Molecules form 2-D patterns never before observed: Experiments produce elusive 5-vertex tilings

Aug 08, 2013,phys.org

The 2-D tessellation pattern known as the "semiregular snub square tiling" stands out clearly in this image, which combines scanning tunneling microscopy with computer graphics. The pattern, observed in a surface architecture just one molecule thick, was formed by self-assembly of linear organic linkers, imaged as rods, and lanthanide cerium centers, visualized as bright protrusions. The area shown measures less than 25 nanometers across. Credit: Barth Lab, copyright TUM

Tessellation patterns that have fascinated mathematicians since Johannes Kepler worked out their systematics 400 years ago – and that more recently have caught the eye of both artists and crystallographers – can now be seen in the laboratory. They first took shape on a surface more perfectly two-dimensional than any sheet of writing paper, a single layer of atoms and molecules atop an atomically smooth substrate. Physicists coaxed these so-called Kepler tilings "onto the page" through guided self-assembly of nanostructures.

The experiments were carried out by postdoctoral researcher David Ecija, PhD candidate Jose Ignacio Urgel and colleagues in the Physics Department of Technische Universitaet Muenchen (TUM), in collaboration with scientists in Karlsruhe and Zurich. They reported their findings in the Proceedings of the National Academy of Sciences.

Results open a new line of research

Organic molecules equipped with functional groups to express distinct linkages to metal atoms were deposited onto a smooth silver substrate under vacuum conditions. Subsequently the organic layer on this platform was exposed to an atomic flux of the lanthanide cerium. At a certain ratio of cerium atoms to molecules, self-assembly produced a symmetrical complex 2-D pattern described originally by Kepler and known today as the snub square tiling. Clearly identifiable through scanning tunneling microscopy was a recurring, five-vertex connecting element less than one nanometer across, a cerium-ligand coordination unit.

That the snub square tiling pattern had never been fabricated and seen at the molecular level by exploiting self-assembly protocols was interesting in itself. Beyond that, the physicists explain, every new surface architecture could potentially open the way to novel physics and chemistry, and until now five-vertex structures have proven elusive. In particular, the fact that the lanthanide element cerium played such a key role marks this as the beginning of a new line of research.

This is the first time the TUM researchers – members of Prof. Johannes Barth's Institute for Molecular Nanoscience and Chemical Physics of Interfaces – have coordinated molecules with a lanthanide, and the first time anyone has done this in 2-D. "And lanthanides are special," David Ecija explains. "They have very intriguing optical, magnetic, and chemical properties that could be interesting for nanoscience, and possibly also for nanotechnology. Now we have a new playground for research with the lanthanides, and beyond."

More information: Five-vertex Archimedean surface tessellation by lanthanide-directed molecular self-assembly. David Ecija, Jose I. Urgel, Anthoula C. Papageorgiou, Sushobhan Joshi, Willi Auwaerter, Ari P. Seitsonen, Svetlana Klyatskaya, Mario Ruben, Sybille Fischer, Saranyan Vijayaraghavan, Joachim Reichert, and Johannes V. Barth. PNAS 2013 Vol. 110 No. 17, pp. 6678-6681. DOI: 10.1073/pnas.1222713110

Journal reference: Proceedings of the National Academy of Sciences

Raman pixel by pixel

New data processing protocol enables feature-based recognition of Surface-enhanced Raman spectra for intracellular molecule probing of biological targets. It relies on locally detecting the most relevant spectra to retrieve all data independently through indexing.

Raman spectroscopy provides molecular specificity through spectrally-resolved measurement of the inelastic scattering under monochromatic excitation. In the context of microscopy, it may serve as label-free cell imaging, providing structural information. However, the very low cross-section of Raman scattering requires long time exposures, which preclude imaging of cellular components with low concentrations. Surface-enhanced Raman spectroscopy (SERS), which relies on the local electromagnetic field enhancement produced by metallic nanostructures, is an approach to drastically increase the sensitivity of the Raman detection while retaining large amounts of spectral information. In cellular imaging, the measurement is usually performed on endocytosed nanostructures. However, the measured SERS signals vary strongly as they depend on excitation beam profile, local particle presence or aggregation and local molecular environment. Identifying and extracting spectra corresponding to molecules of interest within a SERS data set is very difficult.

