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At least 757 records · Page 42

Abiotic phosphorus recycling from adsorbed ribonucleotides on a ferrihydrite-type mineral: Probing solution and surface species

Iron (Fe) (oxyhydr)oxide minerals, which are amongst most reactive minerals in soils and sediments, are known to exhibit strong adsorption of inorganic phosphate (P i ) and organophosphate (P o ) compounds. Beyond synthetic P o compounds, much still remains unknown about the reactivity of these minerals to transform naturally-occurring P o compounds to P i , particularly with respect to solution versus surface speciation of P o hydrolysis. To investigate this reactivity with a ferrihydrite-type mineral and ribonucleotides, we employed high-resolution liquid chromatography-mass spectrometry (LC-MS), X-ray absorption near-edge structure (XANES), Fourier-transform infrared (FTIR) spectroscopy, and molecular modeling. Kinetic experiments were conducted with the mineral (1 g L -1 ) reacted with adenosine monophosphate, diphosphate, or triphosphate (respectively AMP, ADP, ATP; 50 µM). Analysis of solution organic species by LC-MS implied that only adsorption occurred with AMP and ADP but both adsorption and dephosphorylation of ATP were evident. Maximum adsorption capacities per gram of mineral were 40.6 ± 0.8 µmol AMP, 35.7 ± 1.6 µmol ADP, and 10.9 ± 1.0 µmol ATP; solution dephosphorylated by-products accounted for 15% of initial ATP. Subsequent XANES analysis of the surface species revealed that 16% of adsorbed AMP and 30% of adsorbed ATP were subjected to dephosphorylation, which was not fully quantifiable from the solution measurements. Molecular simulations predicted that ADP and ATP were complexed mainly via the phosphate groups whereas AMP binding also involved multiple hydrogen bonds with the adenosine moiety; our FTIR data confirmed these binding confirmations. Lastly, our findings thus imply that specific adsorption mechanisms dictate the recycling and subsequent trapping of Pi from ribonucleotide-like biomolecules reacted with Fe (oxyhydr)oxide minerals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Monte Carlo algorithm for degenerate plasmas

A procedure for performing Monte Carlo calculations of plasmas with an arbitrary level of degeneracy is outlined. It has possible applications in inertial confinement fusion and astrophysics. Degenerate particles are initialised according to the Fermi–Dirac distribution function, and scattering is via a Pauli blocked binary collision approximation. The algorithm is tested against degenerate electron–ion equilibration, and the degenerate resistivity transport coefficient from unmagnetised first order transport theory. The code is applied to the cold fuel shell and alpha particle equilibration problem of inertial confinement fusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Manufactured solutions for the three-dimensional Euler equations with relevance to Inertial Confinement Fusion

We present a set of manufactured solutions for the three-dimensional (3D) Euler equations. The purpose of these solutions is to allow for code verification against true 3D flows with physical relevance, as opposed to 3D simulations of lower-dimensional problems or manufactured solutions that lack physical relevance. Of particular interest are solutions with relevance to Inertial Confinement Fusion (ICF) capsules. While ICF capsules are designed for spherical symmetry, they are hypothesized to become highly 3D at late time due to phenomena such as Rayleigh–Taylor instability, drive asymmetry, and vortex decay. ICF capsules also involve highly nonlinear coupling between the fluid dynamics and other physics, such as radiation transport and thermonuclear fusion. The manufactured solutions we present are specifically designed to test the terms and couplings in the Euler equations that are relevant to these phenomena. Example numerical results generated with a 3D Finite Element hydrodynamics code are presented, including mesh convergence studies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Multilevel Monte Carlo simulation of Coulomb collisions

We present a new, for plasma physics, highly efficient multilevel Monte Carlo numerical method for simulating Coulomb collisions. The method separates and optimally minimizes the finite-timestep and finite-sampling errors inherent in the Langevin representation of the Landau–Fokker–Planck equation. It does so by combining multiple solutions to the underlying equations with varying numbers of timesteps. For a desired level of accuracy ε, the computational cost of the method is O(ε{sup −2}) or O(ε{sup −2}(lnε){sup 2}), depending on the underlying discretization, Milstein or Euler–Maruyama respectively. This is to be contrasted with a cost of O(ε{sup −3}) for direct simulation Monte Carlo or binary collision methods. We successfully demonstrate the method with a classic beam diffusion test case in 2D, making use of the Lévy area approximation for the correlated Milstein cross terms, and generating a computational saving of a factor of 100 for ε=10{sup −5}. We discuss the importance of the method for problems in which collisions constitute the computational rate limiting step, and its limitations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Implementation of a hybrid particle code with a PIC description in r–z and a gridless description in ϕ into OSIRIS

