Effect of lattice mismatch and shell thickness on strain in core@shell nanocrystals
Abstract not provided
Gamler, Jocelyn T.L.↗
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Water adsorption on the LaMnO3 surface
Studying the adsorption of water on the metallic LaMnO3 surface can provide insight into this complicated surface-adsorbate interaction. Using density functional theory, we investigated the adsorption of a water monomer, dimer, trimer, and a monolayer on the surface. The electronic structure of ground state configurations is explored using analysis of density of states, charge density, and crystal orbital overlap populations. We found that the interaction between the surface and water molecules is stronger than hydrogen bonding between molecules, which facilitates wetting of the surface. Adsorbed water molecules form very strong hydrogen bonds, with substantially shifted OH stretch modes. For the monolayer of adsorbed water, a hint of a bilayer is observed with a height separation of only 0.2 A˚. However, simulated scanning tunneling microscopy images and vibrational spectra suggest a significant difference between the two layers due to intermolecular bonding and interaction with the substrate.
Billman, Chris R.↗
Quantitative assessment of fitting errors associated with streak camera noise in Thomson scattering data analysis
Thomson scattering measurements in high energy density experiments are often recorded using optical streak cameras. In the low-signal regime, noise introduced by the streak camera can become an important and sometimes the dominant source of measurement uncertainty. In this paper, we present a formal method of accounting for the presence of streak camera noise in our measurements. We present a phenomenological description of the noise generation mechanisms and present a statistical model that may be used to construct the covariance matrix associated with a given measurement. This model is benchmarked against simulations of streak camera images. We demonstrate how this covariance may then be used to weight fitting of the data and provide quantitative assessments of the uncertainty in the fitting parameters determined by the best fit to the data and build confidence in the ability to make statistically significant measurements in the low-signal regime, where spatial correlations in the noise become apparent. These methods will have general applicability to other measurements made using optical streak cameras.
47 OTHER INSTRUMENTATION↗
Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection
The substrate for ribosomes actively engaged in protein synthesis is a ternary complex of elongation factor Tu (EF-Tu), aminoacyl-tRNA (aa-tRNA), and GTP. EF-Tu plays a critical role in mRNA decoding by increasing the rate and fidelity of aa-tRNA selection at each mRNA codon. Here, using three-color single-molecule fluorescence resonance energy transfer imaging and molecular dynamics simulations, we examine the timing and role of conformational events that mediate the release of aa-tRNA from EF-Tu and EF-Tu from the ribosome after GTP hydrolysis. Our investigations reveal that conformational changes in EF-Tu coordinate the rate-limiting passage of aa-tRNA through the accommodation corridor en route to the peptidyl transferase center of the large ribosomal subunit. Experiments using distinct inhibitors of the accommodation process further show that aa-tRNA must at least partially transit the accommodation corridor for EF-Tu∙GDP to release. aa-tRNAs failing to undergo peptide bond formation at the end of accommodation corridor passage after EF-Tu release can be reengaged by EF-Tu∙GTP from solution, coupled to GTP hydrolysis. These observations suggest that additional rounds of ternary complex formation can occur on the ribosome during proofreading, particularly when peptide bond formation is slow, which may serve to increase both the rate and fidelity of protein synthesis at the expense of GTP hydrolysis.
59 BASIC BIOLOGICAL SCIENCES↗
Mechanical design of the highly porous cuttlebone: A bioceramic hard buoyancy tank for cuttlefish
Cuttlefish, a unique group of marine mollusks, produces an internal biomineralized shell, known as cuttlebone, which is an ultra-lightweight cellular structure (porosity, ~93 vol%) used as the animal’s hard buoyancy tank. Although cuttlebone is primarily composed of a brittle mineral, aragonite, the structure is highly damage tolerant and can withstand water pressure of about 20 atmospheres (atm) for the species Sepia officinalis . Currently, our knowledge on the structural origins for cuttlebone’s remarkable mechanical performance is limited. Combining quantitative three-dimensional (3D) structural characterization, four-dimensional (4D) mechanical analysis, digital image correlation, and parametric simulations, here we reveal that the characteristic chambered “wall–septa” microstructure of cuttlebone, drastically distinct from other natural or engineering cellular solids, allows for simultaneous high specific stiffness (8.4 MN∙m/kg) and energy absorption (4.4 kJ/kg) upon loading. We demonstrate that the vertical walls in the chambered cuttlebone microstructure have evolved an optimal waviness gradient, which leads to compression-dominant deformation and asymmetric wall fracture, accomplishing both high stiffness and high energy absorption. Moreover, the distribution of walls is found to reduce stress concentrations within the horizontal septa, facilitating a larger chamber crushing stress and a more significant densification. Overall, the design strategies revealed here can provide important lessons for the development of low-density, stiff, and damage-tolerant cellular ceramics.
