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At least 1,603 records · Page 89

Capturing Nucleation at 4D Atomic Resolution

Nucleation plays a critical role in many physical and biological phenomena ranging from crystallization, melting and evaporation to the formation of clouds and the initiation of neurodegenerative diseases. However, nucleation is a challenging process to study especially in the early stage when several atoms/molecules start to form a new phase from its parent phase. Here, we advance atomic electron tomography to study early stage nucleation at 4D atomic resolution. Using FePt nanoparticles as a model system, we reveal that early stage nuclei are irregularly shaped, each has a core of a maximum order parameter, and an order parameter gradient points from the core to the boundary of the nucleus. We capture the structure and dynamics of the same nuclei undergoing growth, fluctuation, dissolution, merging and/or division, which are regulated by the distribution of the order parameter and its gradient. These experimental results differ from classical nucleation theory (CNT) and to explain them we propose an order parameter gradient model, which is more general and thermodynamically more favourable than CNT. We further corroborate this model using molecular dynamics simulations of heterogeneous and homogeneous nucleation in the liquid-solid phase transition of Pt. Here, we anticipate that the order parameter gradient model is applicable to different kinds of nucleation processes and our experimental method opens the door to study the structure and dynamics of materials with 4D atomic resolution.

74 ATOMIC AND MOLECULAR PHYSICS↗

Fast Nitrogen Atoms from Dissociative Excitation of N2 by Electron Impact

The Doppler profiles of one of the fine structure lines of the N I (1200 A) g (sup 4)S(sup 0)-(sup 4)P multiplet and of the N II (1085 A) g (sup 3)p(sup O)-(sup 3)D multiplet have been measured. Excitation of the multiplets is produced by electron impact dissociative excitation of N2. The experimental line profiles are evaluated by fast Fourier transform (FFT) techniques and analysis of the profiles yields the kinetic energy distribution of fragments. The full width at half maximum (FWHM) of N I (1200 A) increases from 27+/-6 mA at 30 eV to 37+/-4 mA at 100 eV as the emission cross section of the dissociative ionization excitation process becomes more important relative to the dissociative excitation process. The FWHM of the N II (1085 A) line is 36+/-4 mA at 100 eV. For each multiplet the kinetic energy distribution function of each of the two fragment N atoms (ions) is much broader than thermal with a mean energy above 1.0 eV. The dissociation process with the largest cross section is predissociation and predominantly produces N atoms with kinetic energy distributions having mean energies above 0.5 eV. Dissociative processes can lead to a substantial escape flux of N I atoms from the satellites, Titan and Triton of the outer planets.

Ajello, Joseph M.↗

Building access and community standards for opacity data at the onset of next-generation atmosphere observations

The characterization of a diverse set of exoplanet atmosphere observations, ranging from hot gas giants to small temperate rocky worlds, will be one of the legacies of upcoming facilities such as the James Webb Space Telescope (JWST). Our understanding and interpretation of such observations will hinge on our ability to link observations with atmospheric theoretical studies that critically rely on fundamental molecular and atomic opacities. Computing such opacities is a highly non-trivial and inaccessible process which requires several terabytes of available disk space, hours of CPU time per pressure-temperature combination, and requires users to carefully aggregate line lists data from various sources, which limits access and intercomparison of opacity data in the exoplanet community. Here we present MAESTRO (Molecules and Atoms in Exoplanet Science: Tools and Resources for Opacities) an opacity database that can be accessed by the community via a web interface and python API. MAESTRO was built with community input to create a version-controlled opacity database that is easily queryable, includes informative metadata to ensure reproducibility, and exports relevant citations for inclusion in publications. Scheduled for community release in 2022, MAESTRO will prove to be an invaluable community resource in the era of JWST and beyond.

