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At least 991 records · Page 55

MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

Peptoids (poly-N-substituted glycines) are a class of synthetic polymers that are regioisomers of peptides (poly-C-substituted glycines), in which the point of side-chain connectivity is shifted from the backbone C to the N atom. Peptoids have found diverse applications as peptidomimetic drugs, protein mimetic polymers, surfactants, and catalysts. Computational modeling is valuable in the understanding and design of peptoid-based nanomaterials. In this work, we report the bottom-up parameterization of coarse-grained peptoid force fields based on the MARTINI peptide force field against all-atom peptoid simulation data. Our parameterization pipeline iteratively refits coarse-grained bonded interactions using iterative Boltzmann inversion and nonbonded interactions by matching the potential of mean force for chain extension. We assure good sampling of the amide bond cis/trans isomerizations in the all-atom simulation data using parallel bias metadynamics. We develop coarse-grained models for two representative peptoids—polysarcosine (poly(N-methyl glycine)) and poly(N-((4-bromophenyl)ethyl)glycine)—and show their structural and thermodynamic properties to be in excellent accord with all-atom calculations but up to 25-fold more efficient and compatible with MARTINI force fields. Here, this work establishes a new rigorously parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adult weight change and premenopausal breast cancer risk: A prospective pooled analysis of data from 628,463 women

Early-adulthood body size is strongly inversely associated with risk of premenopausal breast cancer. It is unclear whether subsequent changes in weight affect risk. We pooled individual-level data from 17 prospective studies to investigate the association of weight change with premenopausal breast cancer risk, considering strata of initial weight, timing of weight change, other breast cancer risk factors and breast cancer subtype. Hazard ratios (HR) and 95% confidence intervals (CI) were obtained using Cox regression. Among 628,463 women, 10,886 were diagnosed with breast cancer before menopause. Models adjusted for initial weight at ages 18–24 years and other breast cancer risk factors showed that weight gain from ages 18–24 to 35–44 or to 45–54 years was inversely associated with breast cancer overall (e.g., HR per 5 kg to ages 45–54: 0.96, 95% CI: 0.95–0.98) and with oestrogen-receptor(ER)-positive breast cancer (HR per 5 kg to ages 45–54: 0.96, 95% CI: 0.94–0.98). Weight gain from ages 25–34 was inversely associated with ER-positive breast cancer only and weight gain from ages 35–44 was not associated with risk. None of these weight gains were associated with ER-negative breast cancer. Weight loss was not consistently associated with overall or ER-specific risk after adjusting for initial weight. Weight increase from early-adulthood to ages 45–54 years is associated with a reduced premenopausal breast cancer risk independently of early-adulthood weight. Biological explanations are needed to account for these two separate factors.

60 APPLIED LIFE SCIENCES↗

Sequential Bayesian Parameter Estimation of Stochastic Dynamic Load Models

In this paper we focus on the parameter estimation of dynamic load models with stochastic terms-in particular, load models where protection settings are uncertain, such as in aggregated air conditioning units. We show how the uncertainty in the aggregated protection characteristics can be formulated as a stochastic differential equation with process noise. We cast the parameter inversion within a Bayesian parameter estimation framework, and we present methods to include process noise. We demonstrate the benefits of considering stochasticity in the parameter estimation and the risks of ignoring it.

Bayesian Statistics↗

Ultrafast Carrier–Lattice Interactions and Interlayer Modulations of Bi 2 Se 3 by X-ray Free-Electron Laser Diffraction

We report as a 3D topological insulator, bismuth selenide (Bi 2 Se 3 ) has potential applications for electrically and optically controllable magnetic and optoelectronic devices. Understanding the coupling with its topological phase requires studying the interactions of carriers with the lattice on time scales down to the sub-picosecond regime. Here we investigate the ultrafast carrier-induced lattice contractions and interlayer modulations in Bi 2 Se 3 thin films by time-resolved diffraction using an X-ray free-electron laser. The lattice contraction depends on the carrier concentration and is followed by an interlayer expansion accompanied by oscillations. Using density functional theory (DFT) and the Lifshitz model, the initial contraction can be explained by van der Waals force modulation of the confined free carrier layers. Our theory suggests that band inversion, related to a topological phase transition, is modulated by the expansion of the interlayer distance. These results provide insights into the topological phase control by light-induced structural change on ultrafast timescales.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Valence-band hybridization in sulphides

