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Exploring cryo-electron microscopy with molecular dynamics

Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.

Biochemistry & Molecular Biology↗

A Scalable Online Monitoring System Based on Elasticsearch for Distributed Data Acquisition in Cms

The part of the CMS Data Acquisition (DAQ) system responsible for data readout and event building is a complex network of interdependent distributed applications. To ensure successful data taking, these programs have to be constantly monitored in order to facilitate the timeliness of necessary corrections in case of any deviation from specified behaviour. A large number of diverse monitoring data samples are periodically collected from multiple sources across the network. Monitoring data are kept in memory for online operations and optionally stored on disk for post-mortem analysis. We present a generic, reusable solution based on an open source NoSQL database, Elasticsearch, which is fully compatible and non-intrusive with respect to the existing system. The motivation is to benefit from an off the-shelf software to facilitate the development, maintenance and support efforts. Elasticsearch provides failover and data redundancy capabilities as well as a programming language independent JSON-over-HTTP interface. The possibility of horizontal scaling matches the requirements of a DAQ monitoring system. The data load from all sources is balanced by redistribution over an Elasticsearch cluster that can be hosted on a computer cloud. In order to achieve the necessary robustness and to validate the scalability of the approach the above monitoring solution currently runs in parallel with an existing in-house developed DAQ monitoring system.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Performance and community structure dynamics of microbial electrolysis cells operated on multiple complex feedstocks

Microbial electrolysis is a promising technology for converting aqueous wastes into hydrogen. However, substrate adaptability is an important feature, seldom documented in microbial electrolysis cells (MECs). In addition, the correlation between substrate composition and community structure has not been well established. This study used an MEC capable of producing over 10 L/L-day of hydrogen from a switchgrass-derived bio-oil aqueous phase and investigated four additional substrates, tested in sequence on a mature biofilm. The additional substrates included a red oak-derived bio-oil aqueous phase, a corn stover fermentation product, a mixture of phenol and acetate, and acetate alone. The MECs fed with the corn stover fermentation product resulted in the highest performance among the complex feedstocks, producing an average current density of 7.3 ± 0.51 A/m 2 , although the acetate fed MECs outperformed complex substrates, producing 12.3 ± 0.01 A/m 2 . 16S rRNA gene sequencing showed that community structure and community diversity were not predictive of performance, and replicate community structures diverged despite identical inoculum and enrichment procedure. The trends in each replicate, however, were indicative of the influence of the substrates. Geobacter was the most dominant genus across most of the samples tested, but its abundance did not correlate strongly to current density. High-performance liquid chromatography (HPLC) showed that acetic acid accumulated during open circuit conditions when MECs were fed with complex feedstocks and was quickly degraded once closed circuit conditions were applied. The largest net acetic acid removal rate occurred when MECs were fed with red oak bio-oil aqueous phase, consuming 2.93 ± 0.00 g/L-day. Principal component analysis found that MEC performance metrics such as current density, hydrogen productivity, and chemical oxygen demand removal were closely correlated. Net acetic acid removal was also found to correlate with performance. However, no bacterial genus appeared to correlated to these performance metrics strongly, and the analysis suggested that less than 70% of the variance was accounted for by the two components. This study demonstrates the robustness of microbial communities to adapt to a range of feedstocks and conditions without relying on specific species, delivering high hydrogen productivities despite differences in community structure. The results indicate that functional adaptation may play a larger role in performance than community composition. Further investigation of the roles each microbe plays in these communities will help MECs to become integral in the 21st-century bioeconomy to produce zero-emission fuels.

09 BIOMASS FUELS↗

Advances in bone preservation: Identifying possible collagen preservation using sulfur speciation mapping

The complexity and heterogeneity of bone chemistry makes it difficult to discern information on physiological and taphonomic processes stored within the bone matrix. Analysis of archaeological and palaeontological bone becomes more difficult because in many cases the most pivotal specimens are too scientifically valuable for destructive analysis. Here, this problem is further escalated by the fact that the heterogeneity of the bone may cause small “pockets” of preservation that can be missed during sampling. Therefore, a non-destructive technique that can spatially resolve such heterogeneity within the bone is needed.