Natasha Batalha↗

Disruptive Technology for Carbon Negative Commodity Chemicals

This project was designed to develop an economically attractive process for the carbon negative production of the commodity biochemical succinic acid. To compete against petroleum derived biochemicals, the process must deliver high raw material conversion efficiency and high volumetric productivity to reduce both recurring and capital-related costs, respectively. The proposed process introduces additional electrons sourced from hydrogen into the biosynthetic pathway so that the carbon from two CO2 molecules can be combined with each glucose to significantly increase succinic acid yields. The process also uses ultrafiltration to continuously remove the product from the bioreactor to avoid product inhibition and extend the productive life of the cell extract. Genetic deletions and specific enzyme removal during extract preparation more efficiently direct both atomic and electronic resources toward product formation. A preliminary technoeconomic analysis indicates that these process innovations made possible by cell-free production will enable large scale production with attractive ROI and profitability. This two-year project provided some 29 distinct insights, analytical advances, and process improvements that resulted in a demonstration of process feasibility. However, an estimated two to three years of additional development will be required to achieve convincing pilot scale demonstrations that will motivate large scale investments.

60 APPLIED LIFE SCIENCES↗

Effects of carbon content and size on Ti-C reaction behavior and resultant properties of Cu-Ti-C alloy system

Highlights: • TiC-strengthened Cu alloys were synthesized by an in situ powder metallurgy route. • Effect of C/Ti ratio on electrical and mechanical properties was studied. • Ti-C reaction behavior during powder metallurgy process was discussed. • Microstructure evolution during present process was analyzed. - Abstract: TiC-strengthened Cu alloys with various nominal compositions were prepared by a high-energy ball-milling process, followed by consolidation using spark plasma sintering (SPS), and a subsequent heat treatment. The results indicated that the lower atomic ratio of C/Ti, the more residual Ti in copper matrix, resulting in a lower electrical conductivity but higher microhardness of alloy. The optimal atomic ratio was found to be close to1.0. The reaction behavior of Ti-C in the Cu-Ti-C system during this process was investigated. Microstructural results suggested that TiC formation is through a diffusion-controlled mechanism. A thin TiC layer was formed at the surface of C particles, and the growth of TiC layer was controlled by interdiffusion of C and Ti atoms across the TiC layer. An incomplete chemical reaction between Ti and C, characterized by a core-shell structure, was observed when the initial C particles were large, and the TiC particle size was found to strongly depending on the C particle size.

36 MATERIALS SCIENCE↗

Processing of DNA single-strand breaks with oxidatively damaged ends by LIG1

Abstract DNA ligase 1 (LIG1) seals broken strand breaks by joining two adjacent ends during DNA replication and repair transactions. We previously reported atomic-level insight into the strategies that LIG1 uses to discriminate mismatches or ribonucleotides. However, how LIG1 processes strand breaks with oxidatively damaged ends in the absence and presence of a “wrong” sugar remains unknown. Here, we determined the crystal structures of LIG1/nick DNA complexes with 3′-8-oxodG and 3′-8-oxorG templating A or C during the pre- and post-catalytic steps of the ligation reaction. Our structures demonstrated differences in the distances at the +1 and +2 nucleotides relative to the 3′-end of the nick and a shift in the template base position to accommodate the oxidative lesion depending on the dual coding potential of 8-oxoG, which forms Hoogsteen or Watson–Crick base pairing in -syn or -anti conformation. Furthermore, these structural adjustments lead to mutagenic ligation or non-mutagenic end joining of the nick substrates. Overall, our findings provide mechanistic insight into how LIG1 processes nicks harboring oxidative damage and ribonucleotides to ensure fidelity at the final ligation step of DNA repair and replication to maintain genome integrity.

Balu, Kanal E [Department of Biochemistry and Mole↗

Reversible disorder-order transitions in atomic crystal nucleation

Nucleation in atomic crystallization remains poorly understood, despite advances in classical nucleation theory. The nucleation process has been described to involve a nonclassical mechanism that includes a spontaneous transition from disordered to crystalline states, but a detailed understanding of dynamics requires further investigation. In situ electron microscopy of heterogeneous nucleation of individual gold nanocrystals with millisecond temporal resolution shows that the early stage of atomic crystallization proceeds through dynamic structural fluctuations between disordered and crystalline states, rather than through a single irreversible transition. Our experimental and theoretical analyses support the idea that structural fluctuations originate from size-dependent thermodynamic stability of the two states in atomic clusters. These findings, based on dynamics in a real atomic system, reshape and improve our understanding of nucleation mechanisms in atomic crystallization.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Carbon Monoxide Poisoning Resistance and Structural Stability of Single Atom Alloys

