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At least 577 records · Page 32

Metal–Ligand Bifunctional Catalysis: The “Accepted” Mechanism, the Issue of Concertedness, and the Function of the Ligand in Catalytic Cycles Involving Hydrogen Atoms

For years, following the ideas of Shvo and Noyori, the core assumption of metal–ligand bifunctional molecular catalysis has relied on the direct involvement of the chelating ligand in the catalytic reaction via a reversible proton (H + ) transfer through cleavage/formation of one of its X–H bonds (X = O, N, C). A recently revised mechanism of the Noyori asymmetric hydrogenation reaction (Dub, P. A. et al. J. Am. Chem. Soc. 2014, 136, 3505) suggests that the ligand is rather involved in the catalytic reaction via the stabilization of determining transition states through N–H···O hydrogen-bonding interactions (HBIs) and not via a reversible H + transfer, behaving in a chemically intact manner within the productive cycle or predominantly in a chemically intact manner within productive cycles. By reexamining selected examples of computational mechanistic studies involving bifunctional catalysts from the literature in the years between 2012–2017, the purpose of this paper is to point out common misconceptions in modeling concerted reactions and show that the actual stepwise nature of key transition states unveils a more complicated catalytic reaction pool (all conceivable catalytic pathways and their crossovers). Such a realization can not only potentially result in a reconsideration of the “accepted” mechanism but also lead us to a new conceptual understanding of the role that the ligand plays in the reaction. Finally, the ultimate goal of this paper is, therefore, to encourage the reader to reconsider the function of the ligand in catalytic cycles of hydrogenation/dehydrogenation with bifunctional catalysts, which until recently has relied almost exclusively on a chemically noninnocent ligand.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Néel domain walls with bistable chirality in a perpendicularly magnetized ferrimagnetic insulator

Field-free spin-orbit torque-driven domain wall motion in magnetic thin films with perpendicular magnetic anisotropy (PMA) requires the domain walls to have Néel character. Conventionally, Néel domain walls are stabilized by the Dzyaloshinskii-Moriya interaction (DMI) in ultrathin films. Here, in a europium iron garnet thin film with PMA and an additional uniaxial in-plane anisotropy, we demonstrate two bistable Néel domain wall states in the absence of DMI, and the capability to toggle the wall states with an in-plane field pulse and consequently their directions of motion under a current pulse. We present a phase diagram for the bistable Néel domain wall states as a function of in-plane field pulse width and amplitude. By fitting the experimental data to an analytical model of Néel wall reversal through the nucleation and propagation of Bloch lines, we extract the length of the initial reversed domain wall segment and Bloch line nucleation energy barrier. Current-driven motion of in-plane anisotropy stabilized Néel walls is qualitatively different from that of DMI-stabilized ones owing to the different symmetry of the effective fields that stabilize the Néel configuration. Furthermore, we present a proof of principle demonstration for 2-bit random number generation based on the stochastic reversal of domain wall chirality. These results provide critical insight into the topological energy barrier of Bloch lines and identify paths towards domain wall-based memory and computing devices.

36 MATERIALS SCIENCE↗

Mechanisms of H{sub 2}O desorption from amorphous solid water by 157-nm irradiation: An experimental and theoretical study

The photodesorption of water molecules from amorphous solid water (ASW) by 157-nm irradiation has been examined using resonance-enhanced multiphoton ionization. The rotational temperature has been determined, by comparison with simulations, to be 425 ± 75 K. The time-of-flight spectrum of H{sub 2}O (v= 0) has been fit with a Maxwell-Boltzmann distribution with a translational temperature of 700 ± 200 K (0.12 ± 0.03 eV). H{sup +} and OH{sup +} fragment ions have been detected with non-resonant multiphoton ionization, indicating vibrationally excited parent water molecules with translational energies of 0.24 ± 0.08 eV. The cross section for water removal from ASW by 7.9-eV photons near 100 K is (6.9 ± 1.8) × 10{sup −20} cm{sup 2} for >10 L H{sub 2}O exposure. Electronic structure computations have also probed the excited states of water and the mechanisms of desorption. Calculated electron attachment and detachment densities show that exciton delocalization leads to a dipole reversal state in the first singlet excited state of a model system of hexagonal water ice. Ab Initio Molecular Dynamics simulations show possible desorption of a photo-excited water molecule from this cluster, though the non-hydrogen bonded OH bond is stretched significantly before desorption. Potential energy curves of this OH stretch in the electronic excited state show a barrier to dissociation, lending credence to the dipole reversal mechanism.

