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At least 55 records · Page 3

Spatiotemporal DNA methylome dynamics of the developing mouse fetus

Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited1,2. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders.

59 BASIC BIOLOGICAL SCIENCES↗

THERMAL STRESS ANALYSIS OF A SPENT NUCLEAR FUEL CANISTER

The potential for chloride induced stress corrosion cracking (CISCC) in spent nuclear fuel dry storage canisters is a current topic of research by the US Department of Energy Spent Fuel and Waste Science and Technology program. One of the important prerequisites for CISCC is a tensile residual stress state. This study utilizes computational models to provide an initial analysis of thermal stresses in a generic spent nuclear fuel canister. A STAR-CCM+ thermal fluid model provides a temperature profile analysis of the canister based on four different ambient temperature conditions. An ANSYS APDL finite element model incorporates the temperature profiles to analyze the thermal stresses in the canister. The calculated thermal stress magnitudes are in the range of 10 MPa to 80 MPa, which could be significant for crack propagation through the canister wall. The maximum thermal stress is not a concern for the structural failure of the canister, but it is high enough that it is a significant contribution to the total stress state of the canister wall, which also includes residual stress from fabrication, internal pressure from helium cover gas, and potential transient mechanical loads, such as earthquakes. This paper describes the initial finite element thermal stress analysis that was completed in 2020, reports the initial findings, and identifies areas where model refinement is still needed to complete this work in the future.

Jensen, Ben J.↗

Illumination-induced modulation of conductivity and Gunn oscillation properties in epitaxial GaAs

In this work, we illuminate a gallium arsenide (GaAs) Gunn device and study the light-induced changes of Gunn oscillation properties. We observe that illumination leads to the modulation of the Gunn threshold voltage, the Gunn oscillation magnitude, and the coherency of Gunn oscillation, with the nature of the modulation being closely related to the position of illumination on the device. These effects are attributed to the generation of optically excited carriers, which results in the modulation of conductivity and the electric field profile along the device. The finite element method is used to simulate the change of the field profile of the Gunn device caused by illumination. We also report an unexpected phenomenon of Gunn oscillation property manipulation with an optical chopper. In addition, wavelength-dependent, power-dependent, and pulsed illumination measurements are performed to help with further understanding the observations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Optimizing aluminum oxide passivation layers—Laser-induced plasmas for layer formation, real-time diagnostics, and layer evaluation

Molten salts have beneficial thermophysical and electrolytic properties, but the aggressive nature of molten salts requires corrosion mitigation strategies, such as structural material surface treatment. In this study, a laser-induced breakdown spectroscopy (LIBS) system was used to simultaneously ablate and monitor de-excitation spectra to form and identify dense alumina passivation layers. Additionally, high-frequency (kHz) LIBS imaging allowed rapid elemental mapping and depth profiling for surface O/Al ratios via minimally destructive analysis. The paired t-test rejected the null hypothesis that air and Ar cover gases were equivalent (p = 0.00012), and the analysis of variance (ANOVA) showed that overlap between shots (p = 0.03112) and cover gas flow rate (p = 0.02729) were statistically significant. At 75% overlap, the O/Al ratio increased to 10% ± 2%, and 90% overlap rose further to 31% ± 2%. Regardless of overlap, tuning the gas flow from 0.5 to 2.5 L min −1 enhanced the O/Al ratio by 24% ± 4%. LIBS depth profiling showed a 3× increase in layer thickness from 75% to 90% overlap. Molecular band peaks of AlO, a precursor to Al 2 O 3 found during treatment, suggest that band intensity could be used for real-time Al 2 O 3 optimization. Ultimately, by adjusting laser spot overlap and cover gas flow rate, a 266 nm laser was shown to form Al 2 O 3 layers on an Al6061 sample, with cover gas flow rate primarily affecting the O/Al ratio and layer thickness correlating with laser spot overlap. This combination of molecular spectra collection, imaging, and depth profiling demonstrated the robust layer analysis capabilities of LIBS.

