Influence of water contamination on the sputtering of silicon with low-energy argon ions investigated by molecular dynamics simulations

• Grégoire R. N. Defoort-Levkov,
• Alan Bahm and
• Patrick Philipp

Beilstein J. Nanotechnol. 2022, 13, 986–1003, doi:10.3762/bjnano.13.86

• by molecular dynamics (MD) simulations how one of the most commonly found residual contaminations in vacuum chambers (i.e., water adsorbed on a silicon surface) influences sputtering by 100 eV argon ions. The incidence angle was changed from normal incidence to close to grazing incidence. For the

• ; molecular dynamics; silicon; simulations; water; Introduction Focused ion beams (FIB) play an increasingly important role in materials research areas such as nanoanalysis (e.g., secondary ion mass spectrometry (SIMS) [1][2][3] and sample preparation for transmission electron microscopy (TEM) [4], atom

• extreme cases. Nowadays, very little is known about the influence of contaminations on the amorphization process under ion irradiation. Thanks to molecular dynamics (MD) simulations, a wide range of materials properties and process parameters can be reproduced [27][28][29]. In this paper, we are using MD

Modeling a multiple-chain emeraldine gas sensor for NH₃ and NO₂ detection

• Hana Sustkova and
• Jan Voves

Beilstein J. Nanotechnol. 2022, 13, 721–729, doi:10.3762/bjnano.13.64

• gradient approximated (GGA) Perdew–Burke–Ernzerhof (PBE) exchange–correlation functional was used. Guo et al. [5] investigated the graphene/polyaniline adsorption energy of NH3, CO, NO, and H2 using DFT and molecular dynamics computations. From this, graphene/PANI is highly sensitive to NH3 in comparison

• chosen fixed positions of ammonia and nitrogen dioxide molecules. We have computed the local energy minima through molecular dynamics, which results in the optimized position and orientation of the gas molecule. The spatial orientation of the gas molecules was estimated by these optimizations. Next, one

• as well. The I–V characteristics were computed for several molecule positions near the doped and near the undoped nitrogen atoms, see above. The molecule orientation was estimated through molecular dynamics optimization. The resistance from the linear part of the I–V characteristics was used to

Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking

• Kendra Ramirez-Acosta,
• Ivan A. Rosales-Fuerte,
• J. Eduardo Perez-Sanchez,
• Alfredo Nuñez-Rivera,
• Josue Juarez and
• Ruben D. Cadena-Nava

Beilstein J. Nanotechnol. 2022, 13, 699–711, doi:10.3762/bjnano.13.62

• variants of SARS-CoV-2. This research work will be focused on the molecular docking of peptides by molecular dynamics, in addition to an analysis of the possible interaction of these peptides with physiological proteins. This methodology could be extended to design peptides that are active against other

Comparative molecular dynamics simulations of thermal conductivities of aqueous and hydrocarbon nanofluids

• Adil Loya,
• Antash Najib,
• Fahad Aziz,
• Asif Khan,
• Guogang Ren and
• Kun Luo

Beilstein J. Nanotechnol. 2022, 13, 620–628, doi:10.3762/bjnano.13.54

• ., alkane) the thermal conductivity was increased three times (from 0.1 to 0.4 W·m−1·K−1). This approach to determine the thermal conductivity of metal oxide nanoparticles in aqueous and nonaqueous fluids using visual molecular dynamics and interactive autocorrelations demonstrate a great tool to quantify

• thermophysical properties of nanofluids using a simulation environment. Moreover, this comparison introduces data on aqueous and nonaqueous suspensions in one study. Keywords: alkanes; aqueous solutions; CuO; hydrocarbon solutions; molecular dynamics simulation; nanoparticles; thermal conductivity

• molecules [1]. The molecular dynamics (MD) simulation method is a tool that has been used to effectively predict nanofluid thermal properties with relative accuracy [38][39][40][41][42]. The method relies on computationally solving basic equations of Newton’s laws of motion for interacting particles at the