36 MATERIALS SCIENCE↗

Investigating Kinetic Mechanisms of Soot Formation in Plasma Pyrolysis of Methane via Active Learning (Final Technical Report)

Plasma pyrolysis of methane is an effective route for zero-carbon hydrogen production. Yet, soot generated from pyrolysis of hydrocarbons is detrimental to the climate and human health. There is ample experimental and theoretical evidence that suggests polycyclic aromatic hydrocarbons (PAHs) are the molecular precursors to soot particles. The reaction pathways of PAH formation are intricately dependent on a multitude of process parameters, whose kinetic mechanisms are not well-understood in plasma pyrolysis. This project aims to leverage advances in the kinetic modeling of soot formation in combustion, as well as in surrogate modeling and active learning, to systematically investigate the effects of process parameter on the kinetics of PAH formation in plasma pyrolysis of methane. To this end, we propose to use the PAH formation kinetics model developed by the PPPL/PU group based on the well-established ABF and HACA mechanisms, coupled with low-temperature plasma models. We will develop an active learning (AL) framework based on Bayesian optimization to systematically and data-efficiently explore the complex and multivariable parameter space of plasma pyrolysis in order to quantify the effects of plasma and feed parameters on the ABF and HACA kinetic pathways. AL is the branch of machine learning concerned with systematically querying samples from a system (experimental or computational) to train a data-driven model that maps design parameters to a performance criterion. We will use the data generated via AL to perform global sensitivity analysis, combined with uncertainty quantification, to elucidate the impact of different reaction pathways on minimizing formation of soot precursors. This study will result in an improved understanding of kinetics of PAH formation in plasma pyrolysis and can pave the way for more advanced mechanistic studies (e.g., soot nucleation mechanisms). Additionally, the findings will be useful for establishing practical strategies for increasing the pyrolysis efficiency and producing high-grade carbon for synthesis of nanomaterials.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level

For Diels–Alder (DA) reactions in solution, an accurate and converged free energy (FE) surface at ab initio (ai) quantum mechanical/molecular mechanical (QM/MM) level is imperative for the understanding of reaction mechanism. However, this computation is still far too expensive. In a previous work, we proposed a new method termed MBAR+wTP, with which the computation of the ai FE profile can be accelerated by several orders of magnitude via a three-step procedure: (I) an umbrella sampling (US) using a semi-empirical (SE) QM/MM Hamiltonian is performed; (II) the FE profile is generated using the Multistate Bennett Acceptance Ratio (MBAR) analysis; and (III) a weighted Thermodynamic Perturbation (wTP) from the SE Hamiltonian to the ai Hamiltonian is performed to obtain the ai QM/MM FE profile using weight factors from the MBAR analysis. In this work, this method is extended to the calculations of two-dimensional FE surfaces of two Diels–Alder reactions of cyclopentadiene with either acrylonitrile or 1-4-naphthoquinone at ai QM/MM level. The accurate activation free energies at the ai QM/MM level, which are much closer to the experimental measurements than those calculated by other methods, indicate that this MBAR+wTP method can be applied in the studies of complex reactions in condensed phase with much-enhanced efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Alcock-Paczynski Blinding Scheme for the Ly-$α$ Forest Analysis

We present and validate a blinding method for the Lyman-$α$ (Ly$α$) forest analysis based on a modification of the Alcock-Paczynski test. In order to hide the background expansion history, the method employs a geometrical shift of each quasar (QSO) forest in wavelength space, once the quasar continuum has been fitted and the fluctuation field is extracted. The redshift positions for the QSO sample are also changed in a consistent manner. We show that the method remains effective when applied to real data, where contamination from metals and Lyman-$β$ is intrinsically mixed with the Lyman-$α$ forest. This limitation is primarily visible in the 1D correlation function, where other blinding strategies can mitigate the effect. To assess its effectiveness, the prescription is tested against a series of datasets of increasing complexity: from idealized low-noise mocks, to realistic DESI year one synthetic datasets, and finally to data from DESI first data release (DR1), using both the auto (Ly$α\times$Ly$α$) and cross (Ly$α\times$ QSO) correlations. We find that the method robustly shifts the BAO peak position from the 3D correlation functions to the expected value for cosmology changes of around 5% in the matter content, without altering the shape of the posteriors in the model parameters. In conclusion, this catalog-level blinding strategy is a viable method for cosmological inference with the Lyman-$α$ forest, particularly if a cross-analysis with other tracers using the same blinding strategy is pursued.

