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py_convrot: rotation conventions, to understand and to apply

The Python-based program py_convrot is a universal converter of rigid-body rotation parameters. The program interactively illustrates the action of various rotation parameters and can be used both for teaching goals and for practical applications.




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Local orientational order in self-assembled nanoparticle films: the role of ligand composition and salt

An X-ray cross-correlation study of the impact of ligand composition and salt content on the self-assembly of soft-shell nanoparticles is presented, indicating symmetry-selective formation of order.




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Disorder in La1−xBa1+xGaO4−x/2 ionic conductor: resolving the pair distribution function through insight from first-principles modeling

Ba excess in LaBaGaO4 triggers ionic conductivity together with structural disorder. A direct correlation is found between the density functional theory model energy and the pair distribution function fit residual.




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3D-printed holders for in meso in situ fixed-target serial X-ray crystallography

The design and assembly of two 3D-printed holders for high-throughput in meso in situ fixed-target crystallographic data collection are described.




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Full reciprocal-space mapping up to 2000 K under controlled atmosphere: the multipurpose QMAX furnace

This article presents the capability of the QMAX furnace, devoted to reciprocal space mapping through X-ray scattering at high temperature up to 2000 K.




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Equatorial aberration of powder diffraction data collected with an Si strip X-ray detector by a continuous-scan integration method

Exact and approximate formulas for equatorial aberration of a continuous-scan Si strip detector are compared.




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Orientational disorder of monomethyl-quinacridone investigated by Rietveld refinement, structure refinement to the pair distribution function and lattice-energy minimizations

The crystal structure of the organic pigment 2-monomethyl-quinacridone (Pigment Red 192, C21H14N2O2) was solved from X-ray powder diffraction data. The resulting average structure is described in space group Poverline 1, Z = 1 with the molecule on the inversion centre. The molecules are arranged in chains. The molecules, which have no inversion symmetry, show orientational head-to-tail disorder. In the average structure, the methyl group is disordered and found on both ends of the molecule with an occupancy of 0.5 each. The disorder and the local structure were investigated using various ordered structural models. All models were analysed by three approaches: Rietveld refinement, structure refinement to the pair distribution function (PDF) and lattice-energy minimization. All refinements converged well. The Rietveld refinement provided the average structure and gave no indication of a long-range ordering. The refinement to the PDF turned out to be very sensitive to small structural details, giving insight into the local structure. The lattice-energy minimizations revealed a significantly preferred local ordering of neighbouring molecules along the [0ar 11] direction. In conclusion, all methods indicate a statistical orientational disorder with a preferred parallel orientation of molecules in one direction. Additionally, electron diffraction revealed twinning and faint diffuse scattering.




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A closer look at superionic phase transition in (NH4)4H2(SeO4)3: impedance spectroscopy under pressure

The proton-conducting material (NH4)4H2(SeO4)3 is examined to check whether its conductivity spectra are sensitive to subtle changes in the crystal structure and proton dynamics caused by external pressure. The AC conductivity was measured using impedance spectroscopy, in the frequency range from 100 Hz to 1 MHz, at temperatures 260 K < T < 400 K and pressures 0.1 MPa < p < 500 MPa. On the basis of the impedance spectra, carefully analyzed at different thermodynamic conditions, the p–T phase diagram of the crystal is constructed. It is found to be linear in the pressure range of the experiment, with the pressure coefficient value dTs/dp = −0.023 K MPa−1. The hydrostatic pressure effect on proton conductivity is also presented and discussed. Measurements of the electrical conductivity versus time were performed at a selected temperature T = 352.3 K and at pressures 0.1 MPa < p < 360 MPa. At fixed thermodynamic conditions (p = 302 MPa, T = 352.3 K), the sluggish solid–solid transformation from low conducting to superionic phase was induced. It is established that the kinetics of this transformation can be described by the Avrami model with an effective Avrami index value of about 4, which corresponds to the classical value associated with the homogeneous nucleation and three-dimensional growth of a new phase.




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A closer look at superionic phase transition in (NH4)4H2(SeO4)3: impedance spectroscopy under pressure

The proton-conducting crystal (NH4)4H2(SeO4)3 is examined to check whether its conductivity spectra and the phase transition to the superprotonic phase are sensitive to subtle changes in the crystal structure and proton dynamics caused by various thermodynamic conditions. It is established that the kinetics of this transformation can be described using the Avrami model with an effective Avrami index value associated with homogeneous nucleation and three-dimensional growth of a new phase.




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Orientational disorder of mono­methyl-quinacridone investigated by Rietveld refinement, structure refinement to the pair-distribution function and lattice-energy minimizations

The crystal structure of the nanocrystalline pigment mono­methyl-quinacridone was solved from X-ray powder data. The orientational disorder was investigated using Rietveld refinements, structure refinement to the pair-distribution function, and lattice-energy minimizations of various ordered structural models.




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Synthesis, crystal structure, polymorphism and microscopic luminescence properties of anthracene derivative compounds

Crystal structure and microscopic optical properties of anthracene derivative compounds have been investigated by single-crystal synchrotron X-ray diffraction, laser confocal microscopy and fluorescence lifetime imaging microscopy.




