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At least 361 records · Page 20

Kinetic modeling of neutral transport for a continuum gyrokinetic code

In this work we present the first-of-its-kind coupling of a continuum full- f gyrokinetic turbulence model with a 6D continuum model for kinetic neutrals, carried out using the Gkeyll code. Our objective is to improve the first-principle understanding of the role of neutrals in plasma fueling, detachment, and their interaction with edge plasma profiles and turbulence statistics. Our model includes only atomic hydrogen and incorporates electron-impact ionization, charge exchange, and wall recycling. These features have been successfully verified with analytical predictions and benchmarked with the DEGAS2 Monte Carlo neutral code. We carry out simulations for a scrape-off layer (SOL) with simplified geometry and National Spherical Torus Experiment parameters. We compare these results to a baseline simulation without neutrals and find that neutral interactions reduce the normalized density fluctuation levels and associated skewness and kurtosis, while increasing auto-correlation times. A flatter density profile is also observed, similar to the SOL density shoulder formation in experimental scenarios with high fueling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Interpreting ion-energy distributions using charge exchange emitted from deeply kinetic field-reversed-configuration plasmas

Energy resolving the atomic hydrogen outflux created within plasmas by charge exchange (CX) of hot plasma ions with cooler hydrogen neutrals is used to infer the ion energy distribution within the plasma, IED p . In high- β plasma with field nulls and ion gyro-radii comparable to the plasma size, the measured ion energy distribution (IED m ) of the CX outflux will depend on the viewing angle and position of the detector. Here, we describe the physics for this, results from a synthetic diagnostic code that contrasts the IED m to the IED p within relatively small and hot field-reversed-configuration plasmas, and how these data can show the presence of magnetic nulls and different orbit classes in the plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Continuous wave room temperature operation of the 2 $μ$m GaSb-based photonic crystal surface emitting diode lasers

Continuous wave room temperature operation of 2 μm GaSb-based photonic-crystal surface-emitting diode lasers has been realized. The deep etched square mesa devices showed threshold current densities of 500 A/cm 2 at 20 °C. The epi-side down mounted lasers generated above 10 mW of output power in the continuous wave regime and tens of milliwatts in pulses from the 200 × 200 μm 2 aperture. Here, the breakthrough in the device performance parameters was achieved thanks to a highly homogeneous air-pocket retaining epitaxial regrowth process optimized for a specifically designed antimonide diode laser heterostructure. The nanofabrication method utilizing low temperature atomic hydrogen surface cleaning yielded low disorder square lattice of droplet-shaped voids covered by uniform p-cladding layer. The laser emission spectrum as well as near/far field patterns demonstrated peculiar features presumably linked to deformation of the void shape during regrowth and formation of the array of filaments.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Tunnel ionization within a one-dimensional, undriven plasma sheath

In high density, high temperature plasmas, the plasma sheath that develops can result in extremely high electric fields, on the order of tens to hundreds of V/nm. Under the right conditions, these electric fields can reach magnitudes that can increase the probability of electron tunneling ionization to occur, resulting in one or more electron-ion pairs. The presence of tunneling ionization can then modify the development of the plasma sheath, as well as properties such as the ion and electron densities and plasma potential. The tunnel ionization process for hydrogen atoms is demonstrated, in this work, as implemented in a Sandia National Laboratories, particle-in-cell code Aleph. Results are presented for the application of the tunnel ionization process to a one-dimensional, undriven plasma sheath. Additional results for cases that consider warm ions and neutrals, the inclusion of electron–neutral collisions, and the injection of neutral particles, as well as the application to various plasma devices, will be discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Convergent ab initio analysis of the multi-channel HOBr + H reaction

