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

Influence of grain size and composition, topology and excess free volume on the deformation behavior of Cu–Zr nanoglasses

• Daniel Şopu and
• Karsten Albe

Beilstein J. Nanotechnol. 2015, 6, 537–545, doi:10.3762/bjnano.6.56

• allowing for lateral contraction. The atomic scale deformation mechanisms were analyzed by visualizing the local atomic shear strain [23], calculated with the OVITO analysis and visualization software [24]. A quantitative interpretation of strain localization has been realized by using the strain

Dynamic force microscopy simulator (dForce): A tool for planning and understanding tapping and bimodal AFM experiments

• Horacio V. Guzman,
• Pablo D. Garcia and
• Ricardo Garcia

Beilstein J. Nanotechnol. 2015, 6, 369–379, doi:10.3762/bjnano.6.36

• operations such as data storing and visualization. For the simulations, it is important to choose appropriate values for the numerical integrator, in particular the number of periods, interval of periods (to calculate the steady state), and the average tip–surface distance step to guarantee that the

Synthesis, characterization, monolayer assembly and 2D lanthanide coordination of a linear terphenyl-di(propiolonitrile) linker on Ag(111)

• Zhi Chen,
• Svetlana Klyatskaya,
• José I. Urgel,
• David Écija,
• Olaf Fuhr,
• Willi Auwärter,
• Johannes V. Barth and
• Mario Ruben

Beilstein J. Nanotechnol. 2015, 6, 327–335, doi:10.3762/bjnano.6.31

• and Supporting Information File 1, Figure S2, respectively. Selected bond lengths of these molecules are listed in Supporting Information File 1, Tables S1–4. The visualization of molecule 2 highlights a conformation, in which the central phenyl ring is rotated out of the plane of the two peripheral

• -donor atom from the sterically hindering α-C–H group at the phenyl ring. ORTEP plot of compound 2. Ellipsoids were drawn at a 30% level of probability for all non-hydrogen atoms, indicating the numbering scheme (a); 3D visualization of the molecular conformation (view along direction a) (b); and the

Overview about the localization of nanoparticles in tissue and cellular context by different imaging techniques

• Anja Ostrowski,
• Daniel Nordmeyer,
• Alexander Boreham,
• Cornelia Holzhausen,
• Lars Mundhenk,
• Christina Graf,
• Martina C. Meinke,
• Annika Vogt,
• Sabrina Hadam,
• Jürgen Lademann,
• Eckart Rühl,
• Ulrike Alexiev and
• Achim D. Gruber

Beilstein J. Nanotechnol. 2015, 6, 263–280, doi:10.3762/bjnano.6.25

• their sites of interaction with living structures is essential to complete the picture. In this review we will describe and compare different imaging techniques for localizing inorganic as well as organic nanoparticles in tissues, cells and subcellular compartments. The visualization techniques include

• structured illumination, Raman microspectroscopy and X-ray microscopy. Importantly, all methodologies described allow for the simultaneous visualization of nanoparticles and evaluation of cell and tissue changes that are of prime interest for toxicopathologic studies. However, the different approaches vary

• , local and systemic NP distribution after administration and their final destination is indispensable. For an optimal pathological assessment, it is thus desirable to combine imaging techniques for the visualization of NP with techniques that are classically used for pathological examination of tissue

Kelvin probe force microscopy in liquid using electrochemical force microscopy

• Liam Collins,
• Stephen Jesse,
• Jason I. Kilpatrick,
• Alexander Tselev,
• M. Baris Okatan,
• Sergei V. Kalinin and
• Brian J. Rodriguez

Beilstein J. Nanotechnol. 2015, 6, 201–214, doi:10.3762/bjnano.6.19

• that within the first two PCs, isolated regions or hot spots demonstrate a different electrochemical behavior from their immediate surroundings. This highlights the usefulness of PCA for dimensionality reduction and qualitative visualization of spatial variations in the EcFM measurements. The

