interactions in more complex domains (i.e., configured with a context-dependent mixture of interaction coefficients) as well as in simple domains without further training. In the further test against real biological data obtained through imaging experiments of a binary consortium (Pseudomonas fluorescens and a mutant of Escherichia coli), our model also predicted the dramatic shifts in interactions of the two organisms across different environmental contexts. Through various successful demonstrations in this work, the combined use of the agent-based model and machine learning algorithm provides a means to use new type of data - microscopic images - for extracting microbial interactions, therefore presenting itself as a useful tool for the analysis of more complex microbial community interactions.

Lee, Joon-Yong↗

Conservation laws and effective hadronization models

Hadronization models based on local string-breaking dynamics are typically Markovian by construction, yet the physical ensemble of final states is shaped by global constraints that couple the entire fragmentation trajectory. Recasting hadronization as a conditioned stochastic diffusion process provides a precise mathematical resolution to this tension. In particular, this language reveals explicitly that constraints stemming from conservation laws induce non-Markovian correlations between otherwise independent fragmentation steps, and that these correlations can be absorbed exactly into a renormalization of the local dynamics through a Doob $h$-transform. We develop this formalism for a $q\bar{q}$ string in the chiral limit, where the longitudinal-transverse factorization of the Lund kernel becomes exact, enabling systematic power counting and clean ultraviolet (UV)/infrared (IR) separation. The dynamics organize naturally into a tower of effective theories distinguished by the remaining string mass, spanning a UV fixed point with scale-invariant transport coefficients, an intermediate regime where transverse phase space induces controlled running, and an IR boundary layer where non-local effects enter at leading order. The tower exhibits genuine Wilsonian structure, including $β$-functions, anomalous dimensions, and systematic matching conditions. The resulting framework achieves a clean factorization of universal microscopic fragmentation dynamics from infrared constraint effects, and opens new directions for both the theoretical analysis and practical simulation of hadronization.

Menzo, Tony [Alabama U.; Fermilab] (ORCID:00000002↗

Ice nucleation measurements from DRUM impactors during TRACER campaign in the Houston TX region from July to September 2022