42 ENGINEERING↗
Unveiling the complexity of nanodiamond structures
Understanding nanodiamond structures is of great scientific and practical interest. It has been a long-standing challenge to unravel the complexity underlying nanodiamond structures and to resolve the controversies surrounding their polymorphic forms. Here, we use transmission electron microscopy with high-resolution imaging, electron diffraction, multislice simulations, and other supplementary techniques to study the impacts of small sizes and defects on cubic diamond nanostructures. The experimental results show that common cubic diamond nanoparticles display the (200) forbidden reflections in their electron diffraction patterns, which makes them indistinguishable from new diamond (n-diamond). The multislice simulations demonstrate that cubic nanodiamonds smaller than 5 nm can present the d -spacing at 1.78 Å corresponding to the (200) forbidden reflections, and the relative intensity of these reflections increases as the particle size decreases. Our simulation results also reveal that defects, such as surface distortions, internal dislocations, and grain boundaries can also make the (200) forbidden reflections visible. These findings provide valuable insights into the diamond structural complexity at nanoscale, the impact of defects on nanodiamond structures, and the discovery of novel diamond structures.
36 MATERIALS SCIENCE↗
Wire, hybrid, and laser-cut X-pinches as Talbot–Lau backlighters for electron density diagnostics
Talbot–Lau x-ray deflectometry (TXD) enables refraction-based imaging for high-energy-density physics experiments, and thus, it has been studied and developed with the goal of diagnosing plasmas relevant to inertial confinement and magnetic liner inertial fusion. X-pinches, known for reliably generating fast (~1 ns), small (~1 µm) x-ray sources, were driven on the compact current driver generator for ablation structure and implosion studies (~200 kA, 150 ns) as a potential backlighter source for TXD. Considering that different X-pinch configurations have characteristic advantages and drawbacks as x-ray generating loads, three distinct copper X-pinch configurations were studied: the wire X-pinch, the hybrid X-pinch, and the laser-cut X-pinch. Furthermore, the Cu K-shell emission from each configuration was characterized and analyzed regarding the specific backlighter requirements for an 8 keV TXD system: spatial and temporal resolution, number of sources, time of emission, spectrum, and reproducibility. Recommendations for future experimental improvements and applications are presented. The electron density of static objects was retrieved from Moiré images obtained through TXD. This allowed to calculate the mass density of static samples within 4% of the expected value for laser-cut X-pinches, which were found to be the optimal X-pinch configuration for TXD due to their high reproducibility, small source size (≤5 µm), short duration (~1 ns), and up to 106 W peak power near 8 keV photon energy. Plasma loads were imaged through TXD for the first-time using laser-cut X-pinch backlighting. Experimental images were compared with simulations from the x-ray wave-front propagation code, demonstrating that TXD can be a powerful x-ray refraction-based diagnostic for dense Z-pinch loads. Future plans for Talbot–Lau interferometry diagnostics in the pulsed-power environment are described.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
SkyFACT: high-dimensional modeling of gamma-ray emission with adaptive templates and penalized likelihoods
We present SkyFACT (Sky Factorization with Adaptive Constrained Templates), a new approach for studying, modeling and decomposing diffuse gamma-ray emission. Like most previous analyses, the approach relies on predictions from cosmic-ray propagation codes like GALPROP and DRAGON. However, in contrast to previous approaches, we account for the fact that models are not perfect and allow for a very large number (∼> 10{sup 5}) of nuisance parameters to parameterize these imperfections. We combine methods of image reconstruction and adaptive spatio-spectral template regression in one coherent hybrid approach. To this end, we use penalized Poisson likelihood regression, with regularization functions that are motivated by the maximum entropy method. We introduce methods to efficiently handle the high dimensionality of the convex optimization problem as well as the associated semi-sparse covariance matrix, using the L-BFGS-B algorithm and Cholesky factorization. We test the method both on synthetic data as well as on gamma-ray emission from the inner Galaxy, |ℓ|<90{sup o} and | b |<20{sup o}, as observed by the Fermi Large Area Telescope. We finally define a simple reference model that removes most of the residual emission from the inner Galaxy, based on conventional diffuse emission components as well as components for the Fermi bubbles, the Fermi Galactic center excess, and extended sources along the Galactic disk. Variants of this reference model can serve as basis for future studies of diffuse emission in and outside the Galactic disk.
