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At least 757 records · Page 42

Structures of TOG1 and TOG2 from the human microtubule dynamics regulator CLASP1

Tubulin-binding TOG domains are found arrayed in a number of proteins that regulate microtubule dynamics. While much is known about the structure and function of TOG domains from the XMAP215 microtubule polymerase family, less in known about the TOG domain array found in animal CLASP family members. The animal CLASP TOG array promotes microtubule pause, potentiates rescue, and limits catastrophe. How structurally distinct the TOG domains of animal CLASP are from one another, from XMAP215 family TOG domains, and whether a specific order of structurally distinct TOG domains in the TOG array is conserved across animal CLASP family members is poorly understood. We present the x-ray crystal structures of Homo sapiens (H.s.) CLASP1 TOG1 and TOG2. The structures of H.s. CLASP1 TOG1 and TOG2 are distinct from each other and from the previously determined structure of Mus musculus (M.m.) CLASP2 TOG3. Comparative analyses of CLASP family TOG domain structures determined to date across species and paralogs supports a conserved CLASP TOG array paradigm in which structurally distinct TOG domains are arrayed in a specific order. H.s. CLASP1 TOG1 bears structural similarity to the free-tubulin binding TOG domains of the XMAP215 family but lacks many of the key tubulin-binding determinants found in XMAP215 family TOG domains. This aligns with studies that report that animal CLASP family TOG1 domains cannot bind free tubulin or microtubules. In contrast, animal CLASP family TOG2 and TOG3 domains have reported microtubule-binding activity but are structurally distinct from the free-tubulin binding TOG domains of the XMAP215 family. H.s. CLASP1 TOG2 has a convex architecture, predicted to engage a hyper-curved tubulin state that may underlie its ability to limit microtubule catastrophe and promote rescue. M.m. CLASP2 TOG3 has unique structural elements in the C-terminal half of its α-solenoid domain that our modeling studies implicate in binding to laterally-associated tubulin subunits in the microtubule lattice in a mode similar to, yet distinct from those predicted for the XMAP215 family TOG4 domain. The potential ability of the animal CLASP family TOG3 domain to engage lateral tubulin subunits may underlie the microtubule rescue activity ascribed to the domain. These findings highlight the structural diversity of TOG domains within the CLASP family TOG array and provide a molecular foundation for understanding CLASP-dependent effects on microtubule dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Coupling of Charge Regulation and Geometry in Soft Ionizable Molecular Assemblies

The size, shape, and charge of structures, such as proteins and amphiphile assemblies, respond in an interconnected manner to solution ionic conditions. Here, we analyze assemblies of an amphiphile (C 16 K 2 ), with two ionizable amino acids [lysine (K)] coupled to a 16-carbon alkyl tail, via small-angle X-ray scattering (SAXS), nonlinear Poisson–Boltzmann theory (nl-PB), and hybrid Monte Carlo-molecular dynamics (MC-MD) simulations. SAXS revealed structural transitions from spherical micelles to cylindrical micelles to bilayers with increasing pH. By combining SAXS-determined structural information and nl-PB, we derived the molecular degree of ionization as a function of pH. The back-calculated titration curves matched the experimental data over an extended pH range, without adjustable parameters. Similarly, the SAXS data on the evolution of spherical micelle structure with ionic strength were combined with nl-PB and MC-MD to derive the bare and effective charges. MC-MD, which considered finite ion sizes, showed that bare and effective charges saturate quickly with increasing salt concentration. Furthermore, the calculated effective charges closely matched results from Zeta-potential measurements. The presented approach has advantages over customary methods for charge regulation, such as the Henderson–Hasselbalch (HH) or Hill models, where molecular ionization/deionization in assemblies is described by effective pKs that are distinct from the pK for isolated molecules. However, these models lack a physical explanation for these pK shifts. By contrast, our approach of combining structural details with an electrostatic model and simulations provides a more intuitive understanding of structure-charge coupling and a framework for understanding charge regulation in many synthetic and biological systems.

ionization↗

Dynamic response analysis of geometrically non-linear structures subjected to high impact.

