Frog tongue surface microstructures: functional and evolutionary patterns

• Thomas Kleinteich and
• Stanislav N. Gorb

Beilstein J. Nanotechnol. 2016, 7, 893–903, doi:10.3762/bjnano.7.81

• , captured during micro-CT scanning, we reconstructed image stacks of virtual cross-sections through the entire specimen with the software NRecon (Bruker microCT, Kontich, Belgium). These image stacks were then exported as 16 bit TIFF files, which we analyzed and visualized with the 3D visualization software

Direct formation of gold nanorods on surfaces using polymer-immobilised gold seeds

• Majid K. Abyaneh,
• Pietro Parisse and
• Loredana Casalis

Beilstein J. Nanotechnol. 2016, 7, 809–816, doi:10.3762/bjnano.7.72

• that gold particles are distributed well at the surface of PMMA with mean particles size of 150 nm for P1-20 and 80 nm for P2-20 nanocomposites. Gwyddion, a multi-platform modular free software [37] for visualization and analysis of data from scanning probe microscopes has been used to process the AFM

Hierarchical coassembly of DNA–triptycene hybrid molecular building blocks and zinc protoporphyrin IX

• Rina Kumari,
• Sumit Singh,
• Mohan Monisha,
• Sourav Bhowmick,
• Anindya Roy,
• Neeladri Das and
• Prolay Das

Beilstein J. Nanotechnol. 2016, 7, 697–707, doi:10.3762/bjnano.7.62

• ) in suitable dialysis buffer to exclude small molecule impurities. Denaturing PAGE (20%) was used for visualization and purification of the DNA–TPA conjugates. The desired bands were excised from the PAGE and the DNA–TPA conjugates were purified using extraction buffer and ethanol washing. These

• AFM imaging was employed for the direct visualization of the self-assembled (S1)3–TPA and (S2)3–TPA hybrid conjugates. AFM images show the formation of extended nanofibers through the self-assembly into hierarchically organized structures of DNA–TPA units, when hybridized in the presence of Zn PpIX

Hemolysin coregulated protein 1 as a molecular gluing unit for the assembly of nanoparticle hybrid structures

• Tuan Anh Pham,
• Andreas Schreiber,
• Elena V. Sturm (née Rosseeva),
• Stefan Schiller and
• Helmut Cölfen

Beilstein J. Nanotechnol. 2016, 7, 351–363, doi:10.3762/bjnano.7.32

• elongation of the NPs assembly structures. The decrease in the absorbance between 17 h and 22 h is due to the slight precipitation of large Au Hcp1_cys3 structures. For better visualization of the different Au NP architectures, a cryo-TEM investigation was conducted for 3 samples at 7.5 h, 17 h and 22 h, as

• analysis of the HRTEM images were realized by means of the Digital Micrograph (Gatan, USA) and JEMS (version: 3.5930U2010) software. Visualization of the magnetite crystal models was performed with the VESTA 3 software. The magnetic measurement was accomplished with a SQUID magnetometer, type MPMS XL5 from

Surface coating affects behavior of metallic nanoparticles in a biological environment

• Darija Domazet Jurašin,
• Marija Ćurlin,
• Ivona Capjak,
• Tea Crnković,
• Marija Lovrić,
• Michal Babič,
• Daniel Horák,
• Ivana Vinković Vrček and
• Srećko Gajović

Beilstein J. Nanotechnol. 2016, 7, 246–262, doi:10.3762/bjnano.7.23

• ]. Analytical methods As described in [49], the size and charge of NPs were measured by dynamic (DLS) and electrophoretic light scattering (ELS), respectively, using Zetasizer Nano ZS (Malvern, UK). Visualization of NPs were done using a transmission electron microscope (TEM, Zeiss 902A). Total silver

Plasticity-mediated collapse and recrystallization in hollow copper nanowires: a molecular dynamics simulation

• Amlan Dutta,
• Arup Kumar Raychaudhuri and
• Tanusri Saha-Dasgupta

Beilstein J. Nanotechnol. 2016, 7, 228–235, doi:10.3762/bjnano.7.21

• implemented in the large-scale atomic/molecular massively parallel simulator (LAMMPS) developed at the Sandia National Laboratory [23], while the OVITO [24] visualization tool is employed to view the atomic configuration of the nanowire. Results and Discussion Morphological evolution We start with the

Effects of electronic coupling and electrostatic potential on charge transport in carbon-based molecular electronic junctions

• Richard L. McCreery

Beilstein J. Nanotechnol. 2016, 7, 32–46, doi:10.3762/bjnano.7.4

• experimental results where possible. Experimental Common DFT procedures were used, in part to maximize availability to potential users. Gaussian09 version 9.5 (revision D.01 Windows 64 bit) and Gaussview 5.0.9 software packages were used for all calculations and visualization of molecular structures and