79 ASTRONOMY AND ASTROPHYSICS↗
On determination of charge transfer efficiency of thick, fully depleted CCDs with 55 Fe x-rays
Charge transfer efficiency (CTE) is one of the most important CCD characteristics. Our paper examines ways to optimize the algorithms used to analyze 55 Fe x-ray data on the CCDs, as well as explores new types of observables for CTE determination that can be used for testing LSST CCDs. Furthermore, the observables are modeled employing simple Monte Carlo simulations to determine how the charge diffusion in thick, fully depleted silicon affects the measurement. The data is compared to the simulations for one of the observables, integral flux of the x-ray hit.
79 ASTRONOMY AND ASTROPHYSICS↗
Understanding palladium–tellurium cluster formation on WTe2: From a kinetically hindered distribution to thermodynamically controlled monodispersity
Abstract A fundamental understanding of the transition metal dichalcogenide (TMDC)–metal interface is critical for their utilization in a broad range of applications. We investigate how the deposition of palladium (Pd), as a model metal, on WTe2(001), leads to the assembly of Pd into clusters and nanoparticles. Using X-ray photoemission spectroscopy, scanning tunneling microscopy imaging, and ab initio simulations, we find that Pd nucleation is driven by the interaction with and the availability of mobile excess tellurium (Te) leading to the formation of Pd-Te clusters at room temperature. Surprisingly, the nucleation of Pd-Te clusters is not affected by intrinsic surface defects, even at elevated temperatures. Upon annealing, the Pd-Te nanoclusters adopt an identical nanostructure and are stable up to ∼523 K. Density functional theory calculations provide a foundation for our understanding of the mobility of Pd and Te atoms, preferential nucleation of Pd-Te clusters, and the origin of their annealing-induced monodispersity. These results highlight the role the excess chalcogenide atoms may play in the metal deposition process. More broadly, the discoveries of synthetic pathways yielding thermally robust monodispersed nanostructures on TMDCs are critical to the manufacturing of novel quantum and microelectronics devices and catalytically active nano-alloy centers.
36 MATERIALS SCIENCE↗
Vorticity-induced flow-focusing leads to bubble entrainment in an inkjet printhead: Synchrotron x-ray and volume-of-fluid visualizations
The oscillatory flows present in an inkjet printhead can lead to strong deformations of the air-liquid interface at the nozzle exit. Such deformations may lead to an inward directed air jet with bubble pinch-off and the subsequent entrainment of an air bubble, which is highly detrimental to the stability of inkjet printing. Understanding the mechanisms of bubble entrainment is therefore crucial to improving print stability. Here, in the present work, we use ultrafast x-ray phase-contrast imaging and direct numerical simulations based on the volume-of-fluid method to study the mechanisms underlying the bubble entrainment in a piezoacoustic printhead. We first demonstrate good agreement between experiments and numerics. We then show the different classes of bubble pinch-off obtained in experiments, and that those were also captured numerically. The numerical results are then used to show that the baroclinic torque, which is generated at the gas-liquid interface due to the misalignment of density and pressure gradients, results in a flow-focusing effect that drives the formation of the air jet from which a bubble can pinch off.