During TRACER, three Davis Rotating Uniform size-cut Monitors (DRUM; DRUMAir 4-DRUM) were used to collect aerosols for ice nucleation measurements in the Brooks laboratory at Texas A&M University. The three instruments were located at AMF1 in La Porte, Ancillary site in Guy (ANC), and onboard the Texas A&M Rapid Onsite Atmospheric Measurements Van (ROAM-V). ROAM-V was deployed to capture airmasses behind (maritime) and ahead (continental) of the passage of the sea-breeze front through Houston. On select sampling days, ROAM-V sampled in the morning/mid-day on the coast and then transited to a second inland site for the afternoon/evening. The suite of instruments deployed on ROAM-V included a Condensation Particle Counter (CPC; GRIMM Model 5.403 CPC), Scanning Mobility Particle Sizer (SMPS; TSI 3750 detector, TSI 3082 classifier, TSI 3088 neutralizer, TSI 3081A Differential Mobility Analyzer), Cloud Condensation Nuclei counter (Droplet Measurement Technologies CCN Counter), micro pulse lidar (Droplet Measurement Technologies Micro Pulse LiDAR (miniMPL)), and one of the Davis Rotating Uniform size-cut Monitors (DRUM; DRUMAir 4-DRUM). Before sampling at each location, the latitude and longitude were recorded using the GPS on the phone application “My Altitude”. Each DRUM sampler was operated at a flow rate of 23 LPM. Each DRUM has four stages where the aerodynamic diameter size cuts are as follows: stage 1 larger than 3 μm, stage 2 from 3 to 1.2 μm, stage 3 from 1.2 to 0.34 μm, and stage 4 from 0.34 to 0.15 μm. Pretreated aluminum foil was used as a substrate on all stages. At AMF1 and ANC sites, the DRUMs were operated on the shared aerosol inlet, with generous support of the DOE ARM site staff. These instruments rotated 24 mm per day and only contained aluminum foil substrates. Substrates were changed weekly and transported to Texas A&M for storage in -80C freezer until analysis. The DRUM onboard ROAM-V was operated at a faster rotation rate of 150 mm per day to clearly separate the multiple deployment locations for ROAM-V. For the ROAM-V DRUM, substrates were changed every deployment and transported to Texas A&M for storage in -80C freezer until analysis. At Texas A&M, ice nucleation experiments were conducted to measure the ice nucleation temperature of the ambient aerosol samples collected from the three DRUMs using our previously established procedures (Alsante et al., 2023; Fornea et al., 2009; Matthews et al., 2023). For ice nucleation, only samples collected on stage 3 were analyzed, given that these are the most relevant size (1.2 to 0.34 μm diameter) for potential ice nucleating particles. For the AMF1 and ANC sites, we cut and analyzed 2 mm (2-hour) samples. We analyzed the time periods of the AMF1 site instrument when the ROAM-V was deployed. A 72-hour period from July 11th at 23:49 through July 15th at 1:49 was analyzed from the ANC site instrument. For the ROAM-V instrument, we separated the daily samples by site location. Between 1- and 6-hour independent samples were analyzed at each location. We also cut the ROAM-V samples in half to allow for compositional analysis of the aerosol on the other half of the substrate. All viable samples from the ROAM-V were analyzed. Analysis was done using a custom-built ice nucleation apparatus, recently updated to include an array of 16 individual samples (Matthews et al., 2023). On our experimental setup, we used 100 μL of Ultra-High-Performance Liquid Chromatography (UHPLC) water (Sigma Aldrich, >99.9% purity) to wash off the aerosol from the DRUM substrate. Then, we micropipetted 2 μL droplet samples into each of the 16 wells of the array, using hydrophobically coated microscope slides. Experiments would cycle 28 times from 10 C to -40C over a 20-hour period. During analysis of the TRACER samples, nine experiments were conducted with UHPLC water process blanks that followed an identical preparation procedure. The average freezing temperature and standard deviation for these process blanks is -27.7±2.4 C. This data was collected for ARM Field Campaign AFC07023 and supported by DOE ASR grant DE-SC0021047. For any further questions, please feel free to contact the instrument PI, Sarah D. Brooks, sbrooks@tamu.edu. Alsante, A. N., Thornton, D. C., & Brooks, S. D. (2023). Ice nucleation catalyzed by the photosynthesis enzyme RuBisCO and other abundant biomolecules. Communications Earth & Environment, 4(1), 51. Fornea, A. P., Brooks, S. D., Dooley, J. B., & Saha, A. (2009). Heterogeneous freezing of ice on atmospheric aerosols containing ash, soot, and soil. Journal of Geophysical Research: Atmospheres, 114(D13). DOI:10.1029/2009JD011958 Matthews, B. H., Alsante, A. N., & Brooks, S. D. (2023). Pollen Emissions of Subpollen Particles and Ice Nucleating Particles. ACS Earth and Space Chemistry.

54 ENVIRONMENTAL SCIENCES↗

Utah FORGE: Well 16A(78)-32 Core Analysis Results

This dataset features petrographic, X-Ray Diffraction (XRD), and Scanning Electron Microscopy Analyses of core samples from well 16A(78)-32, which serves as the injection well for the Utah FORGE Enhanced Geothermal System (EGS) project. In addition to an overview of the analysis, the following items have been included here: images of 21 entire thin sections in plane-polarized and cross-polarized light from 16 depths, scanning electron microscope back scatter electron photomosaic maps of 21 thin sections from 16 depths, bulk XRD data from 16 depths, clay-sized XRD patterns from 16 depths, an optical petrography report, and scanning electron microscopy and energy dispersive spectroscopy analyses of eight selected samples.

