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DOE OSTI2022

Trajectory design via unsupervised probabilistic learning on optimal manifolds

Abstract This article illustrates the use of unsupervised probabilistic learning techniques for the analysis of planetary reentry trajectories. A three-degree-of-freedom model was employed to generate optimal trajectories that comprise the training datasets. The algorithm first extracts the intrinsic structure in the data via a diffusion map approach. We find that data resides on manifolds of much lower dimensionality compared to the high-dimensional state space that describes each trajectory. Using the diffusion coordinates on the graph of training samples, the probabilistic framework subsequently augments the original data with samples that are statistically consistent with the original set. The augmented samples are then used to construct conditional statistics that are ultimately assembled in a path planning algorithm. In this framework, the controls are determined stage by stage during the flight to adapt to changing mission objectives in real-time.

42 ENGINEERING↗

DOE OSTI2020

Enhanced Sulfur Dioxide Adsorption in UiO-66 Through Crystal Engineering and Chalcogen Bonding

Adsorption of corrosive SO 2 gas occurs in metal–organic frameworks (MOFs) including UiO-66. Improvements in SO 2 capacity is obtained through the incorporation of residual modulators in the UiO-66 framework by introducing new binding sites in the material, through residual modulators. Four residual modulators were investigated (acetic acid, trifluoroacetic acid, 3-DMAP acid, cyanoacetic acid), and the UiO-66 framework modulated with cyanoacetic acid exhibited nearly twice the SO 2 uptake for the 18:1 modulator/linker synthesis ratio compared with other modulated UiO-66 structures. Density functional theory investigations confirmed that targeted host–guest interactions were maintained after the modulator was incorporated into the framework. The strongest binding energy was between SO 2 and cyanoacetic acid, consistent with dynamic SO 2 adsorption data, and identified contributions from both the SO 2 reacting with the residual modulator and the coordinating linkers. The successful increase in dynamic SO 2 capacity illustrates how often-overlooked non-covalent interactions can be used in targeted adsorption applications. Further investigation into weak electrostatic interactions for adsorption properties is also needed to advance the potential selectivity and capacity in the adsorption sphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Resolving Heterogeneous Dynamics of Excess Protons in Aqueous Solution with Rate Theory

Rate theories have found great utility across the chemical sciences by providing a physically transparent way to analyze dynamical processes. Here we demonstrate the benefits of using transition state theory and Marcus theory to study the rate of proton transfer in HCl solutions. By using long ab initio molecular dynamics simulations we show that good agreement is obtained between these two different formulations of rate theory and how they can be used to study the pathways and life-time of proton transfer in aqueous solution. Since both rate theory formulations utilize identical sets of molecular data, this provides a self-consistent theoretical picture of the rates of aqueous phase proton transfer. Specifically, we isolate and quantify the rates of proton transfer, ion-pair dissociation, and solvent exchange in concentrated HCl solutions. Our analysis predicts a concentration dependence to both proton transfer and ion-pairing. Moreover, our estimate of the life-time for the Zundel species is 0.8 ps and 1.3 ps for 2M and 8M HCl, respectively. In this paper, we demonstrate that concentration effects, can indeed be quantified through the combination of state-of-the-art simulation and theory and provides a picture of the important correlations between the cation (hydronium) and the counter-ion in acid solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Structural Characterization of the Reaction and Substrate Specificity Mechanisms of Pathogenic Fungal Acetyl-CoA Synthetases