Description of an efficient digital computer method for the determination of the propagation of elastic stresses and deformations in certain geometrically nonlinear structures subjected to high impact loading. The finite-element matrix displacement approach utilizing curved quadrilateral shell elements in conjunction with a nodewise predictor-corrector method employing Runge-Kutta extrapolation techniques has been adopted for the present solution. The related computer program written in FORTRAN V for the UNIVAC 1108 computer has proved to be effective for the solution of a range of practical problems including rectangular and cylindrical panels. Numerical results are presented for a relevant structure, the cell container, and the negative electrode of an impact-resistant battery subjected to high impact, simulating its free landing on a planetary surface.

Gupta, K. K.↗

Constraining AGN Torus Sizes with Optical and Mid-infrared Ensemble Structure Functions

We propose a new method to constrain the size of the dusty torus in broad-line active galactic nuclei (AGNs) using optical and mid-infrared (MIR) ensemble structure functions (SFs). Because of the geometric dilution of the torus, the MIR response to optical continuum variations has suppressed variability with respect to the optical that depends on the geometry (e.g., size, orientation, opening angle) of the torus. More extended tori have steeper MIR SFs with respect to the optical SFs. We demonstrate the feasibility of this SF approach using simulated AGN light curves and a geometric torus model. While it is difficult to use SFs to constrain the orientation and opening angle due to the insensitivity of the SF on these parameters, the size of the torus can be well determined. Applying this method to the ensemble SFs measured for 587 SDSS quasars, we measure a torus R–L relation of $\mathrm{log}\,{R}_{\mathrm{eff}}(\mathrm{pc})={0.51}_{-0.04}^{+0.04}\times \mathrm{log}({{L}}_{\mathrm{bol}}/{10}^{46}\,\mathrm{erg}\ {{\rm{s}}}^{-1})-{0.38}_{-0.01}^{+0.01}$ in the WISE W1 band and sizes ~1.4 times larger in the W2 band, which are in good agreement with dust reverberation mapping measurements. Compared with the reverberation mapping technique, the SF method is much less demanding in data quality and can be applied to any optical+MIR light curves for which a lag measurement may not be possible, as long as the variability process and torus structure are stationary. While this SF method does not extract all information contained in the light curves (i.e., the transfer function), it provides an intuitive interpretation for the observed trends of AGN MIR SFs compared with optical SFs.

79 ASTRONOMY AND ASTROPHYSICS↗

The V471 Tauri system: A multi-data-type probe

V471 Tauri, a white dwarf–red dwarf eclipsing binary (EB) in the Hyades, is well known for stimulating development of common envelope theory, whereby novae and other cataclysmic variables form from much wider binaries by catastrophic orbit shrinkage. Our evaluation of a recent imaging search that reported negative results for a much postulated third body shows that the object could have escaped detection or may have actually been seen. The balance of evidence continues to favor a brown dwarf companion about 12 AU from the EB. A recently developed algorithm finds unified solutions from three data types. New radial velocities (RVs) of the red dwarf and BVR{sub C}I{sub C} light curves are solved simultaneously along with white dwarf and red dwarf RVs from the literature, uvby data, the Microvariability and Oscillations of Stars mission light curve, and 40 years of eclipse timings. Precision-based weighting is the key to proper information balance among the various data sets. Timewise variation of modeled starspots allows unified solution of multiple data eras. Light-curve amplitudes strongly suggest decreasing spottedness from 1976 to about 1980, followed by approximately constant spot coverage from 1981 to 2005. An explanation is proposed for lack of noticeable variation in 1981 light curves, in terms of competition between spot and tidal variations. Photometric–spectroscopic distance is estimated. The red dwarf mass comes out larger than normal for a K2 V star, and even larger than adopted in several structure and evolution papers. An identified cause for this result is that much improved red dwarf RV curves now exist.