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The thermodynamic profile and molecular interactions of a C(9)-cytisine derivative-binding acetylcholine-binding protein from Aplysia californica

Cytisine, a natural product with high affinity for clinically relevant nicotinic acetylcholine receptors (nAChRs), is used as a smoking-cessation agent. The compound displays an excellent clinical profile and hence there is an interest in derivatives that may be further improved or find use in the treatment of other conditions. Here, the binding of a cytisine derivative modified by the addition of a 3-(hydroxypropyl) moiety (ligand 4) to Aplysia californica acetylcholine-binding protein (AcAChBP), a surrogate for nAChR orthosteric binding sites, was investigated. Isothermal titration calorimetry revealed that the favorable binding of cytisine and its derivative to AcAChBP is driven by the enthalpic contribution, which dominates an unfavorable entropic component. Although ligand 4 had a less unfavorable entropic contribution compared with cytisine, the affinity for AcAChBP was significantly diminished owing to the magnitude of the reduction in the enthalpic component. The high-resolution crystal structure of the AcAChBP–4 complex indicated close similarities in the protein–ligand interactions involving the parts of 4 common to cytisine. The point of difference, the 3-(hydroxypropyl) substituent, appears to influence the conformation of the Met133 side chain and helps to form an ordered solvent structure at the edge of the orthosteric binding site.




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Study aims to give endangered Shenandoah salamander better odds at survival

Each year thousands of vacationers enjoy the scenery along Virginia’s Skyline Drive, little knowing that for a few brief moments they are passing through the territory of an endangered […]

The post Study aims to give endangered Shenandoah salamander better odds at survival appeared first on Smithsonian Insider.




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Smithsonian Names Eva Pell as Under Secretary for Science

Today the Smithsonian Institution announced Eva J. Pell, Senior Vice President for Research and Dean of the Graduate School at Pennsylvania State University, will be the new Under Secretary for Science at the Institution.

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Females are giants in newly discovered species of golden orb weaver spider

Native to Africa and Madagascar, females of the species have a body length of 1.5 inches and a leg span of 4 to 5 inches. Males are tiny in comparison.

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Drugged spiders’ web spinning may hold keys to understanding animal behavior

“Spinning under the influence” is one way to describe recent activities in the Costa Rican laboratory of Smithsonian scientist William Eberhard. An entomologist at the Smithsonian’s Tropical Research Institute, Eberhard recently carried out a series of experiments in which he observed the web-building behavior of dozens of spiders under the influence of drugs—specifically, a chemical injected into their bodies by parasitic wasps.

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Tiny, new brains prove just as adept as large, mature brains among tropical orb-web spiders

When it comes to brains, is bigger better? Can the tiny brain of a newly hatched spiderling handle problems as adeptly as the brain of a larger adult spider?

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Japanese giant salamanders given to the National Zoo by Asa Zoological Park in Hiroshima

The Smithsonian’s National Zoo recently acquired Japanese giant salamanders given to the Zoo by the City of Hiroshima Asa Zoological Park. This donation will be the foundation of a new long-term breeding program in the United States and may play an important role in saving amphibians around the globe.

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Newly discovered Madagascar spider spins largest, toughest webs on record

Darwin's bark spider cast giant webs across streams, rivers and lakes, suspending the web’s orb above water and attaching it to plants on each riverbank. Bridgelines of these water-spanning webs have been measured as long as 25 meters.

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A Halloween roundup featuring recent articles on spiders, bats and rats

A roundup of recent articles featuring spiders, bats and rats....

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Rutgers glider added to the collections of the National Museum of Natural History

The Scarlet Knight, as the glider is called, made nautical history as the first submersible glider to successfully cross the Atlantic Ocean.

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Smithsonian researchers help block ship-borne bioinvaders with new screening strategy

To help regulators and engineers develop and test such treatment systems, and ultimately enforce these standards, a team of researchers developed a statistical model to see how to count small, scarce organisms in large volumes of water accurately.

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Don’t pick a fight with a eunuch spider. It has nothing to lose

In a recent study of the mating behavior of these Asian spiders, researchers found that 87.5 percent of males had both palps amputated during copulation.

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Scientists show that modern humans never co-existed with Homo erectus

New excavations in Indonesia and dating analyses by scientists at the Smithsonian and their colleagues show that modern humans never co-existed with Homo erectus.

The post Scientists show that modern humans never co-existed with <em>Homo erectus</em> appeared first on Smithsonian Insider.




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Will global warming be hell on the hellbender? Smithsonian study aims to find out.

Now, a new study of hellbenders by scientists at the Smithsonian Conservation Biology Institute will place these amphibians at the center of the conservation of Appalachian salamanders.

The post Will global warming be hell on the hellbender? Smithsonian study aims to find out. appeared first on Smithsonian Insider.