For many plasma physics problems, three-dimensional and kinetic effects are very important. However, such simulations are very computationally intensive. Fortunately, there is a class of problems for which there is nearly azimuthal symmetry and the dominant three-dimensional physics is captured by the inclusion of only a few azimuthal harmonics. Recently, it was proposed [1] to model one such problem, laser wakefield acceleration, by expanding the fields and currents in azimuthal harmonics and truncating the expansion. The complex amplitudes of the fundamental and first harmonic for the fields were solved on an r–z grid and a procedure for calculating the complex current amplitudes for each particle based on its motion in Cartesian geometry was presented using a Marder's correction to maintain the validity of Gauss's law. In this paper, we describe an implementation of this algorithm into OSIRIS using a rigorous charge conserving current deposition method to maintain the validity of Gauss's law. We show that this algorithm is a hybrid method which uses a particles-in-cell description in r–z and a gridless description in ϕ. We include the ability to keep an arbitrary number of harmonics and higher order particle shapes. Examples for laser wakefield acceleration, plasma wakefield acceleration, and beam loading are also presented and directions for future work are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A particle-in-cell method for the simulation of plasmas based on an unconditionally stable field solver

Here, we propose a new particle-in-cell (PIC) method for the simulation of plasmas based on a recently developed, unconditionally stable solver for the wave equation. This method is not subject to a CFL restriction, limiting the ratio of the time step size to the spatial step size, typical of explicit methods, while maintaining computational cost and code complexity comparable to such explicit schemes. We describe the implementation in one and two dimensions for both electrostatic and electromagnetic cases, and present the results of several standard test problems, showing good agreement with theory with time step sizes much larger than allowed by typical CFL restrictions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A unified formulation of splitting-based implicit time integration schemes

Splitting-based time integration approaches such as fractional step, alternating direction implicit, operator splitting, and locally one dimensional methods partition the system of interest into components, and solve individual components implicitly in a cost-effective way. Here this work proposes a unified formulation of splitting time integration schemes in the framework of general-structure additive Runge–Kutta (GARK) methods. Specifically, we develop implicit-implicit (IMIM) GARK schemes, provide the order conditions for this class, and explain their application to partitioned systems of ordinary differential equations. We show that classical splitting methods belong to the IMIM GARK family, and therefore can be studied in this unified framework. New IMIM-GARK splitting methods are developed and tested using parabolic systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

First-passage time statistics on surfaces of general shape: Surface PDE solvers using Generalized Moving Least Squares (GMLS)

Here, we develop numerical methods for computing statistics of stochastic processes on surfaces of general shape with drift-diffusion dynamics d X t = a (X t ) dt + b(X t ) d W t . We formulate descriptions of Brownian motion and general drift-diffusion processes on surfaces. We consider statistics of the form u (x) = E x [$∫^{τ}_{0}$ g (X t ) dt ] + E x [ f (X τ )] for a domain Ω and the exit stopping time τ = inf t { t >0 | X i Ω}, where f , g are general smooth functions. For computing these statistics, we develop high-order Generalized Moving Least Squares (GMLS) solvers for associated surface PDE boundary-value problems based on Backward- Kolmogorov equations. We focus particularly on the mean First Passage Times (FPTs) given by the case f = 0, g = 1 where u (x) = E x [τ]. We perform studies for a variety of shapes showing our methods converge with high-order accuracy both in capturing the geometry and the surface PDE solutions. We then perform studies showing how statistics are influenced by the surface geometry, drift dynamics, and spatially dependent diffusivities.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

On numerical energy conservation for an implicit particle-in-cell method coupled with a binary Monte-Carlo algorithm for Coulomb collisions