Corrosion↗

Inversion of dislocation-impurity interactions in α -Fe under magnetic state changes

Here, in this work, we investigate the dislocation-impurity interaction energies and their profiles for various 3d elements —V, Cr, Mn, Cu, Ni, and Co —in and around 1/2 $\langle111\rangle$ screw dislocations in α -Fe using ab initio methods. We consider the ferromagnetic and paramagnetic states, with the latter being modeled through both the disordered local moment model and a spin-wave approach. Our findings reveal that (1) magnetic effects are large compared to size misfit effects of substitutional impurities, and (2) dislocation-impurity interactions are dependent on the magnetic state of the matrix and thermal lattice expansion. In particular, Cu changes from core-attractive in the ferromagnetic state to repulsive in the paramagnetic state.

36 MATERIALS SCIENCE↗

Niobium's intrinsic coherence length and penetration depth revisited using low-energy muon spin spectroscopy and secondary-ion mass spectrometry

Here, we report direct, simultaneous measurements of the London penetration depth (𝜆 𝐿 ) and Bardeen-Cooper-Schrieffer coherence length (𝜉 0 ) in oxygen-doped niobium, with impurity concentrations spanning the “clean” to “dirty” limits. Two depth-resolved techniques—low-energy muon spin spectroscopy and secondary-ion mass spectrometry—were used to quantify the element's Meissner screening profiles, analyzed within a framework that accounts for nonlocal electrodynamics. The analysis indicates intrinsic length scales of 𝜆 𝐿 = 29.1⁢ (10)⁢ nm and 𝜉 0 = 39.9 ⁢(25)⁢ nm, corresponding to a Ginzburg-Landau parameter 𝜅 = 0.70⁢ (5). The obtained 𝜆 𝐿 and 𝜅 values, accurately quantified at the nanoscale, are smaller than those commonly used in applications and modeling, and indicate that clean niobium lies at the boundary between type-I and type-II superconductivity, supporting the contemporary view that its intrinsic state may be type I.

Particle Accelerator↗

X-Ray Phase Contrast Imaging for Dynamic Material Mix Experiments, LAO-003-17, Year 3 of 3

X-ray phase contrast imaging with transmission gratings for density profile measurements has been developed and tested for dynamic experimental applications. Talbot-Lau x-ray deflectometry is a new method of measuring x-ray refraction in addition to attenuation and ultrasmall-angle scattering that has recently been developed for static imaging, primarily for medical and industrial applications. To obtain density profiles from fast-evolving systems, we must use a flash x-ray source with a spot size much larger than the continuous microfocus sources of static imaging systems, and we can obtain only a single exposure. The challenges to measuring electron density profiles of two mixed elements from a single-image, low spatial resolution system are addressed, and initial results from the first dynamic experiments with one such system, conducted on a gas launcher at the end of FY 2018 and beginning of FY 2019, are presented. In FY 2019, we designed and built a new deflectometer designed for detonator experiments to test new techniques to improve the sensitivity and reliability of the diagnostic.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A Novel Machine Learning Algorithm for Cloud Detection Using AERI Measurement Data

Infrared hyperspectral remote sensing has been widely used in the field of meteorology. Many scientists have carried out research on inversion methods of meteorological elements such as thermodynamic profile, boundary layer height, cloud base height, etc. In this study, a method based on machine learning for cloud detection using ground-based infrared hyperspectral radiation data is proposed. The features of outliers, the cloudy and cloud-free data of Atmospheric Emitted Radiance Interferometer (AERI) radiation are extracted. The “reference values” of cloudy and cloud-free are determined based on the observation data of Vaisala CL31 ceilometer within the time range of 8 min before the corresponding time of AERI. A support vector machine (SVM) algorithm is used for training. The dataset comes from the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) site and North Slope Alaska (NSA) site from 2015 to 2017, and the ARM West Antarctic Radiation Experiment (AWARE) site in 2016 is also analyzed. The instruments used in this paper include AERI, ceilometer, etc. The experimental results reveal that the agreement of cloud detection results between the proposed algorithm and ceilometer is about 93% at each site. However, for high clouds or optically thin clouds, the agreement will decrease.

