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DOE OSTI2015

Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells

Here, a structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffractive imaging (cryo-CDI) can in principle be used to bridge the important resolution gap between optical and electron microscopy in bio-imaging. Here, the first experimental demonstration of cryo-CDI for quantitative three-dimensional imaging of whole frozen-hydrated cells using 8 Kev X-rays is reported. As a proof of principle, a tilt series of 72 diffraction patterns was collected from a frozen-hydrated Neospora caninum cell and the three-dimensional mass density of the cell was reconstructed and quantified based on its natural contrast. This three-dimensional reconstruction reveals the surface and internal morphology of the cell, including its complex polarized sub-cellular structure. Finally, it is believed that this work represents an experimental milestone towards routine quantitative three-dimensional imaging of whole cells in their natural state with spatial resolutions in the tens of nanometres.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2016

Inductively coupled BCl 3 /Cl 2 /Ar plasma etching of Al-rich AlGaN

Varying atomic ratios in compound semiconductors is well known to have large effects on the etching properties of the material. The use of thin device barrier layers, down to 25 nm, adds to the fabrication complexity by requiring precise control over etch rates and surface morphology. The effects of bias power and gas ratio of BCl 3 to Cl 2 for inductively coupled plasma etching of high Al content AlGaN were contrasted with AlN in this study for etch rate, selectivity, and surface morphology. Etch rates were greatly affected by both bias power and gas chemistry. Here we detail the effects of small variations in Al composition for AlGaN and show substantial changes in etch rate with regards to bias power as compared to AlN.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Consistency and reproducibility in atomic layer deposition

Atomic layer deposition (ALD) is a thin film synthesis technique that can provide exquisite accuracy and precision in film thickness and composition even on complex, large area substrates. Based on self-limiting surface chemistry, ALD can be insensitive to process conditions and reactor designs, allowing an ALD process developed in one lab to be easily reproduced in other labs. In practice, however, ALD is sometimes difficult to reproduce or replicate, and the results can vary substantially between ALD reactors and between labs. This is exemplified by large deviations in reports on the growth of, e.g., Al2O3, FeOx, and TiO2 given the same precursors under similar conditions. Furthermore, the problem of irreproducibility seems to be growing as ALD is adopted by more researchers and integrated into new applications. In this article, the authors highlight some of the major sources of variations and errors and common misconceptions related to ALD. In particular, the authors focus on issues related to precursors, substrates, and deposition tools. The authors illustrate these problems through examples from the literature, and they present results from numerical simulations that describe how nonidealities would manifest in thickness profiles in a typical cross-flow reactor. They also describe how reproducibility in ALD is linked to consistent experimental practice and reporting between labs. The authors’ hope is that by educating newcomers to ALD and advocating for consistent reporting of deposition conditions, they can minimize irreproducibility and enable ALD practitioners to realize the full potential afforded by self-limiting surface chemistry.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Infrared reflection absorption spectroscopy and temperature-programmed desorption studies of CO adsorption on Ni/CeO 2 (111) thin films: The role of the ceria support

Ceria-supported Ni has shown unique catalytic activity due to unique properties of small Ni particles and strong metal-support interaction. Identification of adsorption sites and understanding the chemical interaction over Ni-ceria at the fundamental level provide crucial insights into the reaction pathways of complex catalytic processes. In this study, to probe the surface sites, the adsorption of CO was carried out with model Ni/ceria systems consisting of Ni nanoparticles vapor-deposited on well-ordered CeO x (111) (1.5 < x < 2) thin films using infrared reflection absorption spectroscopy (IRRAS) and temperature-programmed desorption (TPD) under ultrahigh vacuum (UHV) conditions. Fully oxidized CeO 2 (111) (Ce 4+ ) and partially reduced CeO 1.75 (111) (Ce 4+ /Ce 3+ ) thin films were grown on Ru(0001) to examine the role of the ceria support. Additionally, Ni with low coverages (e.g., 0.2 ML) grows forming small two-dimensional particles on ceria at 300 K, which develop into three-dimensional clusters after heating to 700 K. In the absence of Ni, CO adsorption at 1 mTorr at 100 K shows distinct IR bands at 2158 cm -1 on CeO 2 and 2165 cm -1 on CeO 1.75 . Bridging and atop IR bands associated with CO adsorption over metallic Ni were observed on the Ni-CeO 1.75 surface at 300 K under UHV conditions. CO adsorption over Ni 0 was also observed over as-deposited Ni on CeO 2 . However, a new IR band at 2146 cm -1 due to CO adsorption over Ni 2+ species was detected at 100 K over the annealed Ni particles on CeO 2 . CO IRRAS data suggest the oxidation of Ni to Ni 2+ on CeO 2 and the formation of predominant Ni 2+ species with heating, which is further confirmed with CO TPD data and previous x-ray photoelectron spectroscopy results.