Investigation of electron-induced cross-linking of self-assembled monolayers by scanning tunneling microscopy

• Patrick Stohmann,
• Sascha Koch,
• Yang Yang,
• Christopher David Kaiser,
• Julian Ehrens,
• Jürgen Schnack,
• Niklas Biere,
• Dario Anselmetti,
• Armin Gölzhäuser and
• Xianghui Zhang

Beilstein J. Nanotechnol. 2022, 13, 462–471, doi:10.3762/bjnano.13.39

• with a scanning tunneling microscope. As the irradiation dose was increased, the cross-linked regions continued to grow and a large number of subnanometer voids appeared. Their equivalent diameter is 0.5 ± 0.2 nm and the areal density is ≈1.7 × 1017 m−2. Supported by classical molecular dynamics

• cross-linked regions appear darker than the structurally ordered domains. At high doses, subnanometer-sized voids are formed preferably in regions of lower structural order and lower density in the monolayer. The formation of carbon nanomembranes was also modeled using classical molecular dynamics

• were analyzed by using an empirical fit. The lateral distribution of subnanometer voids was analyzed by partitioning the surface area into small segments and counting the number of voids in each segment. Classical molecular dynamics simulations The formation of a CNM was modelled using classical

Electrostatic pull-in application in flexible devices: A review

• Teng Cai,
• Yuming Fang,
• Yingli Fang,
• Ruozhou Li,
• Ying Yu and
• Mingyang Huang

Beilstein J. Nanotechnol. 2022, 13, 390–403, doi:10.3762/bjnano.13.32

• et al. [33] used molecular dynamics to compare the adsorption energies of GR-Au and GR-GR structures. The GR-GR structure has a higher adsorption energy of 307 mJ/m2. Mizuta et al. [7][35] assumed that the use of a GR-GR electrode structure could avoid the uncontrollable microscale interactions

Nanoscale friction and wear of a polymer coated with graphene

• Robin Vacher and
• Astrid S. de Wijn

Beilstein J. Nanotechnol. 2022, 13, 63–73, doi:10.3762/bjnano.13.4

• challenging problem due to the complex viscoelastic properties and structure. Using molecular dynamics simulations, we investigate how a graphene sheet on top of the semicrystalline polymer polyvinyl alcohol affects the friction and wear. Our setup is meant to resemble an AFM experiment with a silicon tip. We

• the polymer chains and reduces the indentation depth. Keywords: friction; graphene; molecular dynamics; polymer; Introduction Graphene is a two dimensional material that has remarkable properties, both electronic [1][2] and mechanical [3][4]. Even before anything was known about graphene, the

• . [27][28] show that graphene has a strong effect on the structure and dynamics of the polymer chains near the interface. In this work, we aim to develop our understanding of the frictional behavior of a polymer coated with graphene by using molecular dynamics simulations of a single sliding asperity at

Effect of lubricants on the rotational transmission between solid-state gears

• Huang-Hsiang Lin,
• Jonathan Heinze,
• Alexander Croy,
• Rafael Gutiérrez and
• Gianaurelio Cuniberti

Beilstein J. Nanotechnol. 2022, 13, 54–62, doi:10.3762/bjnano.13.3

• and velocity distribution are not well defined and one has to resort to an atomistic description, for example, via molecular dynamics (MD) simulations. Also, the contact mechanics at the nanoscale is very different from the macroscopic case since specific pair interactions have to be taken into

• only for better visibility since the actual thickness of the lubricant layer is 5.0–5.5 nm to ensure that the gears are immersed. Finally, the whole system is optimized by using the conjugate gradient method implemented within LAMMPS [58]. Molecular dynamics In this study, we use LAMMPS to perform the

Sputtering onto liquids: a critical review

• Anastasiya Sergievskaya,
• Adrien Chauvin and
• Stephanos Konstantinidis

Beilstein J. Nanotechnol. 2022, 13, 10–53, doi:10.3762/bjnano.13.2

A review on slip boundary conditions at the nanoscale: recent development and applications

