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At least 847 records · Page 47

CuXASNet: Rapid and accurate prediction of copper L-edge x-ray absorption spectra using machine learning

In this work, we have developed CuXASNet, a dense neural network that predicts simulated Cu -edge x-ray absorption spectra (XAS) from atomic structures. Featurization of the Cu local environment is performed using a component of M3GNet, a graph neural network developed for predicting the potential energy surface. CuXASNet is trained on simulated spectra from FEFF9 at the multiple scattering level of theory, and can predict the and edges for Cu sites to quantitative accuracy. To validate our approach, we compare 14 experimental spectra extracted from the literature with the predictions of CuXASNet. The agreement of CuXASNet with experiments is shown by an average mean absolute error of 0.125 and an average Spearman's correlation coefficient of 0.891, which is comparable to FEFF9's values of 0.131 and 0.898 for the same metrics. As such, CuXASNet can rapidly predict a large number of -edge XAS spectra at the same accuracy as FEFF9 simulations. This can be used as a drop-in replacement for multiple scattering codes for fast screening of candidate atomic structure models of a measured system. This model establishes a general framework for Cu XAS prediction, and can be extended to more computationally expensive levels of theory and to other transition metal edges.

36 MATERIALS SCIENCE↗

Structural basis for PECAM-1 homophilic binding

Platelet endothelial cell adhesion molecule-1 (PECAM-1) is a 130-kDa member of the immunoglobulin gene superfamily (IgSF) that is present on the surface of circulating platelets and leukocytes, and highly expressed at the junctions of confluent endothelial cell monolayers. PECAM-1–mediated homophilic interactions, known to be mediated by its 2 amino-terminal immunoglobulin homology domains, are essential for concentrating PECAM-1 at endothelial cell intercellular junctions, where it functions to facilitate diapedesis, maintain vascular integrity, and transmit survival signals into the cell. Given the importance of PECAM-1–mediated homophilic interactions in mediating each of these cell physiological events, and to reveal the nature and orientation of the PECAM-1–PECAM-1 homophilic-binding interface, we undertook studies aimed at determining the crystal structure of the PECAM-1 homophilic-binding domain, which is composed of amino-terminal immunoglobulin homology domains 1 and 2 (IgD1 and IgD2). The crystal structure revealed that both IgD1 and IgD2 exhibit a classical IgSF fold, having a β-sandwich topology formed by 2 sheets of antiparallel β strands stabilized by the hallmark disulfide bond between the B and F strands. Interestingly, despite previous assignment to the C2 class of immunoglobulin-like domains, the structure of IgD1 reveals that it actually belongs to the I2 set of IgSF folds. Both IgD1 and IgD2 participate importantly in the formation of the trans homophilic-binding interface, with a total buried interface area of >2300 Å 2 . These and other unique structural features of PECAM-1 allow for the development of an atomic-level model of the interactions that PECAM-1 forms during assembly of endothelial cell intercellular junctions.

59 BASIC BIOLOGICAL SCIENCES↗

Leiomodin creates a leaky cap at the pointed end of actin-thin filaments

Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a “swinging gate” allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.

2D-NMR↗

Multilevel summation methods for efficient evaluation of long-range pairwise interactions in atomistic and coarse-grained molecular simulation.

The availability of efficient algorithms for long-range pairwise interactions is central to the success of numerous applications, ranging in scale from atomic-level modeling of materials to astrophysics. This report focuses on the implementation and analysis of the multilevel summation method for approximating long-range pairwise interactions. The computational cost of the multilevel summation method is proportional to the number of particles, N, which is an improvement over FFTbased methods who s cost is asymptotically proportional to N logN. In addition to approximating electrostatic forces, the multilevel summation method can be use to efficiently approximate convolutions with long-range kernels. As an application, we apply the multilevel summation method to a discretized integral equation formulation of the regularized generalized Poisson equation. Numerical results are presented using an implementation of the multilevel summation method in the LAMMPS software package. Preliminary results show that the computational cost of the method scales as expected, but there is still a need for further optimization.

