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At least 505 records · Page 28

Effects of warming on bacterial growth rates in a peat soil under ambient and elevated CO 2

Boreal peatlands are important global carbon reservoirs that are particularly vulnerable to predicted climate changes such as increasing CO 2 and temperature. Since microbial activities regulate the balance of carbon sequestered into soil organic matter or remineralized to CO 2 , characterizing their response to these environmental factors is critical to predicting how peatland ecosystems will affect climate-carbon cycle feedbacks. Here we examined in-situ taxon-specific variation in microbial growth under long-term elevated CO 2 and across a gradient of warming treatments in a northern Minnesota peat bog using quantitative stable isotope probing with 18 O-water. Across temperatures, bacterial taxa were grouped according to the excess atom fraction 18 O (EAF) of their genomes, a proxy for DNA replication and hence, growth. Taxon-specific growth across CO 2 and temperature treatments clustered into relatively few response patterns. While a large portion of taxa showed little to no growth under ambient CO 2 , many of the same taxa grew rapidly under elevated CO 2 . We found support for phylogenetic conservation of response patterns among Acidobacteria and Proteobacteria, the two most abundant phyla in our data. Our results suggest certain taxa may be primed for new climate conditions and have a greater influence on carbon cycling with implications for future climate mitigation strategies.

16S amplicon sequencing, Carbon Dioxide (CO2), pea↗

Characterization of Two Positional Isomers of the Cs + Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions

Metal ion binding to amino acid residues is an important interaction motif that controls the tertiary structures of oligopeptides. Analyses of the vibrational band patterns displayed by the amino acid scaffolds are commonly used to characterize the local docking motifs. Here we carry out two-color, IR-IR photobleaching measurements to obtain isomer-selective vibrational spectra of the Cs + Gly ion-molecule complex isolated in a cryogenically cooled, radiofrequency ion trap. The distinct band patterns of two non-interconverting isomers are observed and traced to different bidentate binding motifs between Cs + and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid head group yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. Furthermore, the band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.

Infrared spectroscopy↗

Observation of a single protein by ultrafast X-ray diffraction

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Meso bromination and derivatization of synthetic bacteriochlorins

Here, the ability to prepare and tailor synthetic analogues of native bacteriochlorophylls enables diverse applications. A de novo route entails dimerization of a dihydrodipyrrin-acetal to afford the corresponding 5-methoxy and/or 5-unsubstituted bacteriochlorin, wherein each pyrroline ring contains a gem-dimethyl group to ensure stability toward adventitious dehydrogenation. The presence of a 5-methoxy group facilitates bromination at the distal meso-(15-)position. While bromination of 5-unsubstituted bacteriochlorins typically affords a mixture of brominated products, here the presence of two substitution patterns (2,12-dicarboethoxy, 2,12-diacetyl) has been found to facilitate selective meso-bromination in the absence of the methoxy substituent. The introduction of a single meso-bromine atom in a bacteriochlorin opens opportunities for Pd-mediated derivatization, which include (1) preparation of four ethynylphenyl building blocks (and two benchmark bacteriochlorins) with long-wavelength absorption bands tuned across 725–757 nm, for use in preparation of multichromophore arrays; (2) installation of a bioconjugatable group to free base bacteriochlorins or a copper bacteriochlorin, the latter for possible use in photoacoustic imaging; and (3) installation of an S-acetylthio group for surface attachment. Altogether, 25 new bacteriochlorins are described including 5 meso-bromobacteriochlorin intermediates and 12 target bacteriochlorins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

IMPROVED Co i log(gf) VALUES AND ABUNDANCE DETERMINATIONS IN THE PHOTOSPHERES OF THE SUN AND METAL-POOR STAR HD 84937

New emission branching fraction measurements for 898 lines of the first spectrum of cobalt (Co i) are determined from hollow cathode lamp spectra recorded with the National Solar Observatory 1 m Fourier transform spectrometer on Kitt Peak, AZ and a high-resolution echelle spectrometer. Published radiative lifetimes from laser induced fluorescence measurements are combined with the branching fractions to determine accurate absolute atomic transition probabilities for the 898 lines. Hyperfine structure (hfs) constants for levels of neutral Co in the literature are surveyed and selected values are used to generate complete hfs component patterns for 195 transitions of Co i. These new laboratory data are applied to determine the Co abundance in the Sun and metal-poor star HD 84937, yielding log ϵ(Co) = 4.955 ± 0.007 (σ = 0.059) based on 82 Co i lines and log ϵ(Co) = 2.785 ± 0.008 (σ = 0.065) based on 66 Co i lines, respectively. A Saha or ionization balance test on the photosphere of HD 84937 is performed using 16 UV lines of Co ii, and good agreement is found with the Co i result in this metal-poor ([Fe i/H] = −2.32, [Fe ii/H] = −2.32) dwarf star. The resulting value of [Co/Fe] = +0.14 supports a rise of Co/Fe at low metallicity that has been suggested in other studies.