The hybridization state in solids often defines the critical chemical and physical properties of a compound. However, it is difficult to spectroscopically detect and evaluate hybridization beyond just general fingerprint signatures. Here, the valence-band hybridization of metal d-derived bands (short: “metal d bands”) in selected metal sulphides is studied with a combined spectroscopic and theoretical approach to derive deeper insights into the fundamental nature of such compounds. The valence bands of the studied sulphides are comprised of hybrid bands derived from the metal d, S 3s, and S 3p states. Employing S K and L 2,3 X-ray emission spectroscopy and spectra calculations based on density functional theory, the degree of hybridization (i.e., the covalency) of these bands can be directly probed as a function of their relative energies. We find that the relative intensity of the “metal d band” features in the spectra scales with the inverse square of the energy separation to the respective sulfur-derived bands, which can be analytically derived from a simple two-orbital model. This study demonstrates that soft X-ray emission spectroscopy is a powerful tool to study valence state hybridization, in particular in combination with hard X-ray emission spectroscopy, promising a broad impact in many research fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Resonant Frequency Derived from the Rayleigh-Wave Dispersion Image: The High-Impedance Boundary Problem

In this work, we present a simple and automated approach to estimate primary site-response resonance, layer thickness, and shear-wave velocity directly from a dispersion image for a layer over half-space problem. We demonstrate this for high-impedance boundary conditions that lie in the upper tens of meters. Our approach eliminates the need for time-consuming dispersion curve picking and 1D shear-wave velocity inversion for large data volumes that can capture velocity structure in profile. We highlight important relationships between dispersion characteristics and resonance parameters through synthetic modeling and field data acquired over Atlantic Coastal Plain sediments. In this environment, shallow soil conditions are critical to accurately estimate earthquake site response. We suggest that this image processing approach can be applied to a range of high-impedance conditions, at a range of scales, or can provide model constraints for more complex velocity structures.

58 GEOSCIENCES↗

Double exponential approximation and inverse double exponential fit for Bell Labs and International-Military Standard EMP waveforms

We summarize here the double exponential and inverse double exponential approximations for two common EMP waveforms, the Bell Laboratories (Bell Labs) and the International- military standard (IEC-MIL-STD). Both models have been used frequently due to their relatively easy analytical expressions for both the time domain waveforms and their associated frequency domain spectra.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Limits on Astrophysical Antineutrinos with the KamLAND Experiment

Abstract We report on a search for electron antineutrinos ( ν ¯ e ) from astrophysical sources in the neutrino energy range 8.3–30.8 MeV with the KamLAND detector. In an exposure of 6.72 kton-year of the liquid scintillator, we observe 18 candidate events via the inverse beta decay reaction. Although there is a large background uncertainty from neutral current atmospheric neutrino interactions, we find no significant excess over background model predictions. Assuming several supernova relic neutrino spectra, we give upper flux limits of 60–110 cm −2 s −1 (90% confidence level, CL) in the analysis range and present a model-independent flux. We also set limits on the annihilation rates for light dark matter pairs to neutrino pairs. These data improve on the upper probability limit of 8 B solar neutrinos converting into ν ¯ e , P ν e → ν ¯ e < 3.5 × 10 − 5 (90% CL) assuming an undistorted ν ¯ e shape. This corresponds to a solar ν ¯ e flux of 60 cm −2 s −1 (90% CL) in the analysis energy range.

79 ASTRONOMY AND ASTROPHYSICS↗

The Magnificent Five Images of Supernova Refsdal: Time Delay and Magnification Measurements

In late 2014, four images of supernova (SN) "Refsdal," the first known example of a strongly lensed SN with multiple resolved images, were detected in the MACS J1149 galaxy-cluster field. Following the images' discovery, the SN was predicted to reappear within hundreds of days at a new position ~8'' away in the field. The observed reappearance in late 2015 makes it possible to carry out Refsdal's original proposal to use a multiply imaged SN to measure the Hubble constant H0, since the time delay between appearances should vary inversely with H0. Moreover, the position, brightness, and timing of the reappearance enable a novel test of the blind predictions of galaxy-cluster models, which are typically constrained only by the positions of multiply imaged galaxies. We have developed a new photometry pipeline that uses DOLPHOT to measure the fluxes of the five images of SN Refsdal from difference images. We apply four separate techniques to perform a blind measurement of the relative time delays and magnification ratios between the last image SX and the earlier images S1–S4. We measure the relative time delay of SX–S1 to be 376.0$^{+5.6}_{–5.5}$ days and the relative magnification to be 0.30$^{+0.5}_{–0.3}$. This corresponds to a 1.5% precision on the time delay and 17% precision for the magnification ratios and includes uncertainties due to millilensing and microlensing. In an accompanying paper, we place initial and blind constraints on the value of the Hubble constant.