15 GEOTHERMAL ENERGY↗

Analysis of Niobium Electropolishing Using a Generalized Distribution of Relaxation Times Method

Using electrochemical impedance spectroscopy, we have devised a method of sensing the microscopic surface conditions on the surface of niobium as it is undergoing an electrochemical polishing (EP) treatment. The method uses electrochemical impedance spectroscopy (EIS) to gather information on the surface state of the electrode without disrupting the polishing reaction. The EIS data is analyzed using a so-called distribution of relaxation times (DRT) method. Using DRT, the EIS data can be deconvolved into discrete relaxation time peaks without any a priori knowledge of the electrode dynamics. By analyzing the relaxation time peaks, we are able to distinguish two distinct modes of the EP reaction. As the polishing voltage is increased, the electrode transitions from the low voltage EP mode, characterized by a single relaxation time peaks, to the high voltage EP mode, characterized by two relaxation time peaks. We theorize that this second peak is caused by the formation of an oxide layer on the electrode. We also find that this oxide induced peak transitions from to a negative relaxation time, which is indicative of a blocking electrode process. By analyzing EPed samples, we show that samples polished in the low voltage mode have significantly higher surface roughness due to grain etching and faceting. We find that the surface roughness of the samples only improves when the oxide film peak is present and in the negative relaxation time region. This shows that EIS combined with DRT analysis can be used to predict etching on EPed Nb. This method can also be performed before or during the EP, which could allow for adjustment of polishing parameters to guarantee a smooth cavity surface finish.

43 PARTICLE ACCELERATORS↗

Open Source Visualization and Analysis Platform for 3D Reconstructions of Materials by Transmission Electron Microscopy

Three-dimensional characterization of materials at the nano- and meso-scale has become possible with transmission and scanning transmission electron microscopes (S/TEM). Its importance has extended to a wide class of nanomaterials such as hydrogen fuel cells, solar cells, industrial catalysts, new battery materials and semiconductor devices, as well as spanning high-tech industry, universities, and national labs. While capable instrumentation is abundant, this rapidly expanding demand for high-resolution tomography is bottlenecked by software that is instead tailored for lower-dose, biological applications and not optimized for higher-resolution materials applications. Existing tomography fails to utilize the chemical information provided by S/TEM spectrometers. To address this problem, this project delivered a scalable, fully functional, freely-distributable, open Source materials tomography package with a modern user interface that enables automated acquisition, alignment, and real-time reconstruction of raw tomography data, and provides advanced segmentation, three-dimensional chemical visualization and analysis optimized for materials applications. It has established an extendable framework capable of automation for high-throughput for the tomography of materials from data acquisition to visualization. Phase I and II delivered a full-featured, cross-platform, clean and integrated application for S/TEM materials tomography. It can read projection data from the microscope, with graphical tools for alignment of data, tomographic reconstruction, segmentation, and visualization of the reconstructed 3D volume. The entire pipeline can be saved to an XML state file, enabling fully reproducible data processing and analysis with a full Python environment for the development of custom algorithms, processing, and analysis requirements. Phase IIB extended the application to provide real-time tomographic reconstruction, "live updates" as data is processed, analysis of big data, and multi-channel tomography. Here, quantitative assessment of nanomaterials can occur as data is being recorded on a 3D visualization platform that accommodates additional information from multiple channels. We provide unmatched high-throughput tomography, where the complete tomographic pipeline from measurement to 3D visualization can occur rapidly. The project was extended to offer capabilities for micro-CT, X-ray, neutron, focused ion beam, atomic electron tomography and atom probe tomography. With over 600 transmission electron microscopes worldwide and approximately 50 coming online each year, the demand and impact of an open-source tomography tool is large. Significant opportunities exist in high-tech industry, universities, and national labs to enable or enhance three-dimensional imaging at the nanoscale and bring automated high-throughput approaches that will accelerate progress in materials characterization and metrology. The project supports a service based business model by enabling lab-specific acquisition and processing customization and integration-support and development that will be provided into Phase III and beyond.