High-level potential energy surfaces for three reactions of hypobromous acid with atomic hydrogen were computed at the CCSDTQ/CBS//CCSDT(Q)/complete basis set level of theory. Focal point analysis was utilized to extrapolate energies and gradients for energetics and optimizations, respectively. The H attack at Br and subsequent Br–O cleavage were found to proceed barrierlessly. The slightly submerged transition state lies −0.2 kcal mol−1 lower in energy than the reactants and produces OH and HBr. The two other studied reaction paths are the radical substitution to produce H2O and Br with a 4.0 kcal mol−1 barrier and the abstraction at hydrogen to produce BrO and H2 with an 11.2 kcal mol−1 barrier. The final product energies lie −37.2, −67.9, and −7.3 kcal mol−1 lower in energy than reactants, HOBr + H, for the sets of products OH + HBr, H2O + Br, and H2 + BrO, respectively. Additive corrections computed for the final energetics, particularly the zero-point vibrational energies and spin–orbit corrections, significantly impacted the final stationary point energies, with corrections up to 6.2 kcal mol−1.

Chemistry↗

The accuracies of effective interactions in downfolding coupled-cluster approaches for small-dimensionality active spaces

Here, this paper evaluates the accuracy of the Hermitian form of the downfolding procedure using the double unitary coupled cluster (DUCC) ansatz on the benchmark systems of linear chains of hydrogen atoms, H6 and H8. The computational infrastructure employs the occupation-number-representation codes to construct the matrix representation of arbitrary second-quantized operators, allowing for the exact representation of exponentials of various operators. The tests demonstrate that external amplitudes from standard single-reference coupled cluster methods that sufficiently describe external (out-of-active-space) correlations reliably parameterize the Hermitian downfolded effective Hamiltonians in the DUCC formalism. The results show that this approach can overcome the problems associated with losing the variational character of corresponding energies in the corresponding SR-CC theories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Proton diffusion and hydrogen/deuterium exchange in amorphous solid water at temperatures from 114 to 134 K

The reaction coefficient for hydrogen/deuterium (H/D) exchange and the diffusion of hydrated excess protons within amorphous solid water (ASW) are characterized as a function of temperature. For these experiments, water films are deposited on a Pt(111) substrate at 108 K, and reactions with pre-adsorbed hydrogen atoms produce hydrated protons. Upon heating, protons diffuse within the water, and H/D exchange occurs when they encounter D2O probe molecules deposited in the films. The time-dependent concentration of D2O is monitored with infrared spectroscopy, and it indicates the protons diffusion from the substrate and establish an equilibrium distribution prior to significant H/D exchange for temperatures 114 K ≤T≤ 134 K. By controlling the distance between the D2O molecules and the substrate, we probe the distribution of protons within the film. It decays as x−2 for the examined range of x (12–52 nm) due to the electric field that develops between the diffusing protons and their image charges in the metal substrate. This agrees with the theoretical distance scaling for the equilibrated proton concentration in a dielectric near a metal boundary. From the proton concentration and the measured D2O decay rate, a lower bound for the proton diffusion coefficient ranging from 10−20 m2/s at 114 K to 10−18 m2/s at 134 K is estimated. The diffusion coefficient has an activation energy of 0.40 eV, which is comparable to energies reported for molecular translations and rotations of H2O, suggesting they may play a critical role in the proton diffusion mechanism within ASW.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Active Thermochemical Tables: the thermophysical and thermochemical properties of methyl, CH 3 , and methylene, CH 2 , corrected for nonrigid rotor and anharmonic oscillator effects

The thermophysical properties (isobaric heat capacity, entropy, enthalpy increment) of two prominent radicals, methyl, CH 3 , and methylene, CH 2 , were computed using the Nonrigid Rotor Anharmonic Oscillator (NRRAO) approach and compared to their RRHO counterparts, demonstrating significant differences between the results from the two approaches. Methylene presents a typical case in which the NRRAO thermophysical properties have significantly higher values than their RRHO counterparts at higher temperatures. In the case of methyl, the positive anharmonicity of the umbrella motion causes an opposite effect, and the NRRAO corrected thermophysical properties have lower values than their RRHO counterparts. The NRRAO corrected thermophysical properties, in turn, affect the resulting thermochemical properties. Here, two reactions important in combustion modelling were tested: the recombination of methyl radical with hydrogen atoms to form methane, and the recombination of two methyl radicals to form ethane. The related NRRAO equilibrium constants differ significantly from their RRHO analogs, and the consequences for chemical modelling are discussed. Also reported are the most current ATcT enthalpies of formation for CH n (n = 4-0) species and for C 2 H 6 , together with the tightly related sequential bond dissociation enthalpies along with the CHn series.

