Multiscale modelling of biomolecular corona formation on metallic surfaces

• Parinaz Mosaddeghi Amini,
• Ian Rouse,
• Julia Subbotina and
• Vladimir Lobaskin

Beilstein J. Nanotechnol. 2024, 15, 215–229, doi:10.3762/bjnano.15.21

• modelling of the interaction between various surfaces, that is (100), (110), and (111), of fcc aluminum with the most abundant milk proteins and lactose. Our approach combines atomistic molecular dynamics, a coarse-grained model of protein adsorption, and kinetic Monte Carlo simulations to predict the

Thermal transport in kinked nanowires through simulation

• Alexander N. Robillard,
• Graham W. Gibson and
• Ralf Meyer

Beilstein J. Nanotechnol. 2023, 14, 586–602, doi:10.3762/bjnano.14.49

• completely understood. The behaviour of the conductance is examined as kinks of varying angular intensity are included into nanowires. The effects on thermal transport are evaluated through molecular dynamics simulations, phonon Monte Carlo simulations and classical solutions of the Fourier equation. A

• ballistic paths through the wire, or equivalently the LoS. It would instead appear that the changes in conductance in MD results are as much due to the angling of the lattice as the kink effects. In order to further investigate the effects of the kinks, we turn to phonon Monte Carlo simulations. PMC

Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF₃)₄

• Alexey Prosvetov,
• Alexey V. Verkhovtsev,
• Gennady Sushko and
• Andrey V. Solov’yov

Beilstein J. Nanotechnol. 2021, 12, 1151–1172, doi:10.3762/bjnano.12.86

• the FEBID process. The follow-up study [15] introduced a novel multiscale computational methodology that couples Monte Carlo simulations for radiation transport with IDMD for simulating the IDC processes with atomistic resolution. The spatial and energy distributions of secondary and backscattered

Is the Ne operation of the helium ion microscope suitable for electron backscatter diffraction sample preparation?

• Annalena Wolff

Beilstein J. Nanotechnol. 2021, 12, 965–983, doi:10.3762/bjnano.12.73

• interaction volume, a steady-state condition of ion impurity concentration and number of induced defects is reached. The EBSD measurements and Monte Carlo simulations indicate that when this steady-state condition is reached more quickly, which can be achieved using high-energy Ne ions at a glancing incidence

• transmission electron microscopy (STEM), TEM, TEM selected area electron diffraction (SAED), and TEM dark-field (DF) measurements. The results for each experiment are compared to those of a non-irradiated area of the Cu TEM grid. Monte Carlo simulations of the occurring ion–solid interactions are evaluated to

• produce artefacts that would compromise the TEM analysis. Monte Carlo simulations were performed using the program Stopping and Range of Ions in Matter (SRIM) to better understand the underpinning ion–solid interactions for the different settings [22]. The extent of created dislocations, vacancies as well

The role of convolutional neural networks in scanning probe microscopy: a review

• Ido Azuri,
• Irit Rosenhek-Goldian,
• Neta Regev-Rudzki,
• Georg Fantner and
• Sidney R. Cohen

Beilstein J. Nanotechnol. 2021, 12, 878–901, doi:10.3762/bjnano.12.66

A review of defect engineering, ion implantation, and nanofabrication using the helium ion microscope

• Frances I. Allen

Beilstein J. Nanotechnol. 2021, 12, 633–664, doi:10.3762/bjnano.12.52

Surface-enhanced Raman scattering of water in aqueous dispersions of silver nanoparticles

• Paulina Filipczak,
• Krzysztof Hałagan,
• Jacek Ulański and
• Marcin Kozanecki

Beilstein J. Nanotechnol. 2021, 12, 497–506, doi:10.3762/bjnano.12.40

• -donor or electron-acceptor centres is involved in the interaction with the Ag surface [51]. To bring the Monte-Carlo simulations closer to a real system, short-range interactions between the nearest neighbours were also assumed besides the movement rules defined by the DLL algorithm itself (providing an

