The Smithsonian Environmental Research Center in Edgewater, Md., and the Alaska Sea Grant Program of the University of Alaska, Fairbanks, were recently identified as the […]

The post Smithsonian scientists to help identify and eradicate invasive species in Alaskan waters appeared first on Smithsonian Insider.

The post Community ecologist Sunshine Van Bael explains her work in Panama with leafcutting ants appeared first on Smithsonian Insider.

Candy Feller, senior ecologist at the Smithsonian Environmental Research Center in Edgewater, Md., will lead an effort to track more than 100 miles of Florida mangrove forests that are encroaching on salt marshes to the north.

The post NASA to help Smithsonian botanists track northern creep of Florida mangroves appeared first on Smithsonian Insider.

These opportunistic plants quickly fill-in the gap taking advantage of the increased light coming through the tree canopy and the fresh soil at the fallen tree’s turned-up roots.

The post Falling trees help invasive wineberry move into deciduous forests in North America appeared first on Smithsonian Insider.

In 1909, naturalist Dr. Edgar A. Mearns joined Theodore Roosevelt and scientists from the Smithsonian and New York’s American Museum of Natural History on an […]

The post New project will improve access to thousands of scientific field books, journals and notes in Smithsonian collections appeared first on Smithsonian Insider.

The post Introducing Leafsnap, an electronic field guide to North America trees run on a mobile phone app appeared first on Smithsonian Insider.

Recent botanical exploration efforts in the rugged Marquesas Islands (French Polynesia) have increased the known flora of the archipelago by an impressive 20 percent. Field research and collecting in conjunction with the Vascular Flora of the Marquesas Islands and Flore de la Polynesie française projects have yielded 62 new species of ferns and flowering plants bringing the total native species to 360, of which 18 are newly described and illustrated in a special issue of PhytoKeys.

The post Marquesas Islands in French Polynesia yield 18 new species of rare ferns and flowering plants appeared first on Smithsonian Insider.

Nutmeg-loving toucans wearing GPS transmitters recently helped a team of scientists at the Smithsonian Tropical Research Institute in Panama address an age-old problem in plant ecology: accurately estimating seed dispersal.

The post Toucans wearing GPS backpacks help Smithsonian scientists study seed dispersal appeared first on Smithsonian Insider.

A new study shows that as climate change enhances tree growth in tropical forests, the resulting increase in litterfall could stimulate soil micro-organisms leading to a release of stored soil carbon.

The post Increased tropical forest growth may result in release of stored carbon in the soil appeared first on Smithsonian Insider.

Ancient pollen and charcoal preserved in deeply buried sediments in Egypt’s Nile Delta document the region’s ancient droughts and fires, including a huge drought 4,200 years ago associated with the demise of Egypt’s Old Kingdom.

The post Fossil pollen used to augment climate record of Egypt’s Nile Delta appeared first on Smithsonian Insider.

A new genetic analysis has revealed that many Amazon tree species are likely to survive human-caused climate warming in the coming century, contrary to previous findings that temperature increases would cause them to die out.

The post Warming climate unlikely to cause near-term extinction of ancient Amazon trees, study says appeared first on Smithsonian Insider.

Soon after a dirt road through the forests of Lambir Hills National Park in Borneo was improved in 1987, local markets selling the meat of […]

The post Loss of animals spells doom for diversity of rainforest trees appeared first on Smithsonian Insider.

Smooth and shiny, the tough body of the South African beetle Pedinorrhina trivittata, a flower eater, appears to be a non-inviting surface for pollen grains […]

The post Caught on camera: Despite hard shells pollen sticks to South African beetles appeared first on Smithsonian Insider.

Tropical forests speed their own recovery, capturing nitrogen and carbon faster after being logged or cleared for agriculture. Researchers working at the Smithsonian Tropical Research […]

The post Tropical forests “fix” themselves appeared first on Smithsonian Insider.

A joint research initiative carried out by scientists from the Smithsonian Institution, Saint Louis University and the Universidad de Los Andes in Venezuela, has resulted in […]

The post New daisy species discovered in Venezuela appeared first on Smithsonian Insider.