Acetyl CoA synthetases (ACSs) are Acyl-CoA/NRPS/Luciferase (ANL) superfamily enzymes that couple acetate with CoA to generate acetyl CoA, a key component of central carbon metabolism in eukaryotes and prokaryotes. Normal mammalian cells are not dependent on ACSs, while tumor cells, fungi, and parasites rely on acetate as a precursor for acetyl CoA. Consequently, ACSs have emerged as a potential drug target. As part of a program to develop antifungal ACS inhibitors, we characterized fungal ACSs from five diverse human fungal pathogens using biochemical and structural studies. ACSs catalyze a two-step reaction involving adenylation of acetate followed by thioesterification with CoA. Our structural studies captured each step of these two half-reactions including the acetyl-adenylate intermediate of the first half-reaction in both the adenylation conformation and the thioesterification conformation and thus provide a detailed picture of the reaction mechanism. We also used a systematic series of increasingly larger alkyl adenosine esters as chemical probes to characterize the structural basis of the exquisite ACS specificity for acetate over larger carboxylic acid substrates. Consistent with previous biochemical and genetic data for other enzymes, structures of fungal ACSs with these probes bound show that a key tryptophan residue limits the size of the alkyl binding site and forces larger alkyl chains to adopt high energy conformers, disfavoring their efficient binding. Together, our analysis provides highly detailed structural models for both the reaction mechanism and substrate specificity that should be useful in designing selective inhibitors of eukaryotic ACSs as potential anticancer, antifungal, and antiparasitic drugs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Assessment of TMT Labeling Efficiency in Large-Scale Quantitative Proteomics: The Critical Effect of Sample pH

Isobaric labeling via tandem mass tag (TMT) reagents enables sample multiplexing prior to LC–MS/MS, facilitating high-throughput large-scale quantitative proteomics. Consistent and efficient labeling reactions are essential to achieve robust quantification; therefore, embedded in our clinical proteomic protocol is a quality control (QC) sample that contains a small aliquot from each sample within a TMT set, referred to as “Mixing QC.” This Mixing QC enables the detection of TMT labeling issues by LC–MS/MS before combining the full samples to allow for salvaging of poor TMT labeling reactions. While TMT labeling is a valuable tool, factors leading to poor reactions are not fully studied. We observed that relabeling does not necessarily rescue TMT reactions and that peptide samples sometimes remained acidic after resuspending in 50 mM HEPES buffer (pH 8.5), which coincided with low labeling efficiency (LE) and relatively low median reporter ion intensities (MRIIs). To obtain a more resilient TMT labeling procedure, we investigated LE, reporter ion missingness, the ratio of mean TMT set MRII to individual channel MRII, and the distribution of log 2 reporter ion ratios of Mixing QC samples. We discovered that sample pH is a critical factor in LE, and increasing the buffer concentration in poorly labeled samples before relabeling resulted in the successful rescue of TMT labeling reactions. Moreover, resuspending peptides in 500 mM HEPES buffer for TMT labeling resulted in consistently higher LE and lower missing data. By better controlling the sample pH for labeling and implementing multiple methods for assessing labeling quality before combining samples, we demonstrate that robust TMT labeling for large-scale quantitative studies is achievable.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Mo Atom Rearrangement Drives Layer-Dependent Reactivity in Two-Dimensional MoS 2

Two-dimensional (2D) materials offer a valuable platform for manipulating and studying chemical reactions at the atomic level, owing to the ease of controlling their microscopic structure at the nanometer scale. While extensive research has been conducted on the structure-dependent chemical activity of 2D materials, the influence of structural transformation during the reaction has remained largely unexplored. In this work, we report the layer-dependent chemical reactivity of MoS 2 during a nitridation atomic substitution reaction and attribute it to the rearrangement of Mo atoms. Our results show that the chemical reactivity of MoS 2 decreases as the number of layers is reduced in the few-layer regime. In particular, monolayer MoS 2 exhibits significantly lower reactivity compared with its few-layer and multilayer counterparts. Atomic-resolution transmission electron microscopy (TEM) reveals that MoN nanonetworks form as reaction products from monolayer and bilayer MoS 2 , with the continuity of the MoN crystals increasing with layer number, consistent with the local conductivity mapping data. The layer-dependent reactivity is attributed to the relative stability of the hypothetically formed MoN phase, which retains the number of Mo atomic layers present in the precursor. Specifically, the low chemical reactivity of monolayer MoS 2 is attributed to the high energy cost associated with Mo atom diffusion and migration necessary to form multilayer Mo lattices in the thermodynamically stable MoN phase. In conclusion, this study underscores the critical role of lattice rearrangement in governing chemical reactivity and highlights the potential of 2D materials as versatile platforms for advancing the understanding of materials chemistry at the atomic scale.

