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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2023

Kinetic Growth of Multicomponent Microcompartment Shells

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Altogether, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

defects↗
DOE OSTI2023

Yb Substitution and Ultralow Thermal Conductivity of the Ca 3– x Yb x AlSb 3 (0 ≤ x ≤ 0.81(1)) System

Here, a series of Yb-substituted Zintl phases in the Ca 3–x Yb x AlSb 3 (0 ≤ x ≤ 0.81(1)) system has been synthesized by initial arc melting and post-heat treatment, and their isotypic crystal structures were characterized by both powder and single crystal X-ray diffraction analysis. All four title compounds adopted the Ca 3 AlAs 3 -type structure (space group Pnma, Pearson code oP28, Z = 4). The overall structure can be described as a combination of the 1-dimensional (1D) infinite chain of ∞ 1 [Al(Sb 2 Sb 2/2 )] formed by two vertices sharing [AlSb 4 ] tetrahedral moieties and three Ca 2+ /Yb 2+ mixed sites located in between these 1D chains. The charge balance and the resultant independency of the 1D chains in the title system were explained by the Zintl-Klemm formalism [Ca 2+ /Yb 2+ ] 3 [(4b-Al 1– )(1b-Sb 2– ) 2 (2b-Sb 1– ) 2/2 ]. A series of DFT calculations proved that (1) the band overlap between the d-orbital states from two types of cations and the p-orbital states from Sb at the high symmetry Γ point implied a heavily doped degenerate semiconducting behavior of the quaternary Ca 2 YbAlSb 3 model and (2) the site preference of Yb for the M1 site was due to the electronic-factor criterion based on the Q values of each atomic site. The electron localization function calculations also proved that the two different shapes of lone pairs of the Sb atoms—the “umbrella-shape” and the “C-shape”—are determined by local geometry and the coordination environment on the anionic frameworks. Thermoelectric measurements of the quaternary title compound Ca 2.19(1) Yb 0.81 AlSb 3 showed an approximately two times larger ZT value than that of ternary Ca 3 AlSb 3 at 623 K due to increased electrical conductivity and ultralow thermal conductivity originated from Yb substitution for Ca.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana

Two bacterial strains, 1N T and 5N T , were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1N T (0.65×1.85 µm) and 5N T (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5N T elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1N T and 5N T occurred at 25–30 °C, pH 6.5–7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1N T and 5N T were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11 T , Paraburkholderia aspalathi LMG 27731 T and Paraburkholderia caffeinilytica CF1 T . The genomes of 1N T and 5N T had an average nucleotide identity (91.6 and 91.3%) and in silico DNA–DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1N T and 5N T from each other and their closest relatives. The only ubiquinone present in strains 1N T and 5N T was Q-8. The major cellular fatty acids were C 16 : 0 , 3OH-C 16 : 0 , C 17 : 0 cyclo, C 19 : 0 cyclo ω8 c and summed features 2 (3OH-C 14 : 0 / C 16 : 1 iso I), 3 (C 16 : 1 ω6 c /ω7 c ) and 8 (C 18 : 1 ω7 c /ω6 c ). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana . Our polyphasic approach demonstrated that strains 1N T and 5N T represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1N T =DSM 110721 T =LMG 31704 T ) and Paraburkholderia elongata sp. nov. (type strain 5N T =DSM 110722 T =LMG 31705 T ) are proposed.

Microbiology↗
DOE OSTI2018

Spectral and dynamical analysis of a single vortex ring in anisotropic harmonically trapped three-dimensional Bose-Einstein condensates