Bond, Stephen D.↗

Molecular Dynamics-based Simulations of Bulk/Interfacial Structures and Diffusion Behaviors in Nuclear Waste Glasses

This NEUP Project aimed to generate accurate atomic structural models of nuclear waste glasses by using large-scale molecular dynamics-based computer simulations and to use these models to investigate self-diffusion behaviors, interfacial structures, and hydrated gel structures formed during dissolution of these glasses. The goal was to obtain realistic and accurate short and medium range structures of these complex oxide glasses, to provide a mechanistic understanding of the dissolution behaviors, and to generate reliable information with predictive power in designing nuclear waste glasses for long-term geological storage. Looking back of the research accomplishments of this project, most of the scientific goals initially proposed have been achieved through intensive research in the three and a half year period of the project. This project has also generated a wealth of scientific data and vibrant discussions with various groups through collaborations within and outside of this project. Throughout the project one book chapter and 14 peer reviewed journal publications have been generated (including one under review) and 16 presentations (including 8 invited talks) have been made to disseminate the results of this project in national and international conference. Furthermore, this project has trained several outstanding graduate students and young researchers for future workforce in nuclear related field, especially on nuclear waste immobilization. One postdoc and four PhD students have been fully or partially supported through the project with intensive training in the field material science and engineering with expertise on glass science and nuclear waste disposal

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Radiation Tolerance and Mechanical Properties of Nanostructured Amorphous-Ceramic/Metal Composites

The objective of this work was to use a radically non-traditional approach to design amorphous-ceramic/metal composites for service in extreme irradiation environments. The project was built on a strong integration among four research teams for materials synthesis and characterization, ion irradiation, mechanical evaluation, and atomic scale modeling. Rather than try to prevent microstructure changes in polycrystalline aggregates, the research team worked to evolve composite systems where one of the constituents is intentionally synthesized in a non-crystalline or “amorphous” state. Because amorphous materials possess no translational symmetry, such alloys do not contain conventional crystal defects such as vacancies, interstitials, or dislocations. These materials offer the possibility of eliminating the root cause responsible for radiation damage in polycrystalline solids - namely the production of point defects and clusters thereof in collision cascades - and could serve as the basis for developing a new class of structural materials with unprecedented resistance to radiation. The amorphous alloys were used to develop advanced amorphous-ceramic/metal composites with greatly improved radiation tolerance and stability above 500oC, and improved mechanical performance by combining the good properties of amorphous materials (high strength and elastic limit) with those of crystalline materials (high toughness, strain hardening). The ceramic component of the composite consisted of a high crystallization temperature and radiation tolerant amorphous alloy composed of Si-O-C, silicon oxycarbide, while the metal layer was Fe and Fe(Cr), chosen to serve as model materials for steel. A prime hypothesis that drove this work is that the composite interface, together with the composite constituents, would provide significantly enhanced radiation tolerance, similar to or superior to those observed in metallic nanolayered structures, in a more engineering relevant material system. As our experimental data and modeling show, we have successfully developed a new class of ceramic/metal composites that can be adapted for engineering applications, thus significantly impacting improved materials performance for advanced nuclear reactors.

36 MATERIALS SCIENCE↗

Advanced Microscopy and Spectroscopy for Probing and Optimizing Electrode-Electrolyte Interphases in High Energy Lithium Batteries (Final Scientific/Technical Report)

The earliest developed LiCoO 2 layered oxide cathode material sparked the development of other layered cathode materials, dominating the positive electrode materials for lithium ion batteries. Within the practical operating conditions of today, the current generation layered oxide materials do not meet the future energy storage demands of 350 Wh kg -1 at cell level. Li-rich layered oxide (LRLO) materials have the potential to meet the high energy demands. Unlike the classical layered oxides, LRLO materials exhibit capacities that go beyond conventional topotactic mechanistic theoretical values. Despite its high capacities, this material has several challenges (voltage fading, structural instability, sluggish kinetics, cathode electrolyte interphase instability, etc.) that must be overcome in order to reach commercialization. In the past five years, our research group has made great progress on developing advanced characterization techniques coupled with atomic scale modeling to properly characterize the dynamic phenomena that govern the performance limitations of LRLO materials. Furthermore, our efforts have guided the material synthesis and surface modification to improve capacity retention. By carefully controlling the oxygen activities through the creation of uniform oxygen vacancies, we were able to avoid structural decomposition in LRLO. Our materials deliver a discharge capacity as high as 306 mAh g -1 with an initial coulombic efficiency of 90.6%. Furthermore, they do not exhibit obvious capacity decay with a reversible capacity over 300 mAh g -1 after 100 cycles at 0.1 C-rate. Our approach demonstrates the critical needs for advanced diagnosis and characterization. It is through the in-depth understanding of these high voltage cathode materials at atomistic and molecular level and their dynamic changes during the operation of batteries; we can successfully formulate strategies to further optimize this class of cathode materials, especially for the voltage instabilities. The diagnostic tools developed here can also be leveraged to study anode materials such as Li metal anode. The challenge of probing Li metal is the low dose tolerance (high beam sensitivity) of Li metal. We will have to apply cryogenic method (low-temperature) and low-dose electron microscopy and specialized camera to enable the characterization of the lithium metal.

