A novel approach for finding and evaluating structural models of small metallic nanoparticles is presented. Rather than fitting a single model with many degrees of freedom, libraries of clusters from multiple structural motifs are built algorithmically and individually refined against experimental pair distribution functions. Each cluster fit is highly constrained. The approach, called cluster-mining, returns all candidate structure models that are consistent with the data as measured by a goodness of fit. It is highly automated, easy to use, and yields models that are more physically realistic and result in better agreement to the data than models based on cubic close-packed crystallographic cores, often reported in the literature for metallic nanoparticles.

The use of strongly bent crystals in spectrometers for pulses of a hard X-ray free-electron laser is explored theoretically. Diffraction is calculated in both dynamical and kinematical theories. It is shown that diffraction can be treated kinematically when the bending radius is small compared with the critical radius given by the ratio of the Bragg-case extinction length for the actual reflection to the Darwin width of this reflection. As a result, the spectral resolution is limited by the crystal thickness, rather than the extinction length, and can become better than the resolution of a planar dynamically diffracting crystal. As an example, it is demonstrated that spectra of the 12 keV pulses can be resolved in the 440 reflection from a 20 µm-thick diamond crystal bent to a radius of 10 cm.

A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink-beam X-ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit-cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink-beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi-monochromatic X-rays and with electrons the algorithm indexed more patterns than other programs tested.

Entangled embedded periodic nets and crystal frameworks are defined, along with their dimension type, homogeneity type, adjacency depth and periodic isotopy type. Periodic isotopy classifications are obtained for various families of embedded nets with small quotient graphs. The 25 periodic isotopy classes of depth-1 embedded nets with a single-vertex quotient graph are enumerated. Additionally, a classification is given of embeddings of n-fold copies of pcu with all connected components in a parallel orientation and n vertices in a repeat unit, as well as demonstrations of their maximal symmetry periodic isotopes. The methodology of linear graph knots on the flat 3-torus [0,1)3 is introduced. These graph knots, with linear edges, are spatial embeddings of the labelled quotient graphs of an embedded net which are associated with its periodicity bases.

Crystal structure identification of thin organic films entails a number of technical and methodological challenges. In particular, if molecular crystals are epitaxially grown on single-crystalline substrates a complex scenario of multiple preferred orientations of the adsorbate, several symmetry-related in-plane alignments and the occurrence of unknown polymorphs is frequently observed. In theory, the parameters of the reduced unit cell and its orientation can simply be obtained from the matrix of three linearly independent reciprocal-space vectors. However, if the sample exhibits unit cells in various orientations and/or with different lattice parameters, it is necessary to assign all experimentally obtained reflections to their associated individual origin. In the present work, an effective algorithm is described to accomplish this task in order to determine the unit-cell parameters of complex systems comprising different orientations and polymorphs. This method is applied to a polycrystalline thin film of the conjugated organic material 6,13-pentacene­quinone (PQ) epitaxially grown on an Ag(111) surface. All reciprocal vectors can be allocated to unit cells of the same lattice constants but grown in various orientations [sixfold rotational symmetry for the contact planes (102) and (102)]. The as-determined unit cell is identical to that reported in a previous study determined for a fibre-textured PQ film. Preliminary results further indicate that the algorithm is especially effective in analysing epitaxially grown crystallites not only for various orientations, but also if different polymorphs are present in the film.

Recent developments of two-color operation modes at X-ray free-electron laser facilities provide new research opportunities, such as X-ray pump/X-ray probe experiments and multiple-wavelength anomalous dispersion phasing methods. However, most existing indexing methods were developed for indexing diffraction data from monochromatic X-ray beams. Here, a new algorithm is presented for indexing two-color diffraction data, as an extension of the sparse-pattern indexing algorithm SPIND, which has been demonstrated to be capable of indexing diffraction patterns with as few as five peaks. The principle and implementation of the two-color indexing method, SPIND-TC, are reported in this paper. The algorithm was tested on both simulated and experimental data of protein crystals. The results show that the diffraction data can be accurately indexed in both cases. Source codes are publicly available at https://github.com/lixx11/SPIND-TC.