Chemical reactivity↗

DOE OSTI2023

Evaluating EAMv2 Simulated High Latitude Clouds Using ARM Measurements in the Northern and Southern Hemispheres

Here, this study evaluates high latitude stratiform mixed-phase clouds (SMPC) in the atmosphere model of the Energy Exascale Earth System Model version 2 (EAMv2) by utilizing one-year-long ground-based remote sensing measurements from the Atmospheric Radiation and Measurement (ARM) program. A nudging approach is applied to model simulations for a constrained comparison with the ARM observations. Observed and modeled SMPCs are sampled and collocated to address the difference in data resolution, so that we can consistently evaluate their macrophysical properties at the North Slope of Alaska (NSA) site in the Arctic and the McMurdo (AWR) site in the Antarctic. We found that EAMv2 overestimates SMPC frequency of occurrence at both sites. However, the model captures the observed larger cloud frequency of occurrence at the NSA site. For collocated SMPCs, the annual statistics of observed cloud macrophysics are generally reproduced at the NSA site, while at the AWR site, there are larger biases. Compared to the AWR site, the lower cloud top and cloud base and the warmer cloud top temperature observed at NSA are well simulated. On the other hand, simulated cloud phase is substantially biased. The model largely overestimates liquid water path, and the ice water path is underestimated at NSA, but at AWR, the liquid water path is frequently underestimated due to the dominance of snow in Antarctic SMPCs. As a result, the observed hemispheric difference in cloud phase partitioning is misrepresented in EAMv2. This study implies that additional model development is needed for high latitude mixed-phase clouds.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Phase Transitions and Thermal Equation of State of Fe‐9wt.%Si Applied to the Moon and Mercury

Abstract Accurate knowledge of the phase transitions and thermoelastic properties of candidate iron alloys, such as Fe‐Si alloys, is essential for understanding the nature and dynamics of planetary cores. The phase diagrams of some Fe‐Si alloys between 1 atm and 16 GPa have been back‐extrapolated from higher pressures, but the resulting phase diagram of Fe 83.6 Si 16.4 (9 wt.% Si) is inconsistent with temperature‐induced changes in its electrical resistivity between 6 and 8 GPa. This study reports in situ synchrotron X‐ray diffraction (XRD) measurements on pre‐melted and powder Fe 83.6 Si 16.4 samples from ambient conditions to 60 GPa and 900 K using an externally heated diamond‐anvil cell. Upon compression at 300 K, the bcc phase persisted up to ∼38 GPa. The hcp phase appeared near 8 GPa in the pre‐melted sample, and near 17 GPa in the powder sample. The appearance of the hcp phase in the pre‐melted sample reconciles the reported changes in electrical resistivity of a similar sample, thus resolving the low‐pressure region of the phase diagram. The resulting high‐temperature Birch‐Murnaghan equation of state (EoS) and thermal EoS based on the Mie‐Gruneisen‐Debye model of the bcc and hcp structures are consistent with, and complement the literature data at higher pressures. The calculated densities based on the thermal EoS of Fe‐9wt.%Si indicate that both bcc and hcp phases agree with the reported core density estimates for the Moon and Mercury.