36 MATERIALS SCIENCE↗

DOE OSTI2016

SU-F-T-449: Dosimetric Comparison of Acuros XB, Adaptive Convolve in Intensity Modulated Radiotherapy for Head and Neck Cancer

Purpose: There have been several publications focusing on dose calculation in lung for a new dose calculation algorithm of Acuros XB (AXB). AXB could contribute to dose calculation for high-density media for bone and dental prosthesis rather than in lung. We compared the dosimetric performance of AXB, Adaptive Convolve (AC) in head and neck IMRT plans. Methods: In a phantom study, the difference in depth profile between AXB and AC was evaluated using Kodak EDR2 film sandwiched with tough water phantoms. 6 MV x-ray using the TrueBeam was irradiated. In a patient study, 20 head and neck IMRT plans had been clinically approved in Pinnacle3 and were transferred to Eclipse. Dose distribution was recalculated using AXB in Eclipse while maintaining AC-calculated monitor units and MLC sequence planned in Pinnacle. Subsequently, both the dose-volumetric data obtained using the two different calculation algorithms were compared. Results: The results in the phantom evaluation for the shallow area ahead of the build-up region shows over-dose for AXB and under-dose for AC, respectively. In the patient plans, AXB shows more hot spots especially around the high-density media than AC in terms of PTV (Max difference: 4.0%) and OAR (Max. difference: 1.9%). Compared to AC, there were larger dose deviations in steep dose gradient region and higher skin-dose. Conclusion: In head and neck IMRT plans, AXB and AC show different dosimetric performance for the regions inside the target volume around high-density media, steep dose gradient regions and skin-surface. There are limitations in skin-dose and complex anatomic condition using even inhomogeneous anthropomorphic phantom Thus, there is the potential for an increase of hot-spot in AXB, and an underestimation of dose in substance boundaries and skin regions in AC.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

The largest deep-ocean silicic volcanic eruption of the past century

In this paper, the 2012 submarine eruption of Havre volcano in the Kermadec arc, New Zealand, is the largest deep-ocean eruption in history and one of very few recorded submarine eruptions involving rhyolite magma. It was recognized from a gigantic 400-km 2 pumice raft seen in satellite imagery, but the complexity of this event was concealed beneath the sea surface. Mapping, observations, and sampling by submersibles have provided an exceptionally high fidelity record of the seafloor products, which included lava sourced from 14 vents at water depths of 900 to 1220 m, and fragmental deposits including giant pumice clasts up to 9 m in diameter. Most (>75%) of the total erupted volume was partitioned into the pumice raft and transported far from the volcano. The geological record on submarine volcanic edifices in volcanic arcs does not faithfully archive eruption size or magma production.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Parametric dependencies of resonant layer responses across linear, two-fluid, drift-MHD regimes

Non-axisymmetric magnetic fields arising in a tokamak either by external or internal perturbations can induce complex non-ideal MHD responses in their resonant surfaces while remaining ideally evolved elsewhere. This layer response can be characterized in a linear regime by a single parameter called the inner-layer Delta, which enables outer-layer matching and the prediction of torque balance to non-linear island regimes. Here, we follow strictly one of the most comprehensive analytic treatments including two-fluid and drift MHD effects and keep the fidelity of the formulation by incorporating the numerical method based on the Riccati transformation when quantifying the inner-layer Delta. The proposed scheme reproduces not only the predicted responses in essentially all asymptotic regimes but also with continuous transitions as well as improved accuracies. In particular, the Delta variations across the inertial regimes with viscous or semi-collisional effects have been further resolved, in comparison with additional analytic solutions. The results imply greater shielding of the electromagnetic torque at the layer than what would be expected by earlier work when the viscous or semi-collisional effects can compete against the inertial effects, and also due to the intermediate regulation by kinetic Alfven wave resonances as rotation slows down. These are important features that can alter the nonaxisymmetric plasma responses including the field penetration by external fields or island seeding process in rotating tokamak plasmas.