• temperature measurements were carried out by using a single cell Peltier accessory (Varian Inc.), which allows for temperature change of a liquid in the standard 10 mm pathway cuvette with an accuracy of ±0.1 °C. Simulation parameters Experimental works were supported by Monte Carlo simulations performed by

Scanning transmission helium ion microscopy on carbon nanomembranes

• Daniel Emmrich,
• Annalena Wolff,
• Nikolaus Meyerbröker,
• Jörg K. N. Lindner,
• André Beyer and
• Armin Gölzhäuser

Beilstein J. Nanotechnol. 2021, 12, 222–231, doi:10.3762/bjnano.12.18

• detector is able to determine the thickness of membranes with sub-nanometer precision by quantitatively evaluating the image signal and comparing the results with Monte Carlo simulations. The thickness determined by the dark-field transmission detector is compared to X-ray photoelectron spectroscopy and

• between holder in the specimen chamber and objective lens. The required hole sizes depend on the deflection angles, which are determined by beam energy, sample thickness, and sample material. The angles can be predicted using Monte Carlo simulations, which yield information about the relevant range of

• areas of freestanding CNM. Intensity profiles across a feature (a rupture and a fold) show that the portion of direct SE from the CNM is negligible for the STIM analysis (Figure 2c). Monte Carlo simulations and signal/contrast modelling In order to understand the physics behind the STIM signal, the

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

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

• . Simulations for this kind of models have been performed using lattice [34][35] and off-lattice [36][37][38] Monte Carlo simulations, or MD simulations [37][39]. Regarding the latter, we have very recently shown that this methodology is suitable for the representation of tetratopic molecules with different

• . As shown in Figure 1a, we have marked the angle θ between arms B and C. This angle has been set for the models NT and WT to θ =120°and to θ = 60°for the models NL and WL. One has to note that for the latter models we can not reproduce the counterparts in the Monte Carlo simulations on a triangular

• * = 0.01. In the Monte Carlo simulations, we have assumed that one segment can occupy only one vertex of a triangular lattice and the interaction energy between terminal arm segments is taken into account only if the neighboring arms are collinear (→←), resulting in ε = −1 energy contribution. One has to

The effect of heat treatment on the morphology and mobility of Au nanoparticles

• Sven Oras,
• Sergei Vlassov,
• Simon Vigonski,
• Boris Polyakov,
• Mikk Antsov,
• Vahur Zadin,
• Rünno Lõhmus and
• Karine Mougin

Beilstein J. Nanotechnol. 2020, 11, 61–67, doi:10.3762/bjnano.11.6

• the geometry from faceted to more rounded shapes were observed with increasing annealing temperature. Kinetic Monte Carlo simulations indicate that the NPs become rounded due to the minimization of the surface area and the transition to lower energy surface types {111} and {100}. The NPs were

Nitrogen-vacancy centers in diamond for nanoscale magnetic resonance imaging applications

• Alberto Boretti,
• Lorenzo Rosa,
• Jonathan Blackledge and
• Stefania Castelletto

Beilstein J. Nanotechnol. 2019, 10, 2128–2151, doi:10.3762/bjnano.10.207

• obtaining the 3D maps of the magnetic field in the sample from the magnetic field images, Monte Carlo simulations of the nuclear spin T2 decoherence was performed in lattices of representative cells. This was done to connect micrometer-scale magnetic field measurements to the MRI contrast. The predicted

Choosing a substrate for the ion irradiation of two-dimensional materials

• Egor A. Kolesov

Beilstein J. Nanotechnol. 2019, 10, 531–539, doi:10.3762/bjnano.10.54

• defect formation mechanisms. The estimations include Monte Carlo simulations for He, Ar, Xe, C, N and Si ions, performed in the incident ion energy range from 100 eV to 250 MeV. Cu, SiO2, SiC and Al2O3 substrates were analyzed. The considered substrate-related defect formation mechanisms are sputtering

• material structural modification by ion irradiation. Conclusion Monte Carlo simulations were performed to estimate the role of Cu, SiO2, SiC and Al2O3 substrates in the defect formation in 2D materials under irradiation with He, Ar, Xe, C, N and Si ions in the incident ion energy range from 100 eV to 250