36 MATERIALS SCIENCE↗

Automating STEM Aberration Correction via Bayesian Optimization

Multipole aberration correctors have given scanning transmission electron microscopes (STEM) the ability to produce high-quality, atomic-resolution images, enabling STEM to be a key tool in material sciences for characterizing the structure and composition of materials. However, the process of correcting these aberrations typically requires human input and is accomplished using scanned STEM or Ronchigram images at different focii and beam tilts. In this work, we demonstrate an automated on-sample aberration correction system using Bayesian Optimization. We have developed a Python-based server able to communicate with the CEOS DCOR aberration corrector and the Thermo Fischer microscope scripting interface. This server allows us to change aberrations, acquire images and perform basic image analysis.

47 OTHER INSTRUMENTATION↗

Measuring Loss Tangents of Substrates for Superconducting Qubits with Part-per-Billion Precision

We report precision measurements of dielectric loss tangents in substrates for superconducting qubits using an ultra-high quality factor niobium SRF cavity operating at millikelvin temperatures and low electric fields. Multiple substrate types and surface treatments are compared to assess how processing impacts microwave dissipation. The RF results are correlated with materials analysis, including ToF-SIMS and XPS, to identify dominant loss mechanisms. This combined study links microscopic surface chemistry to macroscopic performance and provides a framework for materials-driven improvements in qubit coherence and device design.

Bafia, Daniel [Fermilab]↗

Measuring Loss Tangents of Substrates for Superconducting Qubits with Part-per-Billion Precision

We report precision measurements of dielectric loss tangents in substrates for superconducting qubits using an ultra-high quality factor niobium SRF cavity operating at millikelvin temperatures and low electric fields. Multiple substrate types and surface treatments are compared to assess how processing impacts microwave dissipation. The RF results are correlated with materials analysis, including ToF-SIMS and XPS, to identify dominant loss mechanisms. This combined study links microscopic surface chemistry to macroscopic performance and provides a framework for materials-driven improvements in qubit coherence and device design.

Bafia, Daniel [Fermilab]↗

Post-irradiation characterization of a high burnup mixed oxide fuel rod with minor actinides

The Advanced Fuels Campaign performed a series of irradiation tests of minor actinide-bearing mixed oxide fuel (MA-MOX), the so-called AFC-2C&D experiments, to investigate the transmutation of long-lived transuranic actinide isotopes contained in spent nuclear fuel via fast reactor technology at burnups exceeding 10 % fission of initial metallic atoms. This manuscript reports the test results derived from one of the five MA-MOX rodlets taken to higher burnup in the AFC-2D irradiation. This includes both non-destructive investigations, such as gamma and neutron spectrometry, and destructive investigations, such as fission gas release, ceramography, and chemical burnup analysis. In addition, the microstructure of the fuel was investigated using advanced electron microscopy techniques including electron backscatter diffraction (EBSD) and transmission electron microscopy (TEM). Here, it was observed with EBSD that the pellet had subdivision of the grains and the TEM observed migration of cladding material into the 5 metal precipitates in the fuel which could have been from the higher than desired oxygen/metal ratio. The TEM also showed an enrichment of Cr in fuel clad chemical interaction (FCCI) layer.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Angular correlation between the fission fragment intrinsic spins