MHD instability↗

DOE OSTI2015

Enhanced Soundings for Local Coupling Studies: 2015 ARM Climate Research Facility Field Campaign

Matching observed diurnal cycles is a fundamental yet extremely complex test for models. High temporal resolution measurements of surface turbulent heat fluxes and boundary layer properties are required to evaluate the daytime evolution of the boundary layer and its sensitivity to land-atmosphere coupling. To address this need, (12) one-day intensive observing periods (IOP) with enhanced radiosonding will be carried out at the ARM Southern Great Plains (SGP) Central Facility (CF) during summer 2015. Each IOP will comprise a single launch to correspond with the nighttime overpass of the A-Train of satellites (~0830 UTC) and hourly launches during daytime beginning from 1130 UTC and ending at 2130 UTC. At 3-hourly intervals (i.e., 1140 UTC, 1440 UTC, 1740 UTC, and 2040 UTC) a duplicate second radiosonde will be launched 10 minutes subsequent to launch of the on-hour radiosonde for the purpose of assessing horizontal atmospheric variability. In summary, each IOP will have a 14-sounding supplement to the 6-hourly operational sounding schedule at the ARM-SGP CF. The IOP days will be decided before sunset on the preceding day, according to the judgment of the PI’s and taking into consideration daily weather forecasts and the operability of complimentary ARM-SGP CF instrumentation. An overarching goal of the project is to address how ARM could better observe land-atmosphere coupling to support the evaluation and refinement of coupled weather and climate models.

Ferguson, CR↗

DOE OSTI2016

Running SW4 On New Commodity Technology Systems (CTS-1) Platform

We have recently been running earthquake ground motion simulations with SW4 on the new capacity computing systems, called the Commodity Technology Systems - 1 (CTS-1) at Lawrence Livermore National Laboratory (LLNL). SW4 is a fourth order time domain finite difference code developed by LLNL and distributed by the Computational Infrastructure for Geodynamics (CIG). SW4 simulates seismic wave propagation in complex three-dimensional Earth models including anelasticity and surface topography. We are modeling near-fault earthquake strong ground motions for the purposes of evaluating the response of engineered structures, such as nuclear power plants and other critical infrastructure. Engineering analysis of structures requires the inclusion of high frequencies which can cause damage, but are often difficult to include in simulations because of the need for large memory to model fine grid spacing on large domains.

58 GEOSCIENCES↗

DOE OSTI2021

ParFlow

ParFlow is an open-source, modular, parallel watershed flow model. It includes fully-integrated overland flow, the ability to simulate complex topography, geology and heterogeneity and coupled land-surface processes including the land-energy budget, biogeochemistry and snow (via CLM). It is multi-platform and runs with a common I/O structure from laptop to supercomputer. ParFlow is the result of a long, multi-institutional development history and is now a collaborative effort between CSM, LLNL, UniBonn and UCB. ParFlow has been coupled to the mesoscale, meteorological code ARPS and the NCAR code WRF.

Smith, Steven↗

DOE OSTI2021

ParFlow

Smith, Steven↗

DOE OSTI2014

Clay Minerals

Clay minerals are important components of the environment and are involved or implicated in processes such as the uptake of pollutants and the release of nutrients and as potential platforms for a number of chemical reactions. Owing to their small particle sizes (typically, on the order of microns or smaller) and mixing with a variety of other minerals and soil components, advanced characterization methods are needed to study their structures, dynamics, and reactivities. In this article, we describe the use of solid-state NMR methods to characterize the structures and chemistries of clay minerals. Early one-pulse magic-angle spinning (MAS) NMR studies of 27Al and 29Si have now been enhanced and extended with new studies utilizing advanced methodologies (such as Multiple Quantum MAS) as well as studies of less-sensitive nuclei. In additional work, the issue of reactivity of clay minerals has been addressed, including studies of reactive surface area in the environment. Utilizations of NMR-sensitive nuclides within the clay minerals themselves, and in molecules that react with specific sites on the clay mineral surfaces, have aided in understanding the reactivity of these complex aluminosilicate systems.