25 ENERGY STORAGE↗

Direct Measurement of Mass-Temperature Distributions in the Core of Implosions on the National Ignition Facility (Full Technical Final Report)

Inertial confinement fusion plasmas are characterized by several kilo-electron-volt (keV) electron temperatures and ion and electron densities approaching 100 to 1000 times solid. In these implosions which simulate the dynamics of our sun, spectroscopic dopants can lead to detailed exploration of the plasma gradients that are not possible in other places. This is both in the central core pressure and temperature as well as any “mix” resultant from ablation and hydrodynamic interactions. This work will show new Bayesian atomic physics models applied to ICF plasmas to give both the temperature and density of the internal hot spot to better describe the physical nature of these implosions along with trying to spatially resolve the mix coming from the ablator region. The mission impact is to demonstrate this effect and to lead to a more quantitative description of mix in inertial confinement plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Physics-based Multiscale Additively Manufactured Superalloy Design for Optimized High Cycle Fatigue Life (Final Report)

The objectives of this project are to: (i) Gain fundamental understandings towards the microscopic damage mechanisms, as impacted by pertinent materials properties (e.g. stacking fault energy (SFE) and microstructure (e.g., grain size), leading to high-cycle fatigue (HCF) damage to AM Ni-based superalloy parts; (ii) Provide scientific insight into the effect of testing frequency on damage mechanisms and fatigue life of AM Ni-based superalloy parts under HCF regime, thereby establishing an appropriate correlation between accelerated testing and materials’ true service life; (iii) Devise an accurate, experimentally validated multiscale model across atomic, micro- and meso-scales, to predict the cyclic stress-strain responses and fatigue damage accumulation for AM Ni-based superalloys under various loading frequencies.

36 MATERIALS SCIENCE↗

Overview of NETL’s Low Temperature CO2 Electrolysis Research

This keynote lecture will briefly overview diverse research areas of National Energy Technology Laboratory (NETL) to advance energy and environmental sustainability along with carbon management. Our electrochemistry efforts on carbon conversion directly support the US goal of achieving carbon-free power sector by 2035 and net zero emissions by 2050. Since CO2 electroreduction is highly structure-sensitive, NETL ongoing research has been focused on the rational design and engineering of electrocatalysts to facilitate the CO2 conversion to desirable products with good selectivity, activity, and durability. Different classes and types of electrocatalytic materials will be covered in this talk, from well-defined atomic-scale model catalysts to heterogenous, scalable powder systems at nano- and micro-scale for “real world” performance evaluation. Several spectroscopic, microscopic, and electrochemical characterization techniques along with computational findings will be additionally discussed to gain more insights into the structure-activity relation. The last part of this seminar will provide more detail on how NETL has transitioned from the most common aqueous H-type reactor for lab-scale validation to more realistic full electrolyzer cell in bench-scale prototype. The knowledge, electrocatalytic materials, and device validation achieved from NETL in-house research will be translated to industrial sector for large scale deployment and the anticipated outcome will help advance the development of low temperature CO2 electrolysis technologies.

Nguyen Phan, Thuy Duong↗

A search for O{sub 2} in co-depleted molecular cloud cores with Herschel

The general lack of molecular oxygen in molecular clouds is an outstanding problem in astrochemistry. Extensive searches with the Submillimeter Astronomical Satellite, Odin, and Herschel have only produced two detections; upper limits to the O{sub 2} abundance in the remaining sources observed are about 1000 times lower than predicted by chemical models. Previous atomic oxygen observations and inferences from observations of other molecules indicated that high abundances of O atoms might be present in dense cores exhibiting large amounts of CO depletion. Theoretical arguments concerning the oxygen gas–grain interaction in cold dense cores suggested that, if O atoms could survive in the gas after most of the rest of the heavy molecular material has frozen out onto dust, then O{sub 2} could be formed efficiently in the gas. Using Herschel HIFI, we searched a small sample of four depletion cores—L1544, L694-2, L429, and Oph D—for emission in the low excitation O{sub 2} N {sub J} = 3{sub 3}–1{sub 2} line at 487.249 GHz. Molecular oxygen was not detected and we derive upper limits to its abundance in the range of N(O{sub 2})/N(H{sub 2}) ≈ (0.6--1.6) × 10{sup −7}. We discuss the absence of O{sub 2} in the light of recent laboratory and observational studies.