• of Gaussian09 for Windows. Orbital visualization with Gaussview used the default isovalue of 0.02, which is commonly used to represent the majority of the electron density. Predictions of charge transfer within model molecules used the Mulliken charges calculated during the DFT analysis. There is

Controlled graphene oxide assembly on silver nanocube monolayers for SERS detection: dependence on nanocube packing procedure

• Martina Banchelli,
• Bruno Tiribilli,
• Roberto Pini,
• Luigi Dei,
• Paolo Matteini and
• Gabriella Caminati

Beilstein J. Nanotechnol. 2016, 7, 9–21, doi:10.3762/bjnano.7.2

• rendering was performed using Gwyddion 2.30 SPM data visualization tool (http://gwyddion.net/). UV–vis measurements. UV–vis spectra of the nanocube suspension in ethanol and of monolayers deposited on quartz substrates were recorded using a Jasco V-6 UV–vis–NIR spectrophotometer with 1 nm slit and 200 nm

Plasma fluorination of vertically aligned carbon nanotubes: functionalization and thermal stability

• Claudia Struzzi,
• Mattia Scardamaglia,
• Axel Hemberg,
• Luca Petaccia,
• Jean-François Colomer,
• Rony Snyders and
• Carla Bittencourt

Beilstein J. Nanotechnol. 2015, 6, 2263–2271, doi:10.3762/bjnano.6.232

• grafted species, we first analyze the C 1s, F 1s and O 1s core levels in the XPS spectra acquired after fluorination (labeled RT in the figure). Once the Shirley-type background was subtracted, the C 1s intensities in Figure 1a were normalized to the maximum value, allowing a direct visualization of the

• . Temperature-dependent XPS analysis of functionalized vCNTs. (a) C 1s spectra acquired as a function of heating temperature. The C 1s spectrum recorded just after the fluorination is labelled RT, the pristine spectrum is the bottom curve. The spectra were normalized and stacked for better visualization of

Virtual reality visual feedback for hand-controlled scanning probe microscopy manipulation of single molecules

• Philipp Leinen,
• Matthew F. B. Green,
• Taner Esat,
• Christian Wagner,
• F. Stefan Tautz and
• Ruslan Temirov

Beilstein J. Nanotechnol. 2015, 6, 2148–2153, doi:10.3762/bjnano.6.220

• the analysis of manipulation trajectory data much simpler. It would also help to transfer knowledge between different users and/or experiments, thus facilitating systematic learning during which manipulation protocols are refined and corrected in multiple steps. Visualization of the manipulation

Near-field visualization of plasmonic lenses: an overall analysis of characterization errors

• Jing Wang,
• Yongqi Fu,
• Zongwei Xu and
• Fengzhou Fang

Beilstein J. Nanotechnol. 2015, 6, 2069–2077, doi:10.3762/bjnano.6.211

• University, 300072, P. R. China 10.3762/bjnano.6.211 Abstract Many factors influence the near-field visualization of plasmonic structures that are based on perforated elliptical slits. Here, characterization errors are experimentally analyzed in detail from both fabrication and measurement points of view

Simulation of thermal stress and buckling instability in Si/Ge and Ge/Si core/shell nanowires

• Suvankar Das,
• Amitava Moitra,
• Mishreyee Bhattacharya and
• Amlan Dutta

Beilstein J. Nanotechnol. 2015, 6, 1970–1977, doi:10.3762/bjnano.6.201

• ++ [28] have been employed for performing the simulations. Wherever required, the crystal structure was viewed using the OVITO [29] visualization tool. Measurement of thermal stress As mentioned in the previous section, CSNWs with different core diameters have been simulated for a fixed outer diameter of

Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

• Christina M. Powers,
• Karmann A. Mills,
• Stephanie A. Morris,
• Fred Klaessig,
• Sharon Gaheen,
• Nastassja Lewinski and
• Christine Ogilvie Hendren

Beilstein J. Nanotechnol. 2015, 6, 1860–1871, doi:10.3762/bjnano.6.189

• hold and organize large quantities of data has increased data availability to scientists, engineers, and others in the scientific community. Greater access to data repositories, data sharing platforms, and data visualization tools creates opportunities to compare and integrate information across a

Imaging of carbon nanomembranes with helium ion microscopy

• André Beyer,
• Henning Vieker,
• Robin Klett,
• Hanno Meyer zu Theenhausen,
• Polina Angelova and
• Armin Gölzhäuser

Beilstein J. Nanotechnol. 2015, 6, 1712–1720, doi:10.3762/bjnano.6.175

• range of magnification of a HIM allows for the visualization of TEM grids by recording a single HIM image. The effects of charging as well as background features were discussed. We demonstrated that the sample holder under the CNM surface can induce image artefacts, which are avoidable by mounting the