36 MATERIALS SCIENCE↗

Optical and magneto-optical properties of ferromagnetic monolayer CrBr 3 : A first-principles G W and G W plus Bethe-Salpeter equation study

The discovery of atomically thin two-dimensional (2D) magnetic semiconductors has triggered enormous research interest recently. In this paper, we use first-principles many-body perturbation theory to study a prototypical 2D ferromagnetic semiconductor, monolayer chromium tribromide (CrBr 3 ). With broken time-reversal symmetry, spin-orbit coupling, and excitonic effects included through the full-spinor GW and GW plus Bethe-Salpeter equation (GW-BSE) methods, we compute the frequency-dependent layer polarizability tensor and dielectric function tensor that govern the optical and magneto-optical (MO) properties. In addition, we provide a detailed theoretical formalism for simulating magnetic circular dichroism, MO Kerr effect, and Faraday effect, demonstrating the approach with monolayer CrBr 3 . Due to reduced dielectric screening in 2D and the localized nature of the Cr d orbitals, we find strong self-energy effects on the quasiparticle band structure of monolayer CrBr 3 that give a 3.8 eV indirect bandgap. Also, excitonic effects dominate the low-energy optical and MO responses in monolayer CrBr 3 where a large exciton binding energy of 2.3 eV is found for the lowest bright exciton state with excitation energy at 1.5 eV. We further find that the MO signals demonstrate strong dependence on the excitation frequency and substrate refractive index. Furthermore, our theoretical framework for modeling optical and MO effects could serve as a powerful theoretical tool for future study of optoelectronic and spintronics devices consisting of van der Waals 2D magnets.

36 MATERIALS SCIENCE↗

Improving Uintah's Scalability Through the Use of Portable Kokkos-Based Data Parallel Tasks

The University of Utah’s Carbon Capture Multidisciplinary Simulation Center (CCMSC) is using the Uintah Computational Framework to predict performance of a 1000 MWe ultra-supercritical clean coal boiler. The center aims to utilize the Intel Xeon Phi-based DOE systems, Theta and Aurora, through the Aurora Early Science Program by using the Kokkos C++ library to enable node-level performance portability. This paper describes infrastructure advancements and portability improvements made possible by the integration of Kokkos within Uintah. This integration marks a step towards consolidating Uintah’s MPI+PThreads and MPI+CUDA hybrid parallelism approaches into a single MPI+Kokkos approach. Scalability results are presented that compare serial and data parallel task execution models for a challenging radiative heat transfer calculation, central to the center’s predictive boiler simulations. Here, these results demonstrate both good strong-scaling characteristics to 256 Knights Landing (KNL) processors on the NSF Stampede system, and show the KNL-based calculation to compete with prior GPU-based results for the same calculation.

97 MATHEMATICS AND COMPUTING↗

Radial rib antenna surface deviation analysis program

A digital computer program was developed which analyzes any radial rib antenna with ribs radiating from a central hub. The program has the capability for calculating the antenna surface contour (reversed pillowing effect), the optimum rib shape for minimizing the rms surface error, and the actual rms surface error. Rib deflection due to mesh tension and catenary cable tension can also be compensated for, and the pattern from which the mesh gores are cut can be determined.

Coyner, J. V., Jr.↗

Computation Of Facilitated Transport of O2 In Hemoglobin

Report describes computations of unsteady facilitated transport of oxygen through liquid membrane of hemoglobin. Used here, "facilitated transport" means diffusion of permeant through membrane in which that diffusion enhanced by reversible chemical reaction between permeant and membrane. In this case, reversible reactions between hemoglobin and oxygen.