Multifunctional layered magnetic composites

• Maria Siglreitmeier,
• Baohu Wu,
• Tina Kollmann,
• Martin Neubauer,
• Gergely Nagy,
• Dietmar Schwahn,
• Vitaliy Pipich,
• Damien Faivre,
• Dirk Zahn,
• Andreas Fery and
• Helmut Cölfen

Beilstein J. Nanotechnol. 2015, 6, 134–148, doi:10.3762/bjnano.6.13

• Coomassie blue have been tested successfully in reference experiments (see Figure S3, Supporting Information File 1). For a better visualization of the stained areas in between the layers the light blue stained gelatin (see Supporting Information File 1) has been processed digitally. This means the green

Materials and characterization techniques for high-temperature polymer electrolyte membrane fuel cells

• Roswitha Zeis

Beilstein J. Nanotechnol. 2015, 6, 68–83, doi:10.3762/bjnano.6.8

• ]. Synchrotron X-ray radiography and tomography – acid distribution in HT-PEMFCs Synchrotron X-ray radiography had been successfully applied to LT-PEMFCs for visualization of liquid water profiles under different operating conditions. It was also straightforward to extend the same technique to the studies of

High-frequency multimodal atomic force microscopy

• Adrian P. Nievergelt,
• Jonathan D. Adams,
• Pascal D. Odermatt and
• Georg E. Fantner

Beilstein J. Nanotechnol. 2014, 5, 2459–2467, doi:10.3762/bjnano.5.255

• ; small cantilevers; Introduction The atomic force microscope (AFM) has developed into an extremely useful and versatile tool for nanometre-scale visualization and mechanical characterization. In recent years, several methods have been developed for simultaneous measurement of topographical and

Proinflammatory and cytotoxic response to nanoparticles in precision-cut lung slices

• Stephanie Hirn,
• Nadine Haberl,
• Kateryna Loza,
• Matthias Epple,
• Wolfgang G. Kreyling,
• Barbara Rothen-Rutishauser,
• Markus Rehberg and
• Fritz Krombach

Beilstein J. Nanotechnol. 2014, 5, 2440–2449, doi:10.3762/bjnano.5.253

• 24 h of incubation. Recently, our group has demonstrated that third harmonic generation (THG) microscopy, which is based on optical effects induced by specific inherent physical properties of a specimen, allows high-resolution label-free 3D visualization of cellular and tissue structures in intact

Low-cost plasmonic solar cells prepared by chemical spray pyrolysis

• Erki Kärber,
• Atanas Katerski,
• Ilona Oja Acik,
• Valdek Mikli,
• Arvo Mere,
• Ilmo Sildos and
• Malle Krunks

Beilstein J. Nanotechnol. 2014, 5, 2398–2402, doi:10.3762/bjnano.5.249

• is a unitless characteristic (EQE < 1) given by: where JSC(λ) (A·m−2) is the spectrally resolved short-circuit current of the solar cell, P(λ) (W·m−2) is the calibrated light intensity incident on the solar cell, and hc/qλ is the energy (eV) of a photon as function of wavelength λ. For visualization

Synthesis of radioactively labelled CdSe/CdS/ZnS quantum dots for in vivo experiments

• Gordon M. Stachowski,
• Christoph Bauer,
• Christian Waurisch,
• Denise Bargheer,
• Peter Nielsen,
• Jörg Heeren,
• Stephen G. Hickey and
• Alexander Eychmüller

Beilstein J. Nanotechnol. 2014, 5, 2383–2387, doi:10.3762/bjnano.5.247

• nanomaterials have been developed for applications in the field of bio-labelling. For the visualization of transport processes in the body, organs and cells, luminescent quantum dots (QDs) make for highly useful diagnostic tools. However, intercellular routes, bio-distribution, metabolism during degradation or

Interaction of dermatologically relevant nanoparticles with skin cells and skin

• Annika Vogt,
• Fiorenza Rancan,
• Sebastian Ahlberg,
• Berouz Nazemi,
• Chun Sik Choe,
• Maxim E. Darvin,
• Sabrina Hadam,
• Ulrike Blume-Peytavi,
• Kateryna Loza,
• Jörg Diendorf,
• Matthias Epple,
• Christina Graf,
• Eckart Rühl,
• Martina C. Meinke and
• Jürgen Lademann