47 OTHER INSTRUMENTATION↗

Experimental measurement of the rapid mixing of fuel and air in a multi-element diffusion (Hencken) burner

Flat flame burners are valuable tools for studying complex combustion phenomena like particle synthesis due to the well-controlled and well-behaved initial and boundary conditions. In this study, the methane/air flame temperature and tracer density profiles of a multi-element diffusion burner equipped with a central tube were characterized using krypton (Kr) x-ray fluorescence at the Advanced Photon Source at Argonne National Laboratory. The experiments were performed using a fuel-to-oxygen equivalence ratio of 0.8 and 3.3% Kr by volume was added to the reactant gases. One- and two-dimensional scans of non-combusting (i.e., cold flow) and combusting conditions, both with and without flow through the central tube were performed. Spatially-resolved Kr number density profiles were obtained at different planar locations and heights above the surface of the burner. The results show rapid mixing occurred near the exit-plane of the burner and increased spatial uniformity was achieved from 0.1 mm to 0.5 mm above the surface of the burner. Further, the data also showed the impact of the central tube flow on the main methane/air flame, including evidence of the central tube flow mixing with the main flow. Flame temperatures were calculated from the fluorescence measurements at various heights above the burner surface and were in good agreement with model predictions for a burner stabilized flame. These high-fidelity measurements provide accurate baseline data that are particularly valuable for understanding the effects of fuel and air mixing on downstream phenomena, such as the formation of condensed-phase products.

42 ENGINEERING↗

Efficient sensitivity analysis of the thermal profile in powder bed fusion of metals using hypercomplex automatic differentiation finite element method

Rapid cyclic temperature fluctuation occurring in powder bed fusion of metals using a laser beam (PBF-LB/M) influences the formation of flaws in printed parts. Consequently, there is a pressing need to enhance the quality of printed parts by developing innovative methodologies that can predict thermal histories and help uncover the intricate relationships between process parameters and thermal profiles. Sensitivity Analysis (SA) emerges as an essential tool for this, offering the potential for process optimization and enhanced quality control. Nonetheless, conventional SA methodologies often incur in excessive computational costs and potential numerical approximation errors. Here, to address this technical challenge, we present a novel method for SA that integrates the HYPercomplex-based Automatic Differentiation (HYPAD) technique with transient thermal simulations conducted via the finite element method (FEM). Leveraging this methodology, we efficiently and accurately perform SA for PBF-LB/M processes in a post-processing step. Compared to traditional methods like Finite Differences (FD), HYPAD-FEM required 96 % less computational time for obtaining sensitivities for 22 process parameters, under a comparative study conducted within the context of the 2018–02 AM benchmark of the National Institute of Standards and Technology. In summary, HYPAD-FEM offers superior efficiency and accuracy in SA over conventional methods, delivering the best sensitivity of a model without the need for step-size selection and problem or parameter-based implementations.

36 MATERIALS SCIENCE↗

Predicting Dynamic-to-Static Correction Factor from Petrophysical Data and Chemostratigraphy using Unsupervised Machine Learning