Davis, Sanford↗

Efficient GPU-Accelerated MultiSource Global Fit Pipeline for LISA Data Analysis

The large-scale analysis task of deciphering gravitational-wave signals in the LISA data stream will be difficult, requiring a large amount of computational resources and extensive development of computational methods. Its high dimensionality, multiple model types, and complicated noise profile require a global fit to all parameters and input models simultaneously. In this work, we detail our global fit algorithm, called “Erebor,” designed to accomplish this challenging task. It is capable of analyzing current state-of-the-art datasets and then growing into the future as more pieces of the pipeline are completed and added. We describe our pipeline strategy, the algorithmic setup, and the results from our analysis of the LDC2A Sangria dataset, which contains massive black hole binaries, compact galactic binaries, and a parametrized noise spectrum whose parameters are unknown to the user. The Erebor algorithm includes three unique and very useful contributions: GPU acceleration for enhanced computational efficiency; ensemble Markov Chain Monte Carlo (MCMC) sampling with multiple MCMC walkers per temperature for better mixing and parallelized sample creation; and special online updates to reversible-jump (or transdimensional) sampling distributions to ensure sampler mixing and accurate initial estimates for detectable sources in the data.We recover posterior distributions for all 15 (6) of the injected massive black hole binaries (MBHB) in the LDC2A training (hidden) dataset. We catalog ∼12000 galactic binaries (∼8000 as high confidence detections) for both the training and hidden datasets. All of the sources and their posterior distributions are provided in publicly available catalogs.

LISA↗

Nonlinear Alfvén instability simulation and EP transport for ITER reversed shear (steady-state) and monotonic q-profile regimes *

The nonlinear evolution and dynamics of energetic particle (EP) driven instabilities in both steady-state (reversed shear q-profile) and monotonic q-profile regimes of ITER are examined using the global gyro-Landau closure model FAR3d. Both neutral beam and alpha components are included, leading to synergistic effects between the two populations. In order to maintain computational feasibility, the present nonlinear simulation includes all toroidal mode numbers ranging from n = 0 to 15. It cannot be excluded that n’s above this range could introduce larger linear growth rates; however, as indicated from the results, the n = 0 to 15 range is sufficient to provide a strong linear drive and significant nonlinear transport effects. While the toroidal mode numbers n = 6,13 dominate the linear instability growth phase, nonlinear energy transfers in the saturated phase reverse this trend, leading to the dominance of lower n’s in the saturated phase of the simulation. Zonal flow structure generation and EP density flattening are further consequences of the nonlinear phase. The density profile flattening is caused by collectively driven EP radial transport fluxes, which have non-local characteristics. Instantaneous alpha particle transport fluxes are significant (Γ α ~ 2 x 10 20 m –2 s –1 ) for the reversed shear regime and lower (Γ α ~ 1.1 x 10 20 m –2 s –1 ) for the monotonic q-profile case.

AE↗

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes—in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Furthermore, both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Four-Dimensional Finite-Orbit-Width Fokker-Planck Code with Sources, for Neoclassical/Anomalous Transport Simulation of Ion and Electron (Final Technical Report)

Within the US Department of Energy/Office of Fusion Energy magnetic fusion research program, there is an important whole-plasma-modeling need for a radio-frequency/neutral-beam-injection (RF/NBI) transport-oriented finite-difference Fokker-Planck (FP) code with combined capabilities for 4D (2R2V) geometry near the fusion plasma periphery, and computationally less demanding 3D (1R2V) bounce-averaged capabilities for plasma in the core of fusion devices. Demonstration of proof-of-principle achievement of this goal has been carried out in research carried out under Phase I of the SBIR award. Two DOE-sponsored codes, the CQL3D bounce-average Fokker-Planck code in which CompX has specialized, and the COGENT 4D, plasma edge-oriented Fokker-Planck code which has been constructed by Lawrence Livermore National Laboratory and Lawrence Berkeley Laboratory scientists, where coupled. Coupling was achieved by using CQL3D calculated velocity distributions including an energetic tail resulting from NBI, as boundary conditions for the COGENT code over the two-dimensional velocity space on a spatial interface (flux) surface at a given radius near the plasma periphery. The finite-orbit-width fast ions from the CQL3D distributions penetrated into the peripheral plasma modeled by the COGENT code. This combined code demonstrates the feasibility of the proposed 3D/4D code. By combining these codes, the greatest computational efficiency is achieved subject to present modeling needs in toroidally symmetric magnetic fusion devices. The more efficient 3D code can be used in its regions of applicability, coupled to the more computationally demanding 4D code in higher collisionality edge plasma regions where that extended capability is necessary for accurate representation of the plasma. More efficient code leads to greater use and utility of the model. An ancillary aim of the project is to make the combined 3D/4D code user friendly. Achievement of full-coupling of these two Fokker-Planck codes will advance computational modeling of plasma devices important to the USDOE magnetic fusion energy program, in particular the DIII-D tokamak at General Atomics, San Diego, the NSTX spherical tokamak at Princeton, New Jersey, and the MST reversed-field-pinch Madison, Wisconsin. The validation studies of the code against the experiments will improve understanding of physics important for magnetic fusion, and will increase our design capabilities for achieving the goals of the International Tokamak Experimental Reactor (ITER) project in which the US is a participant and which seeks to demonstrate at least a factor of five in fusion power production divided by input power.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Simulation and Modeling of Time-Resolved X-Ray Detector for the Saturn Accelerator