79 ASTRONOMY AND ASTROPHYSICS↗

Component Assessment of the Electric Transmission Grid to Hurricanes

The increased frequency and intensity of extreme weather events from climate change necessitates understanding impacts on critical infrastructure, particularly electrical transmission grids. One of the foundational concepts of a grid's resilience is its robustness to extreme weather events, such as hurricanes. Resilience of the electric grid to high wind speeds is predicated upon the location and physical characteristics of the system components. Previous modeling assessments of electric grid failure were done at the systems level with assumptions on location and type of specific components. To facilitate more explicit adaptation metrics, accurate component-level information is needed. In this study, we build and utilize a data set of location, physical characteristics, and age of transmission structures for nine counties in the Florida Panhandle. These component characteristics were then simulated for failure under a variety of scenarios using fragility curves. Eight hurricanes were modeled using Hazus from the Federal Emergency Management Administration and the resulting impact to the network was assessed. The network was generated using the transmission lines and towers, showing increasing impacts to network efficiency with larger storms. Although modern transmission structures are built under the more stringent extreme wind loading construction standards, the prevalence of older, wooden transmission structures throughout the region poses a substantial risk to reliable electricity transmission during tropical cyclone events from the Gulf of Mexico.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Features of the Frequency Dependence of Capacitance–Voltage Characteristics of a Semiconductor Structure of a Photoelectric Converter Based on a p–n Junction with an Antireflective Film of Porous Silicon

The frequency dependence of capacitance–voltage characteristics of a semiconductor structure with an antireflective film of porous silicon, which was formed by electrochemical etching above a p–n junction, is studied. Photoluminescence spectra of layers of porous silicon of the experimental samples are also examined. It is demonstrated that the capacitance–voltage curves are shaped by competing influences of capacitances of the p–n junction and the surface structure forming in a porous Si film due to its inhomogeneity. A structural model of layers of the studied semiconductor structure and a capacitance equivalent circuit are proposed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Vibration of a Singly-curved Thin Shell Reflector with a Unidirectional Tension Field

Increased science requirements for space-based instruments over the past few decades have lead to the increased popularity of deployable space structures constructed from thin, lightweight films. Such structures offer both low mass and the ability to be stowed inside conventional launch vehicles. The analysis in this work pertains to large, singly-curved lightweight deployable reflectors commonly used in radar antennas and space telescopes. These types of systems, which can vary a great deal in size, often have frequency requirement that must be met. This work discusses two missions that utilize this type of aperture technology, and then develops a Rayleigh-Ritz model that predicts the natural frequencies and mode shapes for a (nearly) flat and singly-curved reflector with unidirectional in-plane loading. The results are compared with NASTRAN analyses.

singly-curved shell↗

Hydrothermal synthesis, crystal structure and properties of a novel chain coordination polymer constructed by tetrafunctional phosphonate anions and cobalt ions

A novel cobalt phosphonate, [Co(HL)(H{sub 2}O){sub 3}]{sub n} (1) (L=N(CH{sub 2}PO{sub 3}H){sub 3}{sup 3−}) has been synthesized by hydrothermal reaction at 150 °C and structurally characterized by X-ray diffraction, infrared spectroscopy, elemental and thermogravimetric analysis. Complex 1 features a 1D chain structure with double-channel built from CoO{sub 6} octahedra bridged together by the phosphonate groups. Each cobalt ion is octahedrally coordinated by three phosphonate oxygen atoms and three water molecules. The coordinated water molecules can form the hydrogen bonds with the phosphonate oxygen atoms to link the 1D chains, building a 2D layered structure, further resulting in a 3D network. The luminescence spectrum indicates an emission maximum at 435 nm. The magnetic susceptibility curve exhibits a dominant antiferromagnetic behavior with a weakly ferromagnetic component at low temperatures. - Graphical abstract: The connectivity between cobalt ions and the ligands results in a chain structure with a 1D double-channel structure, which is constructed by A-type subrings and B-type subrings. - Highlights: • The tetrafunctional phosphonate ligand was used as the ligand. • A novel chain structure can be formed by A-type rings and B-type rings. • Two types of rings can form a 1D double-channel structure, along the c-axis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Density-Functional Tight-Binding Parameters for Bulk Zirconium: A Case Study for Repulsive Potentials