Platinum group metals (PGMs) serve as highly active catalysts in a variety of heterogeneous chemical processes. Unfortunately, their high activity is accompanied by a high affinity for CO and thus, PGMs are susceptible to poisoning. Alloying PGMs with metals exhibiting lower affinity to CO could be an effective strategy toward preventing such poisoning. In this work, we use density functional theory to demonstrate this strategy, focusing on highly dilute alloys of PGMs (Pd, Pt, Rh, Ir and Ni) with poison resistant coinage metal hosts (Cu, Ag, Au), such that individual PGM atoms are dispersed at the atomic limit forming single atom alloys (SAAs). We show that compared to the pure metals, CO exhibits lower binding strength on the majority of SAAs studied, and we use kinetic Monte Carlo simulation to obtain relevant temperature programed desorption spectra, which are found to be in good agreement with experiments. Additionally, we consider the effects of CO adsorption on the structure of SAAs. We calculate segregation energies which are indicative of the stability of dopant atoms in the bulk compared to the surface layer, as well as aggregation energies to determine the stability of isolated surface dopant atoms compared to dimer and trimer configurations. Our calculations reveal that CO adsorption induces dopant atom segregation into the surface layer for all SAAs considered here, whereas aggregation and island formation may be promoted or inhibited depending on alloy constitution and CO coverage. Furthermore, this observation suggests the possibility of controlling ensemble effects in novel catalyst architectures through CO-induced aggregation and kinetic trapping.

36 MATERIALS SCIENCE↗

Gaussian process based optimization of molecular geometries using statistically sampled energy surfaces from quantum Monte Carlo

Optimization of atomic coordinates and lattice parameters remains a significant challenge to the wide use of stochastic electronic structure methods such as quantum Monte Carlo (QMC). Measurements of the forces and stress tensor by these methods contain statistical errors, challenging conventional gradient-based numerical optimization methods that assume deterministic results. Additionally, forces are not yet available for some methods, wavefunctions, and basis sets and when available may be expensive to compute to sufficiently high statistical accuracy near energy minima, where the energy surfaces are flat. Here, we explore the use of Gaussian process based techniques to sample the energy surfaces and reduce sensitivity to the statistical nature of the problem. We utilize Latin hypercube sampling, with the number of sampled energy points scaling quadratically with the number of optimized parameters. Furthermore, we show these techniques may be successfully applied to systems consisting of tens of parameters, demonstrating QMC optimization of a benzene molecule starting from a randomly perturbed, broken symmetry geometry.

74 ATOMIC AND MOLECULAR PHYSICS↗

PageRank as a Collective Variable to Study Complex Chemical Transformations and Their Energy Landscapes

A reduced set of reaction coordinates are often employed in chemistry to describe the collective change between reactants and products within the context of rare event theories and in the exploration of energy landscapes. While incredibly powerful, use of these collective variables becomes increasingly challenging as the systems under study become more complex. Recent advancement of new descriptions of collective molecular coordinates have included PageRank (PR) analysis of the network of interactions about molecules and atoms within a system. Herein, PR is developed as a continuous variable that not only captures chemical transformations but can also be employed as a collective variable for a process that could span a highly dimensional energy surface. The derivatives of PR with respect to atomic coordinates are presented, and subsequently combined with forces during a chemical transformation within biased molecular dynamics sampling simulations to create the potential of mean force (PMF). This technique is demonstrated for two reactions: 1) the transformation of tetrahedral [Al(OH)4]-(aq) to octahedral [Al(OH)4(H2O)2]-(aq), and 2) the formation of contact ion pairs (CIPs) and solvent separated ion pairs (SSIPs) of Na+ and OH- in bulk water. Comparison of the behavior of the PR collective variable in both examples reveals that the ability of the PR to resolve local versus extended configurational attributes is tuned by the size of the network employed. This is a unique feature of PageRank that enables control over the resolution of the PMF that is produced.

