Cryo-EM structure of Rubisco from Arabidopsis thaliana with the 2B small subunit isoform
Cryo-EM structure of Rubisco from Arabidopsis thaliana with the 2B small subunit isoform
Ceminsky, M.↗
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Atomic-Level Sculpting of Crystalline Oxides: Toward Bulk Nanofabrication with Single Atomic Plane Precision
We demonstrate atomic-level sculpting of 3D crystalline oxide nanostructures from metastable amorphous layer in a scanning transmission electron microscope (STEM). Strontium titanate nanostructures grow epitaxially from the crystalline substrate following the beam path. This method can be used for fabricating crystalline structures as small as 1-2 nm and the process can be observed in situ with atomic resolution. We further demonstrate fabrication of arbitrary shape structures via control of the position and scan speed of the electron beam. Combined with broad availability of the atomic resolved electron microscopy platforms, these observations suggest the feasibility of large scale implementation of bulk atomic-level fabrication as a new enabling tool of nanoscience and technology, providing a bottom-up, atomic-level complement to 3D printing.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
The Reactivity and Structural Dynamics of Supported Metal Nanoclusters Using Electron Microscopy, in-situ X-Ray Spectroscopy, Electronic Structure Theories, and Molecular Dynamics Simulations
This research will provide new methods to determine the structures and compositions of heterogeneous catalysts as they exist in reaction conditions. The new tools will make it possible to understand how extremely small material structures—ones in a size range spanning from single atoms to larger polyatomic clusters—make it possible to carry out highly selective chemical transformations required to synthesize useful materials as well as for efficient energy production and utilization. The tools will make it possible to see how the atomic structures of catalytic materials evolve over time under the conditions of their use, and in this way provide understandings to guide the design of new energy-efficient catalysts. The work will make it possible to answer long standing questions that include the following. How does catalyst structure help guide molecules along specific reaction pathways? What are the important intermediates involved in these transformations? How do the structures and reactivity of catalytic materials, as well as the chemistry of their interfaces, vary with reaction conditions? Is it possible to develop new catalytic materials using new knowledge of the active structures and reaction mechanisms? The work will provide heretofore unavailable experimental tools that can be applied in advanced programs of research addressing such questions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
From Images to Dark Matter: End-to-end Inference of Substructure from Hundreds of Strong Gravitational Lenses
Abstract Constraining the distribution of small-scale structure in our universe allows us to probe alternatives to the cold dark matter paradigm. Strong gravitational lensing offers a unique window into small dark matter halos (<10 10 M ⊙ ) because these halos impart a gravitational lensing signal even if they do not host luminous galaxies. We create large data sets of strong lensing images with realistic low-mass halos, Hubble Space Telescope (HST) observational effects, and galaxy light from HST’s COSMOS field. Using a simulation-based inference pipeline, we train a neural posterior estimator of the subhalo mass function (SHMF) and place constraints on populations of lenses generated using a separate set of galaxy sources. We find that by combining our network with a hierarchical inference framework, we can both reliably infer the SHMF across a variety of configurations and scale efficiently to populations with hundreds of lenses. By conducting precise inference on large and complex simulated data sets, our method lays a foundation for extracting dark matter constraints from the next generation of wide-field optical imaging surveys.
79 ASTRONOMY AND ASTROPHYSICS↗
Examining the Chemical and Structural Properties that Influence the Sensitivity of Energetic Nitrate Esters
The sensitivity of explosives is controlled by factors that span from intrinsic chemical reactivity and chemical intramolecular effects to mesoscale structure and defects, and has been a topic of extensive study for over 50 years. Due to these complex competing chemical and physical elements, a unifying relationship between molecular framework, crystal structure, and sensitivity has yet to be developed. In order to move towards this goal, ideally experimental studies should be performed on systems with small, systematic structural modifications, with modeling utilized to interpret experimental results. Pentaerythritol tetranitrate (PETN) is a common nitrate ester explosive that has been widely studied due to its use in military and commercial explosives. We have synthesized PETN derivatives with modified sensitivity characteristics by substituting the CCH 2 ONO 2 moiety with other substituents, including CH, CNH 2 , CNH3X, CCH 3 , and PO. We relate the handling sensitivity properties of each PETN derivative to its structural properties, and discuss the potential roles of thermodynamic properties such as heat capacity and heat of formation, thermal stability, crystal structure, compressibility, and inter- and intramolecular hydrogen bonding on impact sensitivity. Reactive molecular dynamics (MD) simulations of the C/H/N/O-based PETN-derivatives have been performed under cook-off conditions that mimic those accessed in impact tests. As a result, these simulations infer how changes in chemistry affect the subsequent decomposition pathways.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Wall-Pressure-Array Measurements Beneath a Separating/Reattaching Flow Region
A database of wall-pressure array measurements was compiled for studying the space-time character of the surface-pressure field within a separating/reattaching flow region. The experimental setup consisted of a long splitter plate instrumented with an array of 80 flush-mounted microphones located within the wake of a fence. Data were acquired for a Reynolds number of 7885, based on the fence height. Two distinctive regions, defined based on their location relative to the position of the mean reattachment point (x(sub r)) of the shear layer, emerged from this investigation. Upstream, from the fence to 1/4x(sub r), the surface-pressure signature was dominated by large time scale disturbances and an upstream convecting velocity of 0.21U(sub infinity). Beyond 1/4x(sub r), turbulent structures with small time scales and a downstream convection velocity of 0.57U(sub infinity) generated most of the pressure fluctuations. There was evidence that these structures began to form around 1/4x(sub r) and grew in strength and size with downstream distance before reattaching on the plate. Only the time-averaged results from the microphones have been examined hitherto and will be presented.