Here in the present work, motivated by numerous recent experimental developments we revisit the dynamics of a single vortex ring in anisotropic harmonic traps. At the theoretical level, we start from a general Lagrangian dynamically capturing the evolution of a vortex ring and not only consider its spectrum of linearized excitations, but also explore the full nonlinear dynamical evolution of the ring as a vortical filament. The theory predicts that the ring is stable for 1 ≤ λ ≤ 2, where λ = ω z /ω r is the ratio of the trapping frequencies along the z and r axes, i.e., for spherical to slightly oblate condensates. We compare this prediction with direct numerical simulations of the full three-dimensional Gross-Pitaevskii equation (GPE) capturing the linearization spectrum of the ring for different values of the chemical potential and as a function of the anisotropy parameter λ . We identify this result as being only asymptotically valid as the chemical potential μ → ∞, revealing how the stability interval narrows and, in particular, its upper bound decreases for finite μ. Finally, we compare at the dynamical level the results of the GPE with the ones effectively capturing the ring dynamics, revealing the unstable evolution for different values of λ, as well as the good agreement between the two.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2018

Mathematical Simulation of Humidification of Earth on a Slope and Calculation of Its Safety Factor

This paper presents a mathematical model of the simultaneous processes of moisture, heat, and salt transfer in a porous medium, as well as a pattern of calculation of earth stability on a slope depending on the above factors and nonlinear dependences on them of the strength characteristics of the earth. The corresponding boundary-value problem has been solved by the method of radial basis functions. A comparison has been made between the results of numerical experiments showing the relationship between the change in the value of the safety factor and the position of the slip curve depending on the heat, salt, and moisture transfer.

42 ENGINEERING↗
DOE OSTI2021

tSFM 1.0: tRNA Structure–Function Mapper

Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation P-values can quantify the significance of CIF divergences between two taxa, their naive Monte Carlo approximation is slow and inaccurate. The Peaks-over-Threshold approach of Knijnenburg et al. (2009) promises improvements to both speed and accuracy of permutation P-values, but has no publicly available API. Here, we present tRNA Structure–Function Mapper (tSFM) v1.0, an open-source, multi-threaded application that efficiently computes, visualizes and assesses significance of single- and paired-site CIFs and their evolutionary divergences for any RNA, protein, gene or genomic element sequence family. Multiple estimators of permutation P-values for CIF evolutionary divergences are provided along with confidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A Semi-Empirical Framework for Interpreting Traveling Wave Ion Mobility Arrival Time Distributions

The inherent structural heterogeneity of biomolecules is an important biophysical property that is essential to their function, but is challenging to characterize experimentally. We present a workflow that rapidly and quantitatively assesses the conformational heterogeneity of peptides and proteins in the gas phase using traveling wave ion mobility (TWIM) arrival time distributions (ATDs). We have established a set of semi-empirical equations that model the TWIM ATD peak width and resolution across a wide range of wave amplitudes (V) and wave velocities (v). In addition, a conformational broadening parameter, δ, can be extracted from this analysis that reports on the contribution of conformational heterogeneity to the broadening of TWIM ATD peak width during ion mobility separation. We use this δ value to evaluate the conformational heterogeneity of a set of helical peptides, and our analysis correlates well with previous peak width observations reported for these ions. Furthermore, we use molecular dynamics simulations to independently investigate the general flexibility of these peptides in the gas phase, and generate similar trends found in experimental TWIM data. Finally, we extended our analysis to Avidin, a 64-kDa homotetramer, and quantify the structural heterogeneity of this intact complex using TWIM ATD data as a function of cross-linking. We observe an initial reduction in δ values as a function of cross-linker concentration, demonstrating the sensitivity of our δ value analysis to changes in flexibility of the assembly. .

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Minimum conditions for accurate modeling of urea production via co-electrolysis

Co-electrolysis of carbon oxides and nitrogen oxides promise to simultaneously help restore the balance of the C and N cycles while producing valuable chemicals such as urea. However, co-electrolysis processes are still largely inefficient and numerous knowledge voids persist. Here, we provide a solid thermodynamic basis for modelling urea production via co-electrolysis. First, we determine the energetics of aqueous urea produced under electrochemical conditions based on experimental data, which enables an accurate assessment of equilibrium potentials and overpotentials. Next, we use density functional theory (DFT) calculations to model various co-electrolysis reactions producing urea. The calculated reaction free energies deviate significantly from experimental values for well-known GGA, meta-GGA and hybrid functionals. These deviations stem from errors in the DFT-calculated energies of molecular reactants and products. In particular, the error for urea is approximately -0.25 ± 0.10 eV. Finally, we show that all these errors introduce large inconsistencies in the calculated free-energy diagrams of urea production via co-electrolysis, such that gas-phase corrections are strongly advised.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Exact reaction coordinates for flap opening in HIV-1 protease

