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At least 865 records · Page 48

Structure and magnetic properties of irradiated Fe/Fe oxide core-shell nanoclusters

A cluster deposition method was used to produce a film of loosely aggregated particles of Fe-Fe3O4 core-shell nanoclusters with an 8 nm iron core size and 2 nm oxide shell thickness. The film of particles on a silicon substrate was irradiated with 5.5 MeV Si2+ ions to a fluence of 1016 cm-2 near room temperature, and computer simulations based on the SRIM (Stopping and Range of Ions in Matter) code show that the implanted Si species stops near the film-substrate interface. The ion irradiation creates a structural change in the film with corresponding chemical and magnetic changes. X-ray diffraction shows that the core size and chemistry stay the same but the shell becomes FeO that grows to a thickness of 17 nm. Helium ion microscopy shows that the previously separate particles have densified into a nearly continuous film. Major loop magnetic hysteresis measurements show a decrease in saturation magnetization that we attribute to the presence of the antiferromagnetic (AFM) FeO shell. First-order reversal curve measurements on the irradiated film performed with a vibrating sample magnetometer show that the AFM shell prevents the particles from interacting magnetically, leading to low coercivity from the iron core and little bias field from the core interactions. These results, and others reported previously on different compositions (Fe3O4 or FeO+Fe3N nanoclusters), show that the ion irradiation behavior of nanocluster films such as these depends strongly on the initial nanostructure and chemistry.

Environmental Molecular Sciences Laboratory↗

Elucidation of Peptide-Directed Palladium Surface Structure for Biologically Tunable Nanocatalysts

Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then eluddated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences

atomic pair distribution function↗

Extraordinary Redox Activities in Ladder-Type Conjugated Molecules Enabled by B ← N Coordination-Promoted Delocalization and Hyperconjugation

The introduction of B ← N coordinate bond-isoelectronic to C-C single bond-into π-systems represents a promising strategy to impart exotic redox and electrochromic properties into conjugated organic molecules and macromolecules. To achieve both reductive and oxidative activities using this strategy, a cruciform ladder-type molecular constitution was designed to accommodate oxidation-active, reduction-active, and B ← N coordination units into a compact structure. Two such compounds (BN-F and BN-Ph) were synthesized via highly efficient N-directed borylation. These molecules demonstrated well-separated, two reductive and two oxidative electron-transfer processes, corresponding to five distinct yet stable oxidation states, including a rarely observed boron-containing radical cation. Spectroelectrochemical measurements revealed unique optical characteristics for each of these reduced/oxidized species, demonstrating multicolor electrochromism with excellent recyclability. Distinct color changes were observed between each redox state with clear isosbestic points on the absorption spectra. Here, the underlying redox mechanism was elucidated by a combination of computational and experimental investigations. Single-crystal X-ray diffraction analysis on the neutral state, the oxidized radical cation, and the reduced dianion of BN-Ph revealed structural transformations into two distinct quinonoid constitutions during the oxidation and reduction processes, respectively. B ← N coordination played an important role in rendering the robust and reversible multistage redox properties, by extending the charge and spin delocalization, by modulating the π-electron density, and by a newly established hyperconjugation mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CO 2 adsorption-induced structural changes in coordination polymer ligands elucidated via molecular simulations and experiments

Aiming to elucidate guest-induced structural changes in the coordination polymer CPL-2, grand canonical Monte Carlo (GCMC) simulations were used to predict CO 2 loadings in this material, and the results were compared with experimental isotherms. Our calculations suggest that CPL-2 exhibits more pronounced CO 2 -induced structural changes than previously reported. As the initial evidence, the isotherm simulated in the previously reported CPL-2 structure (experimentally resolved from X-ray diffraction in the “as-synthesized” CPL-2) underestimated the measured CO 2 loadings at high pressure, indicating that CPL-2 might undergo structural changes that enable higher pore volumes at high pressure. GCMC simulations in CPL-2 structures considering moderate unit cell expansions reported in the literature still underestimated high-pressure experimental loadings. However, considering an incremental rotation of the CPL-2 bipyridyl pillars with increasing CO 2 pressure, we were able to trace the measured isotherm with the simulation data. Computational analysis shows that ligand rotation in CPL-2 enables higher pore volumes, which, in turn, accommodate more CO 2 as the gas pressure increases. Desorption measurements suggest that hysteresis in the CO 2 isotherm of CPL-2 may also be linked to ligand rotation, and the measured adsorption/desorption cycles show that the rotation is reversible. Based on our simulations for CPL-4 and CPL-5 and previously reported experimental data, it is likely that these materials, which differ from CPL-2 in the bipyridyl ligand, behave similarly in the presence of CO 2 . Our results help understand the behavior of these materials, which present the kind of structural changes that could be potentially exploited to enhance the CO 2 working capacity of ultra-microporous materials for carbon capture applications.

