Detecting stable adsorbates of (1S)-camphor on Cu(111) with Bayesian optimization

• Jari Järvi,
• Patrick Rinke and
• Milica Todorović

Beilstein J. Nanotechnol. 2020, 11, 1577–1589, doi:10.3762/bjnano.11.140

• structure of complex molecular adsorbates from microscopy images can be difficult, and using atomistic simulations to find the most stable structures is limited to partial exploration of the potential energy surface due to the high-dimensional phase space. In this study, we present the recently developed

• Bayesian Optimization Structure Search (BOSS) method as an efficient solution for identifying the structure of non-planar adsorbates. We apply BOSS with density-functional theory simulations to detect the stable adsorbate structures of (1S)-camphor on the Cu(111) surface. We identify the optimal structure

• surface structures, but interpreting images of bulky three-dimensional molecules on surfaces can be difficult, which prevents an accurate structure determination. In such cases, computations can help in detecting the most stable structures. With atomistic simulations, we can determine the optimal

Electrokinetic characterization of synthetic protein nanoparticles

• Daniel F. Quevedo,
• Cody J. Lentz,
• Adriana Coll de Peña,
• Yazmin Hernandez,
• Nahal Habibi,
• Rikako Miki,
• Joerg Lahann and
• Blanca H. Lapizco-Encinas

Beilstein J. Nanotechnol. 2020, 11, 1556–1567, doi:10.3762/bjnano.11.138

• at the trapping voltage of each particle. For the simulations, a conductivity of 21.3 µS·cm−1 and a relative permittivity of 78.4 for the suspension medium were used, while the substrate was assumed to be an insulator due to the low conductivity of PDMS [58]. The nonlinear empirical electrophoretic

Design of V-shaped cantilevers for enhanced multifrequency AFM measurements

• Mehrnoosh Damircheli and
• Babak Eslami

Beilstein J. Nanotechnol. 2020, 11, 1525–1541, doi:10.3762/bjnano.11.135

• -shaped cantilevers in multifrequency, specifically bimodal, AFM. The optimum geometrical dimensions of V-shaped cantilevers that can provide maximum phase contrast (material composition) are found by simulations. The effect of geometry on static and dynamic parameters of cantilevers such as mass, spring

• of Zc = 6 nm on Au is provided. In this round of simulations, the parameters were L = 85 µm, = 15 µm, bref = 86 µm, tref = 0.4 µm, Rtip = 9 nm, and α = 0° where α is defined as the angle between the cantilever and sample. Since this angle cannot be controlled by the user in AFM experiments, it is

• assumed that the cantilever is parallel to the surface for all simulations and experiments of this work. These results verify that the simulation can capture weakly perturbed oscillations of the V-shaped cantilevers in bimodal AFM. It should also be mentioned that the oscillation amplitudes for the first

Adsorption and self-assembly of porphyrins on ultrathin CoO films on Ir(100)

• Feifei Xiang,
• Tobias Schmitt,
• Marco Raschmann and
• M. Alexander Schneider

Beilstein J. Nanotechnol. 2020, 11, 1516–1524, doi:10.3762/bjnano.11.134

• . During subsequent adsorption studies the molecule and the first CoO bilayer were allowed to relax. Calculations were carried out with an energy cutoff of 400 eV and at the gamma point only, all structures were relaxed until forces were smaller than 0.1 eV/Å. STM simulations were performed employing the

• activation energy of rotational motion is below 200 meV. The orientation is given as the angle of the molecular axis with respect to the direction of the Ir(100) surface. (d, e) Top and side view, respectively, of 2 on 1BL CoO. Insets in (a) and (d) are STM-DFT simulations at bias voltages of −1.6 V and

Controlling the electronic and physical coupling on dielectric thin films

• Philipp Hurdax,
• Michael Hollerer,
• Larissa Egger,
• Georg Koller,
• Xiaosheng Yang,
• Anja Haags,
• Serguei Soubatch,
• Frank Stefan Tautz,
• Mathias Richter,
• Alexander Gottwald,
• Peter Puschnig,
• Martin Sterrer and
• Michael G. Ramsey

