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DOE OSTI2025

MarK, a Novosphingobium aromaticivorans kinase required for catabolism of multiple aromatic monomers

The aromatic compounds used in a variety of industrial products are currently obtained from nonrenewable petroleum sources. Alternatively, the plant polymer lignin is an abundant renewable source of aromatics, and its depolymerization generates a variety of products that can include acetovanillone, a vanillin derivative containing an acetyl side chain. The Alphaproteobacterium Novosphingobium aromaticivorans DSM12444 can metabolize several chemically modified aromatics in deconstructed lignin, but not acetovanillone. In this work, adaptive laboratory evolution identified a single amino acid change in the previously uncharacterized gene product Saro_1862 that is necessary and sufficient for N. aromaticivorans growth with acetovanillone as a sole growth substrate, as well as other aromatic monomers not metabolized by wild-type cells. We show that a glutamate (E) to lysine (K) substitution at amino acid residue 16 of Saro_1862 results in a ~1600-fold increase in the rate of ATP-dependent acetovanillone phosphorylation. We also find that recombinant Saro_1862 E16K phosphorylates several other aromatic compounds in vitro , defining the first reported catalytic activity for the widespread UPF0261 protein domain contained in Saro_1862. Thus, we propose naming Saro_1862 MarK, for multiple aromatic kinase. A 1.57 Å crystal structure of MarK E16K predicts that the E16K substitution lies in a potential ATP binding site, suggesting how this amino acid change increased catalytic activity. A search for homologs of MarK and other proteins required for acetovanillone degradation predicts that this pathway for aromatic metabolism exists throughout the bacterial phylogeny.

Novosphingobium↗

DOE OSTI2020

Deformation behavior of nanoscale Al–Al 2 Cu eutectics studied by in situ micropillar compression

We report deformation behavior of nanoscale laser processed Al–Al 2 Cu eutectics at room temperature is characterized through in situ micro-pillar compression testing in a scanning transmission microscope. Interlamellar spacing of Al–Al 2 Cu eutectics varies from hundreds of nanometers to 20 nm. Three different sizes of micro-pillars are fabricated in order to study the deformation behaviors of single colony and multiple colonies, corresponding to the single crystal and polycrystal respectively. For single colonies, lamellar orientations parallel, normal or inclined to the loading direction were tested. The main findings are: 1) the plasticity mechanisms strongly depend on loading orientation: buckling and kinking in the parallel-loaded eutectics, planar sliding along Al–Al 2 Cu lamellar interfaces in the incline-loaded eutectics and localized shearing in the normal-loaded eutectics. 2) the incline-loaded eutectics exhibits the lowest compression flow strength, and the normal-loaded eutectics has the highest compression flow strength. 3) with decreasing inter-lamellar spacing, the strength increases and plasticity is uniformly distributed, as opposed to shear localization. Highest compressive plasticity is observed in polycrystalline eutectics with an ensemble of lamellar orientations with ~20 nm average spacing: 17.9% at flow stress of 1.63 GPa, and degenerate, bimodal morphology: 11.1% at flow stress of 1.36 GPa.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Anomalous entropy-driven kinetics of dislocation nucleation

The kinetics of dislocation reactions, such as dislocation multiplication, controls the plastic deformation in crystals beyond their elastic limit, therefore critical mechanisms in a number of applications in materials science. We present a series of large-scale molecular dynamics simulations that shows that one such type of reactions, the nucleation of dislocation at free surfaces, exhibit unconventional kinetics, including unexpectedly large nucleation rates under compression, very strong entropic stabilization under tension, as well as strong non-Arrhenius behavior. These unusual kinetics are quantitatively rationalized using a variational transition state theory approach coupled with an efficient numerical scheme for the estimation of vibrational entropy changes. These results highlight the need for a variational treatment of the kinetics to quantitatively capture dislocation reaction kinetics, especially at low-to-moderate strains where large deformations are required to activate reactions. These observations suggest possible explanations to previously observed unconventional deformation kinetics in both molecular dynamics simulations and experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Analytical and numerical modeling of optical second harmonic generation in anisotropic crystals using #SHAARP package