Beilstein J. Nanotechnol. 2014, 5, 2363–2373, doi:10.3762/bjnano.5.245

• cellular uptake (a). Labeling of particles with fluorescein enabled the visualization of particle accumulation on skin sections and in hair follicle openings by using fluorescence microscopy (b). However, single particles on the skin surface could only be visualized after preparation of silica particles

Spectroscopic mapping and selective electronic tuning of molecular orbitals in phosphorescent organometallic complexes – a new strategy for OLED materials

• Pascal R. Ewen,
• Jan Sanning,
• Tobias Koch,
• Nikos L. Doltsinis,
• Cristian A. Strassert and
• Daniel Wegner

Beilstein J. Nanotechnol. 2014, 5, 2248–2258, doi:10.3762/bjnano.5.234

• triazole-Pt-triazole axis. This observation provides indications for an orbital shift of the HOMO–4 towards EF. Our analysis shows that the characterization and visualization of molecular orbitals by STS is not limited to entirely flat molecules, but can also be applied when bulky chemical groups are used

Electrical contacts to individual SWCNTs: A review

• Wei Liu,
• Christofer Hierold and
• Miroslav Haluska

Beilstein J. Nanotechnol. 2014, 5, 2202–2215, doi:10.3762/bjnano.5.229

• characteristics measured at different temperatures. (b) Arrhenius plot with linear fits for different gate biases, Vgs. For the better visualization, only the data points obtained for five different gate voltages: 4 V, −1.15 V, −1.25 V, −1.35 V, −4 V are shown. (c) Activation energy (Ea) as a function of gate

PVP-coated, negatively charged silver nanoparticles: A multi-center study of their physicochemical characteristics, cell culture and in vivo experiments

• Sebastian Ahlberg,
• Alexandra Antonopulos,
• Jörg Diendorf,
• Ralf Dringen,
• Matthias Epple,
• Rebekka Flöck,
• Wolfgang Goedecke,
• Christina Graf,
• Nadine Haberl,
• Jens Helmlinger,
• Fabian Herzog,
• Frederike Heuer,
• Stephanie Hirn,
• Christian Johannes,
• Stefanie Kittler,
• Manfred Köller,
• Katrin Korn,
• Wolfgang G. Kreyling,
• Fritz Krombach,
• Jürgen Lademann,
• Kateryna Loza,
• Eva M. Luther,
• Marcelina Malissek,
• Martina C. Meinke,
• Daniel Nordmeyer,
• Anne Pailliart,
• Jörg Raabe,
• Fiorenza Rancan,
• Barbara Rothen-Rutishauser,
• Eckart Rühl,
• Carsten Schleh,
• Andreas Seibel,
• Christina Sengstock,
• Lennart Treuel,
• Annika Vogt,
• Katrin Weber and
• Reinhard Zellner

Beilstein J. Nanotechnol. 2014, 5, 1944–1965, doi:10.3762/bjnano.5.205

• demonstrated for hMSC, primary T-cells, primary monocytes, and astrocytes. A visualization of particles inside cells is possible by X-ray microscopy, fluorescence microscopy, and combined FIB/SEM analysis. By staining organelles, their localization inside the cell can be additionally determined. While primary

The surface properties of nanoparticles determine the agglomeration state and the size of the particles under physiological conditions

• Christoph Bantz,
• Olga Koshkina,
• Thomas Lang,
• Hans-Joachim Galla,
• C. James Kirkpatrick,
• Roland H. Stauber and
• Michael Maskos

Beilstein J. Nanotechnol. 2014, 5, 1774–1786, doi:10.3762/bjnano.5.188

• film that covers the grid from crystallizing and leads to a fixation of the state in solution. The investigation under frozen–hydrated conditions allows the visualization of a particulate sample under physiological conditions in a state that is as close as possible to its native state in solution [21