Sputtering of silicon nanopowders by an argon cluster ion beam

• Xiaomei Zeng,
• Vasiliy Pelenovich,
• Zhenguo Wang,
• Wenbin Zuo,
• Sergey Belykh,
• Alexander Tolstogouzov,
• Dejun Fu and
• Xiangheng Xiao

Beilstein J. Nanotechnol. 2019, 10, 135–143, doi:10.3762/bjnano.10.13

• under-cosine shape, in other words, the atoms are sputtered mostly in the lateral direction [5]. This effect results in another prominent phenomenon called surface smoothing. Using molecular dynamics (MD) and Monte Carlo simulations it has been shown that the effect of the cluster impact depends on the

• compared to the sputtering of the bulk target. The sputtering yield versus radius of a-Si or SiGe particles scaled to the energy deposition depth has been studied by Nietiadi et al. using MD and Monte Carlo simulations [20][21]. As projectiles, Ar atoms were used with an energy of 20 keV. The sputtering

Site-controlled formation of single Si nanocrystals in a buried SiO₂ matrix using ion beam mixing

• Xiaomo Xu,
• Thomas Prüfer,
• Daniel Wolf,
• Hans-Jürgen Engelmann,
• Lothar Bischoff,
• René Hübner,
• Karl-Heinz Heinig,
• Wolfhard Möller,
• Stefan Facsko,
• Johannes von Borany and
• Gregor Hlawacek

Beilstein J. Nanotechnol. 2018, 9, 2883–2892, doi:10.3762/bjnano.9.267

• between the SiO2 layers and perpendicular to the incident Ne+ beam. Keywords: helium ion microscopy; ion beam mixing; Monte Carlo simulations; phase separation; single electron transistor; Introduction Silicon has been the main material in the semiconductor industry for almost all use cases with the

Charged particle single nanometre manufacturing

• Philip D. Prewett,
• Cornelis W. Hagen,
• Claudia Lenk,
• Steve Lenk,
• Marcus Kaestner,
• Tzvetan Ivanov,
• Ahmad Ahmad,
• Ivo W. Rangelow,
• Xiaoqing Shi,
• Stuart A. Boden,
• Alex P. G. Robinson,
• Dongxu Yang,
• Sangeetha Hari,
• Marijke Scotuzzi and
• Ejaz Huq

Beilstein J. Nanotechnol. 2018, 9, 2855–2882, doi:10.3762/bjnano.9.266

Josephson effect in junctions of conventional and topological superconductors

• Alex Zazunov,
• Albert Iks,
• Miguel Alvarado,
• Alfredo Levy Yeyati and
• Reinhold Egger

Beilstein J. Nanotechnol. 2018, 9, 1659–1676, doi:10.3762/bjnano.9.158

• perturbative cotunneling regime. For the corresponding S–QD–S case, see [58][79]. We note that a full solution of this interacting many-body problem requires a detailed numerical analysis using, e.g., the numerical renormalization group [60][61] or quantum Monte Carlo simulations [59][63], which is beyond the

Gas-assisted silver deposition with a focused electron beam

• Luisa Berger,
• Katarzyna Madajska,
• Iwona B. Szymanska,
• Katja Höflich,
• Mikhail N. Polyakov,
• Jakub Jurczyk,
• Carlos Guerra-Nuñez and
• Ivo Utke

Beilstein J. Nanotechnol. 2018, 9, 224–232, doi:10.3762/bjnano.9.24

• . Four point probe resistivity measurements were conducted with a homebuilt setup containing 4 probes with a possibility of 3-axial movement, a Keithley® 2400 Source Meter nanoamperemeter and self-developed controlling software written in LabView®. Monte Carlo simulations of electron distributions were

Electron beam induced deposition of silacyclohexane and dichlorosilacyclohexane: the role of dissociative ionization and dissociative electron attachment in the deposition process

• Ragesh Kumar T P,
• Sangeetha Hari,
• Krishna K Damodaran,
• Oddur Ingólfsson and
• Cornelis W. Hagen

