An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology

• Richard L. Marchese Robinson,
• Mark T. D. Cronin,
• Andrea-Nicole Richarz and
• Robert Rallo

Beilstein J. Nanotechnol. 2015, 6, 1978–1999, doi:10.3762/bjnano.6.202

• standardised, electronic format that facilitates meaningful exchange of information between different researchers, submission to (web-based) searchable databases, integration with other electronic data resources and analysis via appropriate (modelling) software [9][16][17][18]. This could entail directly

• and/or configuration files do not need to be developed for each new dataset) for the purposes of computational modelling. They also facilitate integration between datasets, partly due to the ease of programmatic analysis and in part because standardisation makes it clearer when two items of (meta)data

• in distinct datasets are related. Data integration within searchable databases supports computational modelling via enabling data from multiple sources to be combined, in principle, for more robust, generalisable analysis and via facilitating the identification of data which are relevant to the needs

Two-phase equilibrium states in individual Cu–Ni nanoparticles: size, depletion and hysteresis effects

• Aram S. Shirinyan

Beilstein J. Nanotechnol. 2015, 6, 1811–1820, doi:10.3762/bjnano.6.185

• , Ukraine) for the help in modelling.

NanoE-Tox: New and in-depth database concerning ecotoxicity of nanomaterials

• Katre Juganson,
• Angela Ivask,
• Irina Blinova,
• Monika Mortimer and
• Anne Kahru

Beilstein J. Nanotechnol. 2015, 6, 1788–1804, doi:10.3762/bjnano.6.183

• regulatory decision making while minimising time-consuming and costly in vivo studies [9]. In addition to high-throughput screening tests, modelling can provide information for rapid assessment of the toxicity mechanisms of ENMs [10]. For instance, models based on dynamic energy budget (DEB) theory have been

• tests for evaluation of ENM related hazards [13]. Currently, there are a few QNAR modelling studies available for NPs [51]. However, these studies are based on relatively limited set of experimental data and therefore, applicable only for a small range of ENMs and organisms. Thus, in order to create a

• model with reasonable predictive power, several physico-chemical properties as well as data on a variety of NPs have to be included into the modelling to correlate the properties with toxic effects [25]. To evaluate whether the data in NanoE-Tox database might be suitable for (QNAR-)modelling, we

Atomic scale interface design and characterisation

• Carla Bittencourt,
• Chris Ewels and
• Arkady V. Krasheninnikov

Beilstein J. Nanotechnol. 2015, 6, 1708–1711, doi:10.3762/bjnano.6.174

• metal-nanostructures contacts, development of new tools for characterization and manipulation nanostructures, atomic-scale quantum chemical modelling, and integration in potential devices. All of these are reflected in the 26 reviews presented here. They appropriately demonstrate the richness and

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

• visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and

• interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure–activity relationships for nanomaterials (NanoQSAR). Keywords: database; EU NanoSafety Cluster; nanoinformatics; nanomaterials; nanomaterials ontology; NanoQSAR; safety

• corresponding protocols and data sources should be added, where available. Clear visualisation of nanomaterials that goes beyond just structural formulae should be available, in order to make the data less abstract biologists with less knowledge about nanomaterials. Support for data analysis The modelling

Influence of surface chemical properties on the toxicity of engineered zinc oxide nanoparticles to embryonic zebrafish

• Zitao Zhou,
• Jino Son,
• Bryan Harper,
• Zheng Zhou and
• Stacey Harper

Beilstein J. Nanotechnol. 2015, 6, 1568–1579, doi:10.3762/bjnano.6.160

• estimation; modelling; nanomaterials; nanotechnology; toxicology; Introduction Accelerated advancements in nanotechnology and nanoscience have found applications in a variety of scientific fields, leading to a rapid increase in the types of engineered nanoparticles on the market. In particular, zinc oxide

Electrical properties and mechanical stability of anchoring groups for single-molecule electronics

• Riccardo Frisenda,
• Simge Tarkuç,
• Elena Galán,
• Mickael L. Perrin,
• Rienk Eelkema,
• Ferdinand C. Grozema and
• Herre S. J. van der Zant

Beilstein J. Nanotechnol. 2015, 6, 1558–1567, doi:10.3762/bjnano.6.159

• -breaking regime, giving rise to more variability in the probed conductance of the self-breaking experiment. To gain more insight in the different anchoring geometry and the observed variations in lifetimes and conductance values, we have performed DFT calculations by modelling the molecule of interest in