Analysis of soil bacteria susceptibility to manufactured nanoparticles via data visualization

• Rong Liu,
• Yuan Ge,
• Patricia A. Holden and
• Yoram Cohen

Beilstein J. Nanotechnol. 2015, 6, 1635–1651, doi:10.3762/bjnano.6.166

• manufactured nanoparticles (MNPs) on soil bacterial communities for different exposure periods and MNP doses was explored via data visualization techniques. Interrelationships between MNP treatments and responses of bacterial taxa were illustrated by bipartite graphs, allowing fast identification of important

• communities exposed to MNPs and thus evaluate the potential for environmental impacts. Keywords: environmental impact; manufactured nanoparticles; nanoinformatics; soil bacteria; visualization; Introduction Manufactured nanoparticles (MNPs) are now routinely used in numerous products and applications due to

• datasets of high dimensionality (e.g., over 105 soil DNA sequences extracted for a treatment) [18][19]. Therefore, advanced data exploration/visualization approaches are required to allow researchers to design subsequent confirmatory experiments and/or perform detailed statistical analyses. Graphical

The eNanoMapper database for nanomaterial safety information

• Nina Jeliazkova,
• Charalampos Chomenidis,
• Philip Doganis,
• Bengt Fadeel,
• Roland Grafström,
• Barry Hardy,
• Janna Hastings,
• Markus Hegi,
• Vedrin Jeliazkov,
• Nikolay Kochev,
• Pekka Kohonen,
• Cristian R. Munteanu,
• Haralambos Sarimveis,
• Bart Smeets,
• Pantelis Sopasakis,
• Georgia Tsiliki,
• David Vorgrimmler and
• Egon Willighagen

Beilstein J. Nanotechnol. 2015, 6, 1609–1634, doi:10.3762/bjnano.6.165

How decision analysis can further nanoinformatics

• Matthew E. Bates,
• Sabrina Larkin,
• Jeffrey M. Keisler and
• Igor Linkov

Beilstein J. Nanotechnol. 2015, 6, 1594–1600, doi:10.3762/bjnano.6.162

• techniques of multicriteria decision analysis (MCDA), value of information (VOI), weight of evidence (WOE), and portfolio decision analysis (PDA) can bridge the gap from current data collection and visualization efforts to present information relevant to specific decision needs. Decision analytic and

• way of supplementing data intensive visualization methods for the goals of risk management [5][13][14]. For a successful nanoinformatics enterprise, top-down decision analytic tools and bottom-up data management methods need to be integrated. Decision analytic tools are able to bridge the gap between

• , sorting, and visualization of data, but the top-down identification of decision-relevant information. The four tools described here can accomplish both facets of that goal, and overall, provide capability to expand the reach of current nanoinformatics tools. Part of this expansion should be accomplished

Atomic force microscopy as analytical tool to study physico-mechanical properties of intestinal cells

• Christa Schimpel,
• Oliver Werzer,
• Eleonore Fröhlich,
• Gerd Leitinger,
• Markus Absenger-Novak,
• Birgit Teubl,
• Andreas Zimmer and
• Eva Roblegg

Beilstein J. Nanotechnol. 2015, 6, 1457–1466, doi:10.3762/bjnano.6.151

• . Organization of F-actin networks were investigated via phalloidin labeling and visualization was performed with confocal laser scanning fluorescence microscopy (CLSM) and scanning electron microscopy (SEM). The results of these various experimental techniques revealed significant differences in the

• hydrated and flexible cells, measurements were performed in a semi-dry state as demonstrated elsewhere [37][38]. Tetramethylrhodamine (TRITC)-phalloidin staining Visualization of the cytoskeletal F-actin network was performed using TRITC-phalloidin (Invitrogen GmbH, Darmstadt, Germany) in a similar manner

Using natural language processing techniques to inform research on nanotechnology

• Nastassja A. Lewinski and
• Bridget T. McInnes

Beilstein J. Nanotechnol. 2015, 6, 1439–1449, doi:10.3762/bjnano.6.149

• frequency. The highly frequent noun phrases are used as topics by the clusterer as well as to support visualization of the search results in the topic mapper. The proposed Patent analyzer supports the basic analysis, content map analysis and citation network analysis. The basic analysis contains traditional

• patent analysis information such as number of patents based on country, institution or technology field. The content map allows for the concepts from multiple patents to be viewed and analyzed over time. The patent citation network allows for the visualization of links between entities such as countries

• provides search capability, visualization and analytical tools to analyze nanotechnology patents from the United States Patent and Trademark Office (USPTO), European Patent Office (EPO), Japan Patent Office (JPO), and grants from the U.S. National Science Foundation (NSF). It includes basic statistics