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Suitor’s gentle massage soothes aggressive, cannibalistic female spiders, researchers find

A new study by a team of scientists from the Smithsonian’s National Museum of Natural History, the National University of Singapore and the Slovenian Academy of Sciences and Arts have unlocked the secret to mate binding in orb web spiders, and revealed just how it calms the cannibalistic female spider.

The post Suitor’s gentle massage soothes aggressive, cannibalistic female spiders, researchers find appeared first on Smithsonian Insider.





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New DNA study suggests coral reef biodiversity is seriously underestimated

The first DNA barcoding survey of crustaceans living on samples of dead coral taken from the Indian, Pacific and Caribbean oceans suggests that the diversity of organisms living on the world’s coral reefs—one of the most endangered habitats on Earth—is seriously underestimated.

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Brains of tiny spiders fill their body cavities and legs, Smithsonian researchers discover

New research on tiny spiders has revealed that their brains are so large that they fill their body cavities and overflow into their legs, say a team of scientists at the Smithsonian Tropical Research Institute in Panama.

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Digital technology allows Alexander Graham Bell’s 1880s disc recordings to be played again

In 2011, scholars from three institutions—National Museum of American History Curators Carlene Stephens and Shari Stout, Library of Congress Digital Conversion Specialist Peter Alyea and Lawrence Berkeley National Laboratory Scientists Carl Haber and Earl Cornell—came together in a newly designed preservation laboratory at the Library of Congress to recover sound from those recordings made more than 100 years ago.

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Male spider’s sexual organs work fastest only when a female breaks them off

In fact, researchers have learned, the detached male pedipalps transfer more sperm faster after copulation is ended by the female rather than the male.

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Fancy footwork and non-stick leg coating helps spiders not stick to their own webs

Researchers at the Smithsonian Tropical Research Institute and University of Costa Rica studying why spiders do not stick to their own sticky webs have discovered that a spider's legs are protected by a covering of branching hairs and by a non-stick chemical coating. Their results are published online in the journal, Naturwissenschaften.

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3-D imaging adds remarkable new understanding of North America’s mysterious Clovis people

The only explanation for such symmetry across these vast distances, explains Smithsonian anthropologist Dennis Stanford, is that the method of creating the points was handed down from person to person.

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New mapping of Mars shows Medusae Fossae Formation older than once thought

Recent geologic mapping of the Medusae Fossae Formation on Mars—an intensely eroded deposit near the northern edge of the cratered highlands—has revealed a wider distribution of its western component than was previously recognized.

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Weight of genitals reduces physical endurance in male orb web spiders, researchers find

The scientists made the spiders exercise by irritating them with a small paint brush and causing them to move around until they became exhausted. Spiders from the group with palps removed were able to travel 300 percent further than spiders with their palps intact.

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Female spiders produce mating plugs to prevent unwanted sex from males

They observed that no plugs were ever formed during mating trials, but instead, females exposed to many males produced the amorphous plugs during the egg-laying process.

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Undersea parasite turns male mud crabs female

One such parasite lurks in Chesapeake Bay: an invasive barnacle that hijacks a mud crab’s reproductive system and impregnates it with parasite larvae—even if the crab is male.

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Female “spidernaut” settles into new home at Smithsonian’s Insect Zoo

The new Sant Director of the National Museum of Natural History, Kirk Johnson, had only been on the job for 26 days when he got […]

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Common tropical bat uses echolocation with precision previously considered impossible, new experiments reveal

Using echolocation alone the bats found, identified and captured insects perched motionless and silent on the leaves of plants.

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“Hear My Voice”: Smithsonian identifies 130-year-old recording as Alexander Graham Bell’s voice

The inventions of Alexander Graham Bell—most famously the telephone but also methods of recording sound—have allowed people to hear each other’s voices for more than […]

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Zoo scientists find sudden stream temperature changes boost hellbender immune systems

Hellbenders, aquatic salamanders from the eastern United States, are surprisingly good at dealing with unpredictable weather. In a recent study published in the Journal of […]

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Panamanian fish catch is vastly under-reported, study reveals

The name Panama is said to mean “abundance of fish.” Now a new study estimates that between 1950 and 2010, the amount of fish taken […]

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Slimy invaders, giant snails: Q&A with mollusk expert Ellen Strong

It is related to one of the world’s most destructive invasive species, and possibly the slimiest. Thirty-five pounds of live giant West African snails (Archachatina […]

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In modern amphibian “ark,” new species added with due diligence

Bright orange with a distinctive call the Panamanian poison dart frog Andinobates geminisae lives in only a small area of the Caribbean Coast of Panama. […]

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Jamestown skeletons identified as colony leaders

Within the 1608 church where Pocahontas and John Rolfe married, the skeletal remains of four early settlers were uncovered during a 2013 archaeological dig at […]

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National Zoo Opens New Home for Appalachian Salamanders

Salamanders are typically elusive animals and adept at hiding, but National Zoo visitors will have a chance to see a variety of different amphibian species […]

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Discovery: trap-jaw spiders snap prey with super-spidey speed and power

New high-speed videos of 14 species of tiny Mecysmaucheniid “trap-jaw” spiders have revealed that some species can snap their mouth parts shut at incredibly fast […]

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