Continuum models of focused electron beam induced processing

• Milos Toth,
• Charlene Lobo,
• Vinzenz Friedli,
• Aleksandra Szkudlarek and
• Ivo Utke

Beilstein J. Nanotechnol. 2015, 6, 1518–1540, doi:10.3762/bjnano.6.157

• . Inclusion of diffusion in continuum FEBIP models adds a layer of complexity to the modelling and to interpretation of the model outputs. It is necessary only if diffusion is a major contribution to the growth rate. We will discuss models that incorporate diffusion in a self-contained section below, but will

Scalable, high performance, enzymatic cathodes based on nanoimprint lithography

• Dmitry Pankratov,
• Richard Sundberg,
• Javier Sotres,
• Dmitry B. Suyatin,
• Ivan Maximov,
• Sergey Shleev and
• Lars Montelius

Beilstein J. Nanotechnol. 2015, 6, 1377–1384, doi:10.3762/bjnano.6.142

• (k0) and apparent bio-electrocatalytic constants (kcatapp, i.e., kcat for BOx adsorbed on a Au surface), were calculated based on mathematical modelling (modelled vs experimental curves are presented in Supporting Information File 1, Figure S8). k0 values for both BOx/Au and BOx/NIL/Au electrodes were

• -electrochemical investigations and modelling. Acknowledgements The authors thank Amano Enzyme, Inc. for the Amano 3 preparation of Myrothecium verrucaria bilirubin oxidase. Technical help from A. Kvennefors and M. Graczyk is highly appreciated. This work has been financially supported by the Swedish Research

Surface excitations in the modelling of electron transport for electron-beam-induced deposition experiments

• Francesc Salvat-Pujol,
• Roser Valentí and
• Wolfgang S. Werner

Beilstein J. Nanotechnol. 2015, 6, 1260–1267, doi:10.3762/bjnano.6.129

• /bjnano.6.129 Abstract The aim of the present overview article is to raise awareness of an essential aspect that is usually not accounted for in the modelling of electron transport for focused-electron-beam-induced deposition (FEBID) of nanostructures: Surface excitations are on the one hand responsible

• present a general perspective of recent works on the subject of surface excitations and on low-energy electron transport, highlighting the most relevant aspects for the modelling of electron transport in FEBID simulations. Keywords: focused-electron-beam-induced deposition (FEBID); Monte Carlo simulation

• of electron transport; surface excitations; secondary-electron emission; Introduction An accurate modelling of the energy losses of electrons traversing a solid surface is instrumental for a quantitative understanding of a series of techniques exploiting transmitted, reflected, or emitted electrons

Probing fibronectin–antibody interactions using AFM force spectroscopy and lateral force microscopy

• Andrzej J. Kulik,
• Małgorzata Lekka,
• Kyumin Lee,
• Grazyna Pyka-Fościak and
• Wieslaw Nowak

Beilstein J. Nanotechnol. 2015, 6, 1164–1175, doi:10.3762/bjnano.6.118

• force spectroscopy or lateral force spectroscopy). This likely indicates some differences in the vertical and lateral unbinding scenarios. The computer modelling of a similar unbinding event in an MCP1-IgG antibody complex showed that lateral unbinding forces are about 30% lower than those

Electronic interaction in composites of a conjugated polymer and carbon nanotubes: first-principles calculation and photophysical approaches

• Florian Massuyeau,
• Jany Wéry,
• Jean-Luc Duvail,
• Serge Lefrant,
• Abu Yaya,
• Chris Ewels and
• Eric Faulques

Beilstein J. Nanotechnol. 2015, 6, 1138–1144, doi:10.3762/bjnano.6.115

• to LDA to some extent counteracts what would otherwise be an overestimation in the modelling of the band gap of the experimental tubes. Specifically, we note that our calculated bandgap for the (7,0) nanotube of 0.08 eV is considerably underestimated compared to experiments, due to the well-known

Experimental determination of the light-trapping-induced absorption enhancement factor in DSSC photoanodes

• Serena Gagliardi and
• Mauro Falconieri

Beilstein J. Nanotechnol. 2015, 6, 886–892, doi:10.3762/bjnano.6.91

• ) AM1.5 illumination, provided by a class A solar simulator (Wacom). Modelling In the zero-order approximation, the only optical phenomenon occurring in the sensitized titania layer is the light absorption by the dye molecules. In this case, for a given dye composition of known molar absorptivity, the