In this work, we present the technology-aided computer design (TCAD) device simulation and modeling of a silicon p-i-n diode for detecting time-dependent X-ray radiation. We show that the simulated forward and reverse breakdown current–voltage characteristics agree well with the measured data under nonradiation environment by only calibrating carrier lifetimes for the forward bias case and avalanche model critical fields for the reverse bias condition. Using the calibrated parameters and other nominal material properties, we simulated the radiation responses of the p-i-n diode and compared with experimental data when the diode was exposed to X-ray radiation at Sandia’s Saturn facility and the Idaho State University (ISU) TriMeV facility. For Saturn’s Gaussian dose-rate pulses, we show three findings from TCAD simulations. First, the simulated photocurrents are in excellent agreement with the measured data for two dose-rate pulses with peak values of 1.16×10 10 and 1.88×10 10 rad(Si)/s. Second, the simulation results of high dose-rate pulses predict increased delayed photocurrents with longer time tails in the diode electrical responses due to excess carrier generation. Third, simulated peak values of diode radiation responses versus peak dose rates at different bias conditions provide useful guidance to determine the dose-rate range that the p-i-n diode can reliably detect in experiment. For TriMeV’s non-Gaussian dose-rate pulse, our simulated diode response is in decent agreement with the measured data without further calibration. We also studied the effects of device geometry, recombination process, and dose-rate enhancement via TCAD simulations to understand the higher measured response in the time after the peak dose-rate radiation for the p-i-n diode exposed to TriMeV irradiation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A Hybridizable Discontinuous Galerkin solver for the Grad–Shafranov equation

In axisymmetric fusion reactors, the equilibrium magnetic configuration can be expressed in terms of the solution to a semi-linear elliptic equation known as the Grad–Shafranov equation, the solution of which determines the poloidal component of the magnetic field. When the geometry of the confinement region is known, the problem becomes an interior Dirichlet boundary value problem. We propose a high order solver based on the Hybridizable Discontinuous Galerkin method. The resulting algorithm (1) provides high order of convergence for the flux function and its gradient, (2) incorporates a novel method for handling piecewise smooth geometries by extension from polygonal meshes, (3) can handle geometries with non-smooth boundaries and x-points, and (4) deals with the semi-linearity through an accelerated two-grid fixed-point iteration. The effectiveness of the algorithm is verified with computations for cases where analytic solutions are known on configurations similar to those of actual devices (ITER with single null and double null divertor, NSTX, ASDEX upgrade, and Field Reversed Configurations).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Giant coercivity and high magnetic blocking temperatures for N 2 3- radical-bridged dilanthanide complexes upon ligand dissociation

Increasing the operating temperatures of single-molecule magnets—molecules that can retain magnetic polarization in the absence of an applied field—has potential implications toward information storage and computing, and may also inform the development of new bulk magnets. Progress toward these goals relies upon the development of synthetic chemistry enabling enhancement of the thermal barrier to reversal of the magnetic moment, while suppressing alternative relaxation processes. Here in this paper, we show that pairing the axial magnetic anisotropy enforced by tetramethylcyclopentadienyl (Cp Me4H ) capping ligands with strong magnetic exchange coupling provided by an N 2 3- radical bridging ligand results in a series of dilanthanide complexes exhibiting exceptionally large magnetic hysteresis loops that persist to high temperatures. Significantly, reducing the coordination number of the metal centers appears to increase axial magnetic anisotropy, giving rise to larger magnetic relaxation barriers and 100-s magnetic blocking temperatures of up to 20 K, as observed for the complex [K(crypt-222)][(Cp Me4H 2 Tb) 2 (μ-N∙ 2</sub)].

