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At least 919 records · Page 51

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH’s global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Mapping Composition Evolution through Synthesis, Purification, and Depolymerization of Random Heteropolymers

Random heteropolymers (RHPs) consisting of three or more comonomers have been routinely used to synthesize functional materials. While increasing the monomer variety diversifies the side-chain chemistry, this substantially expands the sequence space and leads to ensemble-level sequence heterogeneity. Most studies have relied on monomer composition and simulated sequences to design RHPs, but the questions remain unanswered regarding heterogeneities within each RHP ensemble and how closely these simulated sequences reflect the experimental outcomes. Here, we quantitatively mapped out the evolution of monomer compositions in four-monomer-based RHPs throughout a design-synthesis-purification-depolymerization process. By adopting a Jaacks method, we first determined 12 reactivity ratios directly from quaternary methacrylate RAFT copolymerization experiments to account for the influences of competitive monomer addition and the reversible activation/deactivation equilibria. The reliability of in silico analysis was affirmed by a quantitative agreement (<4% difference) between the simulated RHP compositions and the experimental results. Furthermore, we mapped out the conformation distribution within each ensemble in different solvents as a function of monomer chemistry, composition, and segmental characteristics via high-throughput computation based on self-consistent field theory (SCFT). These comprehensive studies confirmed monomer composition as a viable design parameter to engineer RHP-based functional materials as long as the reactivity ratios are accurately determined and the livingness of RHP synthesis is ensured.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Planck 2018 results XII. Galactic astrophysics using polarized dust emission

Observations of the submillimetre emission from Galactic dust, in both total intensity I and polarization, have received tremendous interest thanks to the Planck full-sky maps. In this paper we make use of such full-sky maps of dust polarized emission produced from the third public release of Planck data. As the basis for expanding on astrophysical studies of the polarized thermal emission from Galactic dust, we present full-sky maps of the dust polarization fraction p, polarization angle ψ, and dispersion function of polarization angles S . The joint distribution (one-point statistics) of p and NH confirms that the mean and maximum polarization fractions decrease with increasing NH. The uncertainty on the maximum observed polarization fraction, pmax = 22.0 -1.4 +3.5% at 353 GHz and 80' resolution, is dominated by the uncertainty on the Galactic emission zero level in total intensity, in particular towards diffuse lines of sight at high Galactic latitudes. Furthermore, the inverse behaviour between p and S found earlier is seen to be present at high latitudes. This follows the S ∝ p -1 relationship expected from models of the polarized sky (including numerical simulations of magnetohydrodynamical turbulence) that include effects from only the topology of the turbulent magnetic field, but otherwise have uniform alignment and dust properties. Thus, the statistical properties of p, ψ, and S for the most part reflect the structure of the Galactic magnetic field. Nevertheless, we search for potential signatures of varying grain alignment and dust properties. First, we analyse the product map S × p, looking for residual trends. While the polarization fraction p decreases by a factor of 3-4 between NH = 10 20 cm -2 and NH = 2 x 10 22 cm -2 , out of the Galactic plane, this product S × p only decreases by about 25%. Because S is independent of the grain alignment efficiency, this demonstrates that the systematic decrease in p with N H is determined mostly by the magnetic-field structure and not by a drop in grain alignment. This systematic trend is observed both in the diffuse interstellar medium (ISM) and in molecular clouds of the Gould Belt. Second, we look for a dependence of polarization properties on the dust temperature, as we would expect from the radiative alignment torque (RAT) theory. We find no systematic trend of S × p with the dust temperature T d , whether in the diffuse ISM or in the molecular clouds of the Gould Belt. In the diffuse ISM, lines of sight with high polarization fraction p and low polarization angle dispersion S tend, on the contrary, to have colder dust than lines of sight with low p and high S . We also compare the Planck thermal dust polarization with starlight polarization data in the visible at high Galactic latitudes. The agreement in polarization angles is remarkable, and is consistent with what we expect from the noise and the observed dispersion of polarization angles in the visible on the scale of the Planck beam. The two polarization emission-to-extinction ratios, R P/p and R S/V , which primarily characterize dust optical properties, have only a weak dependence on the column density, and converge towards the values previously determined for translucent lines of sight. We also determine an upper limit for the polarization fraction in extinction, p V /E(B - V), of 13% at high Galactic latitude, compatible with the polarization fraction p ≈ 20% observed at 353 GHz. Taken together, these results provide strong constraints for models of Galactic dust in diffuse gas.