Scientists have long known that in the tropics shade-grown coffee plantations provide critical habitat for migratory and resident birds. Now a new survey conducted in […]

The post Shade-grown coffee plantations are mammal friendly as well, study shows appeared first on Smithsonian Insider.

Residents of the southeastern United States might occasionally come across an oddity along a barbed-wire fence: a series of insects, mice or even small birds […]

The post Tiny, fierce and disappearing: breeding program aims to help the loggerhead shrike appeared first on Smithsonian Insider.

This year’s El Niño event is one of the strongest on record and is still ramping up. Large parts of the tropics are turning into […]

The post Major El Nino Perfect opportunity for Global Change Research appeared first on Smithsonian Insider.

The Smithsonian Tropical Research Institute (STRI) celebrated with Panama the completion of the Panama Canal expansion project on June 26, 2016. The $5.6 billion engineering […]

The post Smithsonian celebrates Panama Canal expansion! appeared first on Smithsonian Insider.

Strategically placed honeybee hives can deter African elephants from raiding crops, but the hives must be actively managed by beekeepers to work, according to a […]

The post Study: Managed beehives can discourage crop-raiding elephants appeared first on Smithsonian Insider.

The Smithsonian-Mason School of Conservation offers a range of compelling residential, hands-on, interdisciplinary programs in conservation biology for undergraduate and graduate students and professionals at […]

The post Field Research: Smithsonian-Mason School of Conservation appeared first on Smithsonian Insider.

Finding a mouse in your morning coffee might give you an unwelcome jolt, but there’s a strong connection between small mammals, birds and the plantations […]

The post Of mice and macchiato: Bird Friendly coffee gives a paw-up to small mammals as well appeared first on Smithsonian Insider.

What might lure someone away from the sunny beaches and lush forests of Brazil to the concrete jungle of Washington, D.C.? For wood anatomist Marcelo […]

The post Rigid yet flexible: Anatomy of woody vines has its grip on botanist Marcelo Pace appeared first on Smithsonian Insider.

Ninety Limosa harlequin frogs (Atelopus limosus) bred in human care are braving the elements of the wild after Smithsonian scientists sent them out into the […]

The post Scientists Release Frogs Wearing Mini Radio Transmitters appeared first on Smithsonian Insider.

Smithsonian’s MarineGEO (Marine Global Earth Observatory) conducts long-term research around the world on coastal marine ecosystems, including at their field station on Carrie Bow Cay […]

The post MarineGEO Field Campaign: Belize appeared first on Smithsonian Insider.

To catch lizards on the offshore islands close to St. Croix in the Caribbean, Smithsonian herpetologist Nicole Angeli uses a lasso of thread looped at […]

The post Mongooses wiped them out. Now Nicole Angeli wants the St. Croix ground lizard home again appeared first on Smithsonian Insider.

Millions, if not billions, of specimens reside in the world’s natural history collections, but most of these have not been carefully studied, or even looked […]

The post Using digitized Botany specimens, AI excels in simple curatorial tasks appeared first on Smithsonian Insider.

This article aims to encourage practitioners, young and seasoned, by enhancing their structure-determination toolboxes with a selection of tips and tricks on recognizing and handling aspects of data collection, structure modelling and refinement, and the interpretation of results.

In the structure of the title salt, second-order Jahn–Teller distortion of the coordination octa­hedra around V ions is reflected by coexistence of short V—O bonds and trans-positioned long V—F bonds, with four equatorial V—F distances being inter­mediate in magnitude. Hydrogen bonding of the anions is restricted to F-atom acceptors only, with particularly strong N–H⋯F inter­actions [N⋯F = 2.5072 (15) Å] established by axial and cis-positioned equatorial F atoms.

The asymmetric unit of the title compound contains two independent mol­ecules, consisting of perimidine and phenol units, which are linked through an N—H⋯O hydrogen bond. Intra­molecular O—H⋯N hydrogen bonds are observed in both independent mol­ecules.