A new approach is presented to obtain candidate structures from atomic pair distribution function (PDF) data in a highly automated way. It fetches, from web-based structural databases, all the structures meeting the experimenter's search criteria and performs structure refinements on them without human intervention. It supports both X-ray and neutron PDFs. Tests on various material systems show the effectiveness and robustness of the algorithm in finding the correct atomic crystal structure. It works on crystalline and nanocrystalline materials including complex oxide nanoparticles and nanowires, low-symmetry and locally distorted structures, and complicated doped and magnetic materials. This approach could greatly reduce the traditional structure searching work and enable the possibility of high-throughput real-time auto-analysis PDF experiments in the future.

The generalized Darwin–Hamilton equations [Wuttke (2014). Acta Cryst. A70, 429–440] describe multiple Bragg reflection from a thick, ideally imperfect crystal. These equations are simplified by making full use of energy conservation, and it is demonstrated that the conventional two-ray Darwin–Hamilton equations are obtained as a first-order approximation. Then an efficient numeric solution method is presented, based on a transfer matrix for discretized directional distribution functions and on spectral collocation in the depth coordinate. Example solutions illustrate the orientational spread of multiply reflected rays and the distortion of rocking curves, especially if the detector only covers a finite solid angle.

As you read here
In a 24-hour-period between July 9 and 10, 2009 a clouded leopard cub, a Przewalski's horse, and a red panda cub were all born at Smithsonian's National Zoo's Conservation and Research Center in Front Royal, Virginia.

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George Smith, a marine biologist at the Smithsonian Environmental Research Center, explains his work of finding ways to prevent invasive species from being released in Baltimore Harbor in the ballast water of large ships.

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Leafcutter Ants—an amazing species that has been employing agriculture and antibiotics for some 50 million years.

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When animal care staff at the Smithsonian's National Zoo need to know when to breed their pandas or when to expect a cub they turn to the Endocrine (Hormones) Research Lab at the Zoo's Front Royal, Va. facility.

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Rick Wunderman of the Global Volcanism Program at the Smithsonian's National Museum of Natural History talks about the current volcanic activity in Iceland.

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Eyjafjallajökull's eruption may be a hassle if you had any transatlantic flights planned this summer. For scientists, however, volcanic eruptions are the only way they can obtain samples from deep within the Earth to learn more about our planet, its formation, and its ongoing evolution. Smithsonian Geologist Liz Cottrell helps put this recent eruption into perspective.

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Keeper Tracey Barnes talks about Billie Jean, an Andean bear, and her two new cubs at the Smithsonian's National Zoo.

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Dr. JoGayle Howard of the Smithsonian's National Zoo discusses her work to breed and study one of the world's most endangered cats, the clouded leopard. More about the National Zoo's work to save clouded leopards: http://nationalzoo.si.edu/SCBI/ReproductiveScience/ConsEn...
http://nationalzoo.si.edu/support/annualappeal/cloudedleo... ... (more info)

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Chip Clark came to the Smithsonian's National Museum of Natural History in 1973, with a degree in biology and an interest in photography. He has been a photographer on staff ever since, documenting thousands of specimens and exhibits, and accompanying scientists on research trips around the world. He died June 12, 2010. This video interview was made by Lauren Dare, an intern with the Smithsonian Institution Archives, on May 27, 2010, as part of an oral history project for the National Museum of Natural History's Centennial (2010-2011). To learn more about Chip Clark, see his page on the Centennial website-- www.mnh.si.edu/onehundredyears/profiles/Chip_Clark.html -- where you also can find more videos and stories about the people and the work of the NMNH.

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Dr. Mary Hagedorn, a marine biologist at the Smithsonian Institution, talks about her research to understand and conserve our oceans' corals. To meet more scientists, visit https://insider.si.edu.

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Here come the stinkbugs...With the cooler temperatures of fall the brown marmorated stinkbug begins a determined quest to find a warm place to spend the winter. Crowding around window screens and searching for other ways to get inside, homeowners in the United States will share their indoor living space this winter with millions of brown marmorated stinkbugs. In this video Gary Hevel, an entomolgist at the Smithsonian's National Museum of Natural History, shares some information about these interesting creatures, as well as some advice about how to deal with those that inevitably gain entry to your home.

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Researchers at the Smithsonian's National Zoo's new genetics lab use animal DNA to diagnose new diseases, discover new species help in conservation efforts and solve mysteries.

