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At least 1,135 records · Page 63

Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner

The reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N 2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Magnetic anisotropy and GGG substrate stray field in YIG films down to millikelvin temperatures

Abstract Quantum magnonics investigates the quantum-mechanical properties of magnons, such as quantum coherence or entanglement for solid-state quantum information technologies at the nanoscale. The most promising material for quantum magnonics is the ferrimagnetic yttrium iron garnet (YIG), which hosts magnons with the longest lifetimes. YIG films of the highest quality are grown on a paramagnetic gadolinium gallium garnet (GGG) substrate. The literature has reported that ferromagnetic resonance (FMR) frequencies of YIG/GGG decrease at temperatures below 50 K despite the increase in YIG magnetization. We investigated a 97 nm-thick YIG film grown on 500 μm-thick GGG substrate through a series of experiments conducted at temperatures as low as 30 mK, and using both analytical and numerical methods. Our findings suggest that the primary factor contributing to the FMR frequency shift is the stray magnetic field created by the partially magnetized GGG substrate. This stray field is antiparallel to the applied external field and is highly inhomogeneous, reaching up to 40 mT in the center of the sample. At temperatures below 500 mK, the GGG field exhibits a saturation that cannot be described by the standard Brillouin function for a paramagnet. Including the calculated GGG field in the analysis of the FMR frequency versus temperature dependence allowed the determination of the cubic and uniaxial anisotropies. We find that the total crystallographic anisotropy increases more than three times with the decrease in temperature down to 2 K. Our findings enable accurate predictions of the YIG/GGG magnetic systems behavior at low and ultralow millikelvin temperatures, crucial for developing quantum magnonic devices.

Serha, Rostyslav O.↗

Carrier recombination dynamics and temperature dependent optical properties of InAs–GaSb heterostructures

Heterostructures with two dissimilar materials could offer unprecedented properties if one can carefully synthesize these heterostructures with atomically smooth interfaces and reduced number of recombination centers. InAs/GaSb-based heterostructures have technological importance for long wavelength infrared photodetectors if one can synthesize these materials with high-optical quality and high-carrier lifetime. In this work, the InAs/GaSb heterostructures with a different number of heterointerfaces and growth conditions were grown by solid source molecular beam epitaxy using valved cracker sources for both arsenic and antimony. Precise control of growth parameters and shutter sequences enabled abrupt InAs/GaSb heterointerfaces, as supported by a high-resolution transmission electron microscopic study. The temperature and power-dependent optical properties by photoluminescence (PL) spectroscopic analysis of InAs/GaSb heterostructures with 4 and 28 heterointerfaces displayed donor to the acceptor and the exciton bound to complex defects (V Ga Ga Sb ) 0 . Since the optical transition in PL measurements serves to determine the quality of the material, and the observed excitonic transitions from these InAs/GaSb heterostructures is an indication of high-quality materials. The high-carrier lifetimes of 139 ns to 185 ns from InAs/GaSb heterostructures were measured using microwave photoconductivity decay (μ-PCD) technique at room temperature. The observed increase in carrier lifetime is due to the decreasing number of Ga-related carrier recombination centers or defect complexes. This is further supported by the PL spectroscopic study. In addition, the carrier lifetime with different injection levels is supported by Shockley–Read–Hall recombination. We report these InAs/GaSb heterostructures with high-optical quality and high-carrier lifetimes would offer a path for the development of high-performance infrared photodetectors.

36 MATERIALS SCIENCE↗

Experimental and modeling study of 1/ f noise in multilayer MoS2 and MoSe2 field-effect transistors

In field-effect transistors (FETs) with two-dimensional (2D) transition metal dichalcogenide channels, the dependence of field-effect mobility on atomic layer thickness has been studied and interpreted in terms of interface scattering and interlayer coupling resistance (Rint). However, a model for 1/f noise, such as in MoS2 and in MoSe2 FETs, for various contact metals and layer number thicknesses has not been reported. In this work, we have experimentally studied current–voltage and 1/f noise on MoS2 and MoSe2 FETs with source and drain contacts of high and low work function metals to understand both the mobility and the noise behavior. We have developed a noise model incorporating layer number dependent Hooge parameters and Rint. The noise and mobility models utilize screening lengths for charge, mobility, and Hooge parameter to describe the variation of these quantities with a layer number. Using our single model topology with appropriate fitting parameters for each material and each contact metal, the model captures the experimentally observed layer thickness dependence of the Hooge parameter. Our noise analysis is fully comprehensive and, hence, could be applied to any 2D layered systems.