DNA–melamine hybrid molecules: from self-assembly to nanostructures

• Rina Kumari,
• Shib Shankar Banerjee,
• Anil K. Bhowmick and
• Prolay Das

Beilstein J. Nanotechnol. 2015, 6, 1432–1438, doi:10.3762/bjnano.6.148

• 300 bp (with respect to the ladder) indicates that few network arrays may be smaller than the linear counterpart in terms of DNA content. The assembly of di-branched conjugates moves in the gel, albeit with a much slower gel mobility than the normal R1–R2 oligomer duplex. For direct visualization of

Influence of the shape and surface oxidation in the magnetization reversal of thin iron nanowires grown by focused electron beam induced deposition

• Luis A. Rodríguez,
• Lorenz Deen,
• Rosa Córdoba,
• César Magén,
• Etienne Snoeck,
• Bert Koopmans and
• José M. De Teresa

Beilstein J. Nanotechnol. 2015, 6, 1319–1331, doi:10.3762/bjnano.6.136

• thicknesses). In principle, a change in the magnetization reversal mode is a good candidate to produce a dependence of HC with thickness presenting a maximum. The micromagnetic simulations in the Fe nanowires permit a direct visualization of the magnetic configuration during magnetization reversal, which

PLGA nanoparticles as a platform for vitamin D-based cancer therapy

• Maria J. Ramalho,
• Joana A. Loureiro,
• Bárbara Gomes,
• Manuela F. Frasco,
• Manuel A. N. Coelho and
• M. Carmo Pereira

Beilstein J. Nanotechnol. 2015, 6, 1306–1318, doi:10.3762/bjnano.6.135

• for lysosomes, despite not having been treated with C6. This fact is justified because both cell lines exhibited autofluorescence in the same emission spectrum as C6 and lysotracker. Lung carcinoma cells did not exhibit this intense autofluorescence, therefore allowing the visualization of the NP

• TEM visualization [42]. Vitamin loading capacity (LC) and the encapsulation efficiency (EE) of PLGA NPs were further indirectly determined. For the quantification of the free vitamin, the NP suspension was centrifuged (14500 rpm, 30 min), and the supernatant analyzed. This step was conducted before

• entrapped in the NP matrix does not leach during the experiment, allowing a fluorescent visualization of the uptake of PLGA NPs [30]. After the incubation period, the cells were rinsed with PBS and fixed using 4% paraformaldehyde for 15 min. The cells were then treated with LysoTracker® Red (a marker of

Electrical characterization of single molecule and Langmuir–Blodgett monomolecular films of a pyridine-terminated oligo(phenylene-ethynylene) derivative

• Henrry M. Osorio,
• Santiago Martín,
• María Carmen López,
• Santiago Marqués-González,
• Simon J. Higgins,
• Richard J. Nichols,
• Paul J. Low and
• Pilar Cea

Beilstein J. Nanotechnol. 2015, 6, 1145–1157, doi:10.3762/bjnano.6.116

• ·molecule−1·min−1. Under these experimental conditions, the isotherms were highly reproducible. A commercial mini-Brewster angle microscope (mini-BAM) from Nanofilm Technologie GmbH, Göttingen, Germany, was employed for the direct visualization of the monolayers at the air–water interface and a commercial

Automatic morphological characterization of nanobubbles with a novel image segmentation method and its application in the study of nanobubble coalescence

• Yuliang Wang,
• Huimin Wang,
• Shusheng Bi and
• Bin Guo

Beilstein J. Nanotechnol. 2015, 6, 952–963, doi:10.3762/bjnano.6.98

• ][9], rapid cryofixation/freeze fracturing [10], neutron reflectometry [11], X-ray reflectivity measurements [12], spectroscopic methods [13], total internal reflection fluorescence excitation [14], and even using an optical visualization approach with a limited resolution [14][15]. NBs have shown

Simulation tool for assessing the release and environmental distribution of nanomaterials

• Haoyang Haven Liu,
• Muhammad Bilal,
• Anastasiya Lazareva,
• Arturo Keller and
• Yoram Cohen

Beilstein J. Nanotechnol. 2015, 6, 938–951, doi:10.3762/bjnano.6.97

• interface for scenario design and results visualization, (2) MendNano, which is a fate and transport model for estimating environmental ENM concentrations, (3) lifecycle environmental assessment for release of nanomaterials (LearNano) model for estimating ENM release rates, (4) a parameter database, and (5

• . Based on the designed scenario, MendNano computes the multimedia mass distribution of ENMs given a release rate and/or initial concentration of the selected ENMs in one or more of the environmental compartments. Simulation results are then graphically represented via visualization modules as well as

• (Supporting Information File 1, Equations S2–S4). Implementation of the LearNano model includes user guidance and visualization tools for data input and simulation results, a model solver, and a parameter database. The analysis scenario (i.e., a given combination of ENM, region, and application(s)) is