79 ASTRONOMY AND ASTROPHYSICS↗

Consequences of Lattice Mismatch for Phase Equilibrium in Heterostructured Solids

Lattice mismatch - the difference in natural bond length between two species comprising a solid is a common occurrence in modern materials. Spatial patterns in certain nanocrystal heterostructures, for instance, are thought to be a result of elastic forces arising from lattice mismatch. However, the role of lattice mismatch in mediating the arrangement of atoms in such materials is incompletely understood. Here we consider a simple microscopic model for lattice mismatch, in which the difference in natural lengths between bonded atoms produces interactions mediated by elastic strain. Computer simulations reveal that the model exhibits rich phase behavior, including structures with periodic order and unusual coexistence scenarios. To explain this phase behavior, we derive an effective pairwise interaction potential between atoms, revealing preferred spatial arrangements of atoms driven by spatial variations in the interaction potential. We then develop a mean field theory based on this effective interaction which qualitatively captures observed transition to phases with modulated order. Finally, we explain the observed scenarios of coexistence between using a graphical construction, based on the realization that the free energy cost of phase separation in elastic systems grows with system size. Here, these results clarify the equilibrium effects of lattice mismatch in macroscopic solids and suggest a role for lattice mismatch in creating spatially heterogeneous compositions in nanoscale materials.

36 MATERIALS SCIENCE↗

Tuning 3-D Nanomaterial Architectures Using Atomic Layer Deposition to Direct Solution Synthesis

The ability to synthesize nanoarchitected materials with tunable geometries provides a means to control their functional properties, with applications in biological, environmental, and energy fields. To this end, various bottom-up and top-down synthesis processes have been developed. However, many of these processes require prepatterning or etching steps, making them challenging to scale-up to complex, nonplanar substrates. Furthermore, the ability to integrate nanomaterials into hierarchical arrays with precise control of feature spacing and orientation remains a challenge. One approach to overcome these patterning challenges is the use of surface modification layers to guide the resulting geometry of nanomaterial architectures grown from the substrate. A powerful strategy to accomplish this is what we will refer to as “surface-directed assembly,” where the resulting geometric parameters (feature size, shape, orientation) are predetermined by the initial surface layer. In particular, the use of Atomic Layer Deposition (ALD) to form a surface layer, followed by solution-based growth processes, has the ability to synthesize architected structures with tunable geometries on complex, nonplanar surfaces. Over the past decade, we have reported a series of studies where surface-directed assembly is used to synthesize ZnO nanowires (NWs) on top of a variety of substrates. In this case, a thin film of ZnO is deposited onto the substrate using ALD, which can guide the NW diameter, spacing, and angular orientation with respect to the substrate by controlling epitaxial relationships. Furthermore, we have shown that by depositing a submonolayer overcoat of a secondary material (e.g., amorphous TiO 2 ), nucleation sites are partially blocked, which can further tune the spacing between nanowires while minimizing changes to their other geometric properties. This approach can be used to generate multilevel hierarchical structures, such as hyperbranched NW arrays with tunable control of each level of hierarchy using ALD. Finally, we have demonstrated that the tunable control of geometric parameters can be scaled-up to curved, nonplanar substrates. This highlights the power of ALD to conformally and uniformly deposit the seed layers on complex substrates with subnanometer precision. To complement these seeded hydrothermal approaches, we expanded this strategy to include conversion chemistry of the initial ALD seed layers. For example, by replacing ZnO with Al 2 O 3 as the seed layer without changing the hydrothermal growth conditions, Al–Zn layered-double hydroxide nanosheets can be formed instead of nanowires. In another example of conversion chemistry, a solution anion-exchange process was used to incorporate sulfur into ALD metal oxide films. In both of these conversion processes, the properties of the initial ALD film enabled tuning of the resulting nanostructure geometry. In this Account, we describe the use of ALD to guide the growth of diverse nanomaterial systems, with tunable control over their geometry and composition. We further show how these approaches can be used to tune functional properties for a range of applications, including superomniphobic surfaces, antibiofouling coatings, and photocatalysis. In conclusion, we conclude with an outlook on how the combination of ALD and solution synthesis can enable future directions in scalable nanomanufacturing to overcome the limitations of traditional top-down and bottom-up approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Non-volatile polarization switch of magnetic domain wall velocity