Electric-dipole optical second harmonic generation (SHG) is a second-order nonlinear process that is widely used as a sensitive probe to detect broken inversion symmetry and local polar order. Analytical modeling of the SHG polarimetry of a nonlinear optical material is essential to extract its point group symmetry and the absolute nonlinear susceptibilities. Current literature on SHG analysis involves numerous approximations and a wide range of (in)accuracies. We have developed an open-source package called the Second Harmonic Analysis of Anisotropic Rotational Polarimetry (#SHAARP.si) which derives analytical and numerical solutions of reflection SHG polarimetry from a single interface (.si) for bulk homogeneous crystals with arbitrary symmetry group, arbitrary crystal orientation, complex and anisotropic linear dielectric tensor with frequency dispersion, a general SHG tensor and arbitrary light polarization. #SHAARP.si enables accurate modeling of polarimetry measurements in reflection geometry from highly absorbing crystals or wedge-shaped transparent crystals. The package is extendable to multiple interfaces.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Visualizing discrete Fermi surfaces and possible nodal-line to Weyl state evolution in ZrSiTe

Topological nodal line semimetals (TNLSMs) represent a quantum state of topological matter. When the crystal/time-reversal symmetry is broken, a nodal line state is expected to evolve into a Dirac semimetal, a Weyl semimetal, or other topological phases according to theoretical studies. Here, we report scanning tunneling microscopy (STM) based quasiparticle interference (QPI) measurements performed on the surface of TNLSM ZrSiTe single crystal. A discrete Fermi surface with multiple electron/hole pockets and the impurity-induced inter-/intra- pockets scatterings are directly visualized from QPI patterns. Moreover, the degenerated Dirac points at X point evolve into the pairs of Weyl nodes when Fe atoms are deposited, suggesting a possible phase transition from the nodal line to the Weyl state. The calculated band structures and the Weyl points by applying Zeeman splitting energies along x-direction, further confirm the existence of Weyl points in the Fe-doped ZrSiTe induced by the broken of time-reversal symmetry.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Dicarbonyl[10,10-dimethyl-5,15-bis(pentafluorophenyl)biladiene]ruthenium(II): discovery of the first ruthenium tetrapyrrole cis -dicarbonyl complex by X-ray and electron diffraction

Dicarbonyl[10,10-dimethyl-5,15-bis(pentafluorophenyl)biladiene]ruthenium(II), [Ru(C 33 H 16 F 10 N 4 )(CO) 2 ] or Ru(CO) 2 [DMBil1], is the first reported ruthenium(II) cis-dicarbonyl tetrapyrrole complex. The neutral complex sports two carbonyls and an oligotetrapyrrolic biladiene ligand. Notably, the biladiene adopts a coordination geometry that is well distorted from square planar and much more closely approximates a seesaw arrangement. Accordingly, Ru(CO) 2 [DMBil1] is not only the first ruthenium cis-dicarbonyl with a tetrapyrrole ligand, but also the first metal biladiene complex in which the tetrapyrrole does not adopt a (pseudo-)square-planar coordination geometry. Ru(CO) 2 [DMBil1] is weakly luminescent, displaying λ em = 552 nm upon excitation at λ ex = 500 nm, supports two reversible 1 e – reductions at –1.45 and –1.73 V (versus Fc + /Fc), and has significant absorption features at 481 and 531 nm, suggesting suitability for photocatalytic and photosensitization applications. While the structure of Ru(CO) 2 [DMBil1] was initially determined by X-ray diffraction, a traditionally acceptable quality structure could not be obtained (despite multiple attempts) because of consistently poor crystal quality. Furthermore, an independent structure obtained from electron diffraction experiments corroborates the structure of this unusual biladiene complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1996