We report conventional particle-in-cell (PIC) methods suffer from enhanced numerical heating (explicit PIC) or cooling (semi-implicit PIC) when coupled with a binary Monte-Carlo algorithm for Coulomb collisions. In this work, a fully-implicit θ-PIC scheme (with adjustable time-biasing parameter 1/2 ≤ θ ≤) is considered. The discrete change in energy of a closed system after a time step for this scheme scales with (1/2 - θ)C θ , where C θ is a positive definite quantity that depends on the frequency spectrum of the energy in the fields. Collisions lead to additional energy in the field fluctuations associated with high-frequency light waves produced by a numerical Bremsstrahlung process, which can result in a large increase in the numerical cooling rate for θ > 1/2. However, for θ = 1/2, energy is exactly conserved. The energy in the field fluctuations on long time scales agrees with that calculated using the equipartition theorem for a classical system in thermodynamic equilibrium.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Electronic structure study of screw dislocation core energetics in Aluminum and core energetics informed forces in a dislocation aggregate

Here we use a real-space formulation of orbital-free DFT to study the core energetics and core structure of an isolated screw dislocation in Aluminum. Using a direct energetics based approach, we estimate the core size of a perfect screw dislocation to be ≈ 7 |b|, which is considerably larger than previous estimates of 1–3 |b| based on displacement fields. The perfect screw upon structural relaxation dissociates into two Shockley partials with partial separation distances of 8.2 Å and 6.6 Å measured from the screw and edge component differential displacement plots, respectively. Similar to a previous electronic structure study on edge dislocation, we find that the core energy of the relaxed screw dislocation is not a constant, but strongly dependent on macroscopic deformations. Next, we use the edge and screw dislocation core energetics data with physically reasonable assumptions to develop a continuum energetics model for an aggregate of dislocations that accounts for the core energy dependence on macroscopic deformations. Further, we use this energetics model in a discrete dislocation network, and from the variations of the core energy with respect to the nodal positions of the network, we obtain the nodal core force which can directly be incorporated into discrete dislocation dynamics frameworks. We analyze and classify the nodal core force into three different contributions based on their decay behavior. Two of these contributions to the core force, both arising from the core energy dependence on macroscopic deformations, are not accounted for in currently used discrete dislocation dynamics models which assume the core energy to be a constant excepting for its dependence on the dislocation line orientation. Using case studies involving simple dislocation structures, we demonstrate that the contribution to the core force from the core energy dependence on macroscopic deformations can be significant in comparison to the elastic Peach–Koehler force even up to distances of 10–15 nm between dislocation structures. Thus, these core effects, whose origins are in the electronic structure of the dislocation core, can play an important role in influencing dislocation-dislocation interactions to much larger distances than considered heretofore.

36 MATERIALS SCIENCE↗

An XPS study on the impact of relative humidity on the aging of UO 2 powders

High resolution x-ray photoemission spectroscopy (XPS) was used to characterize the chemical speciation of high purity uranium dioxide (UO 2 ) powder samples following aging for periods of up to one year under controlled conditions with relative humidity ranging from 34% to 98%. A systematic shift to higher uranium oxidation states, and thus an increase in the mean uranium valence, was found to directly correlate with the dose of water received (i.e. the product of exposure time and relative humidity). Exposure duration was found to have a greater impact on sample aging than relative humidity. Lastly, the sample aged at 98% relative humidity was found to have unique structural differences for exposure time beyond 180 days when observed by scanning electron microscopy (SEM).

36 MATERIALS SCIENCE↗

Tunneling field-effect junctions with WS 2 barrier

Transition metal dichalcogenides (TMDCs), with their two-dimensional structures and sizable bandgaps, are good candidates for barrier materials in tunneling field-effect junctions (TFEJ) formed from atomic precision vertical stacks of graphene and insulating crystals of a few atomic layers in thickness. Here we report first-principles study of the electronic properties of the Graphene/WS 2 /Graphene sandwich structure revealing strong interface effects on dielectric properties and predicting a high ON/OFF ratio with an appropriate WS 2 thickness and a suitable range of the gate voltage. Both the band spin-orbit coupling splitting and the dielectric constant of the WS 2 layer depend on its thickness when in contact with the graphene electrodes, indicating strong influence from graphene across the interfaces. The dielectric constant is significantly reduced from the bulk WS 2 value. The effective barrier height varies with WS 2 thickness and can be tuned by a gate voltage. These results are critical for future nanoelectronic device applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessing the influence of processing parameters and external loading on the nanoporous structure and morphology of nanoporous gold toward catalytic applications