Conventional data analysis methods look for global patterns in the data, whereas the single-molecule sensitivity of SERS can detect independent molecules in each pixel with little correlation between pixels. Nicolas Pavillon and his colleagues from Osaka University now explored different algorithmic methods to automatically discriminate spectra of interest in the measured field of view, without imposing assumptions on the self-similarity of the data. The proposed method relies on the indexing of the positions of relevant spectra, which are selected by the computation of a quality map.

The scientists proposed various criteria to compute spectra extraction, such as the spectral energy, the peak count per spectra, or the projection coefficients on SVD vectors. They assessed each criteria with simulated data and applied this approach to different types of measurements, such as dried Rhodamine 6G adsorbed on gold nanoparticles deposited on a glass substrate, and HeLa cells with endocytosed gold nanoparticles.

The tests with simulated data showed that various criteria can provide satisfactory results. The computation time could be tremendously decreased by discarding irrelevant pixels through a simple criterion based on the spectral energy, reducing the processing time to typically less than 10 seconds for a field of view on the order of 100 X 100 pixels.

The tests performed on Rhodamine 6G measurements demonstrated the validity of the proposed approach, where its known spectrum could be extracted automatically. The peak count criterion was the most suitable for most cases, as it detects various patterns without filtering out any curve which may only appear a single instance in the data set. Such single spectra may be critical important in a given SERS detection experiment. One main feature of the proposed approach is that its output is a localization map of the most relevant spectra in a measurement. The spatial information is retained, making it possible to trace back the positions of several spectra with identical properties, for instance. The optimized method was utilized to extract and classify the complex SERS response behavior of gold nanoparticles taken in live cells.

More information: N. Pavillon, K. Bando, K. Fujita, N. I. Smith, Feature-based recognition of Surface-enhanced Raman spectra for biological targets, J. Biophotonics 6(8),587-597 (2013); dx.doi.org/10.1002/jbio.201200181

Read more at: http://phys.org

INS Arihant reactor goes critical, submarine to start sea trials

India's first indigenously constructed nuclear powered submarine achieved a key milestone when its atomic reactor was switched on in Visakhapatnam last night. Top naval sources confirmed that the Arihant's reactor had "gone critical". With this, a key milestone in the submarine's 'harbour acceptance trials' have been completed. "We have waited a very long time for this," a senior naval official said.

A nuclear submarine armed with nuclear-tipped ballistic missiles is the third leg of the 'triad' of land, air and sea launched nuclear weapons envisaged by India's nuclear doctrine of 1998. The navy wants the submarine ready for deterrent patrol, or when it can sail out with nuclear weapons, by 2014.

The next key milestone will be when the 6000-tonne Arihant begins its sea trials and when its commanding officer Captain Sanjay Mahendru signals "underway on nuclear power", to mean that the submarine is sailing out self-powered. This is likely to be as early as next month when the monsoons subside.

Nuclear submarines use miniaturised atomic reactors to generate tremendous heat that boils water into saturated steam. This steam runs its submarine's propulsion and generates electricity. It is near-identical to a steam-powered turbine plant, except it uses nuclear energy.  

Since its launch in Vizag on 26 July 2009, the Arihant has spent over four years in harbour acceptance trials. Steam from the dockyard was generated and pumped into the submarine to test its major machinery and control systems. With the 80 Megawatt nuclear reactor now switched on, the submarine can generate its own power to test its systems.

The Arihant was launched in Vizag on 26 July 2009. Since then, the ballistic missile submarine (SSBN) has spent over four years in harbor trials that are meant to test whether all its machinery and control systems are functional.

During sea trials, the submarine will test all its parameters: maximum diving depth, speeds and sensors. "It's difficult to put a timeline to these trials because they are event-based and not time-based," says veteran submarine Vice Admiral Arun Kumar Singh (retired). "The crew of the Arihant will have to check off literally hundreds of parameters."

The sea trials will include the submerged test-firing of the 'B-05' ballistic missile. The Arihant can carry 12 of these nuclear-tipped missiles, each of which has a range of 700 km. Sections of a second submarine, to be named Aridaman are already at an advanced stage of outfitting at the Ship Building Centre (SBC) in Vizag. Sources indicate the submarine could be launched by next year. Sections of a third submarine are also under construction at the Larsen & Toubro's Hazira facility. The three SSBNs have been under construction under a secret navy-DRDO-Bhabha Atomic Research Centre (BARC) project called the 'Advanced Technology Vessel' (ATV) project. India's strategic plans call for a fleet of five nuclear powered attack submarines (SSN) and five ballistic missile submarines (SSBN), a goal that is unlikely to be achieved before 2025.

Read more at: http://indiatoday.intoday.in