Meza-Morales, Paul J.↗

The sponge-like topology of large-scale structure in the universe

The relative connectedness of the high- and low-density regions in the universe is studied using a median density contour which divides space into two equal volumes. The CfA data are found to show a sponge-like topology where the highand low-density regions are both interlocking and equivalent. The boundary surface between the two regions has a general negative curvature, and is characterized by a large number of holes. In the initial conditions the connectedness of the two regions must be identical because a change of sign in the random quantum fluctuations would reverse their roles. It is noted that in the cold dark matter and neutrino scenarios the hole sizes are typically of the order of the smoothing diameter or the damping length, whichever is larger. The sponge-like topology is consistent with the universe having a frothy appearance without being divided neatly into cells. A computer algorithm for measuring topology is discussed.

Gott, J. R., III↗

3D Simulations of the Richtmyer-Meshkov Instability with Re-Shock

We present results of inviscid simulations, in three dimensions, of Richtmyer-Meshkov instability for high incident shock Mach number. The growth rate of a single harmonic perturbation is quantified and compared with the results of a 2D calculation. Upon re-shock, the perturbation amplitude undergoes a phase reversal while the mean velocity of the interface is zero. Before re-shock the normalized growth rate of a 2D and 3D interface are nearly the same, but the growth rate after re-shock is significantly larger for the 3D than the 2D case. We also examine the evolution of multiple harmonic perturbations. Computational and parallelization issues of the simulation code will also be briefly discussed. The computations were done on the T3E at Pittsburgh Supercomputing Center.

Meiron, Daniel I.↗

Computational Flow Field in Energy Efficient Engine (EEE)

In this paper, preliminary results for the recently-updated Open National Combustion Code (Open NCC) as applied to the EEE are presented. The comparison between two different numerical schemes, the standard Jameson-Schmidt-Turkel (JST) scheme and the advection upstream splitting method (AUSM), is performed for the cold flow and the reacting flow calculations using the RANS. In the cold flow calculation, the AUSM scheme predicts a much stronger reverse flow in the central recirculation zone. In the reacting flow calculation, we test two cases: gaseous fuel injection and liquid spray injection. In the gaseous fuel injection case, the overall flame structures of the two schemes are similar to one another, in the sense that the flame is attached to the main nozzle, but is detached from the pilot nozzle. However, in the exit temperature profile, the AUSM scheme shows a more uniform profile than that of the JST scheme, which is close to the experimental data. In the liquid spray injection case, we expect different flame structures in this scenario. We will give a brief discussion on how two numerical schemes predict the flame structures inside the EEE using different ways to introduce the fuel injection.

CFD↗

A Step Toward Working with Untrusted Ground Stations

We are witnessing a shift toward outsourcing satellite and ground station services to third-party commercial entities. As with any enterprise, these third parties can be vulnerable to cyber compromise, including image tampering and deepfake injection. The multimedia community is beginning to establish standards and technology to enable authenticity verification of multimedia created and edited by others. While appealing to the remote sensing domain, the nature of raw satellite imagery is incompatible with the proposed change verification tools, resulting in the need for a means to validate updates made to image products. We present a simple method for verifying a specific class of algorithms. Our inverse processing approach eliminates the need to see the original image as the reversed data can be checked against an original digital signature. We demonstrate our approach on basic image restoration routines and conclude with a discussion on open challenges and next steps.

97 MATHEMATICS AND COMPUTING↗

Quantum field as a quantum cellular automaton: The Dirac free evolution in one dimension

We present a quantum cellular automaton model in one space-dimension which has the Dirac equation as emergent. This model, a discrete-time and causal unitary evolution of a lattice of quantum systems, is derived from the assumptions of homogeneity, parity and time-reversal invariance. The comparison between the automaton and the Dirac evolutions is rigorously set as a discrimination problem between unitary channels. We derive an exact lower bound for the probability of error in the discrimination as an explicit function of the mass, the number and the momentum of the particles, and the duration of the evolution. Computing this bound with experimentally achievable values, we see that in that regime the QCA model cannot be discriminated from the usual Dirac evolution. Finally, we show that the evolution of one-particle states with narrow-band in momentum can be efficiently simulated by a dispersive differential equation for any regime. This analysis allows for a comparison with the dynamics of wave-packets as it is described by the usual Dirac equation. This paper is a first step in exploring the idea that quantum field theory could be grounded on a more fundamental quantum cellular automaton model and that physical dynamics could emerge from quantum information processing. In this framework, the discretization is a central ingredient and not only a tool for performing non-perturbative calculation as in lattice gauge theory. The automaton model, endowed with a precise notion of local observables and a full probabilistic interpretation, could lead to a coherent unification of a hypothetical discrete Planck scale with the usual Fermi scale of high-energy physics. - Highlights: • The free Dirac field in one space dimension as a quantum cellular automaton. • Large scale limit of the automaton and the emergence of the Dirac equation. • Dispersive differential equation for the evolution of smooth states on the automaton. • Optimal discrimination between the automaton evolution and the Dirac equation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Brownian dynamics of confined rigid bodies