Nanoporous gold structure gains several unique physical and chemical properties from its nanoscale foam structure composed of ligaments and connected pores. The high specific surface area and interconnected pores make its structure ideal for gas catalysis. Catalytic activity arises in part from the high number density of surface steps and kinks at points of high curvature in the nanoporous structure. However, the structure also makes the material macroscopically brittle and unreliable for many applications due to poor mechanical stability. The ligament diameter, which regulates both desirable chemical properties and mechanical instability, can be tuned to over three orders of magnitude, but few morphology features can be adjusted independently of this. In this report we fabricate nanoporous gold with an average ligament diameter of around 10 nm while varying synthesis parameters and quantify the resulting morphology in order to evaluate the effect of processing on the resulting nanoscale foam structure. In situ tensile experiments are performed to observe how both individual ligaments and the foam structure's features change during deformation in real-time. We found two new morphology features that are independently controllable through synthesis parameters and are likely to influence mechanical stability while preserving or enhancing catalytic activity. The curvature of the ligaments can be increased by stirring the electrolyte during dealloying and the width of the ligament diameter size distribution can be adjusted by controlling the coarsening rate. In situ mechanical tests show that grain boundaries can influence crack propagation and that ligaments removed from the crack tip experience both elastic and plastic stress.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis, structure and canted antiferromagnetism of layered cobalt hydroxide sorbate

Layered hybrid organic–inorganic compounds of the transition metal hydroxides, in which part of the hydroxide ions are exchanged for organic ligands that act as spacers of the 2-dimensional inorganic layers, elicit new or enhanced properties. The interlayer ligands enable fine-tuning of the physicochemical properties of the metal hydroxide layers, including their magnetism. Specifically, within the Co(OH) 2 family of transition ion hydroxides, this approach has been leveraged to stabilize antiferromagnetic and ferrimagnetic ground states for pillared and layered complexes, respectively. Here, in this work, we further investigate the effects of changing dimensionality, local Co coordination, and interlayer spacing on the magnetic ground state of brucite-like β-Co(OH) layered complexes. We report the hydrothermal synthesis of a new crystalline material, Co(OH)(sorb), where the inorganic layers are spaced by monotopic, doubly unsaturated sorbate ligands (sorb = [C 6 H 7 O 2 ] – ). The material was structurally characterized using powder X-ray and neutron diffraction measurements and the crystal structure was solved ab initio from powder diffraction data and refined using the Rietveld method. The magnetic susceptibility and magnetization measurements reveal canted antiferromagnetic ordering with T N = 41.7 K. This report augments our understanding of tuning magnetism through dimensionality in layered complexes and represents a step forward in the design of new 2D layered hybrid compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High temperature infrared absorption cross sections of methane near 3.4 µm in Ar and CO 2 mixtures

In this study, the absorption cross-sections of CH 4 at two wavelengths in the mid-IR region: λ peak = 3403.4 nm and λ valley = 3403.7 nm were measured. Data were taken using three different compositions of non-reactive gas mixtures comprising CH 4 /Ar/CO 2 between 700 < T < 2000 K and 0.1 < P < 1.5 atm in a shock tube utilizing a continuous-wave distributed-feedback quantum cascade laser. Also, broadband room temperature methane cross section measurements were performed using a Fourier transform infrared spectrometer and the cascade laser to gain a better insight into the changes of the line shapes in various bath gasses (Ar, CO 2 , and N 2 ). An application of the high-temperature cross-section data was demonstrated to determine the concentration of methane during oxy-methane combustion in a mixture of CO 2 , O 2 , and Ar. Lastly, current measurements will be valuable addition to the spectroscopy database for methane- an important fuel used for power generation and heating around the world.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural and Magnetic Analysis of Nanocrystalline Lead Europium Sulfide (PbxEuyS)

The authors report the synthesis of nanocrystalline, alloyed PbEuS, a potentially important dilute magnetic semiconductor. The thermolysis of mixed precursors has been adapted for the formation of homogeneous alloyed nanocrystals. X-ray diffraction and magnetization measurements of ternary PbEuS nanocrystals provide convincing evidence that no phase separation occurs in these nanomaterials for europium concentrations up to x = 0.17. X-ray photoelectron spectroscopy provides the atomic composition for PbEuS alloy nanocrystals juxtaposed with the ratio of the starting precursors.

36 MATERIALS SCIENCE↗