Berrada, Meryem↗

DOE OSTI2022

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes dissociation of the S1 domains and exposure of the fusion machinery, although the molecular details of this process have yet to be observed. We report the development of bottom-up coarse-grained (CG) models consistent with cryo-electron tomography data, and the use of CG molecular dynamics simulations to investigate viral binding and S2 core exposure. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces in a manner distinct from binding between soluble proteins, which processively induces S1 dissociation. We also simulate possible variant behavior using perturbed CG models, and find that ACE2-induced S1 dissociation is primarily sensitive to conformational state populations and the extent of S1/S2 cleavage, rather than ACE2 binding affinity. These simulations reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Plutonium oxide melt structure and covalency

Advances in nuclear power reactors include the use of mixed oxide fuel, containing uranium and plutonium oxides. The high-temperature behaviour and structure of PuO 2-x above 1,800 K remain largely unexplored, and these conditions must be considered for reactor design and planning for the mitigation of severe accidents. Here, in this study, we measure the atomic structure of PuO 2-x through the melting transition up to 3,000 +/- 50 K using X-ray scattering of aerodynamically levitated and laser-beam-heated samples, with O/Pu ranging from 1.57 to 1.76. Liquid structural models consistent with the X-ray data are developed using machine-learned interatomic potentials and density functional theory. Molten PuO 1.76 contains some degree of covalent Pu-O bonding, signalled by the degeneracy of Pu 5f and O 2p orbitals. The liquid is isomorphous with molten CeO 1.75 , demonstrating the latter as a non-radioactive, non-toxic, structural surrogate when differences in the oxidation potentials of Pu and Ce are accounted for. These characterizations provide essential constraints for modelling pertinent to reactor safety design. The molten structure of plutonium oxide-a component of mixed oxide nuclear fuels-is measured, showing some degree of covalent bonding. Its atomic structure is similar to that of cerium oxide, which could be a non-radioactive structural surrogate.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

In situ synchrotron diffraction and modeling of non-equilibrium solidification of a MnFeCoNiCu alloy

The solidification mechanism and segregation behavior of laser-melted Mn 35 Fe 5 Co 20 Ni 20 Cu 20 was firstly investigated via in situ synchrotron x-ray diffraction at millisecond temporal resolution. The transient composition evolution of the random solid solution during sequential solidification of dendritic and interdendritic regions complicates the analysis of synchrotron diffraction data via any single conventional tool, such as Rietveld refinement. Therefore, a novel approach combining a hard-sphere approximation model, thermodynamic simulation, thermal expansion measurement and microstructural characterization was developed to assist in a fundamental understanding of the evolution of local composition, lattice parameter, and dendrite volume fraction corresponding to the diffraction data. This methodology yields self-consistent results across different methods. Via this approach, four distinct stages were identified, including: (I) FCC dendrite solidification, (II) solidification of FCC interdendritic region, (III) solid-state interdiffusion and (IV) final cooling with marginal diffusion. It was found out that in Stage I, Cu and Mn were rejected into liquid as Mn 35 Fe 5 Co 20 Ni 20 Cu 20 solidified dendritically. During Stage II, the lattice parameter disparity between dendrite and interdendritic region escalated as Cu and Mn continued segregating into the interdendritic region. After complete solidification, during Stage III, the lattice parameter disparity gradually decreases, demonstrating a degree of composition homogenization. The volume fraction of dendrites slightly grew from 58.3 to 65.5%, based on the evolving composition profile across a dendrite/interdendritic interface in diffusion calculations. Postmortem metallography further confirmed that dendrites have a volume fraction of 64.7 ± 5.3% in the final microstructure.

36 MATERIALS SCIENCE↗

DOE OSTI2022

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Optimization of binding affinities for compounds to their target protein is a primary objective in drug discovery. Herein we report on a collaborative study that evaluates a set of compounds binding to ROS1 kinase. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to rank the binding free energies. The predicted binding free energies from ESMACS simulations show good correlations with experimental data for subsets of the compounds. Consistent binding free energy differences are generated for TIES and ESMACS. Although an unexplained overestimation exists, we obtain excellent statistical rankings across the set of compounds from the TIES protocol, with a Pearson correlation coefficient of 0.90 between calculated and experimental activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Thermoelectric transport of semiconductor full-Heusler VFe 2 Al

Seebeck coefficient of VFe 2 Al over a wide range of doping levels can be explained only with a small band-gap ( E g ) range of 0.02–0.04 eV. This E g value is also consistent with high-temperature resistivity data of nominally stoichiometric VFe 2 Al.