Transmission Electron Microscope Measures Lattice Parameters

Convergent-beam microdiffraction (CBM) in thermionic-emission transmission electron microscope (TEM) is technique for measuring lattice parameters of nanometer-sized specimens of crystalline materials. Lattice parameters determined by use of CBM accurate to within few parts in thousand. Technique developed especially for use in quantifying lattice parameters, and thus strains, in epitaxial mismatched-crystal-lattice multilayer structures in multiple-quantum-well and other advanced semiconductor electronic devices. Ability to determine strains in indivdual layers contributes to understanding of novel electronic behaviors of devices.

Pike, William T.↗

NASA NTRS2017

Valence State Partitioning of Cr and V Between Olivine-Melt and Pyroxene-Melt in Experimental Basalts of a Eucritic Composition

The partitioning of multivalent elements in basaltic systems can elucidate the oxygen fugacity (fO2) conditions under which basalts formed on planetary bodies (Earth, Moon, Mars, asteroids). Chromium and V are minor and trace elements in basaltic melts, partition into several minerals that crystallize from basaltic melts, exist in multiple valence states at differing fO2 conditions, and can therefore be used as oxybarometers for basaltic melts. Chromium is mostly 3+ in terrestrial basaltic melts at relatively high fO2 values (≥ IW+3.5), and mostly 2+ in melts at low fO2 values (≤ IW-1), such as those on the Moon and some asteroids. At intermediate fO2s, (i.e., IW-1 to IW+3.5), basaltic melts contain both Cr3+ and Cr2+. Vanadium in basaltic melts is mostly 4+ at high fO2, mostly 3+ at low fO2, and a mix of V3+ and V4+ at intermediate fO2 con-ditions. Understanding the partitioning of Cr and V into silicate phases with changing fO2 is therefore critical to the employment of Cr and V oxybarometers. In this abstract we examine the equilibrium partitioning of Cr and V between olivine/melt and pyroxene/melt in experimental charges of a eucritic composition produced at differing fO2 conditions. This study will add to the experimental data on DCr and DV (i.e., olivine/melt, pyroxene/melt) at differing fO2, and in turn these D values will be used to assess the fO2 of eucrite basalts and perhaps other compositionally similar planetary basalts.

Karner, J. M.↗

DOE OSTI2025

Strain release by 3D atomic misfit in fivefold twinned icosahedral nanoparticles with amorphization and dislocations

Multiple twinning to form fivefold twinned nanoparticles in crystal growth is common and has attracted broad attention ranging from crystallography research to physical chemistry and materials science. Lattice-misfit strain and defects in multiple twinned nanoparticles (MTP) are key to understand and tailor their electronic properties. However, the structural defects and related strain distributions in MTPs are poorly understood in three dimensions (3D). Here, we show the 3D atomic misfit and strain relief mechanism in fivefold twinned icosahedral nanoparticles with amorphization and dislocations by using atomic resolution electron tomography. We discover a two-sided heterogeneity in variety of structural characteristics. A nearly ideal crystallographic fivefold face is always found opposite to a less ordered face, forming Janus-like icosahedral nanoparticles with two distinct hemispheres. The disordered amorphous domains release a large amount of strain. Molecular dynamics simulations further reveal the Janus-like icosahedral nanoparticles are prevalent in the MTPs formed in liquid-solid phase transition. This work provides insights on the atomistic models for the modelling of formation mechanisms of fivefold twinned structures and computational simulations of lattice distortions and defects. We anticipate it will inspire future studies on fundamental problems such as twin boundary migration and kinetics of structures in 3D at atomic level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2014