• is based on the comparison of the absorbed light fraction as experimentally measured in the electrode with the absorbance of the dye loaded on the titania. Modelling The specific surface area and the N719 dye load in a 6.5 μm thick electrode, with a surface area of 1 cm2, were obtained using the

• method described in the Modelling part of the Experimental section and are reported in Figure 4 as a function of the titania nanoparticle diameter. The nanoparticles contained in the titania paste are 15–20 nm in radius, according to the vendor specifications. This corresponds to an average dye content

Electromagnetic enhancement of ordered silver nanorod arrays evaluated by discrete dipole approximation

• Guoke Wei,
• Jinliang Wang and
• Yu Chen

Beilstein J. Nanotechnol. 2015, 6, 686–696, doi:10.3762/bjnano.6.69

• array arranged in a regular hexagonal pattern. Gap sizes and standard deviations in the target units used in modelling the AgNR 2D random arrays. Acknowledgements G. W. acknowledges financial support from the China Scholarship Council (CSC). Simulation results were obtained by using the EPSRC funded

Influence of size, shape and core–shell interface on surface plasmon resonance in Ag and Ag@MgO nanoparticle films deposited on Si/SiO_x

• Sergio D’Addato,
• Daniele Pinotti,
• Maria Chiara Spadaro,
• Guido Paolicelli,
• Vincenzo Grillo,
• Sergio Valeri,
• Luca Pasquali,
• Luca Bergamini and
• Stefano Corni

Beilstein J. Nanotechnol. 2015, 6, 404–413, doi:10.3762/bjnano.6.40

• of the experimental data [16][17][18], also requires this detailed characterization information as input. In fact, electromagnetic modelling requires knowledge of the NP shape, size and arrangement of the NPs to provide results comparable with experiments. In this work, the results of joint

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

• analytical modelling [61]. Conclusion The feasibility of force-based electrostatic and electrochemical measurements was investigated in liquid by probing the bias- and time-dependent response to a biased probe. The implementation of conventional closed loop-KPFM has been determined to be possible only when

Tunable light filtering by a Bragg mirror/heavily doped semiconducting nanocrystal composite

• Ilka Kriegel and
• Francesco Scotognella

Beilstein J. Nanotechnol. 2015, 6, 193–200, doi:10.3762/bjnano.6.18

• modulation of the transmittance of solar energy [34][35][36][37]. In this study, we propose a tunable filter based on photonic crystals (Bragg mirrors) coupled to heavily doped semiconductor NCs with plasmonic absorption properties. We report the modelling of a Bragg mirror coupled to a dispersion of

• −xSe NCs or an ITO NC film, sketched in dark red. In the following, we demonstrate the modelling of the transmission properties of the proposed device. We first consider the plasmonic absorption properties of the heavily doped NC component and demonstrate its modulated absorption properties through an

Localized surface plasmon resonances in nanostructures to enhance nonlinear vibrational spectroscopies: towards an astonishing molecular sensitivity

• Dan Lis and
• Francesca Cecchet

Beilstein J. Nanotechnol. 2014, 5, 2275–2292, doi:10.3762/bjnano.5.237

• -resonant SFG signal of both the silver film and the LB monolayer. In particular, they highlighted that the SFG signal from the LB film was increased by about 25% and was angularly shifted by comparison with the pure silver film. Combining their experimental results with theoretical calculations modelling

Hybrid spin-crossover nanostructures

• Carlos M. Quintero,
• Gautier Félix,
• Iurii Suleimanov,
• José Sánchez Costa,
• Gábor Molnár,
• Lionel Salmon,
• William Nicolazzi and
• Azzedine Bousseksou

Beilstein J. Nanotechnol. 2014, 5, 2230–2239, doi:10.3762/bjnano.5.232

• Narbonne, 31077 Toulouse, France Department of Chemistry, National Taras Shevchenko University of Kiev, 62 Volodymyrska St. 01601, Ukraine 10.3762/bjnano.5.232 Abstract This review reports on the recent progress in the synthesis, modelling and application of hybrid spin-crossover materials, including core

• the SCO properties and the physical properties (magnetic, photonic, charge transport, etc.) of the surrounding matter. The present review constitutes an overview of these systems including their synthesis, theoretical modelling and future possible technological applications. Indeed, a recent strategy

• nano-objects: towards modelling hybrid systems A reduction in dimensions leads to an inevitable change in the bistability phenomenon for SCO nano-objects [36]. This idea has been experimentally confirmed with the study of spin-crossover nanoparticles [2][3][4][5]. The main observations include the