• Ruifei Wang,
• Jin Chai,
• Bobo Luo,
• Xiong Liu,
• Jianting Zhang,
• Min Wu,
• Mingdan Wei and
• Zhuanyue Ma

Beilstein J. Nanotechnol. 2021, 12, 1237–1251, doi:10.3762/bjnano.12.91

• force [39][40][41][42]. However, compared with experimental methods, numerical simulations, such as the lattice Boltzmann method and molecular dynamics (MD) simulation, are more attractive in many aspects. First, numerical simulations can readily reach the system sizes and timescales of practical

• Beskok compared a slip-modified theoretical model with the molecular dynamics simulation results. They found that the slip enhancement in the electro-osmotic flow is independent of the channel height, which can provide a theoretical basis for membrane fabrication of electrically assisted nanofiltration

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

• presents a detailed computational protocol for the atomistic simulation of formation and growth of metal-containing nanostructures during focused electron beam-induced deposition (FEBID). The protocol is based upon irradiation-driven molecular dynamics (IDMD), a novel and general methodology for computer

• deposition; irradiation-driven molecular dynamics; irradiation-induced chemistry; platinum nanostructures; reactive force fields; Introduction The controllable fabrication of nanostructures with nanoscale resolution remains a considerable scientific and technological challenge [1]. To address this challenge

• up to a few hundred atoms. This makes ab initio approaches of limited use to describe the irradiation-induced chemical transformations occurring during the FEBID process. A breakthrough into the atomistic description of FEBID has been achieved recently by means of irradiation-driven molecular

Effects of temperature and repeat layer spacing on mechanical properties of graphene/polycrystalline copper nanolaminated composites under shear loading

• Chia-Wei Huang,
• Man-Ping Chang and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2021, 12, 863–877, doi:10.3762/bjnano.12.65

• ) composites under shear loading are investigated by molecular dynamics simulations. The effects of different temperatures, graphene chirality, repeat layer spacing, and grain size on the mechanical properties, such as failure mechanism, dislocation, and shear modulus, are observed. The results indicate that

• . Keywords: dislocation; graphene/Cu; molecular dynamics; shear; self-healing; Introduction Graphene is a monolayered hexagonal thin film composed of sp2-bonded carbon atoms and has extraordinary properties for applications in nanoelectronics [1][2][3][4][5][6]. However, because of the two-dimensional

• this work, we focus on temperature and microstructure effects on graphene/polycrystalline copper nanolaminated (GPCuNL) composites. As mentioned above, the microstructure plays a crucial role for the mechanical behavior of GPCuNL composites. Thus, in the present study, molecular dynamics (MD

Reducing molecular simulation time for AFM images based on super-resolution methods

• Zhipeng Dou,
• Jianqiang Qian,
• Yingzi Li,
• Rui Lin,
• Jianhai Wang,
• Peng Cheng and
• Zeyu Xu

Beilstein J. Nanotechnol. 2021, 12, 775–785, doi:10.3762/bjnano.12.61

• can be used to speed up the generation of training data and vary simulation resolution for AFM machine learning. Keywords: atomic force microscopy; Bayesian compressed sensing; convolutional neural network; molecular dynamics simulation; super resolution; Introduction Atomic force microscopy methods

• . The energy maps of the interaction between several tips and samples under different conditions are simulated in dynamic and quasi-static modes. The molecular dynamics simulation details and main steps of reconstruction algorithms are presented. Then, several reconstruction results are conducted to

• dynamics simulation To test the effectiveness of the reconstruction algorithms we perform molecular dynamics simulations of AFM imaging in different conditions. The dynamic process (AM mode) and quasi-static process (the relative position of tip–sample remains unchanged in the simulation) are separately

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

• are faster than molecular dynamics methods. The simulations were performed on a 100×100×32 FCC lattice and averaged over 10 000 time units. Two stiff immobile walls representing Ag {100} surfaces were placed at z = 1 and z = 32. In other directions, (x, y) periodic boundary conditions were used. All