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What does it take to care for a pride of lions? Go behind the scenes with Great Cats Curator Craig Saffoe as he works with animal keepers and veterinarians to prepare the National Zoo's frisky lion cubs for their public debut. For more about the Zoo's growing pride and to watch them on live webcams: http://nationalzoo.si.edu/Animals/GreatCats/default.cfm?cam=LC4

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The three male cheetahs that left the Zoo's D.C. campus in 2009 returned in November and are now on exhibit. The five-and-a-half-year-old brothers―Draco, Granger, and Zabini, named after characters in the Harry Potter stories―have been living at the Zoo's Smithsonian Conservation Biology Institute's Cheetah Science Facility in Front Royal, Virginia.

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The post “How Soil Savvy are You?, is featured in the exhibition “Dig It! The Secrets of Soil,” from the Smithsonian Traveling Exhibition Service appeared first on Smithsonian Insider.

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National Zoo Veterinarian Katharine Hope treats about 2,000 animals from 400 different species. She and her colleagues care for a variety of animals, from small baby flamingos to adult Asian elephants, so there's no such thing as an average day.

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The HSBC Climate Partnership (HCP) is a five-year partnership (2007-2011) between HSBC, The Smithsonian, The Climate Group, Earthwatch Institute and WWF to inspire action on climate change.
Working with these partners and engaging its employees around the world, HSBC hopes to tackle climate change impacts for people, forests, water, and cities. The HCP research of the Smithsonian's Center for Tropical Forest Science (CTFS) focuses on:
• Understanding the role of forests in the global carbon cycle
• Comparing temperate and tropical forests by establishing new plots in the temperate zone
• Quantifying the environmental services provided by tropical forests

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The post Invasive Caribbean lionfish under scrutiny by Smithsonian Tropical Research Institute intern appeared first on Smithsonian Insider.

Paleoecologist Conrad Labandeira travels to the Karoo Basin of South Africa to find leaf fossils from the Permian-Triassic boundary, the time of the Earth's largest mass extinction. What can bug bites on leaves tell us about our own uncertain times?

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This new PBS Newshour video takes a look at a new exhibit at the Air and Space Museum celebrating NASA's space art program.

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In 2010 Dr. Rachel Collin visited her colleagues at the Universidad Austral de Chile in Valdivia to collect some very special snails for her research at the Smithsonian Tropical Research Institute, Panama.

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Digging up early human and animal remains from the field in Africa, performing examination and publishing research about her findings, then enticing and educating the public about the implications are all in a week's work for Briana Pobiner.

The post Meet Our Scientist–Briana Pobiner, human origins researcher at the National Museum of Natural History appeared first on Smithsonian Insider.

Animal care staff at the Smithsonian Conservation Biology Institute in Front Royal, Virginia, are hand-rearing the pair of clouded leopard cubs born on March 28, increasing the chances that the cubs will be more successful at breeding later in their life.

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Keepers at the Smithsonian's National Zoo perform an artificial insemination procedure on a pair of Stanley Cranes. A Stanley Crane chick was successfully hatched on May 23, 2011.

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Tom Crouch, Senior curator in the National Air and Space Museum's Aeronautics Division, discusses Thaddeus Lowe and the birth of American aerial reconnaissance during the Civil War. This presentation was recorded on May 11, 2011 on the National Mall.

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Kari Bruwelheide, forensic anthropologist at the Smithsonian's National Museum of Natural History, discusses how she came to work at the museum, the power of human remains and the information that bones can contain. She and her colleagues continue to discover new ways to interpret evidence from bones and burials.

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What's possibly the most calming yet nerve-racking job in the world? Come behind the scenes of the Smithsonian's Freer Gallery of Art to find out!

The post Zen and the art of fine art conservation: Behind the scenes in the Freer Gallery’s art conservation lab appeared first on Smithsonian Insider.

Meet the Smithsonian's Matthew Carrano, curator of Dinosauria at the Smithsonian's National Museum of Natural History in Washington, D.C. Matthew studies all things dinosaur, but focuses on the evolutionary history of predatory (meat eating) dinosaurs.

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School's nearly back in session, but the seven young lions at the Smithsonian's National Zoo have been working hard through the summer months!

The post Lion cub summer school: Instead of learning their ABCs, the National Zoo’s lion cubs are learning behaviors that will help animal care staff evaluate their health. appeared first on Smithsonian Insider.

Meet Rachel Collin, a staff scientist and director of the Bocas Research Station at the Smithsonian Tropical Research Institute in Panama. Rachel studies the evolution of marine gastropods (snails) and oversees multiple disciplines of marine biology at the Collin Lab in Bocas del Toro.

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Members of the Human Origins Program team at the Smithsonian's National Museum of Natural History describe why they love their job.

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