The Bombardment History of 4 Vesta as Told by Sample Geochronology

The Dawn mission showed asteroid 4 Vesta to be an extensively cratered body, ancient in age, with craters in a variety of morphologies and preservation states [1-3]. Tying Vesta's relative crater ages to an absolute impact history can be accomplished through investigations of the HED (howardite, eucrite, diogenite) meteorites. Eucrites are crustal basalts and gabbros, diogenites are mostly orthopyroxenites representing lower crust or upper mantle materials, and howardites are mixed breccias containing both lithologies. Eucrite 53Mn-53Cr systematics show that the HED parent body globally differentiated by ~4.56 Ga and fully crystallized soon afterwards [4]. Much later, many eucrites were brecciated and heated by large impacts into the parent body surface. Disturbance ages in eucrites show that multiple large impacts occurred within 1 Gyr after crystallization, showing a history that largely resembles that of the Moon [5-7]. Dawn images also showed that Vesta is covered with a well-developed regolith that is spectrally similar to howardite meteorites [8]. Howardites are polymict regolith breccias made up mostly of clasts of eucrites and diogenites, but which also contain clasts formed by melting of the regolith by relatively large, energetic impact events. Impact-melt clast ages from howardites extend our knowledge of the impact history of Vesta, expanding on eucrite disturbance ages and helping give absolute age context to the observed crater-counts produced using Dawn data. The distribution of 40Ar-39Ar ages of impact-melt clasts in howardites shows that they formed within the time period 3.3-3.8 Ga [9]. These, and other impact-melted HED materials, have distinct age and compositional characteristics that suggest they formed in discrete impact events. In order to create these crystalline impact-melt products on the surface of Vesta, the impacts during this time period must have had velocities much higher than 5 km/s, the main belt average [10]. This is inconsistent with formation by a normal distribution of impact velocities and points instead to a unique period where high-velocity collisions were more frequent than currently observed. Until now, impact-reset ages in the HED meteorites have been be interpreted under the umbrella of the canonical lunar cataclysm where an increase in the absolute number of bombarding objects is responsible for creating larger absolute amounts of impact-affected and impact-melted rocks, statistically increasing their chances of being found on Earth and dated. However, the distribution of age among the howardite impact-melt clasts may not necessarily result from an increased number of impacts, but rather result from impacts of higher velocity. The changeover from a typical main belt velocity profile to this regime of increased velocity population at Vesta occurs contemporaneously with a similar transition at the Moon, indicating that howardite impact-melt clast ages reinforce the notion of a dynamically unusual episode of bombardment in the inner solar system beginning at around 4.0 Ga.

Cohen, B. A.↗

DOE OSTI2024

Interplay of coulomb and exciton–phonon coupling controls singlet fission dynamics in two pentacene polymorphs

Pentacene is an important model organic semiconductor in both the singlet exciton fission (SF) and organic electronics communities. We have investigated the effect of changing crystal structure on the SF process, generating multiple triplet excitons from an initial singlet exciton, and subsequent triplet recombination. Unlike for similar organic semiconductors that have strong SF sensitive to polymorphism, we find almost no quantitative difference between the kinetics of triplet pair (TT) formation in the two dominant polymorphs of pentacene. Both pairwise dimer coupling and momentum-space crystal models predict much faster TT formation from the bright singlet excited state of the Bulk vs ThinFilm polymorph, contrasting with the experiment. GW and Bethe–Salpeter equation calculations, including exciton–phonon coupling, reveal that ultrafast phonon-driven transitions in the ThinFilm polymorph compensate the intrinsically slower purely Coulomb-mediated TT formation channel, rationalizing the similarity in observed rates. Taking into account the influence of subtle structural distinctions on both the direct and phonon-mediated SF pathways reveals a predictive capability to these methods, expected to be applicable to a wide variety of molecular crystals.