Estimating static mechanical properties of stratigraphic layers is critical for optimizing subsurface engineering applications. To estimate dynamic-to-static correction factor F ds (static-to-dynamic Young’s modulus ratio) across the Caney shale interval in Oklahoma, USA, we integrated triaxial test measurements and petrophysical data, including well logs and X-ray fluorescence (XRF) using unsupervised machine learning (ML). We used a novel workflow that includes principal component analysis (PCA) to reduce data set dimensionality of well logs and XRF data sets—both separately and combined—creating three scenarios, and later applied inverse distance weighting (IDW) to derive F ds profiles for these scenarios. Furthermore, we applied K-means clustering on each scenario to predict depositional facies, and built a stiffness zonation profile through chemostratigraphic analysis of the terrigenous elements to validate the predicted F ds . The predicted F ds profile from each scenario using the PCA-IDW method was compared with the constant F ds approach from our previous study by calculating the root mean square error (RMSE). The combined data sets scenario yielded the lowest RMSE value of 0.113, while the RMSE values for the well logs and XRF scenarios were 0.131 and 0.129, respectively. In addition, the predicted F ds from the XRF scenario well-matched the stiffness zonation from the chemostratigraphic analysis that was built using the optimized K-means clustering of nine clusters for that scenario. These methods and findings offer a valuable tool for refining lithological classification and improving the F ds profile, potentially enhancing drilling and stimulation strategies for subsurface energy engineering applications.

clastic rock↗

Effect of Soil Properties and Input Motion on Site Amplification Using Validated Nonlinear Soil Model

Here, three-dimensional (3-D) nonlinear site response analyses are conducted using finite element models of actual soil profiles from ten nuclear power plant (NPP) sites in the United States to investigate the effects of soil properties and input motions on site amplification. The modeling approach developed in this study combines several novel elements, such as 3-D analysis (including vertical motions), nonlinear inelastic behavior of soil (strain-dependent shear modulus reduction and hysteretic damping), formulation of nonreflecting boundary conditions at the base, and generation of realistic outcrop ground motions for specific sites. All these elements of the modeling approach are first validated using actual data from five earthquakes at three downhole array stations recorded in the Kiban-Kyoshin network (KiK-net), Japan. The same approach is then used to develop site models of ten NPP sites in the United States and corresponding ground motions that are spectrally matched to the site hazard spectra. Eight sets of three-component input motions are used in the study and are categorized on the basis of presence or absence of a near-field pulse in the seed ground motions used for spectral matching. It is found that all sites retain a definite site amplification function regardless of the input motion, provided that the seed motion is spectrally matched to the site hazard spectra. The magnitude of site amplification and frequencies at which they occur depend upon soil properties, particularly the shear wave velocity profile and the constitutive relationship (strain-dependent shear modulus reduction and hysteretic damping) of soil. Amplification of spectral acceleration in the vertical direction (up-down motion) is found to be just as much as, if not more than, the amplification in the horizontal direction. Peak shear strain is found to be about 20% larger for near-field motions compared to far-field motions whereas maximum horizontal site amplification for far-field motions is found to be consistently larger than that of near-field motions, even though the differences between the two remain within the scatter resulting from individual ground motions.

99 GENERAL AND MISCELLANEOUS↗

Study of Muon Monitor Data to Maintain the Quality of the NuMI Neutrino Beam at Fermilab [Poster]

A muon monitor which measures muon beam profile, is a key beam element to maintain the quality of muon neutrino beam. Three arrays of muon monitors located in the downstream of the hadron absorber provide the measurements of the primary beam quality. We studied the response of muon monitors with the proton beam profile changes and focusing horn current variations. The responses of muon monitors have been used to implement Machine Learning (ML) algorithms to monitor the beam quality.

43 PARTICLE ACCELERATORS↗

Structural stability of thin overhanging walls during material extrusion additive manufacturing of thermoset-based ink