79 ASTRONOMY AND ASTROPHYSICS↗

Local atomic configurations in mechanically alloyed amorphous (FeCoNi) 70 Ti 10 B 20 powders

Here, the atomic structure of amorphous (FeCoNi) 70 Ti 10 B 20 alloy synthesized by mechanical alloying was investigated using high energy synchrotron X-ray diffraction and inverse Monte Carlo simulations of pair distribution functions. Empirical potential structure refinement indicates a chemical short-range order at the length scales of 2.1–2.5 Å via local atomic arrangements forming deformed bcc-like clusters. The structural model obtained was described by bond lengths, coordination numbers, and bond angle distribution functions determined for the first neighbor atoms by x-ray scattering supplemented with 3D Monte Carlo simulations.

36 MATERIALS SCIENCE↗

Atmospheric teleconnection processes linking winter air stagnation and haze extremes in China with regional Arctic sea ice decline

Abstract. Recent studies suggested significant impacts of boreal cryosphere changes on wintertime air stagnation and haze pollution extremes in China. However, the underlying mechanisms of such a teleconnection relationship remains unclear. Here we use the Whole Atmosphere Community Climate Model (WACCM) to investigate dynamic processes leading to atmospheric circulation and air stagnation responses to Arctic sea ice changes. We conduct four climate sensitivity experiments by perturbing sea ice concentrations (SIC) and corresponding sea surface temperature (SST) in autumn and early winter over the whole Arctic and three subregions in the climate model. The results indicate distinct responses in circulation patterns and regional ventilation to the region-specific Arctic changes, with the largest increase of both the probability (by 132 %) and the intensity (by 30 %) of monthly air stagnation extremes being found in the experiment driven by SIC and SST changes over the Pacific sector of the Arctic (the East Siberian and Chukchi seas). The increased air stagnation extremes are mainly driven by an amplified planetary-scale atmospheric teleconnection pattern that resembles the negative phase of the Eurasian (EU) pattern. Dynamical diagnostics suggest that convergence of transient eddy forcing in the vicinity of Scandinavia in winter is largely responsible for the amplification of the teleconnection pattern. Transient eddy vorticity fluxes dominate the transient eddy forcing and produce a barotropic anticyclonic anomaly near Scandinavia and wave train propagation across Eurasia to the downstream regions in East Asia. The piecewise potential vorticity inversion analysis reveals that this long-range atmospheric teleconnection of Arctic origin takes place primarily via the middle and upper troposphere. The anomalous ridge over East Asia in the middle and upper troposphere worsens regional ventilation conditions by weakening monsoon northwesterlies and enhancing temperature inversions near the surface, leading to more and stronger air stagnation and pollution extremes over eastern China in winter. Ensemble projections based on state-of-the-art climate models in the Coupled Model Intercomparison Project Phase 6 (CMIP6) corroborate this teleconnection relationship between high-latitude environmental changes and midlatitude weather extremes, though the tendency and magnitude vary considerably among each participating model.

54 ENVIRONMENTAL SCIENCES↗

The Dirac equation as a model of topological insulators

The Dirac equation with a spatially dependent mass can be used as a simple, exactly soluble, continuum model of a three-dimensional Topological Insulator. For a bulk system, the sign of the mass determines the parity at the only time-reversal point ( k _ = 0 ) and, thus, leads to the designation of the bulk as being topologically trivial or non-trivial. Since the mass changes sign at the interface between a topologically trivial and non-trivial materials, topological surface states appear on that boundary. We present that electron scattering experiments may provide an alternate probe of the topological character of the surface states. For infinitely thick slabs, the states on the opposite sides of the slab decouple. The spatial decoupling results in the surface states become gapless, non-degenerate and, due to the Rashba spin–orbit coupling generated by the loss of inversion symmetry, exhibit spin-momentum locking. We review several characteristic properties of the topological surface states which are dependent on the topological quantum numbers and show that, using this model, they can be calculated exactly using simple approaches.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A mixed, unified forward/inverse framework for earthquake problems: fault implementation and coseismic slip estimate