79 ASTRONOMY AND ASTROPHYSICS↗

Incoherent Thomson scattering system for PHAse space MApping (PHASMA) experiment

A new incoherent Thomson scattering system measures the evolution of electron velocity distribution functions perpendicular and parallel to the ambient magnetic field during kinking of a single flux rope and merging of two flux ropes through magnetic reconnection. The Thom-son scattering system provides sub-millimeter spatial resolution, sufficient to diagnose the several millimeters sized magnetic reconnection electron diffusion region in the PHAse Space MAppgin experiment. Due to the relatively modest plasma density ~ 10 19 m -3 and electron tem-perature ~1 eV, stray light suppression is critical for these measurements. Two volume Bragg gratings are used in series as a notch filter with a spectral bandwidth <0.1 nm in the collection branch. A CCD with a Gen III intensifier with peak quantum efficiency >47% is used as the detector in a 1.3 m spectrometer. Preliminary results of gun plasma electron temperature will be reported and compared with measurements obtained from a triple Langmuir probe.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The effects of display and autopilot functions on pilot workload for Single Pilot Instrument Flight Rule (SPIFR) operations

An analytical and experimental research program was conducted to develop criteria for pilot interaction with advanced controls and displays in single pilot instrument flight rules (SPIFR) operations. The analytic phase reviewed fundamental considerations for pilot workload taking into account existing data, and using that data to develop a divided attention SPIFR pilot workload model. The pilot model was utilized to interpret the two experimental phases. The first experimental phase was a flight test program that evaluated pilot workload in the presence of current and near-term displays and autopilot functions. The second experiment was conducted on a King Air simulator, investigating the effects of co-pilot functions in the presence of very high SPIFR workload. The results indicate that the simplest displays tested were marginal for SPIFR operations. A moving map display aided the most in mental orientation, but had inherent deficiencies as a stand alone replacement for an HSI. Autopilot functions were highly effective for reducing pilot workload. The simulator tests showed that extremely high workload situations can be adequately handled when co-pilot functions are provided.

Hoh, Roger H.↗

Stereo and IMU-Assisted Visual Odometry for Small Robots

This software performs two functions: (1) taking stereo image pairs as input, it computes stereo disparity maps from them by cross-correlation to achieve 3D (three-dimensional) perception; (2) taking a sequence of stereo image pairs as input, it tracks features in the image sequence to estimate the motion of the cameras between successive image pairs. A real-time stereo vision system with IMU (inertial measurement unit)-assisted visual odometry was implemented on a single 750 MHz/520 MHz OMAP3530 SoC (system on chip) from TI (Texas Instruments). Frame rates of 46 fps (frames per second) were achieved at QVGA (Quarter Video Graphics Array i.e. 320 240), or 8 fps at VGA (Video Graphics Array 640 480) resolutions, while simultaneously tracking up to 200 features, taking full advantage of the OMAP3530's integer DSP (digital signal processor) and floating point ARM processors. This is a substantial advancement over previous work as the stereo implementation produces 146 Mde/s (millions of disparities evaluated per second) in 2.5W, yielding a stereo energy efficiency of 58.8 Mde/J, which is 3.75 better than prior DSP stereo while providing more functionality.

Source record↗

Implementation of higher-order velocity mapping between marker particles and grid in the particle-in-cell code XGC

The global total-f gyrokinetic particle-in-cell code XGC, used to study transport in magnetic fusion plasmas or to couple with a core gyrokinetic code while functioning as an edge gyrokinetic code, implements a five-dimensional continuum grid to perform the dissipative operations, such as plasma collisions, or to exchange the particle distribution function information with a core code. To transfer the distribution function between marker particles and a rectangular two-dimensional velocity-space grid, XGC employs a bilinear mapping. The conservation of particle density and momentum is accurate enough in this bilinear operation, but the error in the particle energy conservation can become undesirably large and cause non-negligible numerical heating in a steep edge pedestal. In the present work we update XGC to use a novel mapping technique, based on the calculation of a pseudo-inverse, to exactly preserve moments up to the order of the discretization space. Here we describe the details of the implementation and we demonstrate the reduced interpolation error for a tokamak test plasma using first- and second-order elements with the pseudo-inverse method and comparing with the bilinear mapping.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