Perez-Sanchez, G. [Guanajuato U.] (ORCID:000900096↗

Observational Study of Clogging Specimens from the Tundish Well Showing Origin and Growth of a Clog in an Al-Killed Ti-Alloyed Steel Cast

Post-mortem tundish skull samples of Ti-alloyed, Al-killed IF steel have been studied regarding the formation of clogging. By using modern characterization equipment and applied methods, we performed a detailed characterization of microstructures found in the tundish well. Aside from the primary metallographic examination, newly developed methods of particle size distribution analysis based on population density functions (PDF) and newly developed electron microscope EDS template mapping have been applied, allowing differentiation of complex particles according to phases and interphase contact relationships. Furthermore, detailed EDS analyses of individual inclusions with complex substructure regarding minor and trace elements within the alumina networks have been performed. These composite data on carefully selected clog microstructures allowed us to observe the presence of layering microstructures throughout the clog: “Coarse” layers (abundant microbubbles and internally complex alumina aggregates) and “Fine” layers (no microbubbles and complex alumina aggregates). Two populations of particles: Population I (2 to 5 µm) and a Population II (5 to 20 µm) build up the layers, both having lognormal PDF, in contrast to power-law PDF of secondary metallurgy inclusions. Coarse layers are further distinguished by selective concentrations of spinel with lognormal PDF as well as the occurrence of complex alumina particles with metal sub-inclusions often with elevated Cr, V, and Si content. Based on these observations, we derive a model for the origin and accumulation of the inclusions making up the clog, which suggests that the NMI of the two dominant populations do not come from the bulk steel, although secondary metallurgy-derived inclusions can be traced in the clog. Overall, microstructures show that the clog behaves as a coherent solid, and is able to displace and fracture.

36 MATERIALS SCIENCE↗

Determining Optimal Magnetometer Configuration on MAGIS-100

Long-baseline atom interferometers such as the Matter-wave Atomic Gradiometer Interferometric Sensor (MAGIS-100) require stringent control and continuous characterization of background magnetic fields and spatial gradients to prevent systemic phase shifts that mimic ultralight dark matter or gravitational wave signatures. Because direct sensor placement within the ultra-high vacuum beam pipe is infeasible, in-situ magnetic field monitoring relies on external sensor arrays situated in the surrounding annular region. This work demonstrates a field reconstruction framework for a 5.3-meter MAGIS-100 modular section using finite-element Opera simulations. Transverse magnetic fields are expanded using a cylindrical multipole framework as informed by Fermilab’s Muon g-2 experiment, with magnetometer array configurations optimized via Fisher information matrix D-optimality. Inverting external sensor readings through a Gauss-Newton scheme recovers interior tube fields across distinct axial positions. In the discontinuity-averse uniform region (slice pair P4), the model achieves sub-noise-floor performance with a cross-validated root-mean-square error (RMSE) of $6.7227 \times 10^{-4}\text{ A/m}$ ($0.845\times$ sensor noise floor) and an interior field coefficient of variation of $1.71\%$. An elbow criterion in the Fisher bounds establishes $n_{\text{max}} = 2$ as the optimal multipole truncation order to prevent noise amplification from over-parameterization, with $n_{\text{max}} = 3$ (sextupole) order chosen for analysis to demonstrate further complexity and cross-pair comparison. Furthermore, analytical differentiation of the fitted multipole coefficients yields dense spatial maps of the transverse Jacobian gradient matrix $\nabla \mathbf{H}$ along with propagated $1\sigma$ uncertainty bounds across the beam region ($r \le 2.75\text{ in}$). This operational framework confirms that external magnetometer arrays can reliably monitor magnetic field uniformity and spatial gradients along the 100-meter flight path given appropriate sampling for any complexity order.