Mueller, Karl T.↗

DOE OSTI2019

Real-Time Ice Nuclei Measurements at Oliktok Point Field Campaign Report

The ability of atmospheric particles (aerosols) to serve as heterogeneous ice nuclei (IN) for formation of ice and mixed-phase clouds is one of the least understood microphysical processes resulting in large uncertainties in climate modeling. As stated in the Intergovernmental Panel on Climate Change 2007 report, “The effects of aerosol particles on heterogeneous ice formation are currently insufficiently understood and present another level of challenge for both observations and modeling.” IN can strongly affect cloud radiative properties and precipitation formation. Only a small fraction (often less than 1%) of all aerosol particles act as atmospheric IN. Therefore, it becomes important to identify the active fraction of aerosol particles under a variety of environmental conditions. Proposed IN measurement techniques provide IN concentrations as a function of temperature and humidity conditions, and this unique data set can be analyzed to develop or constrain IN parameterizations that models rely on to calculate primary ice formation. Currently, the processes of ice formation within models are poorly represented, such that climate models often inaccurately partition cloud water between liquid and solid ice. Model studies have shown that uncertainties in cloud phase partitioning induce large uncertainties in the impact of mixedphase clouds on climate change. Arctic clouds composed of ice particles and supercooled liquid droplets at temperatures warmer than -37°C are important for the Arctic’s climate because of their extensive horizontal coverage over long periods, and their impact on the surface radiative balance and thus ice sheet coverage. The complexity of microphysical processes within these clouds and the sensitivity of precipitation to the details of microphysics are not fully understood. In addition, representation of these processes in a variety of cloud models continues to be challenging. Arctic clouds provide unique conditions to understand heterogeneous ice nucleation mechanisms, particularly immersion freezing, and will be the initial focus of the ice nucleation group. The U.S. Department of Energy Atmospheric Radiation Measurement (ARM)-North Slope of Alaska (NSA) site is well equipped with other aerosol measurement (number concentration, size) instruments, and a relationship among long-term IN measurements and aerosol physical and chemical properties under different environmental conditions can be identified and established. The long-term IN measurements will be critical for understanding the ice nucleation process in response to the seasonal variations of aerosol and developing robust ice nucleation parameterizations for cloud and climate models. In the future, IN measurements could also be made at other ARM-NSA sites, specifically, Oliktok Point.

Arctic processes (meteorology), Oliktok Point, aer↗

DOE OSTI2019

Development and Verification of a Numerical Library for Solving Global Terrestrial Multiphysics Problems

Abstract Current generation Land Surface Models (LSMs) routinely simulate many nonlinear multiphysics processes. The complexity of future generation LSMs is expected to increase as critical new biophysical and biogeochemical processes are incorporated. Current generation LSMs have several shortcomings including the lack of robust numerical methods to solve discretized equations, monolithic software design that hinders testing of a process representation in isolation from other components, and absence of a flexible coupling framework to solve tightly coupled multiphysics problems. While the LSMs community vigorously evaluates the accuracy of the conceptual model to represent reality (validation), the accuracy of the numerical implementation of the conceptual model (verification) is seldom examined. Method of Manufactured Solutions is a technique for verifying complex codes when analytical solutions are unavailable. In this work, we present a stand‐alone, open source numerical library for solving global terrestrial multiphysics processes that includes a flexible coupling framework. Robust numerical solution for linear and nonlinear equations is provided via the Portable, Extensible Toolkit for Scientific Computation library. We verify the numerical library using Method of Manufactured Solutions for a range of problems comprising single and multiphysics steady state problems that are applied in one or multiple physical domains. This work provides an example of incorporating code verification as an integral part of Land Surface Model development activities.

58 GEOSCIENCES↗

DOE OSTI2017

Manganese-calcium intermixing facilitates heteroepitaxial growth at the 10 1 ¯ 4 calcite-water interface