42 ENGINEERING↗
Near, far, wherever you are: simulations on the dose efficiency of holographic and ptychographic coherent imaging
Different studies in X-ray microscopy have arrived at conflicting conclusions about the dose efficiency of imaging modes involving the recording of intensity distributions in the near (Fresnel regime) or far (Fraunhofer regime) field downstream of a specimen. A numerical study is presented on the dose efficiency of near-field holography, near-field ptychography and far-field ptychography, where ptychography involves multiple overlapping finite-sized illumination positions. Unlike what has been reported for coherent diffraction imaging, which involves recording a single far-field diffraction pattern, it is found that all three methods offer similar image quality when using the same fluence on the specimen, with far-field ptychography offering slightly better spatial resolution and a lower mean error. These results support the concept that (if the experiment and image reconstruction are done properly) the sample can be near or far; wherever you are, photon fluence on the specimen sets one limit to spatial resolution.
42 ENGINEERING↗
Synthesizing pseudo-Kossel lines from neutron transmission data. I. An analytical approach for recovering single-crystal orientation
The energy-dispersive neutron spectra transmitted through single crystals are characterized by sharp Bragg dips at specific wavelengths, where Bragg's law is being fulfilled for certain crystallographic planes. This phenomenon allows for developing methods for crystal-orientation determination techniques similar to electron backscatter diffraction and X-ray diffraction microscopy. This work presents a new procedure to recover the orientation matrix for single crystals using transmission spectra recorded during rotation of a crystal about an axis perpendicular to a polychromatic neutron beam. The proposed method consists of an initial transformation of the as-collected wavelength–rotation maps to a wavevector $\textit{K}$ space, resulting in linear pseudo-Kossel lines that are suitable for analysis and indexing using image-processing procedures. Further, simulated neutron transmission spectra through a copper crystal with known orientations were used to set and prove the numerical approach. This technique may be expanded for cases where the neutron beam intersects multiple single-crystal grains with different orientations.
36 MATERIALS SCIENCE↗
Towards Interactive, Reproducible Analytics at Scale on HPC Systems
The growth in scientific data volumes has resulted in a need to scale up processing and analysis pipelines using High Performance Computing (HPC) systems. These workflows need interactive, reproducible analytics at scale. The Jupyter platform provides core capabilities for interactivity but was not designed for HPC systems. In this paper, we outline our efforts that bring together core technologies based on the Jupyter Platform to create interactive, reproducible analytics at scale on HPC systems. Our work is grounded in a real world science use case-applying geophysical simulations and inversions for imaging the subsurface. Our core platform addresses three key areas of the scientific analysis workflow-reproducibility, scalability, and interactivity. We describe our implemention of a system, using Binder, Science Capsule, and Dask software. We demonstrate the use of this software to run our use case and interactively visualize real-Time streams of HDF5 data.
containers↗
An engineered design of a diffractive mask for high precision astrometry [Modeling a diffractive mask that calibrates optical distortions]
AutoCAD, Zemax Optic Studio 15, and Interactive Data Language (IDL) with the Proper Library are used to computationally model and test a diffractive mask (DiM) suitable for use in the Gemini Multi-Conjugate Adaptive Optics System (GeMS) on the Gemini South Telescope. Systematic errors in telescope imagery are produced when the light travels through the adaptive optics system of the telescope. DiM is a transparent, flat optic with a pattern of miniscule dots lithographically applied to it. It is added ahead of the adaptive optics system in the telescope in order to produce diffraction spots that will encode systematic errors in the optics after it. Once these errors are encoded, they can be corrected for. DiM will allow for more accurate measurements in astrometry and thus improve exoplanet detection. Furthermore, the mechanics and physical attributes of the DiM are modeled in AutoCAD. Zemax models the ray propagation of point sources of light through the telescope. IDL and Proper simulate the wavefront and image results of the telescope. Aberrations are added to the Zemax and IDL models to test how the diffraction spots from the DiM change in the final images. Based on the Zemax and IDL results, the diffraction spots are able to encode the systematic aberrations.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
MO-FG-CAMPUS-JeP1-01: Prompt Gamma Imaging with a Multi-Knife-Edge Slit Collimator: Evaluation for Use in Proton Beam Range Verification
Purpose: To evaluate and characterize a multi-slit collimated imaging system for use in prompt gamma range verification of proton therapy. Methods: Acrylic (PMMA) targets were irradiated with a 50 MeV proton beam. With the collimator placed 13 cm from the beam axis, photons of energy from 2–7 MeV were measured. Image reconstruction provided 2-dimensional distribution of gamma rays. Estimated Bragg peak location was compared with 1-dimensional profiles of photon images. Shifts in Bragg peak were simulated by physically moving the targets in 1 mm increments. Results: The imaging system measured prompt gamma emissions resulting from a 50 MeV proton beam, at currents up to 2 nA, incident on a PMMA target. Overall system detection efficiency was approximately 2.6×10{sup −5} gamma/proton. With delivery of 1×10{sup 11} protons, shifts of 1 mm in the target location were detected in 2D prompt gamma images and 1D profiles. With delivery of 1×10{sup 8} protons, shifts of approximately 3 mm were detectable. Conclusion: This work has characterized the performance of a prototype multi-slit collimated imaging system. The system can produce 2D images of prompt gamma distributions and detect shifts in Bragg peak location down to 1 mm. These results encourage further development and optimization of the system for clinical proton beam applications. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number: DENA0000979 through the Nuclear Science and Security Consortium.
