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At least 721 records · Page 40

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A spectrometer for ultrashort gamma-ray pulses with photon energies greater than 10 MeV

Herein we present a design for a pixelated scintillator based gamma-ray spectrometer for non-linear inverse Compton scattering experiments. By colliding a laser wakefield accelerated electron beam with a tightly focused, intense laser pulse, gamma-ray photons up to 100 MeV energies and with few femtosecond duration may be produced. To measure the energy spectrum and angular distribution, a 33 × 47 array of cesium-iodide crystals was oriented such that the 47 crystal length axis was parallel to the gamma-ray beam and the 33 crystal length axis was oriented in the vertical direction. Using an iterative deconvolution method similar to the YOGI code, modeling of the scintillator response using GEANT4 and fitting to a quantum Monte Carlo calculated photon spectrum, we are able to extract the gamma ray spectra generated by the inverse Compton interaction.

47 OTHER INSTRUMENTATION↗

Active learning for robust, high-complexity reactive atomistic simulations

Machine learned reactive force fields based on polynomial expansions have been shown to be highly effective for describing simulations involving reactive materials. Nevertheless, the highly flexible nature of these models can give rise to a large number of candidate parameters for complicated systems. In these cases, reliable parameterization requires a well-formed training set, which can be difficult to achieve through standard iterative fitting methods. In this paper, we present an active learning approach based on cluster analysis and inspired by Shannon information theory to enable semi-automated generation of informative training sets and robust machine learned force fields. The use of this tool is demonstrated for development of a model based on linear combinations of Chebyshev polynomials explicitly describing up to four-body interactions, for a chemically and structurally diverse system of C/O under extreme conditions. We show that this flexible training database management approach enables development of models exhibiting excellent agreement with Kohn–Sham density functional theory in terms of structure, dynamics, and speciation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Recent Advances in Small Angle X-ray Scattering for Superlattice Study

Small-angle x-ray scattering is used for the structure determination of superlattice for its superior resolution, nondestructive nature, and high penetration power of x rays. With the advent of high brilliance x-ray sources and innovative computing algorithms, there have been notable advances in small angle x-ray scattering analysis of superlattices. High brilliance x-ray beams have made data analyses less model-dependent. Additionally, novel data acquisition systems are faster and more competitive than ever before, enabling a more accurate mapping of the superlattices' reciprocal space. Fast and high-throughput computing systems and algorithms also make possible advanced analysis methods, including iterative phasing algorithms, non-parameterized fitting of scattering data with molecular dynamics simulations, and the use of machine learning algorithms. As a result, solving nanoscale structures with high resolutions has become an attainable task. In this review, we highlight new developments in the field and introduce their applications for the analysis of nanoscale ordered structures, including nanoparticle supercrystals, nanoscale lithography patterns, and supramolecular self-assemblies. Particularly, we highlight the reciprocal space mapping techniques and the use of iterative phase retrieval algorithms. We also cover coherent-beam-based small angle x-ray scattering techniques such as ptychography and ptycho-tomography in view of the traditional small angle x-ray scattering perspective.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Drift-ordered fluid vorticity equation with energy consistency

Although drift-ordered fluid models are widely applied in tokamak edge turbulence simulations, the models used are acknowledged not to conserve energy or even electrical charge. The present paper aims to remove many of the existing pitfalls in drift-fluid models, however, with the objective of finding a solution simple enough to be implemented in numerical applications. Our main result is an improved version of the drift-Braginskii equations involving a generalized vorticity function. In the new drift-Braginskii system, the quasi-neutrality condition translates into a transport equation for a generalized vorticity, expressed in conservation form, and related to the total mass-weighted circulation. It is found that kinetic energy conservation can be achieved if the polarization flow is defined recursively. In conclusion, the resulting model conserves the kinetic energy associated with E×B and diamagnetic flows and retains the associated perpendicular kinetic energy flux.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Modeling cross-beam energy transfer with sector ray tracing

Ray-based cross-beam energy transfer (CBET) models are an essential feature of the radiation-hydrodynamic codes used to simulate inertial confinement fusion implosions, but full 3D ray-based CBET calculations can have a prohibitively high computational cost. Sector ray tracing can be used to reduce the cost by orders of magnitude in cases where the coronal plasma and laser drive can be approximated as spherically symmetric. An extension of sector ray tracing (section ray tracing) can be used to relax the assumption of a spherically symmetric drive while still retaining most of the computational savings of a sector ray trace. We discuss the foundations of sector and section ray tracing and compare them to full ray tracing.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Desmearing Bonse–Hart USANS data using Bayesian Gaussian process regression