14 SOLAR ENERGY↗

NASA NTRSDate not supplied

Modeling the Crystallization of Martian Igneous Compositions

The martian crust is dominated by basalts and ultramafic rocks [1]. Understanding the crystallization sequence of martian igneous rocks is critical for constraining the petrologic and geochemical evolution of the crust and mantle. Experimental studies have investigated the parental liquid compositions and crystallization behavior using martian meteorite compositions [2-7], as well as compositions measured by rovers on the martian surface [8,9]. While experiments deliver crucial results, they are often limited by time and resources. Therefore, modeling approaches are an ideal tool to complement experimental results. The application of the MELTS software package [10, 11], to calculate the crystallization of martian compositions, reproduces important compositional details of magma crystallization but significant uncertainties regarding the pressure of the olivine-pyroxene multiple saturation point have been reported [12], and in the temperatures of initial crystallization [12, 13]. Recently, a new melting model, MAGMARS, has been shown to reproduce martian primary melts more accurately [14]. Here, we constrain the applicability of Gibbs free energy minimization software Perple_X [15] for martian compositions by comparing our modeled results to experimentally derived crystallization paths for two martian compositions.

J Semprich↗

NASA NTRS1992

Prediction of dislocation generation during Bridgman growth of GaAs crystals

Dislocation densities are generated in GaAs single crystals due to the excessive thermal stresses induced by temperature variations during growth. A viscoplastic material model for GaAs, which takes into account the movement and multiplication of dislocations in the plastic deformation, is developed according to Haasen's theory. The dislocation density is expressed as an internal state variable in this dynamic viscoplastic model. The deformation process is a nonlinear function of stress, strain rate, dislocation density and temperature. The dislocation density in the GaAs crystal during vertical Bridgman growth is calculated using a nonlinear finite element model. The dislocation multiplication in GaAs crystals for several temperature fields obtained from thermal modeling of both the GTE GaAs experimental data and artificially designed data are investigated.

Tsai, C. T.↗

DOE OSTI2025

Multiple Twinning in Nacre and Aragonite

Twinning occurs when two crystals share a coherent interface along which their lattices are mirror symmetric. Here, twinning is investigated in biogenic and geologic aragonite (CaCO 3 ) in columnar nacre from the red abalone Haliotis rufescens, sheet nacre from the black-lip pearl oyster Pinctada margaritifera, and geologic aragonite. All samples exhibit the expected single (110) twins, characterized by a 116.2° rotation of the aragonite a-axis. Surprisingly, multiple twins—double, triple, quadruple—are also observed, each involving successive 116.2° rotations of the a-axis around the c-axis. Multiple twinning is concomitant but distinct from the well-known cyclic twinning of aragonite. Multiple twinning is most prevalent in columnar nacre, reaching up to quadruple twins, most frequently occurring between nacre tablets in the same column, whereas sheet nacre and geologic aragonite exhibit up to triple twins. The frequency of twins decreases with increasing twin multiple, consistent with a physical rather than biological origin. This interpretation is supported by observations in geologic aragonite and by simulations of columnar nacre growth, which incorporate only nucleation rate, growth rate, and basic geometric constraints, yet they reproduce the observed twinning behavior in columnar nacre, reinforcing the conclusion that multiple twinning arises from physical growth mechanisms.

Schmidt, Connor A. [Univ. of Wisconsin, Madison, W↗

DOE OSTI2023

Eulerian finite element implementations of a dislocation density-based continuum model

In Eulerian finite element simulations, the mesh moves relative to the material. After every change of position between the mesh and the material, the state variables are interpolated to the new mesh position, which is referred to as advection. Large strain crystal plasticity models are based on the multiplicative decomposition of the total deformation gradient. Further, the stress is evaluated as a function of the thermoelastic strain, temperature, and other state variables. Advection of tensor quantities, such as the strain, is coupled with possibly significant advection errors. In an effort to reduce the advection errors, we develop two rate forms of an established dislocation density-based continuum model. To that end, we replace the multiplicative decomposition of the deformation gradient with the additive decomposition of the velocity gradient, and define the stress rate instead of the total stress. The Eulerian implementation is compared with Lagrangian calculations, and two numerical examples with severe deformation levels are presented.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Annealing of focused ion beam damage in gold microcrystals: an in situ Bragg coherent X-ray diffraction imaging study