chemistry, theories, PageRank↗

Radiation transfer in the spectra of short-pulse laser-heated targets

The conditions in laser-produced plasmas are frequently determined with x-ray spectroscopy by comparing calculated to measured spectra. Line spectra from K-shell transitions of low- to mid-atomic number elements are most often used since the important physical processes are well understood and reliable spectra can be readily measured and calculated. Radiation transfer effects due to large optical depths of strong lines can influence the spectra. In this work, the effects of radiation transfer on the emission spectra of short-laser pulse-heated targets are studied. The possible errors made in inferring electron temperature by not including radiation transfer are quantified. The inclusion of radiative transfer in spectral calculations improves the accuracy of typical temperature diagnostics and allows the use of strong lines for diagnostics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Differential scattering cross sections for collisions of 0.5-, 1.5-, and 5.0-keV helium atoms with He, H2, N2, and O2

This paper reports the first results of an experimental program established to provide cross section data for use in modeling various atmospheric processes. Absolute cross sections, differential in the scattering angle, have been measured for collisions of 0.5-, 1.5-, and 5.0-keV helium atoms with He, H2, N2, and O2 at laboratory scattering angles between 0.1 deg and 5 deg. The results are the sums of cross sections for elastic and inelastic scattering of helium atoms; charged collision products are not detected. Integration of the differential cross section data yields integral cross sections consistent with measurements by other workers. The apparatus employs a position-sensitive detector for both primary and scattered particles and uses a short target cell with a large exit aperture to ensure a simple and well-defined apparatus geometry.

Newman, J. H.↗

Polar thermospheric Joule heating, and redistribution of recombination energy in the upper mesosphere

Kellogg (1961), suggested that transport of atomic oxygen from the summer into the winter hemisphere and subsequent release of energy by three body recombination, O+O+N2 yields O2+N2+E, may contribute significantly to the so-called mesopause temperature anomaly. Earlier model calculations have shown that Kellogg's mechanism produces about a 10-percent increase in the temperature from summer to winter at 90 km. This process, however, is partly compensated by differential heating from absorption of UV radiation associated with dissociation of O2. In the auroral region of the thermosphere, there is a steady energy dissipation by Joule heating causing a redistribution and depletion of atomic oxygen due to wind-induced diffusion. With the removal of O, latent chemical energy normally released by three body recombination is also removed, and the result is that the temperature decreases by almost 2 percent near 90 km. Through dynamic feedback, this process reduces the depletion of atomic oxygen by about 25 percent and the temperature perturbation in the exosphere from 10 to 7 percent at polar latitudes. Under the influence of the internal dynamo interaction, the prevailing zonal circulation in the upper thermosphere changes direction when the redistribution of recombination energy is considered.

Mayr, H. G.↗

Attosecond Intramolecular Scattering and Vibronic Delays

We study the temporal and vibrational signature of the universal nuclear recoil associated with the electron emission and intramolecular scattering that accompanies the photoelectric effect. We illustrate these phenomena in the photoionization of the CO molecule from the C-1s orbital using an analytical model that reproduces the entangled character of the nuclear and electronic motion in this process. We show that the photoelectron emission delay can be decomposed into its localization and resonant-confinement components. Photoionization by a broadband x-ray pulse results in a coherent vibrational ionic state delayed compared to the classical sudden-photoemission limit.

74 ATOMIC AND MOLECULAR PHYSICS↗

Angstrom-Resolved Interfacial Structure in Buried Organic-Inorganic Junctions

Charge transport processes at interfaces which are governed by complex interfacial electronic structure play a crucial role in catalytic reactions, energy storage, photovoltaics, and many biological processes. Here, the first soft X-ray second harmonic generation (SXR-SHG) interfacial spectrum of a buried interface (boron/Parylene-N) is reported. SXR-SHG shows distinct spectral features that are not observed in X-ray absorption spectra, demonstrating its extraordinary interfacial sensitivity. Comparison to electronic structure calculations indicates a boron-organic separation distance of 1.9 {\AA}, wherein changes as small as 0.1 {\AA} result in easily detectable SXR-SHG spectral shifts (ca. 100s of meV). As SXR-SHG is inherently ultrafast and sensitive to individual atomic layers, it creates the possibility to study a variety of interfacial processes, e.g. catalysis, with ultrafast time resolution and bond specificity.