Kwon, Jiseok↗

Description of longitudinal space charge effects in beams and plasma through dielectric permittivity

We develop a universal framework which allows quickly solve a wide class of problems for longitudinal space charge effects in beams and plasmas in cylindrical geometry. We introduce the longitudinal dielectric permittivity for the beam of charged particles, which describes its collective space charge response. The analysis yields an effective plasma frequency, which depends on the transverse geometry of the system. This dielectric permittivity mirrors the dielectric permittivity of plasma and matches the one dimensional (1D) expression once the transverse size of the beam is large. Several particle species can be included as additive terms describing susceptibility of each specie. The developed approach allows to study stability criteria for collective beam-beam and beam-plasma instabilities for arbitrary transverse distributions in particle densities.

43 PARTICLE ACCELERATORS↗

Exchange–correlation entropy from the generalized thermal adiabatic connection

Warm dense matter is a highly energetic phase characterized by strong correlations, thermal effects, and quantum mechanical electrons. Thermal density functional theory is commonly used in simulations of this challenging phase, driving the development of temperature-dependent approximations to the exchange–correlation free energy. Approaches using the adiabatic connection formula are well known at zero temperature and have been recently leveraged at non-zero temperatures as well. In this work, a generalized thermal adiabatic connection (GTAC) formula is proposed, introducing a fictitious temperature parameter. This allows extraction of the exchange–correlation entropy S XC using simulated interaction strength scaling. Here, this procedure uses a Hellmann–Feynman approach to express the exchange–correlation entropy in terms of a temperature- and interaction strength-dependent exchange–correlation potential energy. In addition, analysis of S XC as a function of interaction strength suggests new forms for approximations, and GTAC itself offers a new framework for exploring both the exact and approximate interplay of temperature, density, and interaction strength across a wide range of conditions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Proton radiation resilience of CdSeTe photovoltaics: High predicted end-of-life performance for space applications

Two types of cadmium selenide telluride (CdSeTe) photovoltaic devices have been exposed to high-energy (150–1500 keV) protons with fluences ranging from 1 × 10 11 to 9 × 10 13 cm −2 . Pre- and post-irradiation current density vs voltage characteristic data were collected and analyzed. Arsenic-doped CdSeTe devices retained 80% of the power conversion efficiency (PCE) relative to control devices after exposure to 10 12 cm −2 650 keV protons, while copper-doped CdSeTe devices retained about 95% of the control PCE under the same irradiation condition. Displacement damage dose analysis coupled with simulations for duration-dependent performance in a medium Earth orbit space mission revealed superior PCE remaining factors, indicating greater resilience to proton bombardment than state-of-the-art multijunction III-V based space photovoltaic technologies.

CdTe solar cells↗

Implications of phonon anisotropy on thermal conductivity of fluorite oxides

Abstract Fluorite oxides are attractive ionic compounds for a range of applications with critical thermal management requirements. In view of recent reports alluding to anisotropic thermal conductivity in this face-centered cubic crystalline systems, we perform a detailed analysis of the impact of direction-dependent phonon group velocities and lifetimes on the thermal transport of fluorite oxides. We demonstrate that the bulk thermal conductivity of this class of materials remains isotropic despite notable anisotropy in phonon lifetime and group velocity. However, breaking the symmetry of the phonon lifetime under external stimuli including boundary scattering present in nonequilibrium molecular dynamics simulations of finite size simulation cell gives rise to apparent thermal conductivity anisotropy. We observe that for accurate determination of thermal conductivity, it is important to consider phonon properties not only along high symmetry directions commonly measured in inelastic neutron or x-ray scattering experiments but also of those along lower symmetry. Our results suggests that certain low symmetry directions have a larger contribution to thermal conductivity compared to high symmetry ones.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Computational Estimation by Scientific Data Mining with Classical Methods to Automate Learning Strategies of Scientists

Experimental results are often plotted as 2-dimensional graphical plots (aka graphs) in scientific domains depicting dependent versus independent variables to aid visual analysis of processes. Repeatedly performing laboratory experiments consumes significant time and resources, motivating the need for computational estimation. The goals are to estimate the graph obtained in an experiment given its input conditions, and to estimate the conditions that would lead to a desired graph. Existing estimation approaches often do not meet accuracy and efficiency needs of targeted applications. We develop a computational estimation approach called AutoDomainMine that integrates clustering and classification over complex scientific data in a framework so as to automate classical learning methods of scientists. Knowledge discovered thereby from a database of existing experiments serves as the basis for estimation. Challenges include preserving domain semantics in clustering, finding matching strategies in classification, striking a good balance between elaboration and conciseness while displaying estimation results based on needs of targeted users, and deriving objective measures to capture subjective user interests. These and other challenges are addressed in this work. The AutoDomainMine approach is used to build a computational estimation system, rigorously evaluated with real data in Materials Science. Our evaluation confirms that AutoDomainMine provides desired accuracy and efficiency in computational estimation. It is extendable to other science and engineering domains as proved by adaptation of its sub-processes within fields such as Bioinformatics and Nanotechnology.