Appleby, Darwin [William Rainey Harper Coll.] (ORC↗

Determining Optimal Magnetometer Configuration on MAGIS-100

Long-baseline atom interferometers such as the Matter-wave Atomic Gradiometer Interferometric Sensor (MAGIS-100) require stringent control and continuous characterization of background magnetic fields and spatial gradients to prevent systemic phase shifts that mimic ultralight dark matter or gravitational wave signatures. Because direct sensor placement within the ultra-high vacuum beam pipe is infeasible, in-situ magnetic field monitoring relies on external sensor arrays situated in the surrounding annular region. This work demonstrates a field reconstruction framework for a 5.3-meter MAGIS-100 modular section using finite-element Opera simulations. Transverse magnetic fields are expanded using a cylindrical multipole framework as informed by Fermilab’s Muon g-2 experiment, with magnetometer array configurations optimized via Fisher information matrix D-optimality. Inverting external sensor readings through a Gauss-Newton scheme recovers interior tube fields across distinct axial positions. In the discontinuity-averse uniform region (slice pair P4), the model achieves sub-noise-floor performance with a cross-validated root-mean-square error (RMSE) of $6.7227 \times 10^{-4}\text{ A/m}$ ($0.845\times$ sensor noise floor) and an interior field coefficient of variation of $1.71\%$. An elbow criterion in the Fisher bounds establishes $n_{\text{max}} = 2$ as the optimal multipole truncation order to prevent noise amplification from over-parameterization, with $n_{\text{max}} = 3$ (sextupole) order chosen for analysis to demonstrate further complexity and cross-pair comparison. Furthermore, analytical differentiation of the fitted multipole coefficients yields dense spatial maps of the transverse Jacobian gradient matrix $\nabla \mathbf{H}$ along with propagated $1\sigma$ uncertainty bounds across the beam region ($r \le 2.75\text{ in}$). This operational framework confirms that external magnetometer arrays can reliably monitor magnetic field uniformity and spatial gradients along the 100-meter flight path given appropriate sampling for any complexity order.

Appleby, Darwin [William Rainey Harper Coll.] (ORC↗

Effect of Collimation on Diffraction Signal-to-Background Ratios at a Neutron Diffractometer

High diffraction signal-to-background ratios (SBRs), the ratios of diffraction peak integrated intensity over its background intensity, are desired for a neutron diffractometer to acquire good statistics for diffraction pattern measurements and subsequent data analysis. For a given detector, while the diffraction peak signals primarily depend on the characteristics of neutron beam and sample coherent scattering, the background largely originates from the sample incoherent scattering and the scattering from the instrument space. In this work, we investigated the effect of collimation on neutron diffraction SBRs of Si powder measurements using one high-angle area detector bank coupled with six different collimation configurations in a large and complex instrument space at the engineering materials diffractometer VULCAN, SNS, ORNL. The results revealed that the diffraction SBRs can be significantly improved by a proper coarse collimator that leaves no gap between the detector and the collimator, and the improvement of SBRs by a fine radial collimator was remarkable with a proper coarse collimator in place but not distinguishable without one. It was also found that the diffraction SBRs were not effectively improved by adding neutron absorbing element boron to the fine radial collimator body, which indicates that either the absorption of secondary scattered neutrons by the added boron is insignificant or the collimator base material (resin and ABS) alone attenuates background scattering sufficiently. These findings could serve as a useful reference for diffractometer developers and/or operators to optimize their collimation to achieve higher diffraction SBRs.

Yu, Dunji↗

A Perspective on the Milky Way Bulge Bar as Seen from the Neutron-capture Elements Cerium and Neodymium with APOGEE

Abstract This study probes the chemical abundances of the neutron-capture elements cerium and neodymium in the inner Milky Way from an analysis of a sample of ∼2000 stars in the Galactic bulge bar spatially contained within ∣X Gal ∣ < 5 kpc, ∣Y Gal ∣ < 3.5 kpc, and ∣Z Gal ∣ < 1 kpc, and spanning metallicities between −2.0 ≲ [Fe/H] ≲ +0.5. We classify the sample stars into low- or high-[Mg/Fe] populations and find that, in general, values of [Ce/Fe] and [Nd/Fe] increase as the metallicity decreases for the low- and high-[Mg/Fe] populations. Ce abundances show a more complex variation across the metallicity range of our bulge-bar sample when compared to Nd, with ther-process dominating the production of neutron-capture elements in the high-[Mg/Fe] population ([Ce/Nd] < 0.0). We find a spatial chemical dependence of Ce and Nd abundances for our sample of bulge-bar stars, with low- and high-[Mg/Fe] populations displaying a distinct abundance distribution. In the region close to the center of the MW, the low-[Mg/Fe] population is dominated by stars with low [Ce/Fe], [Ce/Mg], [Nd/Mg], [Nd/Fe], and [Ce/Nd] ratios. The low [Ce/Nd] ratio indicates a significant contribution in this central region fromr-process yields for the low-[Mg/Fe] population. The chemical pattern of the most metal-poor stars in our sample suggests an early chemical enrichment of the bulge dominated by yields from core-collapse supernovae andr-process astrophysical sites, such as magnetorotational supernovae.