SUMMARY We introduce a new finite-element (FE) based computational framework to solve forward and inverse elastic deformation problems for earthquake faulting via the adjoint method. Based on two advanced computational libraries, FEniCS and hIPPYlib for the forward and inverse problems, respectively, this framework is flexible, transparent and easily extensible. We represent a fault discontinuity through a mixed FE elasticity formulation, which approximates the stress with higher order accuracy and exposes the prescribed slip explicitly in the variational form without using conventional split node and decomposition discrete approaches. This also allows the first order optimality condition, that is the vanishing of the gradient, to be expressed in continuous form, which leads to consistent discretizations of all field variables, including the slip. We show comparisons with the standard, pure displacement formulation and a model containing an in-plane mode II crack, whose slip is prescribed via the split node technique. We demonstrate the potential of this new computational framework by performing a linear coseismic slip inversion through adjoint-based optimization methods, without requiring computation of elastic Green’s functions. Specifically, we consider a penalized least squares formulation, which in a Bayesian setting—under the assumption of Gaussian noise and prior—reflects the negative log of the posterior distribution. The comparison of the inversion results with a standard, linear inverse theory approach based on Okada’s solutions shows analogous results. Preliminary uncertainties are estimated via eigenvalue analysis of the Hessian of the penalized least squares objective function. Our implementation is fully open-source and Jupyter notebooks to reproduce our results are provided. The extension to a fully Bayesian framework for detailed uncertainty quantification and non-linear inversions, including for heterogeneous media earthquake problems, will be analysed in a forthcoming paper.

58 GEOSCIENCES↗

Quasilinear modelling of collisional trapped electron modes

The simplification of collision operators is necessary for quasilinear turbulence modelling used with integrated modelling frameworks, such as the gyrokinetic code QuaLiKiz. The treatment of collisions greatly impacts the accuracy of trapped electron mode (TEM) modelling, which is necessary to predict the electron heat flux and the balance between inward and outward particle fluxes. In particular, accurate particle flux predictions are necessary to successfully model density peaking in the tokamak core. We explored two ways of improving collisional TEM model reduction for tokamak core plasmas. First, we carried out linear GENE simulations to study the complex interplay between collisions and trapped electrons. We then used these simulations to define an effective trapped fraction to characterize the collisional TEM based on two key parameters, the local inverse-aspect ratio $\epsilon$ and the collisionality $\nu ^\ast$. One aspect missing from analytical TEM research is that the collisional frequency and the bounce-transit frequency are both velocity dependent; this effective trapped fraction takes both into account. In doing so, we determined that two parameters are not enough to model the collisional TEM, as an additional third free parameter was necessary. We determined that this model, as currently formulated, is not suitable for integrated modelling purposes. Second, we directly improved QuaLiKiz's Krook operator, which relies on two free parameters. We determined that these parameters required adjustments against higher-fidelity collisional models. In order to improve density profile predictions when paired with integrated models, we refined the Krook operator by using GENE simulations as a higher-fidelity point of comparison. We then demonstrate strong improvement of density peaking predictions of QuaLiKiz within the integrated modelling framework JETTO.

fusion plasma↗

Spread Spectrum Time Domain Reflectometry and Steepest Descent Inversion to Measure Complex Impedance

In this paper, we present a method for estimating complex impedances using reflectometry and a modified steepest descent inversion algorithm. We simulate spread spectrum time domain reflectometry (SSTDR), which can measure complex impedances on energized systems for an experimental setup with resistive and capacitive loads. A parametric function, which includes both a misfit function and stabilizer function, is created. The misfit function is a least squares estimate of how close the model data matches observed data. The stabilizer function prevents the steepest descent algorithm from becoming unstable and diverging. Steepest descent iteratively identifies the model parameters that minimize the parametric function. We validate the algorithm by correctly identifying the model parameters (capacitance and resistance) associated with simulated SSTDR data, with added 3 dB white Gaussian noise. With the stabilizer function, the steepest descent algorithm estimates of the model parameters are bounded within a specified range. Furthermore, the errors for capacitance (220pF to 820pF) and resistance (50 Ω to 270 Ω) are < 10%, corresponding to a complex impedance magnitude |R +1/jωC| of 53 Ω to 510 Ω.