Computer Science↗

Thermal chains and entrainment in cumulus updrafts, Part 2: Analysis of idealized simulations

Research has suggested that the structure of deep convection often consists of a series of rising thermals, or “thermal chain”, which contrasts with existing conceptual models that are used to construct cumulus parameterizations. In this work, simplified theoretical expressions for updraft properties obtained in Part 1 of this study are used to develop a hypothesis explaining why this structure occurs. In this hypothesis, cumulus updraft structure is strongly influenced by organized entrainment below the updraft’s vertical velocity maximum. In a dry environment, this enhanced entrainment can locally reduce condensation rates and increase evaporation, thus eroding buoyancy. For moderate-to-large initial cloud radius R, this breaks up the updraft into a succession of discrete pulses of rising motion (i.e., a thermal chain). For small R, this leads to the structure of a single, isolated rising thermal. In contrast, moist environments are hypothesized to favor plume-like updrafts for moderate-to-large R. In a series of axisymmetric numerical cloud simulations, R and environmental relative humidity (RH) are systematically varied to test this hypothesis. Vertical profiles of fractional entrainment rate, passive tracer concentration, buoyancy, and vertical velocity from these runs agree well with vertical profiles calculated from the theoretical expressions in Part 1. Analysis of the simulations supports the hypothesized dependency of updraft structure on R and RH, that is, whether it consists of an isolated thermal, a thermal chain, or a plume, and the role of organized entrainment in driving this dependency. Additional 3-dimensional (3-D) turbulent cloud simulations are analyzed, and the behavior of these 3-D runs is qualitatively consistent with the theoretical expressions and axisymmetric simulations.

54 ENVIRONMENTAL SCIENCES↗

Characterizing the Sample Selection for Supernova Cosmology

Type Ia supernovae (SNe Ia) are used as distance indicators to infer the cosmological parameters that specify the expansion history of the universe. Parameter inference depends on the criteria by which the analysis SN sample is selected. Only for the simplest selection criteria and population models can the likelihood be calculated analytically, otherwise it needs to be determined numerically, a process that inherently has error. Numerical errors in the likelihood lead to errors in parameter inference. This article presents toy examples where the distance modulus is inferred given a set of SNe at a single redshift. Parameter estimators and their uncertainties are calculated using Monte Carlo techniques. The relationship between the number of Monte Carlo realizations and numerical errors is presented. The procedure can be applied to more realistic models and used to determine the computational and data management requirements of the transient analysis pipeline.

79 ASTRONOMY AND ASTROPHYSICS↗

Eigenmode Analysis of Pulsed Neutron Transport Simulations

We discuss the time dependent behavior of some simple pulsed neutron simulations of subcritical problems in slab geometry. Our intent is to investigate the eigenvalue structure of the discretized neutron transport equation and to show under some reasonable assumptions that a dominant time eigenvalue exists that has a nonnegative eigenvector that determines the long time dependent behavior of the solution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A novel approach for tetrahedral-element-based finite element simulations of anisotropic hyperelastic intervertebral disc behavior

Intervertebral discs are microstructurally complex spinal tissues that add greatly to the flexibility and mechanical strength of the human spine. Attempting to provide an adjustable basis for capturing a wide range of mechanical characteristics and to better address known challenges of numerical modeling of the disc, we present a robust finite-element-based model formulation for spinal segments in a hyperelastic framework using tetrahedral elements. We evaluate the model stability and accuracy using numerical simulations, with particular attention to the degenerated intervertebral discs and their likely skewed and narrowed geometry. To this end, 1) annulus fibrosus is modeled as a fiber-reinforced Mooney-Rivlin type solid for numerical analysis. 2) An adaptive state-variable dependent explicit time step is proposed and utilized here as a computationally efficient alternative to theoretical estimates. 3) Tetrahedral-element-based FE models for spinal segments under various loading conditions are evaluated for their use in robust numerical simulations. For flexion, extension, lateral bending, and axial rotation load cases, numerical simulations reveal that a suitable framework based on tetrahedral elements can provide greater stability and flexibility concerning geometrical meshing over commonly employed hexahedral-element-based ones for representation and study of spinal segments in various stages of degeneration.