In situ atomic force microscopy (AFM) measurements were performed to probe surface precipitates that formed on the (10-14) surface of calcite (CaCO3) single crystals following reaction with Mn2+-bearing aqueous solutions with a range of initial concentrations. Three-dimensional epitaxial islands were observed to precipitate and grow on the surfaces and in situ time-sequenced measurements demonstrated that their growth rates were commensurate with those obtained for epitaxial islands formed on calcite crystals reacted with Cd2+-bearing aqueous solutions of the same range in supersaturation with respect to the pure metal carbonate phase. This finding was unexpected as rhodochrosite (MnCO3) and calcite display a 10% lattice mismatch, based on the area of their (10-14) surface unit cells, whereas the lattice mismatch is only 4% for otavite (CdCO3) and calcite. Coatings of varying thicknesses were therefore synthesized by reacting calcite single crystals with calcite-equilibrated aqueous solutions with concentrations of up to 250 µM MnCl2 and analyzed to determine the composition of the surface precipitates. Ex situ X-ray photoelectron spectroscopy (XPS), scanning transmission electron microscopy (STEM), energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), X-ray reflectivity (XRR), and AFM measurements of the reacted crystals demonstrated the formation of an epitaxial (Mn,Ca)CO3 solid solution with a spatially complex composition atop the calcite surface, whereby the first few nanometers were rich in Ca and the Mn content increased with distance from the original calcite surface, culminating in a topmost region of almost pure MnCO3 for the thickest coatings. These findings explain the measured growth rates (the effective lattice mismatch was much smaller than nominal mismatch) and highlight the strong influence played by the substrate on the composition of surface precipitates in aqueous conditions.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2020

Fermi surface studies of the low-temperature structure of sodium

Sodium is the most abundant alkali-metal element and has one of the simplest electronic structures of any metal. At ambient conditions, sodium forms a body-centered-cubic lattice. However, during cooling, it undergoes a partial martensitic phase transition to a complex mixture of rhombohedral polytypes commencing from 36 K. Although the Fermi surface (FS) of bcc sodium has been extensively studied, not much attention has been given to the FS of the martensite structure. Here we report results for the Fermi surface and quantum oscillation (QO) frequencies of several energetically favorable crystal structures of Na at low temperature from first-principles calculations. Interestingly we find that despite drastic differences in the crystal structures of the candidate low-temperature phases of sodium, for all these phases the strongest quantum oscillation peak is centered at 28 kT. Our theoretical results are accompanied by experimental data of QO on a multigrain sodium sample at T = 0.3 K and B max = 18 T exhibiting a sharp peak at 28 kT, independent of the sample orientation. The persistence of this peak even in the presence of the structural transitions has an implication for using the quantum oscillations of polycrystalline sodium for high magnetic field calibration.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Linking morphology with activity through the lifetime of pretreated PtNi nanostructured thin film catalysts

In this study, the nanoscale morphology of highly active Pt 3 Ni 7 nanostructured thin film fuel cell catalysts is linked with catalyst surface area and activity following catalyst pretreatments, conditioning and potential cycling. The significant role of fuel cell conditioning on the structure and composition of these extended surface catalysts is demonstrated by high resolution imaging, elemental mapping and tomography. The dissolution of Ni during fuel cell conditioning leads to highly complex, porous structures which were visualized in 3D by electron tomography. Quantification of the rendered surfaces following catalyst pretreatment, conditioning, and cycling shows the important role pore structure plays in surface area, activity, and durability.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2014

Radiation increases the cellular uptake of exosomes through CD29/CD81 complex formation

Highlights: • Radiation increases cellular uptake of exosomes. • Radiation induces colocalization of CD29 and CD81. • Exosomes selectively bind the CD29/CD81 complex. • Radiation increases the cellular uptake of exosomes through CD29/CD81 complex formation. - Abstract: Exosomes mediate intercellular communication, and mesenchymal stem cells (MSC) or their secreted exosomes affect a number of pathophysiologic states. Clinical applications of MSC and exosomes are increasingly anticipated. Radiation therapy is the main therapeutic tool for a number of various conditions. The cellular uptake mechanisms of exosomes and the effects of radiation on exosome–cell interactions are crucial, but they are not well understood. Here we examined the basic mechanisms and effects of radiation on exosome uptake processes in MSC. Radiation increased the cellular uptake of exosomes. Radiation markedly enhanced the initial cellular attachment to exosomes and induced the colocalization of integrin CD29 and tetraspanin CD81 on the cell surface without affecting their expression levels. Exosomes dominantly bound to the CD29/CD81 complex. Knockdown of CD29 completely inhibited the radiation-induced uptake, and additional or single knockdown of CD81 inhibited basal uptake as well as the increase in radiation-induced uptake. We also examined possible exosome uptake processes affected by radiation. Radiation-induced changes did not involve dynamin2, reactive oxygen species, or their evoked p38 mitogen-activated protein kinase-dependent endocytic or pinocytic pathways. Radiation increased the cellular uptake of exosomes through CD29/CD81 complex formation. These findings provide essential basic insights for potential therapeutic applications of exosomes or MSC in combination with radiation.

60 APPLIED LIFE SCIENCES↗