14 SOLAR ENERGY↗

Nonlinear magnetohydrodynamic modeling of current-drive-induced sawtooth-like crashes in the W7-X stellarator

Sawtooth-like core electron temperature crashes have been observed in W7-X experiments with electron cyclotron current drive. Here we present nonlinear single-fluid magnetohydrodynamic simulations of this phenomenon using the newly developed stellarator modeling capability of the M3D-C 1 code. The near-axis current drive gives rise to two ι = 1 resonances in the equilibrium rotational transform profile so that two consecutive (1, 1) internal kink modes are seen in the simulations. A small-amplitude crash at the inner resonance occurs first, which may correspond to the sawtooth precursors observed in the experiments. A bigger crash at the outer resonance then flattens the core temperature profile, which shows semi-quantitative agreements with experimental measurements on certain metrics such as the crash amplitude and the inversion radius of the temperature change. These results illustrate a likely mechanism of the current-drive-induced sawtooth-like crashes in W7-X and, to some extent, validate the stellarator modeling capability of M3D-C 1 .

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Seismotectonic evidence for subduction beneath the Eastern Greater Caucasus

SUMMARY We generated high-resolution 3-D seismic velocity models as well as a relocated earthquake catalogue across the eastern Greater Caucasus and Kura basins. This work was done using data from the recently upgraded Republic Seismological Survey Center's (RSSC) seismic network. We generated our tomographic images of crustal velocity structure in Azerbaijan using double-difference inversions (i.e. tomoDD and hypoDD). Earthquake catalogues from the RSSC between 2011 and 2016 were used; these catalogues include absolute arrival times of 103 288 P- and 120 952 S-wave traveltime picks for 7574 events recorded at 35 stations in Azerbaijan. Beginning with a layered, 1-D velocity model that was estimated using VELEST, we inverted simultaneously for relative location, Vp and Vs on a 3-D grid with dimensions 670 × 445 × 45 km, with a uniform grid spacing of 55 × 55 × 5 km for all of Azerbaijan. We observe that the relocated hypocentres cluster into two depth ranges, at the surface and at depth, that appear to correspond to major fault zones and the top of a subducting plate. Additionally, we note intermediate depth seismicity (∼50–60 km) beneath the Kura Basin, and a northward deepening of earthquake depths. Seismic velocities vary significantly throughout the study region; we observe very slow velocities throughout the Kura Basin between 5 and 15 km, and elevated velocities at 20–35 km. The wholesale velocity structure and seismic structure of Kura Basin strongly mirrors that of the Caspian Sea, which suggests that the geodynamics of the Caspian continue westwards into Azerbaijan. The key results of this study suggest that the northward subduction observed in the Caspian Sea continues beneath the Eastern Greater Caucasus, as well as provides evidence for active faulting along the southern margin of the mountain range.

Gunnels, Michael↗

Multi-scale dynamics of magnetic flux tubes and inverse magnetic energy transfer

Here, we report on an analytical and numerical study of the dynamics of a three-dimensional array of identical magnetic flux tubes in the reduced-magnetohydrodynamic description of the plasma. We propose that the long-time evolution of this system is dictated by flux-tube mergers, and that such mergers are dynamically constrained by the conservation of the pertinent (ideal) invariants, viz. the magnetic potential and axial fluxes of each tube. We also propose that in the direction perpendicular to the merging plane, flux tubes evolve in a critically balanced fashion. These notions allow us to construct an analytical model for how quantities such as the magnetic energy and the energy-containing scale evolve as functions of time. Of particular importance is the conclusion that, like its two-dimensional counterpart, this system exhibits an inverse transfer of magnetic energy that terminates only at the system scale. We perform direct numerical simulations that confirm these predictions and reveal other interesting aspects of the evolution of the system. We find, for example, that the early time evolution is characterized by a sharp decay of the initial magnetic energy, which we attribute to the ubiquitous formation of current sheets. We also show that a quantitatively similar inverse transfer of magnetic energy is observed when the initial condition is a random, small-scale magnetic seed field.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