59 BASIC BIOLOGICAL SCIENCES↗

PDADMAC/PSS Oligoelectrolyte Multilayers: Internal Structure and Hydration Properties at Early Growth Stages from Atomistic Simulations

We analyze the internal structure and hydration properties of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) oligoelectrolyte multilayers at early stages of their layer-by-layer growth process. Our study is based on large-scale molecular dynamics simulations with atomistic resolution that we presented recently [Sánchez et al., Soft Matter 2019, 15, 9437], in which we produced the first four deposition cycles of a multilayer obtained by alternate exposure of a flat silica substrate to aqueous electrolyte solutions of such polymers at 0.1M of NaCl. In contrast to any previous work, here we perform a local structural analysis that allows us to determine the dependence of the multilayer properties on the distance to the substrate. We prove that the large accumulation of water and ions next to the substrate observed in previous overall measurements actually decreases the degree of intrinsic charge compensation, but this remains as the main mechanism within the interface region. We show that the range of influence of the substrate reaches approximately 3 nm, whereas the structure of the outer region is rather independent from the position. This detailed characterization is essential for the development of accurate mesoscale models able to reach length and time scales of technological interest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nature and Scalings of Density Fluctuations of Compressible Magnetohydrodynamic Turbulence with Applications to the Solar Wind

Abstract The solar wind is a magnetized and turbulent plasma. Its turbulence is often dominated by Alfvénic fluctuations and often deemed as nearly incompressible far away from the Sun, as shown by in situ measurements near 1 au. However, for solar wind closer to the Sun, the plasma β decreases (often lower than unity) while the turbulent Mach number M t increases (can approach unity, e.g., transonic fluctuations). These conditions could produce significantly more compressible effects, characterized by enhanced density fluctuations, as seen by several space missions. In this paper, a series of 3D MHD simulations of turbulence are carried out to understand the properties of compressible turbulence, particularly the generation of density fluctuations. We find that, over a broad range of parameter space in plasma β , cross helicity, and polytropic index, the turbulent density fluctuations scale linearly as a function of M t , with the scaling coefficients showing weak dependence on parameters. Furthermore, through detailed spatiotemporal analysis, we show that the density fluctuations are dominated by low-frequency nonlinear structures, rather than compressible MHD eigenwaves. These results could be important for understanding how compressible turbulence contributes to solar wind heating near the Sun.

79 ASTRONOMY AND ASTROPHYSICS↗

Constraining non-standard neutrino interactions with neutral current events at long-baseline oscillation experiments

We explore, for the first time, neutral-current events at long-baseline experiments to constrain vector and axial-vector neutrino non-standard interactions (NSI) with quarks. We leverage the flavor dependence of NSIs to perform an oscillation analysis in the neutral- current channel. We first introduce a framework to parametrize the effect of NSI on the cross section. Then, as an example, we analyze NOvA neutral-current data which provides significantly improved constraints on the axial-vector NSI parameters $ {\varepsilon}_{\mu \mu}^A $,$ {\varepsilon}_{\tau \tau}^A $ and $ {\varepsilon}_{e\mu}^A $. This is highly complementary to constraints from SNO data, which, differently from long-baseline neutral current data, is not sensitive to isospin conserving NSIs $ {\varepsilon}_u^A $ = $ {\varepsilon}_d^A $. Additionally, we disfavor large values of the diagonal vectorial NSI $ {\varepsilon}_{\mu \mu}^{VV} $ and $ {\varepsilon}_{\tau \tau}^V $ which originate from the LMA-Dark solution. We also highlight the complementarity between NSI searches at oscillation experiments using charged current and neutral current channels.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

CondiDiag1.0: a flexible online diagnostic tool for conditional sampling and budget analysis in the E3SM atmosphere model (EAM)

Abstract. Numerical models used in weather and climate prediction take into account a comprehensive set of atmospheric processes (i.e., phenomena) such as the resolved and unresolved fluid dynamics, radiative transfer, cloud and aerosol life cycles, and mass or energy exchanges with the Earth's surface. In order to identify model deficiencies and improve predictive skills, it is important to obtain process-level understanding of the interactions between different processes. Conditional sampling and budget analysis are powerful tools for process-oriented model evaluation, but they often require tedious ad hoc coding and large amounts of instantaneous model output, resulting in inefficient use of human and computing resources. This paper presents an online diagnostic tool that addresses this challenge by monitoring model variables in a generic manner as they evolve within the time integration cycle. The tool is convenient to use. It allows users to select sampling conditions and specify monitored variables at run time. Both the evolving values of the model variables and their increments caused by different atmospheric processes can be monitored and archived. Online calculation of vertical integrals is also supported. Multiple sampling conditions can be monitored in a single simulation in combination with unconditional sampling. The paper explains in detail the design and implementation of the tool in the Energy Exascale Earth System Model (E3SM) version 1. The usage is demonstrated through three examples: a global budget analysis of dust aerosol mass concentration, a composite analysis of sea salt emission and its dependency on surface wind speed, and a conditionally sampled relative humidity budget. The tool is expected to be easily portable to closely related atmospheric models that use the same or similar data structures and time integration methods.

58 GEOSCIENCES↗