79 ASTRONOMY AND ASTROPHYSICS↗

ZEEMAN DOPPLER MAPS: ALWAYS UNIQUE, NEVER SPURIOUS?

Numerical models of atomic diffusion in magnetic atmospheres of ApBp stars predict abundance structures that differ from the empirical maps derived with (Zeeman) Doppler mapping (ZDM). An in-depth analysis of this apparent disagreement investigates the detectability by means of ZDM of a variety of abundance structures, including (warped) rings predicted by theory, but also complex spot-like structures. Even when spectra of high signal-to-noise ratio are available, it can prove difficult or altogether impossible to correctly recover shapes, positions, and abundances of a mere handful of spots, notwithstanding the use of all four Stokes parameters and an exactly known field geometry; the recovery of (warped) rings can be equally challenging. Inversions of complex abundance maps that are based on just one or two spectral lines usually permit multiple solutions. It turns out that it can by no means be guaranteed that any of the regularization functions in general use for ZDM (maximum entropy or Tikhonov) will lead to a true abundance map instead of some spurious one. Attention is drawn to the need for a study that would elucidate the relation between the stratified, field-dependent abundance structures predicted by diffusion theory on the one hand, and empirical maps obtained by means of “canonical” ZDM, i.e., with mean atmospheres and unstratified abundances, on the other hand. Finally, we point out difficulties arising from the three-dimensional nature of the atomic diffusion process in magnetic ApBp star atmospheres.

79 ASTRONOMY AND ASTROPHYSICS↗

H β and H γ Absorption-line Profile Inconsistencies in Laboratory Experiments Performed at White Dwarf Photosphere Conditions

The spectroscopic method relies on hydrogen Balmer absorption lines to infer white dwarf (WD) masses. These masses depend on the choice of atmosphere model, hydrogen atomic line shape calculation, and which Balmer series members are included in the spectral fit. In addition to those variables, spectroscopic masses disagree with those derived using other methods. Here we present laboratory experiments aimed at investigating the main component of the spectroscopic method: hydrogen line shape calculations. These experiments use X-rays from Sandia National Laboratories’ Z-machine to create a uniform ~15 cm 3 hydrogen plasma and a ~4 eV backlighter that enables recording high-quality absorption spectra. The large plasma, volumetric X-ray heating that fosters plasma uniformity, and the ability to collect absorption spectra at WD photosphere conditions are improvements over past laboratory experiments. Analysis of the experimental absorption spectra reveals that electron density (n e ) values derived from the Hγ line are ~34% ± 7.3% lower than from Hβ. Two potential systematic errors that may contribute to this difference were investigated. A detailed evaluation of self-emission and plasma gradients shows that these phenomena are unlikely to produce any measurable Hβ–Hγ n e difference. WD masses inferred with the spectroscopic method are proportional to the photosphere density. Hence, the measured Hβ–Hγ n e difference is qualitatively consistent with the trend that WD masses inferred from their Hβ line are higher than that resulting from the analysis of Hβ and Hγ. In conclusion, this evidence may suggest that current hydrogen line shape calculations are not sufficiently accurate to capture the intricacies of the Balmer series.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Io's sodium emission cloud

Strong evidence that Io's sodium emission is due to resonant scattering is given by our observations which show a monotonic increase of emission intensity with residual solar intensity. In addition we detected no emission during three eclipse observations of Io. We propose a resonant scattering model with two spacial components comprising an optically thick atmosphere extending 1000 km above Io's surface surrounded by an optically thin cloud which forms a partial torus around Jupiter. In this model, sodium atoms are sputtered from Io's surface by heavy energetic ions which are accelerated in a plasma sheath around Io. The atoms sputtered from the surface collide with atoms in Io's atmosphere so the equipartition of kinetic energy is established. During Io's day, sodium and other atmospheric constituents are ionized, giving rise to the ionosphere observed by Pioneer 10. Atoms escape by means of Jeans escape from the critical level, which is at the top of the atmosphere and the base of the cloud.

Macy, W. W., Jr.↗

The energetics of hydrogen atom recombination - Analysis, experiments, and modeling

A theoretical investigation of the effect of the microscopic energetics of the recombination reaction on the performance of a microwave-plasma electrothermal propulsion system is described, and the results of the analysis are presented. A series of experiments to test the concept is described and analyzed by comparison with a computer model of the recombination reaction. It is concluded that internal energy considerations are not likely to significantly affect the design of a microwave-plasma electrothermal rocket. The experimental results indicate that the microwave power is far higher than the capacity of the gas to absorb it; the cooling needed to control the energy dominates the experimental results.

Filpus, J. W.↗