Astronomy & Astrophysics↗

In-Situ Magnetic Field Reconstruction in the MAGIS-100 Experiment

Long-baseline atom interferometers such as the Matter-wave Atomic Gradiometer Interferometric Sensor (MAGIS-100) require stringent control and continuous characterization of background magnetic fields and spatial gradients to prevent systemic phase shifts that mimic ultralight dark matter or gravitational wave signatures. Because direct sensor placement within the ultra-high vacuum beam pipe is infeasible, in-situ magnetic field monitoring relies on external sensor arrays situated in the surrounding annular region. This work demonstrates a field reconstruction framework for a 5.3-meter MAGIS-100 modular section using finite-element Opera simulations. Transverse magnetic fields are expanded using a cylindrical multipole framework as informed by Fermilab’s Muon g-2 experiment, with magnetometer array configurations optimized via Fisher information matrix D-optimality. Inverting external sensor readings through a Gauss-Newton scheme recovers interior tube fields across distinct axial positions. In the discontinuity-averse uniform region (slice pair P4), the model achieves sub-noise-floor performance with a cross-validated root-mean-square error (RMSE) of $6.7227 \times 10^{-4}\text{ A/m}$ ($0.845\times$ sensor noise floor) and an interior field coefficient of variation of $1.71\%$. An elbow criterion in the Fisher bounds establishes $n_{\text{max}} = 2$ as the optimal multipole truncation order to prevent noise amplification from over-parameterization, with $n_{\text{max}} = 3$ (sextupole) order chosen for analysis to demonstrate further complexity and cross-pair comparison. Furthermore, analytical differentiation of the fitted multipole coefficients yields dense spatial maps of the transverse Jacobian gradient matrix $\nabla \mathbf{H}$ along with propagated $1\sigma$ uncertainty bounds across the beam region ($r \le 2.75\text{ in}$). This operational framework confirms that external magnetometer arrays can reliably monitor magnetic field uniformity and spatial gradients along the 100-meter flight path given appropriate sampling for any complexity order.

Appleby, Darwin [William Rainey Harper Coll.; Ferm↗

Wabash CarbonSAFE Subtask 7.1 – Pre-drilling Site Assessment Topical Report: DOE-FE0031626-1

The Wabash CarbonSAFE project will drill a stratigraphic test well at the Wabash Valley Resources facility near Terre Haute, Indiana. Lithologic, geomechanical, and geophysical data collected from samples testing and an extensive geophysical logging suite will be used to determine the feasibility for the geologic sequestration of 50 million metric tons or more of injected carbon dioxide. The primary target reservoir and caprock to be investigated for the Wabash CarbonSAFE project are the Mt. Simon Sandstone and Eau Claire Shale, respectively. The project team has assessed the planned Wabash #1 drilling site using subsurface geologic data and analyses from both Illinois and Indiana. These data were used to generate geologic structure and isopach thickness maps for target reservoir and caprock layers which were incorporated into a detailed discussion of the nature of the Illinois Basin’s Cambro-Ordovician carbon dioxide storage complex at the drilling site. Formation tops were prognosed for 19 lithologic units to aid drilling and coring procedures. Additional GIS analysis indicates that no known structural features will negatively impact the target storage reservoir or caprock, nor will protected and sensitive areas, groundwater resources, or existing resource development be negatively affected by Wabash #1 drilling activities. The Wabash #1 Geologic/Structure Test well drilling permit was awarded by Indiana Department of Natural Resources (IN-DNR) – Division of Oil and Gas on November 12th, 2019, and the well is expected to be drilled to a total depth of approximately 8,350 feet. Potential impacts on drilling progress include abandoned underground coal mines which mined the Springfield and Survant coals until 1964 and 1954, respectively, and a lost circulation zone in the Potosi Dolomite, which has been demonstrated to have intermittent cavernous porosity from karstification. This document also details the coring and sampling program, proposed logging suite, and well testing program, all of which will be dynamically reviewed as drilling progresses.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Eocene-Oligocene Metamorphism, Fluid Flow and Deformation in the Ruby Mountains-East Humboldt Range Metamorphic Core Complex