Controlled propagation speed of individual magnetic domains in metal channels at the room temperature is obtained via the non-volatile field effect associated with the switchable polarization of P(VDF-TrFE) (polyvinylidene fluoride-trifluoroethylene) ferroelectric polymer. Polarization domains directly written using conducting atomic force microscope probe locally accelerate/decelerate the magnetic domains in the 0.6 nm thick Co film. The change of the magnetic domain wall velocity is consistent with the magnetic anisotropy energy modulation through the polarization upward/downward orientation. Excellent retention is observed. The demonstrated local non-destructive and reversible change of magnetic properties via rewritable patterning of ferroelectric domains could be attractive for exploring the ultimate limit of miniaturization in devices based on ferromagnetic/ferroelectric bilayers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Influence of molecular clustering on the interpretation of diffractograms of hydrocarbon films from tokamak T-10

The influence of molecular clustering on the formerly suggested interpretation of diffraction patterns of hydrocarbon films formed in the vacuum vessel of the tokamak T-10 is analyzed numerically. The simulation of clustering of simple hydrocarbon molecules C(D, H){sub 4}, C{sub 2}(D, H){sub 4}, and C{sub 6}(D, H){sub 6} and molecules composed of curved graphene (fullerenes and toroidal nanotubes) is carried out with the rigid body molecular dynamics method. It is shown that formerly neglected atomic correlations C–C and C–D(H) in the amorphous hydrocarbon component decrease the calculated values of the scattered intensity in the range of scattering vector modulus 5 < q < 20 nm{sup –1} because of homogenization of scatters on the spatial scale of ∼1 nm. The allowance for these correlations does not change the diffraction patterns in the range q > 20 nm{sup –1}. The results suggest the necessity to introduce to the procedure of determining the structural content of the films, similar to those from the tokamak T-10, the clusters formed by the van der Waals adhesion of hydrocarbon molecules to “graphene” nanoparticles. This simplifies the mathematical optimization to the former level of complexity—but for an extended ensemble of objects—and makes it possible to calculate the diffraction patterns of these objects using the distributed computing resources. A modified algorithm of structural content identification on the basis of joint X-ray and neutron diffractometry is suggested.

36 MATERIALS SCIENCE↗

EUV Spectra and Line Ratios of Multiply Ionized Calcium and Argon Atoms in a Laboratory Plasma

The utility of Ca in the EUV spectral range of astrophysical observations is limited by a fragmentary and incomplete record of laboratory data. In order to obtain a more comprehensive survey of the Ca line emission in the EUV, we have used a tokamak plasma discharge in hydrogen carrying some Ar and intermittently seeded with Ca as a tool for investigating the emission line intensity pattern of highly charged Ca and Ar ions in the wavelength range 100–285 Å with 0.35 Å spectral resolution. Here, we compare our data to wavelengths and line ratios in much-used databases, especially CHIANTI, and we discuss apparent inconsistencies.

79 ASTRONOMY AND ASTROPHYSICS↗

Compositional patterning in irradiated alloys: Effective potentials and effective interfacial energy

Compositional patterning (CP) in binary alloys during energetic particle irradiation is studied using a kinetic model that considers two competing kinetic processes, a thermally activated one promoting macroscopic phase separation (MPS) of the concentration field c(r,t) and a forced one resulting in finite-range random atomic mixing. The forced mixing is modeled by a Gaussian relocation distribution with a characteristic distance R. A series of approximate kinetic models are introduced by expanding the mixing function into a series of n terms, thus replacing the non-local evaluations of the concentration field c(r'-r,t) by local derivatives of c(r,t). This approach makes it possible to obtain exact effective potentials and build steady-state diagrams for each order-n model. Phase field (PF) simulations using these order-n models reveal that near the onset of patterning, phase evolution is accurately described using an order-3 model, which changes smoothly from an extended Cahn-Hilliard free energy in the MPS regime to a one-mode Swift-Hohenberg functional in the CP regime. Deeper into the patterning regime, higher-order models are required to achieve convergence, yielding square-like concentration profiles characteristic of a strong segregation regime. These higher-order effective free energies are analogous to multimodal Swift-Hohenberg functionals. Here, a new definition for the effective interfacial energy is proposed in the CP regime, since the interfacial area is no longer an excess quantity in that regime, precluding the use of the standard thermodynamic definition of interfacial energy.