The primary goal of protein science is to understand how proteins function, which requires understanding the functional dynamics responsible for transitions between different functional structures of a protein. A central concept is the exact reaction coordinates that can determine the value of committor for any protein configuration, which provide the optimal description of functional dynamics. Despite intensive efforts, identifying the exact reaction coordinates (RCs) in complex molecules remains a formidable challenge. Using the recently developed generalized work functional, we report the discovery of the exact RCs for an important functional process—the flap opening of HIV-1 protease. Our results show that this process has six RCs, each one is a linear combination of ~240 backbone dihedrals, providing the precise definition of collectivity and cooperativity in the functional dynamics of a protein. Applying bias potentials along each RC can accelerate flap opening by 10 3 to 10 4 folds. The success in identifying the RCs of a protein with 198 residues represents a significant progress beyond that of the alanine dipeptide, currently the only other complex molecule for which the exact RCs for its conformational changes are known. Our results suggest that the generalized work functional (GWF) might be the fundamental operator of mechanics that controls protein dynamics.

Science & Technology - Other Topics↗
DOE OSTI2023

Effect of the Nature of Both Cation and Anion Substitution on the Structural Symmetry of Li‐Rich 3 d ‐Metal Chalcogenide Electrodes

Abstract Li‐rich layered chalcogenides have recently led to better understanding of the anionic redox process and its associated high capacity while providing ways to overcome its practical limitations of voltage fade and irreversibility. This study reports on the feasibility of triggering anionic activity in Li 2 TiS 3 , through anionic substitution (Se for S) or cationic substitution (Fe for Ti). Herein, the chalcogenide chemical space is further explored to prepare mono‐substituted Li 1.7 Ti 0.85 Mn 0.45 Ch 3 (Ch = S/Se) and doubly substituted cationic and anionic phases (Li 1.7 Ti 0.85 Fe 0.45 S 3‐z Se z ) which crystallize either in the O3‐ or O1‐type structures depending upon substituents. All series show a bell‐shape capacity variation as function of the transition metal (TM) substitution degree with values up to 240 mAh g −1 . For specific compositions, a structural O3 to O1 phase transition is observed upon Li removal, which is not reversible upon Li re‐insertion due to kinetic limitations and negatively affects long‐term cycling performance. Density functional theory (DFT) calculations confirm the O3/O1 relative stability along the different series and point subtle electronic differences in the TM‐doping, rationalizing the structural and electrochemical behaviors of these phases upon cycling. These findings provide further insights into the link between structural and electronic stability, which is of key importance for designing chalcogenide‐based anionic redox compounds.

Chemistry↗
DOE OSTI2022

The binding of atomic hydrogen on graphene from density functional theory and diffusion Monte Carlo calculations

In this research, density functional theory (DFT) and diffusion Monte Carlo (DMC) methods are used to calculate the binding energy of a H atom chemisorbed on the graphene surface. The DMC value of the binding energy is about 16% smaller in magnitude than the Perdew–Burke–Ernzerhof (PBE) result. The inclusion of exact exchange through the use of the Heyd–Scuseria–Ernzerhof functional brings the DFT value of the binding energy closer in line with the DMC result. It is also found that there are significant differences in the charge distributions determined using PBE and DMC approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