The title compound, 1-(2,5-di­meth­oxy­phen­yl)-2,2,6,6-tetra­methyl­piperidine, was synthesized as a side-product during the synthesis of the inter­mediate, methyl 3,6-dimeth­oxy-2-(2-meth­oxy-2-oxoeth­yl)benzoate, necessary for the total synthesis of the isocoumarin 5,8-dimeth­oxy-3-methyl-1H-isochromen-1-one.

The title compound exhibits exceptionally weak inter­molecular C—H⋯π hydrogen bonding of the ethynyl groups, with the corresponding H⋯π separations [2.91 (2) and 3.12 (2) Å] exceeding normal vdW distances. This bonding compliments distal contacts of the CH (aliphatic)⋯π type [H⋯π = 3.12 (2)–3.14 (2) Å] to sustain supra­molecular layers.

The dihedral angle between the two aromatic rings of the title compound is 64.12 (14)°. The crystal structure is stabilized by a short Cl⋯H contact, C—Cl⋯π and van der Waals inter­actions.

The title complex, Cu(L)2 or [Cu(C15HF10O2)2], comprising one copper ion and two fully fluorinated ligands (L−), was crystallized with 3,4-ethyl­ene­dioxy­thio­phene (EDOT, C6H6O2S) as a guest mol­ecule to give in a di­chloro­methane solution a unique co-crystal, Cu(L)2·3C6H6O2S.

This work presents a technique for extracting the detailed shape of peaks with extended, overlapping tails in an X-ray powder diffraction pattern. The application discussed here concerns crystallite size broadening, though the technique can be applied to spectra of any origin and without regard to how the profiles are to be subsequently analyzed. Historically, the extraction of profile shapes has been difficult due to the complexity of determining the background under the peak, resulting in an offset of the low-frequency components of the Fourier transform of the peak known as the `hook' problem. The use of a carefully considered statistical weighting function in a non-linear least-squares fit, followed by summing the residuals from such a fit with the fit itself, allows one to extract the full shape of an isolated peak, without contributions from either the background or adjacent peaks. The extracted shape, consisting of the fit function recombined with the residuals, is not dependent on any specific shape model. The application of this to analysis of microstructure is performed independently of global parametric models, which would reduce the number of refined parameters; therefore the technique requires high-quality data to produce results of interest. The effectiveness of the technique is demonstrated by extraction of Fourier transforms of peaks from two sets of size-broadened materials with two differing pieces of equipment.

The development of antiviral strategies requires a clear understanding of the principles that control the protein arrangements in viral shells. Considered here are those capsids that violate the paradigmatic Caspar and Klug (CK) model, and it is shown that the important structural features of such anomalous shells from the Picobirnaviridae, Flaviviridae and Leviviridae families can be revealed by models in the form of spherical icosahedral packings of equivalent rhombic structural units (SUs). These SUs are composed of protein dimers forming the investigated capsids which, as shown here, are based on the rhombic triacontahedron (RT) geometry. How to modify the original CK approach in order to make it compatible with the considered rhombic tessellations of a sphere is also discussed. Analogies between capsids self-assembled from dimers and trimers are demonstrated. This analysis reveals the principles controlling the localization of receptor proteins (which recognize the host cell) on the capsid surface.

The unit-cell reduction described by Selling and used by Delone (whose early publications were under the spelling Delaunay) is explained in a simple form. The transformations needed to implement the reduction are listed. The simplicity of this reduction contrasts with the complexity of Niggli reduction.

Compared with X-rays, electron diffraction faces a crucial challenge: dynamical electron scattering compromises structure solution and its effects can only be modelled in specific cases. Dynamical scattering can be reduced experimentally by decreasing crystal size but not without a penalty, as it also reduces the overall diffracted intensity. In this article it is shown that nanometre-sized crystals from organic pharmaceuticals allow positional refinement of the hydrogen atoms, even whilst ignoring the effects of dynamical scattering during refinement. To boost the very weak diffraction data, a highly sensitive hybrid pixel detector was employed. A general likelihood-based computational approach was also introduced for further reducing the adverse effects of dynamic scattering, which significantly improved model accuracy, even for protein crystal data at substantially lower resolution.