The generation of fission fragment (FF) spins and of their relative orbital angular momentum has been debated for more than six decades, and no consensus has been achieved so far. The interpretation of recent experimental results of Wilson et al., has been challenged by several recent theoretical studies, which are not in agreement with one another. According to the interpretation by Wilson et al., the FF spins emerge very long after scission occurrs. Randrup and Vogt, while agreeing that the FF spins are uncorrelated, conclude on the basis of a phenomenological model that these spins are uncorrelated already before scission. Bulgac et al., in a fully microscopic study demonstrate that the primordial FF spin final values are defined before the emission of prompt neutrons and statistical gammas and are strongly correlated with a relative angle between spins close to 2π/3, a result in full agreement with the present independent analysis. The prompt neutrons and statistical gammas carry a significant amount of angular momentum according to the study of Stetcu et al. which can lead to a decorrelation of the FF bandhead spins of the yrast lines measured by Wilson et al., and which also provides arguments why these measured spins are so different from the primordial FF spins evaluated by Bulgac et al.. Here, I show that the unexpected character of the angular correlation between the primordial FF intrinsic spins, recently evaluated by Bulgac et al., which favors FF intrinsic spins pointing predominantly in opposite directions, can be understood by using simple general phase space arguments. The observation by Wilson et al., that the FF spins are uncorrelated follows from both the results of the microscopic calculation of Bulgac et al., and the present analysis of the full correlated probability distribution of the FF spins together with the relative orbital angular momentum of the primordial FFs. These arguments may apply also to heavy-ion collisions and, since there is no use of specifics of the particle interactions, the present results might apply to atomic and molecular systems as well.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Investigating the relation between instantaneous driving decisions and safety critical events in naturalistic driving environment

The availability of large-scale naturalistic driving data provides enormous opportunities for studying relationships between instantaneous driving decisions prior to involvement in safety critical events (SCEs). This study investigates the role of driving instability prior to involvement in SCEs. While past research has studied crash types and their contributing factors, the role of pre-crash behavior in such events has not been explored as extensively. The research demonstrates how measures and analysis of driving volatility can be leading indicators of crashes and contribute to enhancing safety. Highly detailed microscopic data from naturalistic driving are used to provide the analytic framework to rigorously analyze the behavioral dimensions and driving instability that can lead to different types of SCEs such as roadway departures, rear end collisions, and sideswipes. Modeling results reveal a positive association between volatility and involvement in SCEs. Specifically, increases in both lateral and longitudinal volatilities represented by Bollinger bands and vehicular jerk lead to higher likelihoods of involvement in SCEs. Further, driver behavior related factors such as aggressive driving and lane changing also increases the likelihood of involvement in SCEs. Driver distraction, as represented by the duration of secondary tasks, also increases the risk of SCEs. Likewise, traffic flow parameters play a critical role in safety risk. The risk of involvement in SCEs decreases under free flow traffic conditions and increases under unstable traffic flow. Further, the model shows prediction accuracy of 88.1 % and 85.7 % for training and validation data. These results have implications for proactive safety and providing in-vehicle warnings and alerts to prevent the occurrence of such SCEs.

99 GENERAL AND MISCELLANEOUS↗

Pu 5f Occupation in Plutonium Dioxide

Herein an actinide N 4,5 branching ratio analysis of PuO 2 and UO 2 has been performed, including measurements with a scanning transmission electron microscope at the Advanced Light Source. It is shown that the 5f occupation of the Pu in plutonium dioxide is n = 5. This is contrary to recent results from another technique.

36 MATERIALS SCIENCE↗

Review of multi-faceted morphologic signatures of actinide process materials for nuclear forensic science

Particle morphology is an emerging signature that has the potential to identify the processing history of unknown nuclear materials. Using readily available scanning electron microscopes (SEM), the morphology of nearly any solid material can be measured within hours. Coupled with robust image analysis and classification methods, the morphological features can be quantified and support identification of the processing history of unknown nuclear materials. The viability of this signature depends on developing databases of morphological features, coupled with a rapid data analysis and accurate classification process. With developed reference methods, datasets, and throughputs, morphological analysis can be applied within days to (i) interdicted bulk nuclear materials (gram to kilogram quantities), and (ii) trace amounts of nuclear materials detected on swipes or environmental samples. In conclusion, this review aims to develop validated and verified analytical strategies for morphological analysis relevant to nuclear forensics.