A quantum hydrodynamical description for scrambling and many-body chaos

Recent studies of out-of-time ordered thermal correlation functions (OTOC) in holographic systems and in solvable models such as the Sachdev-Ye-Kitaev (SYK) model have yielded new insights into manifestations of many-body chaos. So far the chaotic behavior has been obtained through explicit calculations in specific models. In this paper we propose a unified description of the exponential growth and ballistic butterfly spreading of OTOCs across different systems using a newly formulated “quantum hydrodynamics,” which is valid at finite ℏ and to all orders in derivatives. The scrambling of a generic few-body operator in a chaotic system is described as building up a “hydrodynamic cloud,” and the exponential growth of the cloud arises from a shift symmetry of the hydrodynamic action. The shift symmetry also shields correlation functions of the energy density and flux, and time ordered correlation functions of generic operators from exponential growth, while leads to chaotic behavior in OTOCs. The theory also predicts an interesting phenomenon of the skipping of a pole at special values of complex frequency and momentum in two-point functions of energy density and flux. This pole-skipping phenomenon may be considered as a “smoking gun” for the hydrodynamic origin of the chaotic mode. Here, we also discuss the possibility that such a hydrodynamic description could be a hallmark of maximally chaotic systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Electronic Structure and Linhard Function of Iron-Based Superconductor La{sub 0.5−x}Na{sub 0.5 + x}Fe{sub 2}As{sub 2}

We perform theoretical studies of the iron-based superconductor La{sub 0.5−x}Na{sub 0.5 + x}Fe{sub 2}As{sub 2}. Using density functional calculation with virtual crystal approximation, band structures, density of states, and Fermi surfaces are obtained for different La/Na composition by varying x value. Furthermore, the nesting property is also investigated using the Linhard function. Our main findings are as follows: For undoped (x = 0.0) case, the magnetic and electronic structure share great similarities with extensively studied BaFe{sub 2}As{sub 2}. Upon hole doping (x = 0.3), the Q = (π,π) nesting property are preserved. However, upon electron doping (x = -0.3), the Fermi surfaces undergo a dramastic change into 3D and complex structure. We find this change is attributed to the comprehensive influence of band filling and chemical pressure of La{sup 3+}. We propose the asymmetric change of Fermi surfaces upon doping may in some sense explain the electron-hole asymmetry in phase diagram.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Thermofield Theory for Finite-Temperature Electronic Structure

Wave function methods have offered a robust, systematically improvable means to study ground-state properties in quantum many-body systems. Theories like coupled cluster and their derivatives provide highly accurate approximations to the energy landscape at a reasonable computational cost. Analogues of such methods to study thermal properties, though highly desirable, have been lacking because evaluating thermal properties involve a trace over the entire Hilbert space, which is a formidable task. Besides, excited-state theories are generally not as well studied as ground-state ones. In this mini-review, we present an overview of a finite-temperature wave function formalism based on thermofield dynamics to overcome these difficulties. Thermofield dynamics allows us to map the equilibrium thermal density matrix to a pure state, i.e., a single wave function, albeit in an expanded Hilbert space. Ensemble averages become expectation values over this so-called thermal state. Around this thermal state, we have developed a procedure to generalize ground-state wave function theories to finite temperatures. As explicit examples, we highlight formulations of mean-field, configuration interaction, and coupled cluster theories for thermal properties of Fermions in the grand-canonical ensemble. To assess the quality of these approximations, we also show benchmark studies for the one-dimensional Hubbard model, while comparing against exact results. We will see that the thermal methods perform similarly to their ground-state counterparts, while merely adding a prefactor to the asymptotic computational cost. Furthermore, they also inherit all the properties, good or bad, from the ground-state methods, signifying the robustness of our formalism and the scope for future development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Plasma thermal transport with a generalized 8-moment distribution function

Moment equations that model plasma transport require an ansatz distribution function to close the system of equations. The resulting transport is sensitive to the specific closure used, and several options have been proposed in the literature. Two different 8-moment distribution functions can be generalized to form a single-parameter family of distribution functions. The transport coefficients resulting from this generalized distribution function can be expressed in terms of this free parameter. This provides the flexibility of matching the 8-moment model to some validating result at a given magnetization value, such as Braginskii’s transport, or the more recent results of Davies et al. [Physics of Plasma, 28, 012305 (2021)]. Here, this process can be thought of as solving for the 8-moment distribution function that matches the value of a transport coefficient given by a Chapman-Enskog expansion, while retaining the improved physical properties, such as finite propagation speeds and time dependence which belong to the hyperbolic moment models. Since the presented generalized distribution function only has a single free parameter, only a single transport coefficient can be matched at a time. However, this generalization process may be extended to provide multiple free parameters. The focus of this Brief Communication is on the dramatically improved thermal conductivity of the proposed model compared to the two base moment models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