36 MATERIALS SCIENCE↗

Enhanced phase contrast transfer using ptychography combined with a pre-specimen phase plate in a scanning transmission electron microscope

We report the ability to image light elements in both crystalline and noncrystalline materials at near atomic resolution with an enhanced contrast is highly advantageous to understand the structure and properties of a wide range of beam sensitive materials including biological specimens and molecular hetero-structures. This requires the imaging system to have an efficient phase contrast transfer at both low and high spatial frequencies. Here, we introduce a new phase contrast imaging method in a scanning transmission electron microscope (STEM) using a pre-specimen phase plate in the probe forming aperture, combined with a fast pixelated detector to record diffraction patterns at every probe position, and phase reconstruction using ptychography. The phase plate significantly enhances the contrast transfer of low spatial frequency information, and ptychography maximizes the extraction of the phase information at all spatial frequencies. In addition, the STEM probe with the presence of the phase plate retains its atomic resolution, allowing simultaneous incoherent Z-contrast imaging to be obtained along with the ptychographic phase image. An experimental image of Au nanoparticles on a carbon support shows high contrast for both materials. Multislice image simulations of a DNA molecule shows the capability of imaging soft matter at low dose conditions, which implies potential applications of low dose imaging of a wide range of beam sensitive materials.

36 MATERIALS SCIENCE↗

Structure and morphology evolution of silica-modified pseudoboehmite aerogels during heat treatment

Silica-modified pseudoboehmite aerogels (0, 10, 20 at% of Si) were prepared by sol–gel method followed by supercritical drying. The phase transformations, changes in structure and morphology upon calcination were thoroughly investigated by advanced X-Ray diffraction (XRD) techniques and high-resolution transmission electron microscopy (HRTEM). Obtained pseudoboehmite samples had specific nanostructure: ultrathin two-dimensional (2D) crystallites were loosely packed. The silica dopant drastically enhanced the crystallite anisotropy. Thus, the aerogel with Al:Si atomic ratio of 9:1 consisted of the pseudoboehmite nanosheets with thickness of one unit cell (average dimensions of 14.0×1.2×14.5 nm). The specific nanostructure caused remarkable features of experimental XRD patterns, including anisotropic peak broadening and appearance of forbidden reflection. Direct simulation of XRD patterns with using the Debye Scattering Equation allowed the size and morphology of pseudoboehmite crystallites to be determined. The silica addition strongly delayed formation of γ-alumina and further phase transformations upon calcinaton. Thermal stability of alumina was suggested to be affected by the particle morphology inherited from the pseudoboehmite precursor. - Graphical abstract: Pseudoboehmite samples had specific nanostructure: ultrathin two-dimensional (2D) crystallites were loosely packed. - Highlights: • Silica-doped boehmites were prepared by sol–gel method with supercritical drying. • Ultrathin two-dimensional crystallites of pseudoboehmite were obtained. • Changes in structure and morphology upon calcination were studied. • Simulation of XRD patterns was performed with use of the Debye Scattering Equation. • Thermal stability of alumina depended on morphology inherited from pseudoboehmite.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Diffractive imaging of a rotational wavepacket in nitrogen molecules with femtosecond megaelectronvolt electron pulses

Imaging changes in molecular geometries on their natural femtosecond timescale with sub-Angström spatial precision is one of the critical challenges in the chemical sciences, as the nuclear geometry changes determine the molecular reactivity. For photoexcited molecules, the nuclear dynamics determine the photoenergy conversion path and efficiency. Here we report a gas-phase electron diffraction experiment using megaelectronvolt (MeV) electrons, where we captured the rotational wavepacket dynamics of nonadiabatically laser-aligned nitrogen molecules. We achieved a combination of 100 fs root-mean-squared temporal resolution and sub-Angstrom (0.76 Å) spatial resolution that makes it possible to resolve the position of the nuclei within the molecule. In addition, the diffraction patterns reveal the angular distribution of the molecules, which changes from prolate (aligned) to oblate (anti-aligned) in 300 fs. Lastly, our results demonstrate a significant and promising step towards making atomically resolved movies of molecular reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Relationship between magnetoresistance behavior and magnetic states in intercalated compounds Fe x TiS 2