Density-functional tight-binding (DFTB) parameters are presented for the simulation of the bulk phases of zirconium. Electronic parameters were obtained using a band structure fitting strategy, while two-center repulsive potentials were created by particle swarm optimization. As objective functions for the repulsive potential fitting, we employed the Birch–Murnaghan equations of state for hexagonal close-packed (HCP), body-centered cubic (BCC) and ω phases of Zr from density-functional theory (DFT). When fractional atomic coordinates are not allowed to change in the generation of the equation-of-state curves, long-range repulsive DFTB potentials are able to almost perfectly reproduce equilibrium structures, relative DFT energies of the bulk phases, and bulk moduli. However, the same potentials lead to artifacts in the DFTB potential energy surfaces when atom positions in the unit cell are allowed to fully relax during the change of unit cell parameters. Finally, conventional short-range repulsive DFTB potentials, while inferior in their ability to reproduce DFT bulk energetics, are able to correctly reproduce the qualitative shape of the DFT potential energy surfaces, including the location of global minima, and can therefore be considered more transferable.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Prediction of Cooling Curves for Controlled Unidirectional Solidification Under the Influence of Shrinkage: A Semi-analytical Approach

Quality of casting products can be significantly improved by controlling the crystal growth rate. Both dendritic and equiaxed grain structures depend strongly on crystal growth rate along the crystallographic direction. Uncontrolled solidification processes may lead to the formation of porous and columnar material with an extremely non-homogeneous composition distribution. These undesirable micro-structures can be avoided by adopting an optimal cooling rate (K/s) during the crystal growth. The present work focuses on determining suitable cooling curves to obtain desired unidirectional crystal growth rates, by implementing a semi-analytical model. Here, we defined cooling curve as the time history of temperature evolution at the cold boundary. The proposed semi-analytical heat transfer model is diffusion driven and accounts for shrinkage effect during solidification. The proposed model is found capable of predicting cooling curves for prescribed interface velocities. The model is self-sufficient in validating itself by means of solving inverse and forward problems. The cooling curve prediction by the model is validated by using it as the transient boundary condition for an existing enthalpy updating scheme-based numerical model. The proposed model is also applied to empirical data reported in literature, to validate the model against experimental results. All the validations showcased excellent fit. The proposed model will facilitate controlled unidirectional crystal growth rate by providing cooling rate (K/s) as an input for the experiments involving directional solidification.

36 MATERIALS SCIENCE↗

AEOLUS: A MARKOV CHAIN MONTE CARLO CODE FOR MAPPING ULTRACOOL ATMOSPHERES. AN APPLICATION ON JUPITER AND BROWN DWARF HST LIGHT CURVES

Deducing the cloud cover and its temporal evolution from the observed planetary spectra and phase curves can give us major insight into the atmospheric dynamics. In this paper, we present Aeolus, a Markov chain Monte Carlo code that maps the structure of brown dwarf and other ultracool atmospheres. We validated Aeolus on a set of unique Jupiter Hubble Space Telescope (HST) light curves. Aeolus accurately retrieves the properties of the major features of the Jovian atmosphere, such as the Great Red Spot and a major 5 μm hot spot. Aeolus is the first mapping code validated on actual observations of a giant planet over a full rotational period. For this study, we applied Aeolus to J- and H-band HST light curves of 2MASS J21392676+0220226 and 2MASS J0136565+093347. Aeolus retrieves three spots at the top of the atmosphere (per observational wavelength) of these two brown dwarfs, with a surface coverage of 21% ± 3% and 20.3% ± 1.5%, respectively. The Jupiter HST light curves will be publicly available via ADS/VIZIR.