A Review of the Influence of Processing Parameters on ODS Steels Produced via Additive Manufacturing Techniques

Abstract This paper reviews current observations regarding processing conditions for oxide dispersion-strengthened steels consolidated through additive manufacturing techniques. Variations in ODS steels observed across process parameters include changes in grain size, grain texture, oxide size, density of oxides, porosity, melt pool characteristics, and mechanical properties. These properties were then compared across techniques to understand which techniques and processing conditions lead to the highest strength, ductility, and oxide density. Current literature suggests that a mix of grain types, in the form of either morphology or phase, can significantly increase the strength of printed ODS steels. Meanwhile, the most ductile samples, regardless of consolidation technique or matrix material, were made from feedstock with oxide additions located on the powder surface. Reported grain and oxide sizes were plotted against the ratio of laser power to scan speed, volumetric energy density, and normalized enthalpy. No strong correlation between these values and microstructural features was observed. The plots that were made suggest that a larger data set, more in-depth representative equations, and more defined material properties as a function of specific feedstock used are necessary to determine a value that can be correlated to the printed ODS steel microstructure.

deJong, Matthew↗
DOE OSTI2026

A comparison of the dielectric function for p-point water models

We compute the longitudinal dielectric function ɛl(k) for p-point water models, p = 3 (SPC/E, TIP3P), p = 4 (TIP4P-EW, OPC), and p = 5 (TIP5P-E) from the charge–charge fluctuation function SZZ(k), obtained from two methods: average of the charge in k-space (method:sum) and from the pair distribution function in Fourier space (method:integral). The latter requires a continuation to small k-values, which we thoroughly discuss. We conclude with a detailed comparison of the longitudinal dielectric function for the different p-point models and its main characteristics: small k and large k limits, position of the poles, and its (complex) zeros.

Shevy, Noah [Ames National Laboratory, Department ↗
DOE OSTI2019

Photoelectron spectroscopy of [Mo6X14]2− dianions (X = Cl–I)

Photoelectron spectroscopy and theoretical investigations have been performed to systematically probe the intrinsic electronic properties of [Mo6X14]2− (X = halogen). All three PE spectra of gaseous [Mo6X14]2− (X = Cl, Br, I) dianions, which were generated by electrospray ionization, exhibit multiple resolved peaks in the recorded binding energy range. Theoretical investigations on the orbital structure and charge distribution were performed to support interpretation of the observed spectra and were further extended onto [Mo6F14]2−, a dianion that was not available for the experimental study. The measured adiabatic (ADE) and vertical detachment energies (VDE) for X = Cl–I were well reproduced by density functional theory calculations (accuracy ∼0.1 eV). Corresponding ADE/VDE values for the dianions were found to be 1.48/2.13 (calc.) and 2.30/2.65, 2.30/2.62, and 2.20/2.42 eV (all expt.) for X = F, Cl, Br, and I, respectively, showing an interesting buckled trend of electron binding energy (EBE) along the halogen series, i.e., EBE (F) ≪ EBE (Cl) ∼ EBE (Br) > EBE (I). Molecular orbital analyses indicate different mixing of metal and halogen atomic orbitals, which is strongly dependent on the nature of X, and suggest that the most loosely bound electrons are detached mainly from the metal core for X = F and Cl, but from halide ligands for X = Br and I. The repulsive Coulomb barrier (RCB), estimated from the photon energy dependent spectra, decreases with increasing halogen size, from 1.8 eV for X = Cl to 1.6 eV for X = I. Electrostatic potential modeling confirms the experimental RCB values and predicts that the most favorable electron detaching pathway should lie via the face-bridging halide ligands.

Li, Ren-Zhong↗