Recent developments have enabled material extrusion additive manufacturing of thermoset-based composite inks on the large scale. In addition, printing out-of-plane components is of broad interest to the polymer material extrusion community. Here, we address some of the challenges associated with both large-scale and out-of-plane thermoset material extrusion additive manufacturing by studying the height at which thin overhanging walls collapse. Walls at a range of overhang angles were printed until they collapsed. An optical camera captured the profile of each wall throughout the print, allowing the collapse height to be identified and the geometric fidelity to the programmed angle to be evaluated. Using previously measured rheological properties, predictive models were generated to approximate the collapse height and profile of the deflected walls. First, an analytical model was created to predict the height at which the walls would yield. The analytical model assumes the walls exhibit a perfectly linear profile; however, experiments proved this assumption to be false. Therefore, a finite element simulation was developed to account for the elastic deflection that occurs during printing. The finite element simulation predicts both the yield height and the deflected profile after the deposition of each layer. For the properties of the thermoset ink used here, the yield height predicted by the analytical model and finite element simulation are virtually identical. These predictions match experimental data reasonably well, but minor errors are observed. Accounting for the fully plastic moment appears to explain the small mismatch between experimental data and predictions. Additionally, the finite element simulation provides an excellent prediction of the deflected profile before the wall begins to collapse. Finally, by demonstrating that the collapse height and deflected profile of thin overhanging walls can be predicted, this work illustrates how the soft viscoelastic properties of thermoset-based composite inks limit the scale of a key feature required to print some nonplanar components. It also provides a basis to tailor in-process curing systems to suppress deflection and collapse of thin overhanging walls.

36 MATERIALS SCIENCE↗

Validating the rhenium proxy for rock organic carbon oxidation using weathering profiles

Chemical weathering over geological timescales acts as a source or sink of atmospheric carbon dioxide (CO 2 ), while influencing long-term redox cycling and atmospheric oxygen (O 2 ) at Earth's surface. There is a growing recognition that the oxidative weathering of rock organic carbon (OC petro ) can release more CO 2 than is locally drawn down by silicate weathering, and may vary due to changes in erosion and climate. The element rhenium (Re) has emerged as a proxy to track the oxidative weathering of OC petro , yet uncertainties in its application remain namely that we lack a systematic assessment of the comparative mobility of Re and OC petro during sedimentary rock weathering. Here we measure Re and OC petro loss across gradients in rock weathering at 9 global sites, spanning a range of initial OC petro values from ~0.2 % to >10 %. We use titanium to account for volume changes during weathering and assess Re and OC petro loss alongside major elements that reflect silicate (Na, Mg), carbonate (Ca, Mg) and sulfide (S) weathering. Across the dataset, Re loss is correlated with OC petro loss but not with loss of any other major element. Further, across the weathering profiles, the average molar ratio of OC petro to Re loss was 0.84 ± 0.15, with 8 out of 9 sites having a ratio >0.74. At one site (Marcellus Shale), the average ratio was lower at 0.58 ± 0.11. The excess loss of Re matches expectations that, typically, between ~0 and 20 % of the Re liberated by sedimentary rock weathering derives from silicate or sulfide phases, while some OC petro may be physically or chemically protected from weathering. Overall, our measurements provide validation for the Re proxy of OC petro oxidation and allow future work to further improve our knowledge of regional and global-scale rates of this important source of CO 2 in the geochemical carbon cycle.

58 GEOSCIENCES↗

Layer Time Control for Large Scale Additive Manufacturing Using High Performance Computing

This work proposes to optimize an additive manufacturing AM process to reduce energy and printing cost. The polymer AM process is inherently dependent on the time-temperature history of each layer to maintain geometric tolerances and mechanical integrity. Our preliminary study shows that regression-based layer time control model using thermal images could result in up to 30% build time reduction for simple geometries. This proposed work would use high-performance computing (HPC) to couple the data-driven model with thermal simulation for better predicting layer temperature profiles, improving throughput of large-scale additive manufacturing, and reducing its energy cost. We have developed a method to optimize a layer deposition time (a.k.a. layer time) for large-scale AM via physics-based simulations. A long layer time leads to an over-cooled surface on which a new layer is deposited, and therefore, it may result in a weak bonding or debonding between layers, cracking, or warping. A short layer time leads to a high temperature of the structure due to insufficient cooling, and therefore, the structure may not be stiff enough and may collapse during manufacturing. Therefore, it is important to estimate the optimal layer time in additive manufacturing for a high-quality product. The temperature of a top layer right before deposition is recommended to be slightly higher than the glass temperature of the material. A temperature cooling was approximated to an exponential function of time, and the optimized layer time was obtained based on a target temperature while maintaining a minimal printing time. The material used is carbon fiber-reinforced polycarbonate (CF/PC), and the large-scale deposition system used is LSAM TM from Thermwood Corporation. Three different layer time cases were used for experiments, and a series of thermal images were obtained via an infra-red (IR) camera during the entire AM processes. AM process simulations were performed using a finite element method and the temperature profiles from the simulation were in good agreements with those from experiments. The layer time optimization was performed based on the temperature profiles from the simulations. A layer temperature with the optimal layer time was confirmed as the target temperature through simulation. In addition to the development of a layer time optimization method, we have developed a numerical framework for AM simulation with element activations in sync with toolpath, based on an open source finite element framework, DEAL.II. A major portion of this work was presented at SAMPE 2022 Conference and Exhibition on May 2022, and published in Proceedings of SAMPE 2022.