74 ATOMIC AND MOLECULAR PHYSICS↗

Dipolar focusing in laser-assisted positronium formation

Abstract We consider positronium formation in collisions of positrons with excited hydrogen atoms H(n) in an infrared laser field theoretically. This process is assisted by the dipolar focusing effect: a positron moving in a superposition of a laser field and the dipolar field can approach the atomic target even if its trajectory starts with a very large impact parameter, leading to a significant enhancement of the Ps formation cross section. The classical trajectory Monte Carlo method, which is justified for n ⩾ 3 , allows efficient calculation of this enhancement. A similar effect can occur in collisions of positrons with other atoms in excited states, which can lead to improvements in the efficiency of positronium formation.

Optics↗

Distinguishing the XUV-induced Coulomb explosion dynamics of iodobenzene using covariance analysis

The primary and secondary fragmentation dynamics of iodobenzene following its ionization at 120 eV were determined using three-dimensional velocity map imaging and covariance analysis. Site-selective iodine 4d ionization was used to populate a range of excited polycationic parent states, which primarily broke apart at the carbon-iodine bond to produce I+ with phenyl or phenyl-like cations (C n H x + or C n H, with n = 1 – 6 and x = 1 – 5). The molecular products were produced with varying degrees of internal excitation and dehydrogenation, leading to stable and unstable outcomes. This further allowed the secondary dynamics of C 6 H x 2+ intermediates to be distinguished using native-frame covariance analysis, which isolated these processes in their own centre-of-mass reference frames. Furthermore, the mass resolution of the imaging mass spectrometer used for these measurements enabled the primary and secondary reaction channels to be specified at the level of individual hydrogen atoms, demonstrating the ability of covariance analysis to comprehensively measure the competing fragmentation channels of aryl cations, including those involving intermediate steps.

74 ATOMIC AND MOLECULAR PHYSICS↗

Importance of gas heating in capacitively coupled radiofrequency plasma-assisted synthesis of carbon nanomaterials

In pursuit of diamond nanoparticles, a capacitively-coupled radio frequency flow-through plasma reactor was operated with methane-argon gas mixtures. Signatures of the final product obtained microscopically and spectroscopically indicated that the product was an amorphous form of graphite. This result was consistent irrespective of combinations of the macroscopic reactor settings. To explain the observed synthesis output, measurements of C 2 and gas properties were carried out by laser-induced fluorescence and optical emission spectroscopy. Strikingly, the results indicated a strong gas temperature gradient of 100 K per mm from the center of the reactor to the wall. Based on additional plasma imaging, a model of hot constricted region (filamentation region) was then formulated. It illustrated that, while the hot constricted region was present, the bulk of the gas was not hot enough to facilitate diamond sp 3 formation: characterized by much lower reaction rates, when compared to sp 2 , sp 3 formation kinetics are expected to become exponentially slow. This result was further confirmed by experiments under identical conditions but with a H 2 /CH 4 mixture, where no output material was detected: if graphitic sp 2 formation was expected as the main output material from the methane feedstock, atomic hydrogen would then be expected to etch it away in situ, such that the net production of that sp 2 -hybridized solid material is nearly a zero. Finally, the crucial importance of gas heating was corroborated by replacing RF with microwave source whereby facile sp 3 production was attained with H 2 /CH 4 gas mixture.