Focused ion beam (FIB) techniques are commonly used to machine, analyse and image materials at the micro- and nanoscale. However, FIB modifies the integrity of the sample by creating defects that cause lattice distortions. Methods have been developed to reduce FIB-induced strain; however, these protocols need to be evaluated for their effectiveness. Here, non-destructive Bragg coherent X-ray diffraction imaging is used to study the in situ annealing of FIB-milled gold microcrystals. Two non-collinear reflections are simultaneously measured for two different crystals during a single annealing cycle, demonstrating the ability to reliably track the location of multiple Bragg peaks during thermal annealing. The thermal lattice expansion of each crystal is used to calculate the local temperature. This is compared with thermocouple readings, which are shown to be substantially affected by thermal resistance. To evaluate the annealing process, each reflection is analysed by considering facet area evolution, cross-correlation maps of the displacement field and binarized morphology, and average strain plots. The crystal's strain and morphology evolve with increasing temperature, which is likely to be caused by the diffusion of gallium in gold below ~280°C and the self-diffusion of gold above ~280°C. The majority of FIB-induced strains are removed by 380–410°C, depending on which reflection is being considered. These observations highlight the importance of measuring multiple reflections to unambiguously interpret material behaviour.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Dynamics of self-hybridized exciton–polaritons in 2D halide perovskites

Abstract Excitons, bound electron–hole pairs, in two-dimensional hybrid organic inorganic perovskites (2D HOIPs) are capable of forming hybrid light-matter states known as exciton-polaritons (E–Ps) when the excitonic medium is confined in an optical cavity. In the case of 2D HOIPs, they can self-hybridize into E–Ps at specific thicknesses of the HOIP crystals that form a resonant optical cavity with the excitons. However, the fundamental properties of these self-hybridized E–Ps in 2D HOIPs, including their role in ultrafast energy and/or charge transfer at interfaces, remain unclear. Here, we demonstrate that >0.5 µm thick 2D HOIP crystals on Au substrates are capable of supporting multiple-orders of self-hybridized E–P modes. These E–Ps have high Q factors (>100) and modulate the optical dispersion for the crystal to enhance sub-gap absorption and emission. Through varying excitation energy and ultrafast measurements, we also confirm energy transfer from higher energy E–Ps to lower energy E–Ps. Finally, we also demonstrate that E–Ps are capable of charge transport and transfer at interfaces. Our findings provide new insights into charge and energy transfer in E–Ps opening new opportunities towards their manipulation for polaritonic devices.

42 ENGINEERING↗

DOE OSTI2024

Light-enhanced oxygen degradation of MAPbBr 3 single crystal

Organometal halide perovskites are promising materials for optoelectronic applications, whose commercial realization depends critically on their stability under multiple environmental factors. In this study, a methylammonium lead bromide (MAPbBr 3 ) single crystal was cleaved and exposed to simultaneous oxygen and light illumination under ultrahigh vacuum (UHV). The exposure process was monitored using X-ray photoelectron spectroscopy (XPS) with precise control of the exposure time and oxygen pressure. It was found that the combination of oxygen and light accelerated the degradation of MAPbBr 3 , which could not be viewed as a simple addition of that by oxygen-only and light-only exposures. The XPS spectra showed significant loss of carbon, bromine, and nitrogen at an oxygen exposure of 10 10 Langmuir with light illumination, approximately 17 times of the additive effects of oxygen-only and light-only exposures. It was also found that the photoluminescence (PL) emission was much weakened by oxygen and light co-exposure, while previous reports had shown that PL was substantially enhanced by oxygen-only exposure. Measurements using a scanning electron microscope (SEM) and focused ion beam (FIB) demonstrated that the crystal surface was much roughened by the co-exposure. Furthermore, Density functional theory (DFT) calculations revealed the formation of superoxide and oxygen induced gap state, suggesting the creation of oxygen radicals by light illumination as a possible microscopic driving force for enhanced degradation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