Hudy, Laura M.↗
Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein
Ligand-binding promiscuity in detoxification systems protects the body from toxicological harm but is a roadblock to drug development due to the difficulty in optimizing small molecules to both retain target potency and avoid metabolic events. Immense effort is invested in evaluating metabolism of molecules to develop safer, more effective treatments, but engineering specificity into or out of promiscuous proteins and their ligands is a challenging task. To better understand the promiscuous nature of detoxification networks, we have used X-ray crystallography to characterize a structural feature of pregnane X receptor (PXR), a nuclear receptor that is activated by diverse molecules (with different structures and sizes) to up-regulate transcription of drug metabolism genes. We found that large ligands expand PXR’s ligand-binding pocket, and the ligand-induced expansion occurs through a specific unfavorable compound-protein clash that likely contributes to reduced binding affinity. Removing the clash by compound modification resulted in more favorable binding modes with significantly enhanced binding affinity. We then engineered the unfavorable ligand-protein clash into a potent, small PXR ligand, resulting in marked reduction in PXR binding and activation. Structural analysis showed that PXR is remodeled, and the modified ligands reposition in the binding pocket to avoid clashes, but the conformational changes result in less favorable binding modes. Thus, ligand-induced binding pocket expansion increases ligand-binding potential of PXR but is an unfavorable event; therefore, drug candidates can be engineered to expand PXR’s ligand-binding pocket and reduce their safety liability due to PXR binding.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structure and evolution of small-amplitude intermediate shock waves
A simplified set of equations is derived that approximates the magnetohydrodynamic (MHD) Navier-Stokes equations for weakly nonlinear disturbances whose speeds are close to the MHD intermediate speed. Its shock structure solutions are then examined. The fast and slow shock solutions are uniquely specified by their Rankine-Hugoniot relations. However, the intermediate shock solutions, which are not unique, are characterized by the integral through the shock of the noncoplanar component of the magnetic field. For situations in which this integral is conserved, the Riemann problem is well defined and predicts the evolution of intermediate shocks. This analysis is substantiated by numerical computations.
Kennel, C. F.↗
Volcanism in the cratered terrain hemisphere of Mars
Four kinds of Martian volcanoes and their prevalences in the cratered terrain hemisphere (generally the southern hemisphere) are described. Patera, which are large low-profile volcanic structures, appear to be either older shield volcanoes or a unique type of volcano. 'Plains' volcanics represent low-volume eruptions that formed cones, low shields, and other small-scale structures. Flood volcanics are produced by high-volume eruptions, post-date the older and more degraded plateau plains, and occur mostly as basin-fill materials. Plateau plains, the Martian intercrater plains, contain many wrinkle ridges and floor-fractured craters. It is suggested that volcanic processes as well as erosional processes have been important in obliterating small Martian craters and that volcanic products may constitute a significant fraction (up to 44%) of the surface rocks in the cratered terrain
Greeley, R.↗
Small-scale plasma, magnetic, and neutral density fluctuations in the nightside Venus atmosphere
The evolution of the Venus small-scale waves as they propagate into the nightsite is examined, and the small-scale structures are compared with the waves in the three components of the magnetic field, magnetic dip angle, and neutral density. It is demonstrated that the small-scale fluctuations evolve between the transterminator and antisolar regions. It is shown that atmospheric gravity waves may also be producing some of the fluctuations observed at longer wavelengths. The electron temperature and density are shown to be approximately 180 deg out of phase and exhibiting the highest correlation of any pair of variables. Waves in the electron and neutral densities are found to be correlated moderately on most orbits, while the average electron temperature is higher when the average magnetic field is more horizontal.
Hoegy, W. R.↗
Coordinated Observations of X-ray and High-resolution EUV Active Region Dynamics
The recently-launched High-resolution Coronal imager (Hi-C) sounding rocket provided the highest resolution images of coronal loops and other small-scale structures in the 193 Angstrom passband to date. With just 5 minutes of observations, the instrument recorded a variety of dynamic coronal events -- including even a small B-class flare. We will present our results comparing these extreme-ultraviolet (EUV) observations with X-ray imaging from Hinode/XRT as well as EUV AIA data to identify sources of hot plasma rooted in the photosphere and track their affect on the overall topology and dynamics of the active region.