42 ENGINEERING↗

Composition Quantification of SiGeSn Alloys Through Time-of-Flight Secondary Ion Mass Spectrometry: Calibration Methodologies and Validation With Atom Probe Tomography

Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) is a powerful technique for elemental compositional analysis and depth profiling of materials. However, it encounters the problem of matrix effects that hinder its application. In this work, we introduce a pioneering ToF-SIMS calibration method tailored for SixGeySnz ternary alloys. SixGe1-x and Ge1-zSnz binary alloys with known compositions are used as calibration reference samples. Through a systematic SIMS quantification study of SiGe and GeSn binary alloys, we unveil a linear correlation between secondary ion intensity ratio and composition ratio for both SiGe and GeSn binary alloys, effectively mitigating the matrix effects. Extracted relative sensitivity factor (RSF) value from SixGe1-x (0.07 < x < 0.83) and Ge1-zSnz (0.066 < z < 0.183) binary alloys are subsequently applied to those of SixGeySnz (0.011 < x < 0.113, 0.863 < y < 0.935 and 0.023 < z < 0.103) ternary alloys for elemental compositions quantification. These values are cross-checked by Atom Probe Tomography (APT) analysis, an indication of the great accuracy and reliability of as-developed ToF-SIMS calibration process. Furthermore, the proposed method and its reference sample selection strategy in this work provide a low-cost as well as simple-to-follow calibration route for SiGeSn composition analysis, thus driving the development of next-generation multifunctional SiGeSn-related semiconductor devices.

36 MATERIALS SCIENCE↗

MHz free electron laser x-ray diffraction and modeling of pulsed laser heated diamond anvil cell

A new diamond anvil cell experimental approach has been implemented at the European x-ray Free Electron Laser, combining pulsed laser heating with MHz x-ray diffraction. In this report we use this setup to determine liquidus temperatures under extreme conditions, based on the determination of time-resolved crystallization. The focus is on a Fe-Si-O ternary system, relevant for planetary cores. This time-resolved diagnostic is complemented by a finite-element model, reproducing temporal temperature profiles measured experimentally using streaked optical pyrometry. This model calculates the temperature and strain fields by including (i) pressure and temperature dependencies of material properties, and (ii) the heat-induced thermal stress, including feedback effect on material parameter variations. Making our model more realistic, these improvements are critical as they give 7000 K temperature differences compared to previous models. Laser intensities are determined by seeking minimal deviation between measured and modeled temperatures. Combining models and streak optical pyrometry data extends temperature determination below detection limit. The presented approach can be used to infer the liquidus temperature by the appearance of SiO 2 diffraction spots. In addition, temperatures obtained by the model agree with crystallization temperatures reported for Fe–Si alloys. Our model reproduces the planetary relevant experimental conditions, providing temperature, pressure, and volume conditions. Those predictions are then used to determine liquidus temperatures at experimental timescales where chemical migration is limited. This synergy of novel time-resolved experiments and finite-element modeling pushes further the interpretation capabilities in diamond anvil cell experiments.

36 MATERIALS SCIENCE↗