Ultra-small-angle neutron scattering (USANS) enables access to micrometer-scale structures but is intrinsically affected by strong, anisotropic resolution smearing arising from slit-geometry optics. As a result, recovery of the intrinsic scattering intensity constitutes an ill-posed inverse problem, and commonly used iterative desmearing methods lack rigorous uncertainty quantification. We present a Bayesian desmearing framework for slit-geometry USANS based on Gaussian process regression. In this approach, the scattering intensity is modeled as a smooth random function, and the instrumental point spread function is incorporated explicitly as a forward operator. The resulting formulation yields a closed-form maximum a posteriori solution with well-defined credibility intervals. Computational benchmarks and experimental validation using combined USANS and small-angle neutron scattering (SANS) measurements demonstrate that the framework enables stable desmearing, suppresses experimental noise, and preserves physically meaningful structural features under realistic conditions.

Tung, Chi-Huan [Oak Ridge National Laboratory (ORN↗

Dynamic phasing of multichannel cw laser radiation by means of a stochastic gradient algorithm

The phasing of a multichannel laser beam by means of an iterative stochastic parallel gradient (SPG) algorithm has been numerically and experimentally investigated. The operation of the SPG algorithm is simulated, the acceptable range of amplitudes of probe phase shifts is found, and the algorithm parameters at which the desired Strehl number can be obtained with a minimum number of iterations are determined. An experimental bench with phase modulators based on lithium niobate, which are controlled by a multichannel electronic unit with a real-time microcontroller, has been designed. Phasing of 16 cw laser beams at a system response bandwidth of 3.7 kHz and phase thermal distortions in a frequency band of about 10 Hz is experimentally demonstrated. The experimental data are in complete agreement with the calculation results. (control of laser radiation parameters)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Scheme of a hydrogen-molecule quantum simulator based on two ultracold rubidium atoms

A scheme is proposed for implementing a hydrogen-molecule quantum simulator based on two ultracold rubidium atoms trapped into spatially separated optical dipole traps. The scheme includes the adiabatic preparation of the initial quantum state of two atoms and the iterative quantum phase estimation. The accuracy of measuring the ground state energy of a molecule is numerically calculated as a function of the number of iterations. The simulation is performed using two-qubit gates based on the dipole blockade effect under short-term excitation of atoms into the Rydberg states with allowance for the finite lifetime of Rydberg states and the finite energies of the van der Waals interaction. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An iterative approach to non-overdetermined inverse scattering at fixed energy

We present an iterative approximate reconstruction algorithm for non-overdetermined inverse scattering at fixed energy E with incomplete data, where the dimension d≥2. In particular, we obtain rapidly converging approximate reconstructions for this inverse scattering for E→+∞. Bibliography: 38 titles.

97 MATHEMATICS AND COMPUTING↗

Weighted inequalities for quasilinear integral operators on the semi-axis and applications to Lorentz spaces

A precise characterization of inequalities in weighted Lebesgue spaces with positive quasilinear integral operators of iterative type on the half-axis is given. All cases of positive integration parameters are treated, including the case of supremum. Applications to the solution of the well-known problem of the boundedness of the Hardy-Littlewood maximal operator in weighted Lorentz Γ-spaces are given. Bibliography: 41 titles.

97 MATHEMATICS AND COMPUTING↗

Advanced Reactor Control and Operations (ARCO): A University Research Facility for Developing Optimized Digital Control Rooms

The Advanced Reactor Control and Operations (ARCO) facility was constructed in January 2018 to serve as a test bed for advanced reactor control rooms and operator support systems. Since then, it has supported human-machine interface user experience research, fault detection and mitigation technology development, control room concept of operations development, and remote operations research. ARCO serves as the control room for the Compact Integral Effects Test (CIET) facility, which replicates the primary-side flow paths and thermal-hydraulic behavior of a fluoride-salt-cooled high-temperature reactor (FHR) using simulant fluids and scaling principles. New reactor designs feature different operating conditions and scenarios than those in existing reactors. ARCO supports the research and development of digital tools for operator communications, intuitive real-time data analysis, online health monitoring and prognostics, and control room cybersecurity. By integrating these different technologies, ARCO acts as a prototypical control system to iteratively develop methods and tools of operation in advanced small modular nuclear reactors. This paper describes the features of and challenges to operating advanced small modular reactors underlying the design basis for ARCO and its operator support systems.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