Savage, Sabrina↗
Coordinated Observations of X-ray and High-Resolution EUV Active Region Dynamics
The recently-launched High-resolution Coronal imager (Hi-C) sounding rocket provided the highest resolution images of coronal loops and other small-scale structures in the 193 Angstrom passband to date. With just 5 minutes of observations, the instrument recorded a variety of dynamic coronal events -- including even a small B-class flare. We will present our results comparing these extreme-ultraviolet (EUV) observations with X-ray imaging from Hinode/XRT as well as EUV AIA data to identify sources of hot plasma rooted in the photosphere and track their affect on the overall topology and dynamics of the active region.
Savage, Sabrina↗
De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals
Abstract Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan , respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.
59 BASIC BIOLOGICAL SCIENCES↗
Anisotropy effects on the kinetics of colloidal crystallization and melting: comparison of spheres and ellipsoids
We use alternating current (AC) electric field assisted self-assembly to produce two-dimensional, millimeter scale arrays of ellipsoidal colloids and study the kinetics of their phase reconfiguration by means of confocal microscopy, light scattering, and computer simulation. We find that the kinetics of orientational and positional ordering can be manipulated by changing the shape of the colloids: ellipsoids with aspect ratio 2.0 melt into disordered structures 5.7 times faster compared to spheres. On the other hand, ellipsoids self-assemble into ordered crystals at a similar rate to spheres. Confocal microscopy is used to directly visualize defects in the self-assembled structures. Small-angle light scattering (SALS) quantifies the light diffraction response, which is sensitive to the kinetics of positional and orientational ordering in the self-assembled anisotropic structures. We find three different light diffraction patterns: a phase with high orientational order (with chain-like structure in real space), a phase with high positional and orientational order (characteristic of a close-packed structure), and a phase that is disordered in position but with intermediate orientational order. The large influence of aspect ratio on the kinetics of the positionally and orientationally ordered phase is explored through simulation; it is found that the number of particle degrees of freedom controls the difference between the melting rates of the ellipsoids and spheres. This research contributes to the understanding of reconfiguration kinetics and optical properties of colloidal crystals produced from anisotropic colloids.
36 MATERIALS SCIENCE↗
Record-breaking protein images have applications for drug discovery
Thanks to new electron detectors, cryoelectron microscopy is experiencing a revolution. It can now solve the structures of small biomolecules at high resolution.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Photocatalytic activities of ultra-small β-FeOOH and TiO{sub 2} heterojunction structure under simulated solar irradiation
Highlights: • Ultra small β-FeOOH with TiO{sub 2} in heterojunction showed good photocatalytic activity under simulated solar irradiation. • Significant improvement of photocatalytic activity compared to pristine TiO{sub 2}. • The as prepared catalyst decoloured industrial textile effluent within 30 min. - Abstract: Photocatalytic performance of β-FeOOH/TiO{sub 2} heterojunction structure, created from ultra-small β-FeOOH nanorods (2–6 nm diameter) and spherical anatase phase of TiO{sub 2} nanoparticles (∼100 nm), is reported in this study. Three different β-FeOOH mol% of (2, 5 and 10%) β-FeOOH/TiO{sub 2} composite was prepared. 5% β-FeOOH/TiO{sub 2} composite material showed the highest photocatalytic activity. XRD, high temperature XRD, FTIR, TEM, UV–vis diffuse reflectance spectra (DRS) were used to characterise the prepared catalyst. The developed catalyst showed excellent photocatalytic activity in photodegradation of methyl orange (MO) than β-FeOOH and TiO{sub 2} under simulated solar irradiation. Two commercial metal complex dyes and real textile effluent were efficiently photodegraded under identical conditions. The developed catalyst exhibited good recyclability without the need of sintering. No significant loss in efficiency was observed during the recycling cycle. These characteristics highlight the potential application of the developed photocatalyst in textile effluent treatment via photocatalysis. The enhanced photocatalytic activity was attributed to the relative energy band positions and very good electron, e{sup −} and hole, h{sup +} conduction ability of TiO{sub 2} and β-FeOOH particles respectively.
36 MATERIALS SCIENCE↗
The optical structure of the Crab Nebula's 'jet'
A deep, high-resolution forbidden O III image of the Crab Nebula's northern 'jet' is presented which reveals considerably finer details than visible on previous photographs. The jet's small-scale structure appears composed of numerous emission-line filaments and knots which collectively exhibit a strong alignment having well-defined east-west boundaries. Comparison with an earlier published image suggests a proper motion northward for one of the jet's emission knots of 0.22 + or - 0.05 arcsec/yr. The jet's optical morphology is discussed and its properties compared to predictions of several proposed models. The 'shadowed flow' model suggested by Morrison and Roberts (1985) appears to explain best the jet's known properties.
Fesen, R. A.↗