Beilstein J. Nanotechnol. 2017, 8, 2376–2388, doi:10.3762/bjnano.8.237

• than for SCH, this difference is still within the accuracy of our measurements, and we do not consider this observation to give any conclusive information on the role of DEA, beyond that of DI in this process. According to the current Monte Carlo simulations, about 50% of all secondary electrons

• assistance with the Monte Carlo simulations of Figure 10. OI acknowledges supported from the Icelandic Center of Research (RANNIS) Grant No. 13049305(1-3) and the University of Iceland Research Fund. RKTP acknowledges a doctoral grant from the University of Iceland Research Fund and financial support from

Electronic structure, transport, and collective effects in molecular layered systems

• Torsten Hahn,
• Tim Ludwig,
• Carsten Timm and
• Jens Kortus

Beilstein J. Nanotechnol. 2017, 8, 2094–2105, doi:10.3762/bjnano.8.209

• interaction can be treated essentially exactly using Monte Carlo simulations [15]. The main idea is to use the sequential-tunneling rates, which are analogous to Equation 5 and uniform throughout the monolayer, to determine the probabilities of local Monte Carlo updates. Importantly, these rates depend on the

• independent of the occupation of the neighboring sites. Thus the layer decouples into independent sites. Moreover, forward and backward rates are always equal, Rn→m = Rm→n, so that the system is equivalent to a model at infinite temperature. For the other regions, we have performed Monte Carlo simulations as

Investigation of growth dynamics of carbon nanotubes

• Marianna V. Kharlamova

Beilstein J. Nanotechnol. 2017, 8, 826–856, doi:10.3762/bjnano.8.85

• dependent on the synthesis time. At short times (40 s and 2 min), the perpendicular growth was observed, whereas at long times (10 and 30 min) the tangential mode was dominant. Using tight binding Monte Carlo simulations, it was shown that the tangential growth occurs at reaction conditions that are close

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

• the dominating mechanism. Accordingly, analytical theories and Monte Carlo simulations based on the process of thermally activated diffusion process have been developed and carried out [12]. However, the proposed mechanism of collapse via migration of vacancies from the inner core to the outer surface

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

• literature. Monte Carlo simulations were used to normalize and aggregate individual criteria distributions into distributions of overall performance using criteria weights associated with preferences of different key stakeholders [20]. After developing result distributions that reflect current uncertainties

• , the study evaluated research that might best improve decision confidence. Monte Carlo simulations of possible research outcomes (to reduce uncertainty in the input data) and decision outcomes (resulting reduced uncertainty in the distributions of overall scores) were produced for each nanomaterial

• means of MCDA. Uncertainties derived from expert judgment were considered in Monte Carlo simulations [24]. As with MCDA, once the WOE hazard score is determined, each contributor to the hazard score can be further reviewed to see which had the largest effect on the score and which might benefit from

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

• of partial-wave calculations [48][49]. Inelastic scattering is accounted for by the DIIMFPs described above. Monte-Carlo simulations of electron transport (bulk losses only) for typical geometries in FEBID experiments have been previously considered [2][7]. The inclusion of surface excitations

• Figure 5. The Monte Carlo simulations further allow one to discern the processes that give rise to the different regions of the coincidence spectrum [55]. Thus, it was found that any realistic model of SE emission and low-energy electron transport near solid surfaces must account for surface excitations

Scanning reflection ion microscopy in a helium ion microscope

• Yuri V. Petrov and
• Oleg F. Vyvenko

Beilstein J. Nanotechnol. 2015, 6, 1125–1137, doi:10.3762/bjnano.6.114

• reflection coefficient of the ions, which are incident and reflected at low grazing angles, is not sensitive to the atomic number of the sample material, and the contrast in RI images is determined mostly by the surface morphology. This experimental fact is in agreement with the results of the Monte Carlo

• simulations of the angular dependence of the ion reflection coefficient. Accordingly, RIM can be used for the imaging of surface morphology but not for the imaging of surface composition. The obtained experimental results show that there are some quantitative differences in the surface morphology imaging