Anand, Shashwat↗

DOE OSTI2020

Correlations in the Initial Conditions of Heavy-Ion Collisions

Ultracentral collisions of heavy nuclei, in which the impact parameter is nearly zero, are especially sensitive to the details of the initial state model and the microscopic mechanism for collective flow. In a hydrodynamic “flow” picture, the final state momentum correlations are a direct response to the fluctuating initial geometry, although models of the initial geometry differ widely. Alternatively, dynamical mechanisms based in the color glass condensate (CGC) formalism can naturally lead to many-body correlations with very different systematics. Here we present a calculation of event-by-event elliptic flow in both the hydrodynamic and CGC paradigms and show that they can be qualitatively distinguished in ultracentral collisions of deformed nuclei. Specifically, the multiplicity dependence in such collisions is qualitatively opposite, with the CGC correlations increasing with multiplicity while the hydrodynamic correlations decrease. The consistency of the latter with experimental data on UU collisions appears to rule out a CGC-mediated explanation. We find that these qualitative features also persist in small deformed systems and can therefore be a valuable test of the microscopic physics in that regime.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Self-similar Reynolds-averaged mechanical–scalar turbulence models for Rayleigh–Taylor, Richtmyer–Meshkov, and Kelvin–Helmholtz instability-induced mixing in the small Atwood number limit

Analytical self-similar solutions to two-, three-, and four-equation Reynolds-averaged mechanical–scalar turbulence models describing incompressible turbulent Rayleigh–Taylor, Richtmyer–Meshkov, and Kelvin–Helmholtz instability-induced mixing in planar geometry are derived in the small Atwood number (Boussinesq) limit. The models are based on the turbulent kinetic energy K and its dissipation rate ε, together with the scalar (heavy-fluid mass fraction) variance S and its dissipation rate Χ modeled either differentially or algebraically. The models allow for a simultaneous description of mechanical and scalar mixing, i.e., mixing layer growth and molecular mixing, respectively. Mixing layer growth parameters and other physical observables relevant to each instability are obtained explicitly as functions of the model coefficients. The turbulent fields are also expressed in terms of the model coefficients, with their temporal power-law scalings obtained by requiring that the self-similar equations are explicitly time-independent. The model calibration methodology is described and discussed. Expressions for a subset of the various physical observables are used to calibrate each of the two-, three-, and four-equation models, such that the self-similar solutions are consistent with experimental and numerical simulation data corresponding to these values of the observables and to specific canonical Rayleigh–Taylor, Richtmyer–Meshkov, and Kelvin–Helmholtz turbulent flows. A calibrated four-equation model is then used to reconstruct the mean and turbulent fields, and late-time turbulent equation budgets for each instability-induced flow across the mixing layer. The reference solutions derived here can provide systematic calibrations and better understanding of mechanical–scalar turbulence models and their predictions for instability-induced turbulent mixing in the very large Reynolds number limit.