We introduce numerical methods for simulating the diffusive motion of rigid bodies of arbitrary shape immersed in a viscous fluid. We parameterize the orientation of the bodies using normalized quaternions, which are numerically robust, space efficient, and easy to accumulate. We construct a system of overdamped Langevin equations in the quaternion representation that accounts for hydrodynamic effects, preserves the unit-norm constraint on the quaternion, and is time reversible with respect to the Gibbs-Boltzmann distribution at equilibrium. We introduce two schemes for temporal integration of the overdamped Langevin equations of motion, one based on the Fixman midpoint method and the other based on a random finite difference approach, both of which ensure that the correct stochastic drift term is captured in a computationally efficient way. We study several examples of rigid colloidal particles diffusing near a no-slip boundary and demonstrate the importance of the choice of tracking point on the measured translational mean square displacement (MSD). We examine the average short-time as well as the long-time quasi-two-dimensional diffusion coefficient of a rigid particle sedimented near a bottom wall due to gravity. For several particle shapes, we find a choice of tracking point that makes the MSD essentially linear with time, allowing us to estimate the long-time diffusion coefficient efficiently using a Monte Carlo method. However, in general, such a special choice of tracking point does not exist, and numerical techniques for simulating long trajectories, such as the ones we introduce here, are necessary to study diffusion on long time scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

LDV measurements on a rectangular wing with a simulated glaze ice accretion

LDV measurement results are presented for the upper surface of a rectangular semispan wing with and without simulated glaze ice accretion. Inspection of the model centerline flow field indicates that a large region of reverse flow exists aft of the ice horn on the iced model. At alpha = 0 deg, this region extends to 7 percent chord, while at alpha = 4 deg the bubble grows to more than 12 percent chord. At alpha = 8 deg, the time-averaged separation bubble is measured well beyond 50 percent chord. Experimental and computational flow visualization support these findings. The flow in the vicinity of the ice shape contains many of the features of flow over a backward-facing step.

Khodadoust, A.↗

Random Forests and Networks Analysis

Wilson (Proceedings of the twenty-eight annual acm symposium on the theory of computing, pp. 296–303, 1996) in the 1990s described a simple and efficient algorithm based on loop-erased random walks to sample uniform spanning trees and more generally weighted trees or forests spanning a given graph. This algorithm provides a powerful tool in analyzing structures on networks and along this line of thinking, in recent works (Avena and Gaudillière in A proof of the transfer-current theorem in absence of reversibility, in Stat. Probab. Lett. 142, 17–22 (2018); Avena and Gaudillière in J Theor Probab, 2017. https://doi.org/10.1007/s10959-017-0771-3 ; Avena et al. in Approximate and exact solutions of intertwining equations though random spanning forests, 2017. arXiv:1702.05992v1 ; Avena et al. in Intertwining wavelets or multiresolution analysis on graphs through random forests, 2017. arXiv:1707.04616 , to appear in ACHA (2018)) we focused on applications of spanning rooted forests on finite graphs. The resulting main conclusions are reviewed in this paper by collecting related theorems, algorithms, heuristics and numerical experiments. A first foundational part on determinantal structures and efficient sampling procedures is followed by four main applications: (1) a random-walk-based notion of well-distributed points in a graph, (2) a framework to describe metastable-like dynamics in finite settings by means of Markov intertwining dualities, (3) coarse graining schemes for networks and associated processes, (4) wavelets-like pyramidal algorithms for graph signals.