On the Sampling-Based Computation of Nash Equilibria Under Uncertainty via the Nikaido–Isoda Function

We consider the computation of an equilibrium of a stochastic Nash equilibrium problem, where the player objectives are assumed to be L 0 -Lipschitz continuous and convex, given rival decisions with convex and closed player-specific feasibility sets. To address this problem, we consider minimizing a suitably defined value function defined using the Nikaido–Isoda function. Such an avenue does not necessitate either monotonicity properties of the concatenated gradient map or potentiality requirements on the game but does require a suitable regularity requirement under which a stationary point is a Nash equilibrium. We design and analyze a sampling-enabled projected-gradient-response method, reliant on inexact resolution of a player-level best-response subproblem. Here, by deriving suitable Lipschitzian guarantees on the value function, we derive both asymptotic guarantees for the sequence of generated iterates as well as rate and complexity guarantees for computing a stationary point by appropriate choices of the sampling rate and inexactness sequence.

Nikaido-Isoda function↗

Selective radiant temperature mapping using a layered classifier

A method of measuring temperatures of selected ground-cover types using remotely sensed multispectral scanner data and a layered classification approach is described. A brief review of radiation theory is presented to show that for the wavelength bands and temperature ranges involved in remote sensing applications, a linear calibration function can be satisfactorily utilized. An example of the application of the layered classifier for temperature mapping of water is shown.

Bartolucci, L. A.↗

Continuous dependence of fixed points of condensing maps

Many problems in analysis are concerned with the dependence upon parameters of fixed points of maps. For contraction mappings, criteria are relatively easy to obtain and have been known for some time. In the study of solutions of functional differential equations, more general results were needed. It is the purpose of this paper to give a rather general fixed-point theorem for condensing maps depending on a parameter, to prove continuous dependence and to indicate how many of the previous results are special cases.

Hale, J. K.↗

Massive νs through the CNN lens: interpreting the field-level neutrino mass information in weak lensing

Modern cosmological surveys probe the Universe deep into the nonlinear regime, where massive neutrinos suppress cosmic structure. Traditional cosmological analyses, which use the 2-point correlation function to extract information, are no longer optimal in the nonlinear regime, and there is thus much interest in extracting beyond-2-point information to improve constraints on neutrino mass. Quantifying and interpreting the beyond-2-point information is thus a pressing task. We study the field-level information in weak lensing convergence maps using convolution neural networks. We find that the network performance increases as higher source redshifts and smaller scales are considered — investigating up to a source redshift of 2.5 and ℓ max ≃ 10 4 — verifying that massive neutrinos leave a distinct effect on weak lensing. However, the performance of the network significantly drops after scaling out the 2-point information from the maps, implying that most of the field-level information can be found in the 2-point correlation function alone. We quantify these findings in terms of the likelihood ratio and also use Integrated Gradient saliency maps to interpret which parts of the map the network is learning the most from. We find that, in the absence of noise, the network extracts a similar amount of information from the most overdense and underdense regions. However, upon adding noise, the information in underdense regions is distorted as noise disproportionately washes out void-like structures.

Golshan, Malika [University of California, Berkele↗

Enhancing the efficiency of time-dependent density functional theory calculations of dynamic response properties

X-ray Thomson scattering (XRTS) constitutes an essential technique for diagnosing material properties under extreme conditions, such as high pressures and intense laser heating. Time-dependent density functional theory (TDDFT) is one of the most accurate available ab initio methods for modeling XRTS spectra, as well as a host of other dynamic material properties. However, strong thermal excitations, along with the need to account for variations in temperature and density as well as the finite size of the detector significantly increase the computational cost of TDDFT simulations compared to ambient conditions. In this work, we present a broadly applicable method for optimizing and enhancing the efficiency of TDDFT calculations. Our approach is based on a one-to-one mapping between the dynamic structure factor and the imaginary time density–density correlation function, which naturally emerges in Feynman’s path integral formulation of quantum many-body theory. Specifically, we combine rigorous convergence tests in the imaginary time domain with a constraints-based attenuation of narrow-band fluctuations to improve the efficiency of TDDFT modeling without the introduction of any significant bias. As a result, we can report a speed-up by up to an order of magnitude, thus substantially reducing the burden of computational cost required for XRTS analysis.