It is shown how to reconstruct the stacking sequence from the pairwise correlation functions between layers in close-packed structures. First, of theoretical interest, the analytical formulation and solution of the problem are presented when the exact pairwise correlation counts are known. In the second part, the practical problem is approached. A simulated annealing procedure is developed to solve the problem using as initial guess approximate solutions from previous treatments. The robustness of the procedure is tested with synthetic data, followed by an experimental example. The developed approach performs robustly over different synthetic and experimental data, comparing favorably with the reported methods.

The methods for X-ray crystal orientation are rapidly evolving towards versatility, fewer goniometry measurements, automation, high accuracy and precision. One method that attracts a lot of attention is energy-dispersive X-ray diffraction (EDXRD) which is based on detecting reflections from crystallographic planes in a crystal at fixed angles of a parallel polychromatic X-ray incident beam. In theory, an EDXRD peak can move in a diffraction pattern as a function of a crystallographic plane d-spacing and its orientation relative to a fixed direction in space can change also. This is equivalent to the possibility of measuring the orientation of single crystals. The article provides a modeling for the EDXRD method whose main feature is the nonmoving crystal in the sense of traditional goniometry where the angle measurements of diffracting planes are a must. The article defines the equation of orientation for the method and shows the derivation in great detail. It is shown that the exact solutions of the equations can be obtained using the generalized reduced gradient method, a mathematical subroutine that is implemented in Excel software. The significance and scientific impact of the work are discussed along with the validated tested results.

A new aspherical scattering factor formalism has been implemented in the crystallographic least-squares refinement program SHELXL. The formalism relies on Gaussian functions and can optionally complement the independent atom model to take into account the deformation of electron-density distribution due to chemical bonding and lone pairs. Asphericity contributions were derived from the electron density obtained from quantum-chemical density functional theory computations of suitable model compounds that contain particular chemical environments, as defined by the invariom formalism. Thanks to a new algorithm, invariom assignment for refinement in SHELXL is automated. A suitable parameterization for each chemical environment within the new model was achieved by metaheuristics. Figures of merit, precision and accuracy of crystallographic least-squares refinements improve significantly upon using the new model.

Diffuse scattering is a rich source of information about disorder in crystalline materials, which can be modelled using atomistic techniques such as Monte Carlo and molecular dynamics simulations. Modern X-ray and neutron scattering instruments can rapidly measure large volumes of diffuse-scattering data. Unfortunately, current algorithms for atomistic diffuse-scattering calculations are too slow to model large data sets completely, because the fast Fourier transform (FFT) algorithm has long been considered unsuitable for such calculations [Butler & Welberry (1992). J. Appl. Cryst. 25, 391–399]. Here, a new approach is presented for ultrafast calculation of atomistic diffuse-scattering patterns. It is shown that the FFT can actually be used to perform such calculations rapidly, and that a fast method based on sampling theory can be used to reduce high-frequency noise in the calculations. These algorithms are benchmarked using realistic examples of compositional, magnetic and displacive disorder. They accelerate the calculations by a factor of at least 102, making refinement of atomistic models to large diffuse-scattering volumes practical.

In a Model block, if the instance-specific value of a model argument has an anonymous structure type, an update diagram reports an error when there are multiple bus types that match that anonymous structure type.This bug exists in the following release(s):
R2020a

This bug has a workaround

Interested in Upgrading?

Simulink might produce an incorrect sorted order for a model that meets all of the following conditions:

• The model contains blocks from the SoC Blockset
• The Signal logging option is selected in the model configuration set
• Signals using asynchronous sample time are configured for logging

When the Signal Editor is saving data, the indicator that the save is occurring does not appear.  You might notice a delay when saving large data files.This bug exists in the following release(s):
R2020a

Interested in Upgrading?