36 MATERIALS SCIENCE↗

Improved representation of black carbon mixing structures suggests stronger direct radiative heating

Black carbon significantly influences the Earth system because of its strong solar radiation absorption. However, its direct radiative effect remains poorly understood in current climate models, partly because current climate models oversimplify the diverse structures formed when black carbon mixes with other atmospheric components. Here we show that incorporating more realistic, multi-mixing-structure representations of black carbon increases the direct radiative effect. We find that aged black carbon particles, with thicker coatings and higher embedded fractions, enhance the direct radiative effect more efficiently. Using machine learning alongside the Community Earth System Model, we show that the direct radiative effect at the top of the atmosphere in regions with heavy black carbon pollution is 31.6% greater when multi-mixing structures are considered. These findings highlight the importance of modeling complex mixing structures of particle-resolved black carbon to accurately capture their warming impacts on global atmosphere, particularly in highly polluted regions.

54 ENVIRONMENTAL SCIENCES↗

Mechanistic Insights into Superlattice Transformation at a Single Nanocrystal Level Using Nanobeam Electron Diffraction

Understanding the mechanism and ultimately directing nanocrystal (NC) superlattice assembly and attachment have important implications on future advances in this emerging field. Here, we use 4D-STEM to investigate a monolayer of PbS NCs at various stages of the transformation from a hexatic assembly to a nonconnected square-like superlattice over large fields of view. Maps of nanobeam electron diffraction patterns acquired with an electron microscope pixel array detector (EMPAD) offer unprecedented detail into the 3D crystallographic alignment of the polyhedral NCs. Our analysis reveals that superlattice transformation is dominated by translation of prealigned NCs strongly coupled along the <11n>AL direction and occurs stochastically and gradually throughout single grains. We validate the generality of the proposed mechanism by examining the structure of analogous PbSe NC assemblies using conventional transmission electron microscopy and selected area electron diffraction. Here, the experimental results presented here provide new mechanistic insights into NC self-assembly and oriented attachment.

36 MATERIALS SCIENCE↗

Acoustic cavities in 2D heterostructures

Two-dimensional (2D) materials offer unique opportunities in engineering the ultrafast spatiotemporal response of composite nanomechanical structures. In this work, we report on high frequency, high quality factor ( Q ) 2D acoustic cavities operating in the 50–600 GHz frequency ( f ) range with f × Q up to 1 × 10 14 . Monolayer steps and material interfaces expand cavity functionality, as demonstrated by building adjacent cavities that are isolated or strongly-coupled, as well as a frequency comb generator in MoS 2 /h-BN systems. Energy dissipation measurements in 2D cavities are compared with attenuation derived from phonon-phonon scattering rates calculated using a fully microscopic ab initio approach. Phonon lifetime calculations extended to low frequencies (<1 THz) and combined with sound propagation analysis in ultrathin plates provide a framework for designing acoustic cavities that approach their fundamental performance limit. These results provide a pathway for developing platforms employing phonon-based signal processing and for exploring the quantum nature of phonons.

36 MATERIALS SCIENCE↗

Fingerprinting triangular-lattice antiferromagnet by excitation gaps

CeCd 3 As 3 is a rare-earth triangular-lattice antiferromagnet with large inter-layer separation. Here, our field-dependent heat capacity measurements at dilution fridge temperatures allow us to trace the field-evolution of the spin-excitation gaps throughout the antiferromagnetic and paramagnetic regions. The distinct gap evolution places strong constraints on the microscopic pseudo-spin model, which, in return, yields a close quantitative description of the gap behavior. This analysis provides crucial insights into the nature of the magnetic state of CeCd 3 As 3 , with a certainty regarding its stripe order and low-energy model parameters that sets a compelling paradigm for exploring and understanding the rapidly growing family of the rare-earth-based triangular-lattice systems

36 MATERIALS SCIENCE↗