36 MATERIALS SCIENCE↗

Isotopic mass effects of tritium-fueled high-performance TFTR supershots

An increase in total stored energy correlated with the addition of tritium fuel was observed in supershots during the TFTR DT campaign. This supershot regime had strikingly high, centrally peaked ion and electron temperatures, and the largest neutron emission rates observed in TFTR. This paper presents a study of the causes of this increase in stored energy in supershots. Twenty-six supershots have been recently reanalyzed with the TRANSP plasma analysis code. Early TRANSP simulations did not accurately match the measured magnitude and time evolutions of the neutron emission rates. This mismatch is attributed to neglecting apparent increases of trace amounts of heavy impurities during neutral beam injection. The new TRANSP runs were tuned to accommodate this and match the measured global neutron emission rates. These new runs also had improved fidelity in predicting the time histories and radial dependencies of measured DT neutron emission rates. That in turn adds confidence in the simulated thermal deuterium and tritium density profiles that are needed for calculating the average hydrogenic atomic mass profiles. Six subsets of these supershots had well matched toroidal field B tor , plasma current I p , flux geometry, and total injected neutral beam power. The mix of D and T beam ions was varied for different discharges. The magnitude of the increase of the thermal ion energy W i with added tritium was relatively small, and the total W tot increase is dominated by the increase in fast beam ions with T. Analyses at times before the occurrences of deleterious MHD instabilities yielded scaling of W tot with the volume-average isotopic mass consistent with previous publications. The relative fraction of fast energy ions is expected to be small in practical tokamak reactors. Thus the increase in stored energy W tot observed in TFTR supershots does not appear likely to be significantly helpful for producing useful fusion energy.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A scaling law of the neutral penetration length and Balmer- α wing shape in high-temperature plasmas

Hydrogen atoms penetrating deep inside high-temperature magnetically confined plasmas by repetitive charge-exchange collisions result in a particle source of the plasma, which affects the plasma transport significantly. In this paper, we present an approximate solution of the fluid equations for neutral transport and an analytical representation of the neutral penetration length, in a simplified plasma geometry. This analysis predicts a power-law decay in the Balmer-α line wings which reflects the velocity distribution of the neutral atoms, with the power-law exponent analytically represented as well. These scaling laws are compared with a simple Monte–Carlo simulation and spectroscopic observations of Large Helical Device plasmas. Since the Balmer-α line wings are experimentally accessible, our formulation opens the possibility to quickly estimate the neutral penetration length from spectroscopic observations.

neutral opacity↗

The population of galaxies that contribute to the H i mass function

ABSTRACT We look at the contribution of different galaxy populations to the atomic hydrogen (H i) mass function (HIMF) and the H i density parameter, ΩH i, in the local Universe. Our analysis is based on a sample of 7857 H i selected galaxies selected from a volume common to the Sloan Digital Sky Survey (SDSS) and Arecibo Fast Legacy ALFA (40 per cent catalogue – α.40) surveys. We define different populations of galaxies in the colour (u − r)–magnitude (Mr) plane and compute the HIMF for each of them. Additionally we compute the HIMF for dark galaxies; these are undetected in SDSS and represent $\sim 2{{\ \rm per\ cent}}$ of the total sample. We find that the luminous red population dominates the total HIMF for $\log _{10}(M_{\rm{H\,{\small I}}}h^2_{70}/M_{\odot }) \ge 10.4$. The full red population – luminous and faint – represents about $\sim 17{{\ \rm per\ cent}}$ of the ΩH i budget, while that of the dark population is $\sim 3{{\ \rm per\ cent}}$. The HIMF about the knee, $\log _{10}(M_{\rm{H\,{\small I}}}h^2_{70}/M_{\odot }) \in [8,10.4]$, is dominated by the faint and luminous blue populations, the latter dominating at larger masses in this interval. Their total contribution to ΩH i is $\sim 55\!-\!70{{\ \rm per\ cent}}$, the variation depending on the definition of population. The dominant populations at the low-mass end, $\log _{10}(M_{\rm{H\,{\small I}}}h^2_{70}/M_{\odot }) \le 8.0$ are the faint blue and faint bluer populations, the latter’s dominance being sensitive to its definition. The full blue (blue–bluer luminous and faint) population represents $\sim 80{{\ \rm per\ cent}}$ of ΩH i. A bimodal HIMF suggested by our results is however not seen since the amplitude of the HIMF of the luminous red population is small compared to that of the luminous blue population.