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Inverse design of two-dimensional materials with invertible neural networks

The ability to readily design novel materials with chosen functional properties on-demand represents a next frontier in materials discovery. However, thoroughly and efficiently sampling the entire design space in a computationally tractable manner remains a highly challenging task. To tackle this problem, we propose an inverse design framework (MatDesINNe) utilizing invertible neural networks which can map both forward and reverse processes between the design space and target property. This approach can be used to generate materials candidates for a designated property, thereby satisfying the highly sought-after goal of inverse design. We then apply this framework to the task of band gap engineering in two-dimensional materials, starting with MoS 2 . Within the design space encompassing six degrees of freedom in applied tensile, compressive and shear strain plus an external electric field, we show the framework can generate novel, high fidelity, and diverse candidates with near-chemical accuracy. We extend this generative capability further to provide insights regarding metal-insulator transition in MoS 2 which are important for memristive neuromorphic applications, among others. This approach is general and can be directly extended to other materials and their corresponding design spaces and target properties.

36 MATERIALS SCIENCE↗

Identifying amyloid-related diseases by mapping mutations in low-complexity protein domains to pathologies

Proteins including FUS, hnRNPA2, and TDP-43 reversibly aggregate into amyloid-like fibrils through interactions of their low-complexity domains (LCDs). Mutations in LCDs can promote irreversible amyloid aggregation and disease. We introduce a computational approach to identify mutations in LCDs of disease-associated proteins predicted to increase propensity for amyloid aggregation. We identify several disease-related mutations in the intermediate filament protein keratin-8 (KRT8). Atomic structures of wild-type and mutant KRT8 segments confirm the transition to a pleated strand capable of amyloid formation. Biochemical analysis reveals KRT8 forms amyloid aggregates, and the identified mutations promote aggregation. Aggregated KRT8 is found in Mallory–Denk bodies, observed in hepatocytes of livers with alcoholic steatohepatitis (ASH). We demonstrate that ethanol promotes KRT8 aggregation, and KRT8 amyloids co-crystallize with alcohol. Lastly, KRT8 aggregation can be seeded by liver extract from people with ASH, consistent with the amyloid nature of KRT8 aggregates and the classification of ASH as an amyloid-related condition.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring drift effects in TCV single-null plasmas with the UEDGE code

This study explores the effects of particle drifts across the magnetic field in TCV single-null plasmas using the two-dimensional edge plasma transport code UEDGE. In particular, it aims to reproduce a double-peaked density target profile, a feature which has been observed both at JET and in a TCV forward-field (${\rm{\nabla }}B$ drift of core ions towards the X-point) discharge. Initial simulations are performed with drift effects turned off. This allows identification of the input parameters that strongly influence the computed steady-state but are not well known from the experiment. Including cross-field drifts self-consistently in the simulations brings computed profiles at the inner target closer to the experiment, with the double peak being reproduced for the density. In agreement with the experiment, simulations of a similar reversed-field shot yield lower n e and higher T e at the inner target, as well as unchanged temperatures at the outer plate. However, several discrepancies remain. In the forward field case, the inner target density peak near the separatrix is much sharper than seen experimentally. Furthermore, simulations show a strong dependence of the outer plate density and of the outer/inner power sharing on toroidal field direction. Experimentally, no such dependencies are observed. In the simulations, the changes of target profiles with field direction are mainly due to E × B drifts in the divertor region. Finally, while these simulations highlight the importance of E × B drifts in these TCV plasmas, the remaining differences with the experiment indicate that their role is overestimated in the simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Invariant regimes of Spencer scaling law for magnetic compression of rotating FRC plasma

Abstract The scaling laws for the magnetic compression of a toroidally rotating field reversed configuration (FRC) have been investigated in this work. The magnetohydrodynamics (MHD) simulations of the magnetic compression on rotating FRCs employing the NIMROD code (Sovinec et al 2004 J. Comput. Phys. 195 355), are compared with the Spencer’s one-dimensional (1D) theory (Spencer et al 1983 Phys. Fluids 26 1564) for a wide range of initial flow speeds and profiles. The toroidal flow can influence the scalings directly through the alteration of the compressional work as also evidenced in the 1D adiabatic model, and indirectly by reshaping the initial equilibrium. However, in comparison to the static initial FRC equilibrium cases, the pressure and the radius scalings remain invariant for the magnetic compression ratio B w 2 / B w 1 up to 6 in presence of the initial equilibrium flow, suggesting a broader applicable regime of the Spencer scaling law for FRC magnetic compression. The invariant scaling has been proven a natural consequence of the conservation of angular momentum of both fluid and magnetic field during the dynamic compression process.

Ma, Yiming↗