74 ATOMIC AND MOLECULAR PHYSICS↗

Wigner time delay in photodetachment

Using Cl - as a test case,Wigner time delay in the photodetachment process has been investigated theoretically, along with the photoionization of the isoelectronic Ar atom, for the outer 3p shell using the relativistic-random-phase approximation (RRPA). Time delay was probed in these systems from threshold to 80 eV, to investigate threshold effects, the centrifugal barrier shape resonance, and the Cooper minimum region. This study focuses on Cl - because, for negative ions, the phase of the photoemission process is not dominated by the Coulomb phase as it is in photoionization. The results show significant differences, both qualitative and quantitative, between the time delays for Cl - and Ar photoemission at low photoelectron energy, but they are rather similar in the Cooper minimum region, where the Coulomb phase is small. In particular, the Wigner time delay in Cl - exhibits a dramatic energy dependence just above threshold, and a rapidly increasing time delay in the vicinity of the shape resonance. A strong angular dependence of time delay has also been found near the threshold region for the Cl - case, and is absent in the case of the photoionization of Ar. The origin of these phenomenologies is explained and a prospectus for future work is presented.

74 ATOMIC AND MOLECULAR PHYSICS↗

Investigating calcite growth rates using a quartz crystal microbalance with dissipation (QCM-D)

Calcite precipitation plays a significant role in processes such as geological carbon sequestration and toxic metal sequestration and, yet, the rates and mechanisms of calcite growth under close to equilibrium conditions are far from well understood. In this study, a quartz crystal microbalance with dissipation (QCM-D) was used for the first time to measure macroscopic calcite growth rates. Calcite seed crystals were first nucleated and grown on sensors, then growth rates of calcite seed crystals were measured in real-time under close to equilibrium conditions (saturation index, SI = log ({Ca 2+ }/{CO 3 2– }/ K sp ) = 0.01–0.7, where {i} represent ion activities and K sp = 10 –8.48 is the calcite thermodynamic solubility constant). At the end of the experiments, total masses of calcite crystals on sensors measured by QCM-D and inductively coupled plasma mass spectrometry (ICP-MS) were consistent, validating the QCM-D measurements. Calcite growth rates measured by QCM-D were compared with reported macroscopic growth rates measured with auto-titration, ICP-MS, and microbalance. Calcite growth rates measured by QCM-D were also compared with microscopic growth rates measured by atomic force microscopy (AFM) and with rates predicted by two process-based crystal growth models. The discrepancies in growth rates among AFM measurements and model predictions appear to mainly arise from differences in step densities, and the step velocities were consistent among the AFM measurements as well as with both model predictions. Using the predicted steady-state step velocity and the measured step densities, both models predict well the growth rates measured using QCM-D and AFM. Furthermore, this study provides valuable insights into the effects of reactive site densities on calcite growth rate, which may help design future growth models to predict transient-state step densities.

58 GEOSCIENCES↗

High-throughput manufacturing of epitaxial membranes from a single wafer by 2D materials-based layer transfer process

Layer transfer techniques have been extensively explored for semiconductor device fabrication as a path to reduce costs and to form heterogeneously integrated devices. These techniques entail isolating epitaxial layers from an expensive donor wafer to form freestanding membranes. However, current layer transfer processes are still low-throughput and too expensive to be commercially suitable. Here we report a high-throughput layer transfer technique that can produce multiple compound semiconductor membranes from a single wafer. We directly grow two-dimensional (2D) materials on III–N and III–V substrates using epitaxy tools, which enables a scheme comprised of multiple alternating layers of 2D materials and epilayers that can be formed by a single growth run. Each epilayer in the multistack structure is then harvested by layer-by-layer mechanical exfoliation, producing multiple freestanding membranes from a single wafer without involving time-consuming processes such as sacrificial layer etching or wafer polishing. Moreover, atomic-precision exfoliation at the 2D interface allows for the recycling of the wafers for subsequent membrane production, with the potential for greatly reducing the manufacturing cost.

77 NANOSCIENCE AND NANOTECHNOLOGY↗