Dutta, Saili↗

WALLABY pilot survey: H i gas disc truncation and star formation of galaxies falling into the Hydra I cluster

ABSTRACT We present results from our analysis of the Hydra I cluster observed in neutral atomic hydrogen (H i) as part of the Widefield ASKAP L-band Legacy All-sky Blind Survey (WALLABY). These WALLABY observations cover a 60-square-degree field of view with uniform sensitivity and a spatial resolution of 30 arcsec. We use these wide-field observations to investigate the effect of galaxy environment on H i gas removal and star formation quenching by comparing the properties of cluster, infall, and field galaxies extending up to ∼5R200 from the cluster centre. We find a sharp decrease in the H i-detected fraction of infalling galaxies at a projected distance of ∼1.5R200 from the cluster centre from $\sim 85{{\ \rm per\ cent}}$ to $\sim 35{{\ \rm per\ cent}}$. We see evidence for the environment removing gas from the outskirts of H i-detected cluster and infall galaxies through the decrease in the H i to r-band optical disc diameter ratio. These galaxies lie on the star-forming main sequence, indicating that gas removal is not yet affecting the inner star-forming discs and is limited to the galaxy outskirts. Although we do not detect galaxies undergoing galaxy-wide quenching, we do observe a reduction in recent star formation in the outer disc of cluster galaxies, which is likely due to the smaller gas reservoirs present beyond the optical radius in these galaxies. Stacking of H i non-detections with H i masses below $M_{\rm {HI}}\lesssim 10^{8.4}\, \rm {M}_{\odot }$ will be required to probe the H i of galaxies undergoing quenching at distances ≳60 Mpc with WALLABY.

Reynolds, T. N. (ORCID:0000000266065953)↗

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Abstract Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.

Sehnal, David↗

Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure

The ribose 2'-hydroxyl is the key chemical difference between RNA and DNA and primary source of their divergent structural and functional characteristics. Macromolecular X-ray diffraction experiments typically do not reveal the positions of hydrogen atoms. Thus, standard crystallography cannot determine 2'-OH orientation (H2'-C2'-O2'-HO2' torsion angle) and its potential roles in sculpting the RNA backbone and the expansive fold space. Here, we report the first neutron crystal structure of an RNA, the Escherichia coli rRNA Sarcin-Ricin Loop (SRL). 2'-OD orientations were established for all 27 residues and revealed O-D bonds pointing toward backbone (O3', 13 observations), nucleobase (11) or sugar (3). Most riboses in the SRL stem region show a 2'-OD backbone-orientation. GAGA-tetraloop riboses display a 2'-OD base-orientation. An atypical C2'-endo sugar pucker is strictly correlated with a 2'-OD sugar-orientation. Neutrons reveal the strong preference of the 2'-OH to donate in H-bonds and that 2'-OH orientation affects both backbone geometry and ribose pucker. We discuss 2'-OH and water molecule orientations in the SRL neutron structure and compare with results from a solution phase 10 μs MD simulation. We demonstrate that joint cryo-neutron/X-ray crystallography offers an all-in-one approach to determine the complete structural properties of RNA, i.e. geometry, conformation, protonation state and hydration structure.

59 BASIC BIOLOGICAL SCIENCES↗

Mechanical form factors and densities of nonrelativistic fermions

The hadron physics community has been actively debating the interpretation of so-called mechanical properties of hadrons. Nonrelativistic quantum-mechanical systems like the hydrogen atom have been appealed to in these debates as analogies. Since such appeals are likely to continue, it is important to have Galilei-covariant expressions for matrix elements of the energy-momentum tensor. In this work, I obtain Galilei-covariant breakdowns of such matrix elements into mechanical form factors, with a special focus on spin-half states. I additionally study the spatial densities associated with these form factors, using the pilot wave interpretation to guide their breakdown into contributions from internal structure and from quantum-mechanical effects such as wave packet dispersion. For completeness, I also obtain nonrelativistic Breit frame densities.

form factors↗