Beilstein J. Nanotechnol. 2020, 11, 1492–1503, doi:10.3762/bjnano.11.132

• geometry of the molecules from which they are emitted [28]. The experimental maps in Figure 3a and Figure 3b are in very good agreement with the simulations of the HOMO and LUMO for 6P having two orthogonal orientations. The observation of the LUMO emission clearly shows that charge transfer has occurred

• intensity used in the following angle-resolved ultraviolet photoemission spectroscopy experiments is marked with crosses. Deviations from the simulations for isolated molecules are a result of MgO and Ag(100) sp-band emissions. Films of 6P were grown and measured at room temperature. He I ARUPS spectra for

Self-assembly and spectroscopic fingerprints of photoactive pyrenyl tectons on hBN/Cu(111)

• Domenik M. Zimmermann,
• Knud Seufert,
• Luka Ðorđević,
• Tobias Hoh,
• Sushobhan Joshi,
• Tomas Marangoni,
• Davide Bonifazi and
• Willi Auwärter

Beilstein J. Nanotechnol. 2020, 11, 1470–1483, doi:10.3762/bjnano.11.130

• allows the determination of the electronic properties of the pyrene adsorbates by STM and STS", and the comparison with the gaps estimated by theoretical simulations in vacuum and by UV-vis spectroscopies in solution. Remarkably, the electronic states of the pyrene adsorbates near the Fermi level, probed

Protruding hydrogen atoms as markers for the molecular orientation of a metallocene

• Linda Laflör,
• Michael Reichling and
• Philipp Rahe

Beilstein J. Nanotechnol. 2020, 11, 1432–1438, doi:10.3762/bjnano.11.127

• Figure 2e) evolve on one side of a sharp line connecting the weights of the dumbbells. For an interpretation of the NC-AFM contrast, we run simulations based on the probe particle model [23] for three molecules aligned along , each molecule being in the DFT-optimised adsorption geometry geo 1 [22], as

• similarity to the experimental data. The change from the ellipse to the dumbbell shape is reproduced as well as the evolution of a sharp line connecting the two dumbbell weights (Figure 2h,l). The characteristic contrast features appear in the simulations at different heights for the different tips, a

• is in turn caused by attractive forces acting between the tip and other atoms of the FDCA molecule. Thus, the PPM simulations allow for the assignment of the dumbbell shape to a single FDCA molecule and, in turn, the orientation of the dumbbell precisely defines the axis between the top hydrogen

On the frequency dependence of viscoelastic material characterization with intermittent-contact dynamic atomic force microscopy: avoiding mischaracterization across large frequency ranges

• Enrique A. López-Guerra and
• Santiago D. Solares

Beilstein J. Nanotechnol. 2020, 11, 1409–1418, doi:10.3762/bjnano.11.125

• viscoelastic properties). To obtain further insight, we now examine the force trajectories for the above simulations, which are shown in Figure 4 for an amplitude setpoint of approximately 55% (in the repulsive branch). Figure 4a confirms that the indentation is ca. 1.9 nm greater for material 1 than for

• calculation using Equation 2 and Equation 4 shows that the storage and loss moduli of material 2 have increased by factors of approximately 4.9 and 3.7, respectively. The above simulations illustrate the frequency dependence of the AFM observables for specific materials, along with the challenges involved in

• approach can help to avoid some of the mischaracterization issues discussed above, especially in combination with numerical simulations of quasi-static [14][33][34] and dynamic AFM [35] measurements, which incorporate viscoelastic models such as those depicted in Figure 1. Conclusion We have presented an

Transient coating of γ-Fe₂O₃ nanoparticles with glutamate for its delivery to and removal from brain nerve terminals

• Konstantin Paliienko,
• Artem Pastukhov,
• Michal Babič,
• Daniel Horák,
• Olga Vasylchenko and
• Tatiana Borisova