THE EFFECTS OF CLOSE COMPANIONS (AND ROTATION) ON THE MAGNETIC ACTIVITY OF M DWARFS

We present a study of close white dwarf and M dwarf (WD+dM) binary systems and examine the effect that a close companion has on the magnetic field generation in M dwarfs. We use a base sample of 1602 white dwarf main-sequence binaries from Rebassa-Mansergas et al. to develop a set of color cuts in GALEX, SDSS, UKIDSS, and 2MASS color space. Then using the SDSS Data Release 8 spectroscopic database, we construct a sample of 1756 WD+dM high-quality pairs from our color cuts and previous catalogs. We separate the individual WD and dM from each spectrum using an iterative technique that compares the WD and dM components to best-fit templates. Using the absolute height above the Galactic plane as a proxy for age, and the H{alpha} emission line as an indicator for magnetic activity, we investigate the age-activity relation for our sample for spectral types {<=} M7. Our results show that early-type M dwarfs ({<=}M4) in close binary systems are more likely to be active and have longer activity lifetimes compared to their field counterparts. However, at a spectral type of M5 (just past the onset of full convection in M dwarfs), the activity fraction and lifetimes of WD+dM binary systems become more comparable to that of the field M dwarfs. One of the implications of having a close binary companion is presumed to be increased stellar rotation through disk disruption, tidal effects, or angular momentum exchange. Thus, we interpret the similarity in activity behavior between late-type dMs in WD+dM pairs and late-type field dMs to be due to a decrease in sensitivity in close binary companions (or stellar rotation), which has implications for the nature of magnetic activity in fully convective stars. Using the WD components of the pairs, we find WD cooling ages to use as an additional constraint on the age-activity relation for our sample. We find that, on average, active early-type dMs tend to be younger and that active late-type dMs span a much broader age regime making them indistinguishable from the inactive late-type population. We also show that magnetic strength, as measured by H{alpha}, is comparable between paired and field M dwarfs until a spectral type of M6/M7 where M dwarf activity for stars with close companions becomes much stronger. In addition, we present 37 very close candidate pairs with fast-moving orbits that display radial velocity changes over hour timescales.

79 ASTRONOMY AND ASTROPHYSICS↗

THE McGill PLANAR HYDROGEN ATMOSPHERE CODE (McPHAC)

The McGill Planar Hydrogen Atmosphere Code (McPHAC) v1.1 calculates the hydrostatic equilibrium structure and emergent spectrum of an unmagnetized hydrogen atmosphere in the plane-parallel approximation, at surface gravities appropriate for neutron stars. McPHAC incorporates several improvements over previous codes for which tabulated model spectra are available: (1) Thomson scattering is treated anisotropically, which is shown to result in a 0.2%-3% correction in the emergent spectral flux across the 0.1-5 keV passband; (2) the McPHAC source code is made available to the community, allowing it to be scrutinized and modified by other researchers wishing to study or extend its capabilities; and (3) the numerical uncertainty resulting from the discrete and iterative solution is studied as a function of photon energy, indicating that McPHAC is capable of producing spectra with numerical uncertainties <0.01%. The accuracy of the spectra may at present be limited to {approx}1%, but McPHAC enables researchers to study the impact of uncertain inputs and additional physical effects, thereby supporting future efforts to reduce those inaccuracies. Comparison of McPHAC results with spectra from one of the previous model atmosphere codes (NSA) shows agreement to {approx}<1% near the peaks of the emergent spectra. However, in the Wien tail a significant deficit of flux in the spectra of the previous model is revealed, determined to be due to the previous work not considering large enough optical depths at the highest photon frequencies. The deficit is most significant for spectra with T{sub eff} < 10{sup 5.6} K, though even there it may not be of much practical importance for most observations.