42 ENGINEERING↗

DOE OSTI2022

Modeling of a 43 GHz microplasma within a photonic crystal

The electron density (n e ) and argon metastable density (1 s 5 ) of a 43GHz microplasma are obtained using the zero-dimensional plasma kinetics solver (ZDPlasKin®) for an incident power of 160 and 1000mW and argon pressures of 10–600Torr (1.3 ×10 3 to 8.0 × 10 4 Pa). These simulations are compared with previously published experimental data. To determine the self-consistent electric field in the modeled plasma, the three-dimensional millimeter wave fields are computed as a function of electron density using ANSYS EM19.2, HFSS®. This electromagnetic field model is coupled to ZDPlasKin such that any increase in the simulated plasma density correctly attenuates the simulated electric field within the microplasma. The electron density is found to be sensitive to argon gas temperature, so a two-zone temperature model was needed to obtain agreement with experimental measurements. The temperature in the central core of the microplasma was determined by a previous experimental study. That temperature was used as an input to the model for the simulation of volume recombination losses. The outer regions of the microplasma are assumed to be in equilibrium with the walls (300K). This second temperature was used in the model to determine diffusion losses. The modeled electron and metastable densities are of the order 10 20 and 10 18 m –3 , respectively. This is in good agreement with those measured experimentally as long as the two-zone temperature model is used. In the absence of a hot gas core, the modeled three-body recombination rates are excessive and the simulation severely under-predicts the electron density and over-estimates the metastable density. We conclude that the millimeter wave microplasma has a hot core (2500K at 600 Torr) that rarifies the argon gas and effectively reduces three-body recombination. Furthermore, this allows one to achieve high electron density on the order of 10 20 m –3 with only 100mW of wave power.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Self-similar Reynolds-averaged mechanical–scalar turbulence models for Rayleigh–Taylor mixing induced by power-law accelerations in the small Atwood number limit

Analytical self-similar solutions to two-, three-, and four-equation Reynolds-averaged mechanical–scalar turbulence models describing turbulent Rayleigh–Taylor mixing driven by a temporal power-law acceleration are derived in the small Atwood number (Boussinesq) limit. The solutions generalize those previously derived for constant acceleration Rayleigh–Taylor mixing for models based on the turbulent kinetic energy K and its dissipation rate ε, together with the scalar variance S and its dissipation rate χ [O. Schilling, “Self-similar Reynolds-averaged mechanical–scalar turbulence models for Rayleigh–Taylor, Richtmyer–Meshkov, and Kelvin–Helmholtz instability-induced mixing in the small Atwood number limit,” Phys. Fluids 33, 085129 (2021)]. The turbulent fields are expressed in terms of the model coefficients and power-law exponent, with their temporal power-law scalings obtained by requiring that the self-similar equations are explicitly time-independent. Mixing layer growth parameters and other physical observables are obtained explicitly as functions of the model coefficients and parameterized by the exponent of the power-law acceleration. Values for physical observables in the constant acceleration case are used to calibrate the two-, three-, and four-equation models, such that the self-similar solutions are consistent with experimental and numerical simulation data corresponding to a canonical (i.e., constant acceleration) Rayleigh–Taylor turbulent flow. The calibrated four-equation model is then used to numerically reconstruct the mean and turbulent fields, and turbulent equation budgets across the mixing layer for several values of the power-law exponent. Finally, the reference solutions derived here can be used to understand the model predictions for strongly accelerated or decelerated Rayleigh–Taylor mixing in the large Reynolds number limit.

42 ENGINEERING↗

DOE OSTI2024

Runaway electron plateau current profile reconstruction from synchrotron imaging and Ar-II line polarization angle measurements in DIII-D

Abstract Current profile reconstructions are obtained for high current ( I p ≃ 550 kA) post-disruption runaway electron (RE) plateau plasmas in DIII-D. Two novel methods of measuring the RE current profile in high-current RE plateaus are introduced and compared: localization of the q = 2 rational surface using visible synchrotron emission (SE) imaging and the measurement of the polarization angle of line-integrated Ar-II line emission. The two methods are found to be consistent with each other within the data uncertainties. Different simulations of the RE current profile are compared with the measurements: the toroidal fluid RE model is found to best fit the data, within the measurement uncertainties. In addition to introducing two novel methods to measure the RE current profile and validating present simulation capabilities, this work demonstrates that instabilities can grow at q = 2 and q = 1 surfaces without necessarily causing a RE final loss instability. Numerical simulations are also presented to elucidate the role of these instabilities on synchrotron emission.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