Metamorphic core complexes are ubiquitous in collapsed orogens globally and play a primary role in crustal exhumation. Here, we investigate the metamorphic history of the Ruby Mountains-East Humboldt Range metamorphic core complex, Nevada, using petrochronology to understand how magmatism, metamorphism and deformation interact to modulate crustal rheology, and the timing of exhumation within the Sevier orogenic belt. Field study, microstructural analysis, thermobarometry and laser ablation split-stream monazite, titanite and allanite petrochronology of the mylonitic footwall were integrated to elucidate the pressure-temperature-time (P-T-t) evolution. Major-, trace-element and quartz-in-garnet thermobarometry show peak metamorphism occurred at 5.5–6 kbar and 600–650°C across the study area. Monazite and titanite U-(Th)-Pb petrochronology constrain this episode of metamorphism to 88–81 Ma with the structurally deepest samples yielding dates down to ca. 71 Ma. The preservation of peak metamorphic mineral assemblages indicates these rocks remained at near-peak temperature conditions into the Cenozoic. Cenozoic metamorphism occurred during a punctuated episode contemporaneous with the Great Basin ignimbrite flare up. All samples show a distinct 39–37 Ma population of monazite, titanite and allanite dates that correlate with the emplacement of quartz diorite and gabbro intrusions throughout the footwall. Accessory phases contain zoning textures in backscattered electron images that are consistent with fluid-mediated dissolution-reprecipitation reactions. The U-(Th)-Pb analyses from these zones yield 39–27 Ma dates interpreted as the timing of fluid flow. The results of this study elucidate the integrated importance of magmatism, melting and fluid flow in driving the coupled evolution of Late Cretaceous metamorphism within the Sevier hinterland and the subsequent Cenozoic metamorphic core complex development that exhumed the middle crust.

58 GEOSCIENCES↗

Improved Infrared Optical Constants from Pressed Pellets: II. Ellipsometric n and k Values for Ammonium Sulfate with Variability Analysis

Infrared spectral imaging is facilitated via the comparison of spectra recorded in situ to a databank of actual or synthetic infrared reflectance spectra. It has recently been shown that reference spectra corresponding to the many different morphological forms of the same chemical can be generated synthetically using the imaginary, k, and real, n, components of the complex refractive index, n~ = n + ik. One method to obtain the n and k vectors is infrared ellipsometry, which measures the changes in amplitude, tan ?, and phase, ?, of polarized light reflected from the sample both as a function of wavenumber and angle of incidence. The method requires specularly reflected light so best results are usually obtained with polished planar samples of large surface area. Due to the difficulties of obtaining such samples, however, we investigate the possibility of pressing powders of neat materials and obtaining the corresponding optical constants from the pellets. In this paper, variability in the sample pellet and preparation method is investigated, as is variability in the fitting procedure for the derived optical constants. The n/k vectors are derived from the measured ellipsometric parameters, tan ? and ?, as they are fit by an oscillator model which yield n(?) and k(?) vectors as a function of wavenumber, ?. Construction of the oscillator model is not automatic and depends on significant input from the analyst as well as the sample’s physical characteristics. For the pellet pressing, the experimental variability was found to be minimized for size-selected powdered samples as gauged by the minimal variance in ? and ? for three different pellets; similarly, the analytical precision for multiple measurements of the same pellet was also quite good, suggesting that a pressed pellet is a viable sample preparation method. The greatest variability came in the analytic fitting procedure with differences up to 20% arising from four different fits to the same data set. The final ellipsometric n/k data are compared to literature values obtained from crystalline (NH4)2SO4 samples as well as single-angle reflectance measurements that also used pressed pellets. Comparison with the previous literature values shows generally good agreement although higher k-values are observed for the independent sets of data derived from pressed pellets. These data are suggested as an improved set of optical constants for (NH4)2SO4.

optical constants, ellipsometry, ammonium sulfate,↗

Probing Light Atoms at Subnanometer Resolution: Realization of Scanning Transmission Electron Microscope Holography

Atomic resolution imaging of light elements in electron-transparent materials has long been a challenge. Biomolecular materials, for example, are rapidly altered by incident electrons. We demonstrate a scanning transmission electron microscopy (STEM) technique, called STEM holography, capable of efficient structural analysis of beam-sensitive nanomaterials. STEM holography measures the absolute phase and amplitude of electrons passed through a specimen via interference with a vacuum reference wave. We use an amplitude-dividing nanofabricated grating to prepare multiple beams focused at the sample. We configure the postspecimen microscope imaging system to overlap the beams, forming an interference pattern. We record and analyze the pattern at each 2D-raster-scan-position, reconstructing the complex object wave. As a demonstration, we image gold nanoparticles on an amorphous carbon substrate at 2.4 Å resolution. In conclusion STEM holography offers higher contrast of the carbon while maintaining gold atomic lattice resolution compared to high angle annular dark field STEM.

4D-STEM↗