79 ASTRONOMY AND ASTROPHYSICS↗

Application of the Nonballistic Model to the Black Hole Candidate XTE J1752-223 and the Quasar NRAO 150

Optical and radio observations of the black hole candidate XTE J1752-223 have exhibited a slightly curved motion of the jet components, which is associated with its radio light curve. In addition, observations of the quasar NRAO 150 have revealed a core–jet structure wobbling with a high angular speed. In this paper, the phenomena displayed in these two different sources are interpreted as the precession of a bent jet. In such a scenario, hot spots reproduced at different separations from the core precess on the same precession cone, in which different components correspond to different propagation times to the observer. By fitting the kinematics of the components of XTE J1752-223 and its light curve with a curved pattern of precession period 314 days, we find that the propagation time can make an earlier event appear later, and the jet axis can oscillate during its precession. Simulating the quasar NRAO 150 with the same scenario reveals that the knots at larger separation from the core precess at a slower speed than those closer in. A possible mechanism relating to the cooling time of a component is proposed. These three new results are of importance in understanding the physics underlying the curved jet as well as the activity of the central engine of different black hole systems.

79 ASTRONOMY AND ASTROPHYSICS↗

Discrete-Direct Model Calibration and Uncertainty Propagation Method Confirmed on Multi-Parameter Plasticity Model Calibrated to Sparse Random Field Data

A discrete direct (DD) model calibration and uncertainty propagation approach is explained and demonstrated on a 4-parameter Johnson-Cook (J-C) strain-rate dependent material strength model for an aluminum alloy. The methodology's performance is characterized in many trials involving four random realizations of strain-rate dependent material-test data curves per trial, drawn from a large synthetic population. The J-C model is calibrated to particular combinations of the data curves to obtain calibration parameter sets which are then propagated to “Can Crush” structural model predictions to produce samples of predicted response variability. These are processed with appropriate sparse-sample uncertainty quantification (UQ) methods to estimate various statistics of response with an appropriate level of conservatism. This is tested on 16 output quantities (von Mises stresses and equivalent plastic strains) and it is shown that important statistics of the true variabilities of the 16 quantities are bounded with a high success rate that is reasonably predictable and controllable. The DD approach has several advantages over other calibration-UQ approaches like Bayesian inference for capturing and utilizing the information obtained from typically small numbers of replicate experiments in model calibration situations—especially when sparse replicate functional data are involved like force–displacement curves from material tests. The DD methodology is straightforward and efficient for calibration and propagation problems involving aleatory and epistemic uncertainties in calibration experiments, models, and procedures.

42 ENGINEERING↗

Realization of Magnetostructural Transition and Magnetocaloric Properties of Ni–Mn–Mo–Sn Heusler Alloys

As magnetic cooling refrigerant, Ni–Mn–Sn Heusler alloys have gained significant potentials for a wide range of practical applications as compared with other expensive Ga-doped Ni–Mn based Heusler alloys, toxic As and P doped Mn-based alloys and rare-earth elements like Gd-based alloys. Consequently, an inclusive investigation on magnetostructural transition and magnetocaloric features of Ni{sub 43}Mn{sub 47−x}Mo{sub x}Sn{sub 10} alloys is carried out. The alloys are assembled through arc-melting technique and their X-ray diffraction analysis confirms their B{sub 2}-type crystal structure at room temperature. As the Mo contents are increased, the magnetostructural transition temperature increases for a temperature range between Curie temperature of austenite and martensite phases. Obvious metamagnetic behavior and magnetic hysteresis are observed in isothermal magnetization curves, suggesting that the temperature and magnetic field can be used as robust tools for tuning the structural transformation in Heusler alloys. The noticeable magnetocaloric effect suggests that the prepared alloys can be an attractive choice for magnetic refrigeration applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