Beilstein J. Nanotechnol. 2020, 11, 1381–1393, doi:10.3762/bjnano.11.122

• mode v1.61. The laser correlation spectrometer was equipped with a multi-computing correlator type 7032 CE. Simulation of spatial structure of γ-Fe2O3 nanoparticles coated with blood plasma protein biocorona Simulations of biocorona formation at the surface of γ-Fe2O3 nanoparticles were performed using

• structure of a maghemite nanoparticle coated with blood plasma protein biocorona Interaction of the nanoparticles and plasma proteins was also analyzed with computer modeling and simulations of spatial structures using the programs LeadIT 2.3.2, ArgusLab 4.0.1 and Material Science Suite 2015, and the online

Atomic defect classification of the H–Si(100) surface through multi-mode scanning probe microscopy

• Jeremiah Croshaw,
• Thomas Dienel,
• Taleana Huff and
• Robert Wolkow

Beilstein J. Nanotechnol. 2020, 11, 1346–1360, doi:10.3762/bjnano.11.119

• of the H-terminated Si(100)-2 × 1 surface, its structural features, and defects. Six different scanning probe imaging modes are performed using both STM and nc-AFM. By combining the accessible information with probe particle simulations [23][24] (presented in Supporting Information File 1) of the

• structure negatively charged. We demonstrate the tip-induced removal of the weakly bound H atom, leaving the site neutral. While we present an extensive experimental analysis supplemented with simple simulations of common surface defects on H-terminated silicon, we anticipate that the provided assignments

• stronger repulsive component is observed for the more inert H-functionalized tip probing the H-atom (bright contrast), while the more reactive Si-terminated tip (dark contrast) leads to a stronger attractive interaction (more negative Δf) at the same site [39][40][41][43][44][45]. Simulations of the STHM

Controlling the proximity effect in a Co/Nb multilayer: the properties of electronic transport

• Sergey Bakurskiy,
• Mikhail Kupriyanov,
• Nikolay V. Klenov,
• Igor Soloviev,
• Andrey Schegolev,
• Roman Morari,
• Yury Khaydukov and
• Anatoli S. Sidorenko

Beilstein J. Nanotechnol. 2020, 11, 1336–1345, doi:10.3762/bjnano.11.118

• transitions of individual superconducting layers (or groups of layers) in the multilayer structure. As explained previously in the simulations (Figure 2 and Figure 3), the effective critical temperature of the s-layers within the multilayer structure (i.e., the temperature in which the superconducting order

3D superconducting hollow nanowires with tailored diameters grown by focused He⁺ beam direct writing

• Rosa Córdoba,
• Alfonso Ibarra,
• Dominique Mailly,
• Isabel Guillamón,
• Hermann Suderow and
• José María De Teresa

Beilstein J. Nanotechnol. 2020, 11, 1198–1206, doi:10.3762/bjnano.11.104

• , whereas the volatile products ones are pumped out of the process chamber. Normally, the final deposit is a mixture of carbon, metallic elements and oxygen. As clearly described using analytical modelling [29] and Monte-Carlo simulations [30], the vertical growth of 3D nano-objects by He+ FIBID is mainly

Monolayers of MoS₂ on Ag(111) as decoupling layers for organic molecules: resolution of electronic and vibronic states of TCNQ

• Asieh Yousofnejad,
• Gaël Reecht,
• Nils Krane,
• Christian Lotze and
• Katharina J. Franke

Beilstein J. Nanotechnol. 2020, 11, 1062–1071, doi:10.3762/bjnano.11.91

• properties of the substrate, we refrain from a definite assignment. In any case, our data clearly shows that the HOMO is at or within the conduction band of MoS2. By comparison with simulations, we thus arrive at a clear identification of the energy level alignment. Most notably, we find that the LUMO