60 APPLIED LIFE SCIENCES↗
TU-AB-BRC-10: Modeling of Radiotherapy Linac Source Terms Using ARCHER Monte Carlo Code: Performance Comparison of GPU and MIC Computing Accelerators
Purpose: (1) To perform phase space (PS) based source modeling for Tomotherapy and Varian TrueBeam 6 MV Linacs, (2) to examine the accuracy and performance of the ARCHER Monte Carlo code on a heterogeneous computing platform with Many Integrated Core coprocessors (MIC, aka Xeon Phi) and GPUs, and (3) to explore the software micro-optimization methods. Methods: The patient-specific source of Tomotherapy and Varian TrueBeam Linacs was modeled using the PS approach. For the helical Tomotherapy case, the PS data were calculated in our previous study (Su et al. 2014 41(7) Medical Physics). For the single-view Varian TrueBeam case, we analytically derived them from the raw patient-independent PS data in IAEA’s database, partial geometry information of the jaw and MLC as well as the fluence map. The phantom was generated from DICOM images. The Monte Carlo simulation was performed by ARCHER-MIC and GPU codes, which were benchmarked against a modified parallel DPM code. Software micro-optimization was systematically conducted, and was focused on SIMD vectorization of tight for-loops and data prefetch, with the ultimate goal of increasing 512-bit register utilization and reducing memory access latency. Results: Dose calculation was performed for two clinical cases, a Tomotherapy-based prostate cancer treatment and a TrueBeam-based left breast treatment. ARCHER was verified against the DPM code. The statistical uncertainty of the dose to the PTV was less than 1%. Using double-precision, the total wall time of the multithreaded CPU code on a X5650 CPU was 339 seconds for the Tomotherapy case and 131 seconds for the TrueBeam, while on 3 5110P MICs it was reduced to 79 and 59 seconds, respectively. The single-precision GPU code on a K40 GPU took 45 seconds for the Tomotherapy dose calculation. Conclusion: We have extended ARCHER, the MIC and GPU-based Monte Carlo dose engine to Tomotherapy and Truebeam dose calculations.
60 APPLIED LIFE SCIENCES↗
Simulation Based Inference with Domain Adaptation for Strong Gravitational Lensing
Simulation based inference leverages machine learning to carry out Bayesian inference for systems with intractable likelihoods. However, transitioning a network trained on simulated data to real data runs the risk of encountering domain shift, leading to performance losses. We attempt to implement domain adaptation into the sbi neural posterior estimation framework using the Maximum Mean Discrepancy as an additional network loss. We test two network architectures and use masked autoregressive flow for density estimation. We test the network on a set of 400,000 simulated strong gravitational lensing images generated using deeplenstronomy. The source domain is defined as low noise whereas the target domain has a noise profile sampled from experimentally derived DES survey conditions. We find that, while DA does lead to performance improvements, they are marginal at ~6% less inference error. We also find a similar marginal improvement in uncertainty calibration at around 8%.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