Optical properties and electrical transport of thin films of terbium(III) bis(phthalocyanine) on cobalt

• Peter Robaschik,
• Pablo F. Siles,
• Daniel Bülz,
• Peter Richter,
• Manuel Monecke,
• Michael Fronk,
• Svetlana Klyatskaya,
• Daniel Grimm,
• Oliver G. Schmidt,
• Mario Ruben,
• Dietrich R. T. Zahn and
• Georgeta Salvan

Beilstein J. Nanotechnol. 2014, 5, 2070–2078, doi:10.3762/bjnano.5.215

• granted in both cases, since the condition is that the amount of injected carriers is low compared to that of thermally generated carriers. Once the modelling of the current density characteristics for TbPc2 thin films is derived from cs-AFM measurements, it is necessary to account for the electrode

• geometry in the AFM electrical experiments (AFM probe geometry). We apply the modelling approach described in [26], as we use the same AFM probe geometry. Here, the system is treated as an intermediate case between a situation with infinite plane–plane electrodes and a situation with point–plane electrodes

Carbon-based smart nanomaterials in biomedicine and neuroengineering

• Antonina M. Monaco and
• Michele Giugliano

Beilstein J. Nanotechnol. 2014, 5, 1849–1863, doi:10.3762/bjnano.5.196

• or nanoscale roughness (Figure 3c). Moreover, in the same work, mathematical modelling and electrophysiology were used to probe a contingent connection between the effects observed at single-neuron level and those detected at the level of neuronal networks, leading to the speculation that the tight

Silicon and germanium nanocrystals: properties and characterization

• Ivana Capan,
• Alexandra Carvalho and
• José Coutinho

Beilstein J. Nanotechnol. 2014, 5, 1787–1794, doi:10.3762/bjnano.5.189

• regard to growth, characterization and modeling of silicon and germanium nanocrystals and related materials. Keywords: characterization; germanium; modelling; nanocrystals; silicon; Review I Introduction Nanocrystals (NCs) have emerged as one of the preferred ways to control quantum phenomena at the

• MBE. From the experimental point of view, the synthesis of free-standing NCs will not be covered within this review. However, those issues are visited in Section III of this paper, which deals with the first principles modelling of the NCs. II.1 Magnetron co-sputtering This is basically a technique

Controlling the dispersion of supported polyoxometalate heterogeneous catalysts: impact of hybridization and the role of hydrophilicity–hydrophobicity balance and supramolecularity

• Gijo Raj,
• Colas Swalus,
• Eglantine Arendt,
• Pierre Eloy,
• Michel Devillers and
• Eric M. Gaigneaux

Beilstein J. Nanotechnol. 2014, 5, 1749–1759, doi:10.3762/bjnano.5.185

• , Supporting Information File 1). Molecular modelling by Polarz et al. [19] show that the DODA–POM hybrids consist of defined units, in which the cationic surfactant has all protons replaced and is strongly attached to the POM cluster. However, a close examination of our AFM images shows that the nanorods are

Current state of laser synthesis of metal and alloy nanoparticles as ligand-free reference materials for nano-toxicological assays

• Christoph Rehbock,
• Jurij Jakobi,
• Lisa Gamrad,
• Selina van der Meer,
• Daniela Tiedemann,
• Ulrike Taylor,
• Wilfried Kues,
• Detlef Rath and
• Stephan Barcikowski

Beilstein J. Nanotechnol. 2014, 5, 1523–1541, doi:10.3762/bjnano.5.165

• . Theoretical modelling indicates deviations from a linear correlation for silver rich particles [142]. Laser-based synthesis of AuAg alloy nanoparticles may be conducted by two different methods both avoiding chemical precursors and stabilizing ligands. The first one is based on laser post irradiation of

Mimicking exposures to acute and lifetime concentrations of inhaled silver nanoparticles by two different in vitro approaches

• Fabian Herzog,
• Kateryna Loza,
• Sandor Balog,
• Martin J. D. Clift,
• Matthias Epple,
• Peter Gehr,
• Alke Petri-Fink and
• Barbara Rothen-Rutishauser

Beilstein J. Nanotechnol. 2014, 5, 1357–1370, doi:10.3762/bjnano.5.149

• inhalation, NP concentration simulating occupational exposure, and a 3D in vitro lung-cell culture model simulating the human epithelial alveolar/airway barrier. In addition, the effects of aerosolized Ag NPs with Ag NPs applied in suspension were compared and by modelling the deposited Ag NP dose with the