• excited state allowed us to resolve vibronic states of the transiently negatively charged TCNQ molecule albeit only up to approx. 200 meV above the LUMO resonance, where contributions of MoS2 bands at Γ become strong. Our simulations reproduce the experimental satellite structure of the LUMO very well

A new photodetector structure based on graphene nanomeshes: an ab initio study

• Babak Sakkaki,
• Hassan Rasooli Saghai,
• Ghafar Darvish and
• Mehdi Khatir

Beilstein J. Nanotechnol. 2020, 11, 1036–1044, doi:10.3762/bjnano.11.88

• , and then proceed with the design of the photodetector based on a suitable material. We further calculate the transport and photocurrent of the devices. To demonstrate improved performance of the proposed devices, we perform simulations on three types of devices. Graphene, GNMs and GNRs are materials

• simulations. We assumed a finite GNM length between the two contacts. The channel of the photodetector has three GNM supercells along the transport direction (X direction), while in the perpendicular direction the channel length is defined to be infinite. To compare the designed devices with other

Three-dimensional solvation structure of ethanol on carbonate minerals

• Hagen Söngen,
• Ygor Morais Jaques,
• Peter Spijker,
• Christoph Marutschke,
• Stefanie Klassen,
• Ilka Hermes,
• Ralf Bechstein,
• Lidija Zivanovic,
• John Tracey,
• Adam S. Foster and
• Angelika Kühnle

Beilstein J. Nanotechnol. 2020, 11, 891–898, doi:10.3762/bjnano.11.74

• molecular dynamics (MD) simulations. Within a single AFM data set we are able to resolve both the first laterally ordered solvation layer of ethanol on the calcite surface as well as the following solvation layers that show no lateral order. Our experimental results are in excellent agreement with MD

• simulations. The qualitative difference in the lateral order can be understood by the differing chemical environment: While the first layer adopts specific binding positions on the ionic carbonate surface, the second layer resides on top of the organic ethyl layer. A comparison of calcite and magnesite

• has been investigated theoretically by using both density functional theory (DFT) [12][13] and molecular dynamics (MD) simulations [14][15][16][17]. It has been found that ethanol molecules strongly bind towards calcite (10.4) terraces – even stronger than water [12][14][16][17]. Ethanol molecules

Simulations of the 2D self-assembly of tripod-shaped building blocks

• Łukasz Baran,
• Wojciech Rżysko and
• Edyta Słyk

Beilstein J. Nanotechnol. 2020, 11, 884–890, doi:10.3762/bjnano.11.73

• triangular lattice. We have shown that the constraints present in the latter method can enforce the formation of completely different structures, not reproducible with off-lattice simulations. In addition to that, we have characterized the obtained structures regarding various parameters such as theoretical

• diffraction pattern and average association number. Keywords: 2D materials; coarse-grained model; molecular simulations; self-assembly; structural characterization; tripod building blocks; Introduction On-surface synthesis is a newly developing field in chemistry that aims at making use of solid surfaces as

• computer modeling, which allows for a versatile examination of various thermodynamic conditions in acceptable time frames. Additionally, it is also a convenient tool to vary multiple factors such as the shape of the molecules, and the type of solvent and substrate. The insight gained from the simulations

Transition from freestanding SnO₂ nanowires to laterally aligned nanowires with a simulation-based experimental design

• Jasmin-Clara Bürger,
• Sebastian Gutsch and
• Margit Zacharias

Beilstein J. Nanotechnol. 2020, 11, 843–853, doi:10.3762/bjnano.11.69

• Jasmin-Clara Burger Sebastian Gutsch Margit Zacharias Laboratory for Nanotechnology, Department of Microsystems Engineering (IMTEK), University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany 10.3762/bjnano.11.69 Abstract In this study, we used simulations as a guide for

• experiments in order to switch freestanding nanowire growth to a laterally aligned growth mode. By means of finite element simulations, we determined that a higher volumetric flow and a reduced process pressure will result in a preferred laterally aligned nanowire growth. Furthermore, increasing the