X-Ray Afterglows from the Gamma-Ray Burst “Large-angle” Emission

In this work, we derive basic analytical results for the timing and decay of the gamma-ray burst (GRB) counterpart and delayed afterglow light curves for a brief emission episode from a relativistic surface endowed with angular structure, consisting of a uniform core of size ${\theta }_{c}$ (Lorentz factor ${{\rm{\Gamma }}}_{c}$ and surface emissivity ${i}_{\nu ^{\prime} }^{{\prime} }$ are angle independent) and an axially symmetric power-law envelope (${\rm{\Gamma }}\sim {\theta }^{-g}$). In this "large-angle emission" model, radiation produced during the prompt emission phase (GRB) at angles $\theta \gt {\theta }_{c}$ arrives at the observer well after the burst (delayed emission). The dynamical time range of the very fast decaying GRB "tail" and of the flat afterglow "plateau" and the morphology of the GRB counterpart/afterglow are all determined by two parameters: the core's parameter ${{\rm{\Gamma }}}_{c}{\theta }_{c}$ and the envelope's Lorentz factor index g, leading to three types of light curves that display three post-GRB phases (type 1: tail, plateau/slow decay, post-plateau/normal decay), two post-GRB phases (type 2: tail and fast decay), or just one (type 3: normal decay). We show how X-ray light-curve features can be used to determine core and envelope dynamical and spectral parameters. Testing of the large-angle emission model is done using the Swift/XRT X-ray emission of two afterglows of type 1 (GRB 060607A, GRB 061121), one of type 2 (GRB 061110A), and one of type 3 (GRB 061007). We find that the X-ray afterglows with plateaus require an envelope Lorentz factor ${\rm{\Gamma }}\sim {\theta }^{-2}$ and a comoving-frame emissivity ${i}_{\nu ^{\prime} }^{{\prime} }\sim {\theta }^{2}$; thus, for a typical afterglow spectrum ${F}_{\nu }\sim {\nu }^{-1}$, the lab-frame energy release is uniform over the emitting surface.

79 ASTRONOMY AND ASTROPHYSICS↗

Degradation of proton depth dose distributions attributable to microstructures in lung-equivalent material

Purpose: The purpose of the work reported here was to investigate the influence of sub-millimeter size heterogeneities on the degradation of the distal edges of proton beams and to validate Monte Carlo (MC) methods’ ability to correctly predict such degradation. Methods: A custom-designed high-resolution plastic phantom approximating highly heterogeneous, lung-like structures was employed in measurements and in Monte Carlo simulations to evaluate the degradation of proton Bragg curves penetrating heterogeneous media. Results: Significant differences in distal falloff widths and in peak dose values were observed in the measured and the Monte Carlo simulated curves compared to pristine proton Bragg curves. Furthermore, differences between simulations of beams penetrating CT images of the phantom did not agree well with the corresponding experimental differences. The distal falloff widths in CT image-based geometries were underestimated by up to 0.2 cm in water (corresponding to 0.8–1.4 cm in lung tissue), and the peak dose values of pristine proton beams were overestimated by as much as ~35% compared to measured curves or depth-dose curves simulated on the basis of true geometry. The authors demonstrate that these discrepancies were caused by the limited spatial resolution of CT images that served as a basis for dose calculations and lead to underestimation of the impact of the fine structure of tissue heterogeneities. A convolution model was successfully applied to mitigate the underestimation. Conclusions: The results of this study justify further development of models to better represent heterogeneity effects in soft-tissue geometries, such as lung, and to correct systematic underestimation of the degradation of the distal edge of proton doses.

60 APPLIED LIFE SCIENCES↗

Fantômas unconfined: global QCD fits with Bézier parameterizations

Fantômas is a C++ toolkit for exploring the parametrization dependence of parton distribution functions (PDFs) and other correlator functions in quantum chromodynamics (QCD). Fantômas facilitates the generation of adaptable polynomial parametrizations for PDFs, called metamorphs, to find best-fit PDF solutions and quantify the epistemic uncertainty associated with the parametrizations during their fitting. The method employs Bézier curves as universal approximators for a variety of PDF shapes. Integrated into the xFitter framework for the global QCD analysis, Fantômas provides a foundation for general models of PDFs, while reducing the computational time compared to the approaches utilizing traditional polynomial parametrizations as well as providing an interpretable alternative to neural-network-based models. This paper outlines the structure and practical usage of the Fantômas toolkit, including its inputs, outputs, and implementation within xFitter. It also provides a practical example of using Fantômas for uncertainty quantification as well as the combination of PDF fits into a single ensemble.

Bézier curves↗