Here, temperature and field-dependent neutron powder diffraction (NPD) measurements have been performed to reveal the nature of the unusual evolution of the magnetoresistance behavior with increasing Fe content in the intercalated compounds Fe x TiS 2 (with x=0.25,0.33,0.50,0.55) synthesized by solid-phase reaction method with prolonged homogenization heat treatment. As derived from neutron diffraction measurements, both the Fe 0.25 TiS 2 and the Fe 0.50 TiS 2 compound exhibit an antiferromagnetic (AFM) order below their respective Néel temperatures T N ≈52 K and T N ≈140K, which results in the presence of a large magnetoresistance accompanying the field-induced phase transition from AFM to the ferromagnetic (FM) state. At low temperatures, this AFM-FM transition is irreversible, confirmed by the irreversibility of changes in the NPD patterns and the presence of remnant magnetoresistance. In contrast, Fe 0.33 TiS 2 shows short-range magnetic order at T f ≈44 K due to a triangular network of intercalated Fe atoms and frustrations of exchange interactions with a field-induced FM alignment of Fe magnetic moments in an applied magnetic field as revealed by NPD measurements. The field-induced transformations of the cluster glass magnetic state in this compound lead to a significant decrease in electrical resistivity. According to NPD data, a reduced impact of an external magnetic field on the electrical resistivity of the compound Fe 0.55 TiS 2 can be ascribed to the presence of ferromagnetic or ferrimagnetic order in compounds with the Fe concentrations above x=0.50. The results obtained indicate that the distribution of the Fe atoms, along with their concentration in Fe x TiS 2 layered compounds, plays a decisive role in the formation of the magnetic state and the behavior of the magnetoresistance.

36 MATERIALS SCIENCE↗

Novel Charge-Ordered States in 1 T -IrTe 2

1T-IrTe 2 exhibits an intriguing series of charge-ordered states in both bulk and atomically thin layers. The charge orders in IrTe 2 emerge with consecutive first-order structural transitions involving in-plane Ir–Ir dimerization and interlayer Te–Te depolymerization, resulting in stripe patterns with various periods. Upon chemical doping, 1T-IrTe 2 can also be driven into a superconductor. Despite the intense research effort, a comprehensive understanding of the nature of the charge ordering and its relation to the superconductivity is yet to be reached. This review provides an overview of the novel charge orders and the emergence of superconductivity in IrTe 2 . Finally, we further introduce the recent studies on IrTe 2 nanoflake, in which novel charge orders attainable only in two-dimensional limits lay the grounds for an exotic phase diagram.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

X‑ray Coherent Diffractive Imaging of Large Helium Nanodroplets Doped with Small Molecules

We report the first X-ray coherent diffractive imaging experiment on molecule-doped helium nanodroplets. It complements previous work, where we reported single-shot X-ray coherent diffractive imaging studies of Xe dopant clusters formed in 4He and 3He droplets. These noble gas clusters were used to visualize the impact of rotational excitation of the droplets on the spatial distribution of atomic dopants within the droplets, and to study the differences and connections between quantum and classical droplet rotational motion. Here, we expand our studies to the molecular dopants CF4, CHF3, CH3CN, and SF6, imaged with 1.5 keV photons. We find multiple Bragg spots in the diffraction patterns of molecule-doped droplets with radii of approximately 600 nm, which provide evidence that molecules form elongated clusters with preferential alignment along the angular momentum axis of the 4He droplets, in agreement with our previous results on the aggregation of Xe clusters on quantum vortices. Real-space reconstructions of molecular dopant cluster density profiles are obtained for droplets with smaller radii of approximately 300 nm. The diffuse images suggest the formation of low-density, potentially porous, molecular clusters upon aggregation at T = 0.4 K in 4He droplets. In the normal fluid 3He droplets, molecules aggregate into loose clusters on the droplets' equator, similar to previous observations for Xe atoms. Time-of-flight mass spectra reveal that the doped helium nanodroplet moieties fragment extensively into constituent atomic ions, producing only a small fraction of molecular fragment ions. The findings are discussed in the context of previously proposed schemes to use He droplets as potential tamper materials for ultrafast X-ray imaging experiments.

Feinberg, AlexandraJ↗

The effect of hydrogen embrittlement on the localized plastic deformation of aluminum alloy

The effect of hydrogen embrittlement on the localized plastic deformation of aluminum alloy D1 was investigated. The studies were performed for the test samples of aluminum alloy subjected to electrolytic hydrogenation. It is found that the mechanical properties and localized plastic deformation parameters of aluminum alloy are affected adversely by hydrogen embrittlement. The hydrogenated counterpart of alloy has a lower degree of ductility relative to the original alloy; however, the plastic flow behavior of material remains virtually unaffected. Using scanning electron and atomic force microscopy methods, the changes in the fracture surface were investigated. The deformation diagrams were examined for the deformed samples of aluminum alloy. These are found to show all the plastic flow stages: the linear, parabolic and pre-failure stages would occur for the respective values of the exponent n from the Ludwik-Holomon equation. Using digital speckle image technique, the local strain patterns were being registered for the original alloy D1 and the counterpart subjected to electrolytic hydrogenation for 100 h.

36 MATERIALS SCIENCE↗