97 MATHEMATICS AND COMPUTING↗

Exact-two-component block-localized wave function: A simple scheme for the automatic computation of relativistic ΔSCF

Block-localized wave function is a useful method for optimizing constrained determinants. In this article, we extend the generalized block-localized wave function technique to relativistic two-component framework. Optimization of excited state determinants for two-component wave functions presents a unique challenge because the excited state manifold is often quite dense with degenerate states. Furthermore, we test the degree to which certain symmetries result naturally from the ΔSCF optimization such as time reversal symmetry and symmetry with respect to the total angular momentum operator on a series of atomic systems. Variational optimizations may often break symmetry in order to lower the overall energy, just as unrestricted Hartree-Fock breaks spin symmetry. Overall, we demonstrate that time reversal symmetry is roughly maintained when using Hartree-Fock, but less so when using Kohn-Sham density functional theory. Additionally, maintaining total angular momentum symmetry appears to be system dependent and not guaranteed. Finally, we were able to trace the breaking of total angular momentum symmetry to the relaxation of core electrons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Managing a Cray supercomputer as a git branch

Summary Modern software engineering/DevOps techniques applied to Cray XC Series systems management enable higher fidelity translation from test to production environments, reduce administration costs by avoiding duplicate efforts, and increase reliability. This can be done by using a git repository to track and manage all system configurations on the SMW(s) (System Management Workstation) and then adapt a gitflow‐like development methodology. Using git improves change management with peer review of changes, identification of who made a change, knowing why a change was made, facilitating easier reversion of bad changes, and enables a workflow using the ideas from gitflow with individual branches for preparing, maintaining, and recording releases. Using branches enables multiple contributors to work on different types of changes without getting unexpected changes from another feature area. We will describe a process similar to that used at NERSC (National Energy Research Scientific Computing Center) to extract/abstract configuration data, manage it using git, and then re‐apply changes to the SMW(s).

Jacobsen, Douglas M.↗

Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae

Bacterial heme nitric oxide/oxygen (H-NOX) domains are nitric oxide (NO) or oxygen sensors. This activity is mediated through binding of the ligand to a heme cofactor. However, H-NOX from Vibrio cholerae (Vc H-NOX) can be easily purified in a heme-free state that is capable of reversibly responding to oxidation, suggesting a heme-independent function as a redox sensor. This occurs by oxidation of Cys residues at a zinc-binding site conserved in a subset of H-NOX homologs. Remarkably, zinc is not lost from the protein upon oxidation, although its ligation environment is significantly altered. Using a combination of computational and experimental approaches, we have characterized localized structural changes that accompany the formation of specific disulfide bonds between Cys residues upon oxidation. Furthermore, the larger-scale structural changes accompanying oxidation appear to mimic those changes observed upon NO binding to the heme-bound form. Thus, Vc H-NOX and its homologs may act as both redox and NO sensors by completely separate mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Efficient Schottky-like junction GaAs nanowire photodetector with 9 GHz modulation bandwidth with large active area

Efficient, low capacitance density GaAs/Indium-Tin-Oxide Schottky-like junction photodetectors with a 50 μm square active are fabricated for operation in the gigahertz range. Modulation bandwidth is experimentally measured up to 10 GHz at various applied reverse biases and optical intensities to explore the effects of photo-generated carrier screening on modulation bandwidth. Last, the bandwidth dependence on applied reverse bias and optical intensity is simulated as a means to quantify average carrier velocities in nanowire material systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Molecular processes in comets

Potential energy curves for the two lowest 2 sigma- states of OH are computed at the configuration-interaction level using four different basis sets. Electronic transition dipole moments connecting the excited 1 2 sigma- and 2(D) 2 sigma- states with each other and with he ground X2pi state are presented as functions of internuclear distance. The theoretical absorption oscillator strengths for the D 2 sigma-(v prime=0) reverser to X 2pi (v prime prime=0) transition are in good agreement with the empirical value derived from astronomical measurements. The photodissociation cross sections for absorption rom the v prime prime=0,1, and levels of the ground state into the continuum of the 1 2 sigma- state are calculated, and the interstellar and cometary photodissociation rates are derived.

Dalgarno, A.↗

Calculating Conductance of Ion Channels

We have simulated two small ion channels in a water/membrane system, which consists of 71,000-72,000 atoms, and have estimated the conductance by way of counting ions crossing these channels in applied field. The calculated values of conductance have been compared with predictions of the electrodiffusion model. In a recently developed theoretical framework, all commonly used assumptions of the model can be tested. If they are satisfied, which is often the case, the approach provides a rigorous way to extrapolate conductance calculated at one voltage to other voltages. This, in turn, allows for efficient estimations of current-voltage dependence, examining rectifying behavior of channels and calculating the reversal potential. Furthermore, the consistency of the results can be precisely tested. Simulations at microsecond time scales are required to sufficiently reduce statistical errors and separate them from possible systematic errors. Only then the accuracy of the proposed approach can be properly tested. Linking simulations with electrophysiology provides a stringent, highly relevant test for the correctness of computer simulations of ion channels. Considering biological, medical and pharmaceutical importance of these proteins, results of the proposed study might motivate the development of improved hardware and software that would enable applying a similar strategy to more complex channels at longer times.

Ion↗