The role of gold atom concentration in the formation of Cu–Au nanoparticles from the gas phase

• Yuri Ya. Gafner,
• Svetlana L. Gafner,
• Darya A. Ryzkova and
• Andrey V. Nomoev

Beilstein J. Nanotechnol. 2021, 12, 72–81, doi:10.3762/bjnano.12.6

• composition; however, the size of the resulting particles varies significantly. To solve this issue, we studied the formation of Cu–Au nanoparticles with different chemical compositions from a gaseous medium using computer molecular dynamics (MD) simulation. The aim was to determine the effect of the

• initial vapor phase, basically corresponded to a given target composition. Keywords: binary nanoparticles; computer simulation; copper; gold; molecular dynamics; Introduction The nanometer-sized Cu–Au compounds are being studied quite actively [1][2][3][4][5][6][7][8] because of their potential

• energy effects but also by kinetic effects. By using molecular dynamics methods, we tried to determine the chemical ordering of Cu–Au particles in these synthesis processes and to elucidate some of their formation mechanisms. In particular, it was found that an increase in the relative number of gold

Scanning transmission imaging in the helium ion microscope using a microchannel plate with a delay line detector

• Eduardo Serralta,
• Nico Klingner,
• Olivier De Castro,
• Michael Mousley,
• Santhana Eswara,
• Serge Duarte Pinto,
• Tom Wirtz and
• Gregor Hlawacek

Beilstein J. Nanotechnol. 2020, 11, 1854–1864, doi:10.3762/bjnano.11.167

• channeling effect in the HIM has also been studied using Monte Carlo [21] and molecular dynamics [22] simulations. Measuring the energy of the transmitted particles is a novel technique that adds an information channel to the previously discussed transmission imaging modes. It will provide information on the

Nanomechanics of few-layer materials: do individual layers slide upon folding?

• Ronaldo J. C. Batista,
• Rafael F. Dias,
• Ana P. M. Barboza,
• Alan B. de Oliveira,
• Taise M. Manhabosco,
• Thiago R. Gomes-Silva,
• Matheus J. S. Matos,
• Andreij C. Gadelha,
• Cassiano Rabelo,
• Luiz G. L. Cançado,
• Ado Jorio,
• Hélio Chacham and
• Bernardo R. A. Neves

Beilstein J. Nanotechnol. 2020, 11, 1801–1808, doi:10.3762/bjnano.11.162

• methods; atomic force microscopy (AFM); molecular dynamics (MD); Raman spectroscopy; nanostructured materials; Introduction Layered materials such as graphite, talc, and transition metal dichalcogenides (TMDs), held together by strong covalent bonds within layers and relatively weak van der Waals

• folded 2D material. In principle, the model describes any 2D material, and its predictions are corroborated by comparison with classical molecular dynamics simulations and to results of previous investigations on graphene and talc. Because folds naturally occur in flakes of varying thickness

Molecular dynamics modeling of the influence forming process parameters on the structure and morphology of a superconducting spin valve

• Alexander Vakhrushev,
• Aleksey Fedotov,
• Vladimir Boian,
• Roman Morari and
• Anatolie Sidorenko

Beilstein J. Nanotechnol. 2020, 11, 1776–1788, doi:10.3762/bjnano.11.160

• molecular dynamics method using the many-particle potential of the modified embedded-atom method. In the calculation process the temperature was controlled using the Nose–Hoover thermostat. The simulation of the atomic nanolayer formation was performed by alternating the directional deposition of different

• atomic structures depending on the main parameters of the deposition process. Keywords: hybrid nanostructure; mathematical modeling; modified embedded-atom method; molecular dynamics; spintronics; spin valve; vacuum deposition; Introduction Multilayer superconductor/ferromagnetic (S/F) hybrid