• can be changed to the growth of laterally aligned NWs. By comparison of numerical simulations with systematic experiments, we discuss how the process parameters for freestanding SnO2 NWs have to be modified to achieve a laterally aligned NW growth mode. Experimental Substrate preparation The

Integrated photonics multi-waveguide devices for optical trapping and Raman spectroscopy: design, fabrication and performance demonstration

• Gyllion B. Loozen,
• Arnica Karuna,
• Mohammad M. R. Fanood,
• Erik Schreuder and
• Jacob Caro

Beilstein J. Nanotechnol. 2020, 11, 829–842, doi:10.3762/bjnano.11.68

• the influence of surfaces. We report the design (including simulations), fabrication and performance demonstration for multi-waveguide devices, using our Si3N4 waveguiding platform as the basis. The designed ridge waveguides, optimized for trapping and Raman spectroscopy, emit narrow beams. Multiple

• focused Gaussian beam traps and are confirmed by our own simulations. The Raman spectra of the beads (in this work measured via an objective) show clear peaks that are characteristic of polystyrene. In the low-wavenumber range, the spectra have a background that most likely originates from the Si3N4

• maximum obtainable value for the TM polarization, as a result of optimum constructive interference. For transverse electric (TE) polarization, for which the electric field vector of the beams is oriented in the x–y plane, the resulting light concentration is lower. In the simulations, the refractive

Adsorption behavior of tin phthalocyanine onto the (110) face of rutile TiO₂

• Lukasz Bodek,
• Mads Engelund,
• Aleksandra Cebrat and
• Bartosz Such

Beilstein J. Nanotechnol. 2020, 11, 821–828, doi:10.3762/bjnano.11.67

• measurements of single molecules reveal the coexistence of two conformations of molecules on the TiO2 surface. Density functional theory-based simulations (DFT) indicate that the difference originates from the position of the tin atom protruding from the molecule plane. The irreversible switching of Sn-up

• interactions between SnPc molecules and the rutile surface, while DFT-based simulations combined with high-resolution STM images imply that a Sn-down geometry may be preferred as a consequence of steric adjustment between the molecular shape and the corrugated (110) surface. Experimental The experiment was

• creation of additional bonds between the carboxylic groups and the surface. Conclusion The adsorption process of SnPc molecules on the (110) face of rutile TiO2 was studied by microscopic techniques supported by XPS analysis and DFT simulations. At room temperature, single molecules adsorb onto the TiO2

Hexagonal boron nitride: a review of the emerging material platform for single-photon sources and the spin–photon interface

• Stefania Castelletto,
• Faraz A. Inam,
• Shin-ichiro Sato and
• Alberto Boretti

Beilstein J. Nanotechnol. 2020, 11, 740–769, doi:10.3762/bjnano.11.61

• relevant property for SPE. The SPE was modeled with a 3-level system with ≈ 2.2 ns, ≈ 2.2 ns and ≈ 67.9 ns. Ab-initio simulations have confirmed that VNNB is likely the color center associated with the SPE [111] (Figure 3), and this defect has been modeled as a candidate to provide optical spin readout

Quantitative determination of the interaction potential between two surfaces using frequency-modulated atomic force microscopy

• Nicholas Chan,
• Carrie Lin,
• Tevis Jacobs,
• Robert W. Carpick and
• Philip Egberts

Beilstein J. Nanotechnol. 2020, 11, 729–739, doi:10.3762/bjnano.11.60

• . It also determines interfacial properties, such as adhesion and friction, and is a key input into mechanics models and atomistic simulations of contacts. We have developed a novel methodology to experimentally determine interaction potential parameters, given a particular potential form, using

• mechanics models [22][23][24][25] to allow better visualization of surface interactions. While useful insights can be obtained using fully atomistic simulations, such as molecular dynamics simulations or density functional theory, these techniques are impractical for describing larger contacts with a large

• representing interactions between mismatched materials, many simulations in tribology and interfacial science also use the LJ potential or potentials based on it [27][28][29][30][31]. However, there is little direct experimental validation of this numerical integration approach. Here, we demonstrate a novel