79 ASTRONOMY AND ASTROPHYSICS↗

DERIVING PLASMA DENSITIES AND ELEMENTAL ABUNDANCES FROM SERTS DIFFERENTIAL EMISSION MEASURE ANALYSIS

We use high-resolution spectral emission line data obtained by the SERTS instrument during three rocket flights to demonstrate a new approach for constraining electron densities of solar active region plasma. We apply differential emission measure (DEM) forward-fitting techniques to characterize the multithermal solar plasma producing the observed EUV spectra, with constraints on the high-temperature plasma from the Yohkoh Soft X-ray Telescope. In this iterative process, we compare line intensities predicted by an input source distribution to observed line intensities for multiple iron ion species, and search a broad range of densities to optimize {chi}{sup 2} simultaneously for the many available density-sensitive lines. This produces a density weighted by the DEM, which appears to be useful for characterizing the bulk of the emitting plasma over a significant range of temperature. This 'DEM-weighted density' technique is complementary to the use of density-sensitive line ratios and less affected by uncertainties in atomic data and ionization fraction for any specific line. Once the DEM shape and the DEM-weighted density have been established from the iron lines, the relative elemental abundances can be determined for other lines in the spectrum. We have also identified spectral lines in the SERTS wavelength range that may be problematic.

79 ASTRONOMY AND ASTROPHYSICS↗

ON THE GRAVITATIONAL FIELDS OF MACLAURIN SPHEROID MODELS OF ROTATING FLUID PLANETS

Hubbard recently derived an important iterative equation for calculating the gravitational coefficients of a Maclaurin spheroid that does not require an expansion in a small distortion parameter. We show that this iterative equation, which is based on an incomplete solution of the Poisson equation, diverges when the distortion parameter is not sufficiently small. We derive a new iterative equation that is based on a complete solution of the Poisson equation and, hence, always converges when calculating the gravitational coefficients of a Maclaurin spheroid.

79 ASTRONOMY AND ASTROPHYSICS↗

POINT-SPREAD FUNCTIONS FOR THE EXTREME-ULTRAVIOLET CHANNELS OF SDO/AIA TELESCOPES

We present the stray-light point-spread functions (PSFs) and their inverses we characterized for the Atmospheric Imaging Assembly (AIA) EUV telescopes on board the Solar Dynamics Observatory (SDO) spacecraft. The inverse kernels are approximate inverses under convolution. Convolving the original Level 1 images with them produces images with improved stray-light characteristics. We demonstrate the usefulness of these PSFs by applying them to two specific cases: photometry and differential emission measure (DEM) analysis. The PSFs consist of a narrow Gaussian core, a diffraction component, and a diffuse component represented by the sum of a Gaussian-truncated Lorentzian and a shoulder Gaussian. We determined the diffraction term using the measured geometry of the diffraction pattern identified in flare images and the theoretically computed intensities of the principal maxima of the first few diffraction orders. To determine the diffuse component, we fitted its parameterized model using iterative forward-modeling of the lunar interior in the SDO/AIA images from the 2011 March 4 lunar transit. We find that deconvolution significantly improves the contrast in dark features such as miniature coronal holes, though the effect was marginal in bright features. On a percentage-scattering basis, the PSFs for SDO/AIA are better by a factor of two than that of the EUV telescope on board the Transition Region And Coronal Explorer mission. A preliminary analysis suggests that deconvolution alone does not affect DEM analysis of small coronal loop segments with suitable background subtraction. We include the derived PSFs and their inverses as supplementary digital materials.

79 ASTRONOMY AND ASTROPHYSICS↗

FOCAL PLANE WAVEFRONT SENSING USING RESIDUAL ADAPTIVE OPTICS SPECKLES

Optical imperfections, misalignments, aberrations, and even dust can significantly limit sensitivity in high-contrast imaging systems such as coronagraphs. An upstream deformable mirror (DM) in the pupil can be used to correct or compensate for these flaws, either to enhance the Strehl ratio or suppress the residual coronagraphic halo. Measurement of the phase and amplitude of the starlight halo at the science camera is essential for determining the DM shape that compensates for any non-common-path (NCP) wavefront errors. Using DM displacement ripples to create a series of probe and anti-halo speckles in the focal plane has been proposed for space-based coronagraphs and successfully demonstrated in the lab. We present the theory and first on-sky demonstration of a technique to measure the complex halo using the rapidly changing residual atmospheric speckles at the 6.5 m MMT telescope using the Clio mid-IR camera. The AO system's wavefront sensor measurements are used to estimate the residual wavefront, allowing us to approximately compute the rapidly evolving phase and amplitude of speckle halo. When combined with relatively short, synchronized science camera images, the complex speckle estimates can be used to interferometrically analyze the images, leading to an estimate of the static diffraction halo with NCP effects included. In an operational system, this information could be collected continuously and used to iteratively correct quasi-static NCP errors or suppress imperfect coronagraphic halos.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