Moldabekov, Zhandos A. [Helmholtz-Zentrum Dresden-↗

Robustness of cement-based materials: From dosage variations to yield stress fluctuations

The idea behind the present work is to assess robustness of fresh cement-based materials (i.e. their ability to display the same properties when submitted to variations in the way they are produced) from a generic and analytical point of view. First, analytical models from literature relating components proportions and yield stress are combined into a multi-scale and physical approach and compared to our experimental yield stress measurements. In the second part, the derivation of these analytical relationships is used to assess robustness as a function of components proportions, which allows for the most sensitive variations to be mapped onto component dosage from a yield stress point of view. In the case of fluid concretes, this approach showcases the interest of working at slightly higher water content and slightly lower aggregates fraction along with benefits of viscosity modifying agents / plasticizers combination.

36 MATERIALS SCIENCE↗

Relevance of ERTS to the State of Ohio

The author has identified the following significant results. A significant result was the fabrication of an image transfer and comparison device. To avoid problems and high costs encountered in manual drafting methods, Battelle staff members have fabricated an inexpensive, yet effective, technique for transferring ERTS-1 analysis displays from the Spatial Data 32-Color Viewer to maps and/or aircraft imagery. In brief, the image transfer-comparison device consists of a 2-way mirror which functions similar to a zoom transfer scope. However, the device permits multiuser viewing and real time photographic recording (35-mm and Polaroid) of enhanced ERTS-1 imagery superimposed over maps and aircraft photography. Thirty-five mm, 70 mm, and 4 in. x 5 in. photographs are taken of 80% of the TV screen of the Spatial Data Density Slicing Viewer. The resulting black and white and color imagery is then used in transparent overlays, viewgraphs, 35-mm and 70-mm transparencies, and paper prints for reports and publications. Annotations can be added on the TV screen or on the finished product.

Sweet, D. C.↗

Identification of nonlinear structural elements by force-state mapping

A major contributor to the passive damping and potentially nonlinear behavior of large space structures is the behavior of the joints. Proposed is an experimental technique called 'force-state mapping' that will allow ground testing of these key structural elements. The technique includes the use of very accurate instrumentation to measure the force transmission properties of a structural element as a function of its mechanical state. When these data are presented in the form of a force-state map, the nonlinearities exhibit distinctively recognizable patterns. This presentation of the data allows the extraction of the describing parameters of the linear and nonlinear behavior and the energy dissipation characteristics of the joint. A series of tests were carried out on an idealized laboratory test article to demonstrate the technique. Strong structural nonlinearities, including a cubic hardening spring, friction, and impact phenomena, were introduced and measured. Parameters identified by the force-state mapping technique are compared with those made by traditional techniques and the errors involved in the measurement are estimated.

Crawley, E. F.↗

Multi-element flow-driven spectral chaos (ME-FSC) method for uncertainty quantification of dynamical systems

The flow-driven spectral chaos (FSC) is a recently developed method for tracking and quantifying uncertainties in the long-time response of stochastic dynamical systems using the spectral approach. The method uses a novel concept called enriched stochastic flow maps as a means to construct an evolving finite-dimensional random function space that is both accurate and computationally efficient in time. In this paper, we present a multi-element version of the FSC method (the ME-FSC method for short) to tackle (mainly) those dynamical systems that are inherently discontinuous over the probability space. In ME-FSC, the random domain is partitioned into several elements, and then the problem is solved separately on each random element using the FSC method. Subsequently, results are aggregated to compute the probability moments of interest using the law of total probability. To demonstrate the effectiveness of the ME-FSC method in dealing with discontinuities and long-time integration of stochastic dynamical systems, four representative numerical examples are presented in this paper, including the Van-der-Pol oscillator problem and the Kraichnan-Orszag three-mode problem. Results show that the ME-FSC method is capable of solving problems that have strong nonlinear dependencies over the probability space, both reliably and at low computational cost.

97 MATHEMATICS AND COMPUTING↗