Effect of Ag loading position on the photocatalytic performance of TiO₂ nanocolumn arrays

• Jinghan Xu,
• Yanqi Liu and
• Yan Zhao

Beilstein J. Nanotechnol. 2020, 11, 717–728, doi:10.3762/bjnano.11.59

• between the nanocolumns at the height of 50–120 nm. Figure 8 (b1–4) shows results from the simulations of the ACT3 structure. Ag was filled between the nanocolumns, and a layer of 15 nm thick Ag film was covered on the top of the array. It can be seen from the figure that the Ag coating hinders the

• ) kinetics of different samples, (d) recycling of AFT3 and ACT3. FDTD simulations of the electric field distribution of Ag-loaded TiO2 nanocolumns with different structures. a1) Wavelength 457 nm TNC cross section, a2) wavelength 320 nm TNC cross section, a3) wavelength 457 nm TNC longitudinal section, a4

Stochastic excitation for high-resolution atomic force acoustic microscopy imaging: a system theory approach

• Edgar Cruz Valeriano,
• José Juan Gervacio Arciniega,
• Christian Iván Enriquez Flores,
• Susana Meraz Dávila,
• Joel Moreno Palmerin,
• Martín Adelaido Hernández Landaverde,
• Yuri Lizbeth Chipatecua Godoy,
• Aime Margarita Gutiérrez Peralta,
• Rafael Ramírez Bon and
• José Martín Yañez Limón

Beilstein J. Nanotechnol. 2020, 11, 703–716, doi:10.3762/bjnano.11.58

• modulus in the measurement. In this work, Equation 21 and Equation 27 are useful because these give a quantitative relationship between a set of resonance frequencies and an indentation modulus using white-noise excitation. The validation of this model requires simulations and measurements, which are

• cantilever with L = 400 µm is used and its contact stiffness is changed, it can be seen how the resonance frequencies increase with increasing contact stiffness. Three simulations are shown for contact stiffness values of = 1, 10 and 100 N/m (Figure 4c). The simulation results offer enough support for an

Effect of substitutional defects on resonant tunneling diodes based on armchair graphene and boron nitride nanoribbons lateral heterojunctions

• Majid Sanaeepur

Beilstein J. Nanotechnol. 2020, 11, 688–694, doi:10.3762/bjnano.11.56

• substitutional defects (including BC, NC, CB, and CN) at the interface of graphene and boron nitride nanoribbons on the negative differential resistance behavior of the proposed resonant tunneling diode is investigated. Transport simulations are carried out in the framework of tight-binding Hamiltonians and non

• the conduction band edge [40]. Room temperature (300 K) is considered in all simulations. Results and Discussion Substitutional carbon atoms in boron or nitrogen sublattices (CB and CN) as well as boron or nitrogen atoms on carbon sites (BC and NC) are considered (Figure 2). Each defect could occur

Electromigration-induced directional steps towards the formation of single atomic Ag contacts

• Atasi Chatterjee,
• Christoph Tegenkamp and
• Herbert Pfnür

Beilstein J. Nanotechnol. 2020, 11, 680–687, doi:10.3762/bjnano.11.55

• simulations, partly going far beyond the free-electron model, give clear evidence for the existence of quantized conductance in atomic point contacts. The exact conductance values, however, turn out to depend significantly on the local contact configurations so that they may deviate from integer multiples of

• only observed for alkali metals, but also in monovalent noble metals such as Ag and Au [10][11]. These experimental findings could be very well correlated with the theoretical simulations of conductance histograms [7][12][13]. The theoretical calculation of conductance histograms is based on the semi

• can be suppressed to a large extent, in agreement with our own simulations [26]. This situation differs from most previous EM experiments, in which it was difficult to separate EM from thermal effects. For our experiments we use ultrathin Ag films (thickness 5 nm), which exhibit Stranski–Krastanov