• spintronics applications were studied by the molecular dynamics method [33][34]. Molecular dynamics describes the motion of each nanosystem atom at a certain point in time, therefore, it is possible to reproduce the detailed evolution of nanoelements and their properties. The basis of the method is the

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

• -terminated tips In Figure 3, we compare AFM line profiles taken across the defect of interest (blue) and a corresponding defect-free region (grey) with a simple theoretical structure optimized by molecular dynamics calculations (see Methods for parameters). A preliminary comparison of Figure 3 with the

• above the defect in 4t show a reduced minimum, as well as a horizontal shift in position towards the defect centre due to a polaronic distortion induced by the vacancy’s localized negative charge. Molecular dynamics relaxation was unable to capture this effect as part of the modelling, so the ball and

• terminations. The defect free H–Si ball and stick model was the same as used in [43], with defects manually inserted using Avogadro [94][95]. The geometry of the defect atoms within the lattice were optimized using molecular dynamics relaxation with a Merck molecular force field (MMFF94) [96]. Images of the

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

• 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

• Information File 1, where we also discuss the robustness and reproducibility of the AFM results. Molecular dynamics simulations We employed molecular dynamics simulations to model both calcite and magnesite with their (10.4) surface exposed as a nine layer crystal with three surface unit cells in the

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

• Lukasz Baran Wojciech Rzysko Edyta Slyk Department for Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University in Lublin, Poland. 10.3762/bjnano.11.73 Abstract We introduce a molecular dynamics (MD) coarse-grained model for the description of

• can lead to valuable conclusions, which can be further explored and proved by experimental studies. To date, there are two main approaches that can complement the results obtained in experiments. The first one involves the use of all-atom simulations by molecular dynamics (MD) [27][28][29][30]. Even

• ” active sites, respectively. In a) we can see that the arms are marked as A, B, and C. e) Parameters of the molecular dynamics model. Part of the configurations for a) NT111 at T* = 0.58, b) NL111 at T* = 0.54, and c) WT111 at T* = 0.58, all with ρ* = 0.2. d) Corresponding Monte Carlo simulation on a

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

• 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

A novel dry-blending method to reduce the coefficient of thermal expansion of polymer templates for OTFT electrodes

• Xiangdong Ye,
• Bo Tian,
• Yuxuan Guo,
• Fan Fan and
• Anjiang Cai

Beilstein J. Nanotechnol. 2020, 11, 671–677, doi:10.3762/bjnano.11.53

• the influence of fullerene (C60) on the CTE of Araldite LY 5052/Aradur HY 5052 cross-linked epoxy resin by molecular dynamics simulations. The CTE was minimized by adding a maximum of 15.9 wt % fullerene to the LY/HY/C60 epoxy system. Liu et al. [14] selected MCM-41 mesoporous silica nanoparticles

Understanding nanoparticle flow with a new in vitro experimental and computational approach using hydrogel channels

• Armel Boutchuen,
• Dell Zimmerman,
• Abdollah Arabshahi,
• John Melnyczuk and
• Soubantika Palchoudhury

Beilstein J. Nanotechnol. 2020, 11, 296–309, doi:10.3762/bjnano.11.22

• applicable for modeling smaller NP systems or optimizing less detailed simulations due to their increased complexity and computational cost [17]. The coarse grained molecular dynamics simulations can characterize larger systems over time scales greater than 1 ms [21]. These slightly coarser models simulate a

• group of atoms or molecular fragment instead of an individual atom to incorporate a larger system. However, molecular dynamics models in general are more appropriate in understanding the size, surface, interaction, and uptake of a NP rather than their flow over larger dimensions as it models the

Rational design of block copolymer self-assemblies in photodynamic therapy

• Maxime Demazeau,
• Laure Gibot,
• Anne-Françoise Mingotaud,
• Patricia Vicendo,
• Clément Roux and
• Barbara Lonetti

Beilstein J. Nanotechnol. 2020, 11, 180–212, doi:10.3762/bjnano.11.15