Intuitive human interface to a scanning tunnelling microscope: observation of parity oscillations for a single atomic chain

• Sumit Tewari,
• Jacob Bakermans,
• Christian Wagner,
• Federica Galli and
• Jan M. van Ruitenbeek

Beilstein J. Nanotechnol. 2019, 10, 337–348, doi:10.3762/bjnano.10.33

• –machine augmented system in which the operator and the machine are connected by a real-time simulation. Here, a 3D motion control system is integrated with an ultra-high vacuum (UHV) low-temperature scanning tunnelling microscope (STM). Moreover, we coupled a real-time molecular dynamics (MD) simulation

• and combined it with a molecular dynamics (MD) simulator that simulates in real-time the manipulation process going on in the STM. The MD simulation not only provides information about the atomic scale structure of the junction, but also serves as a visual feedback to the operator in real-time who can

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

Hydrogen-induced plasticity in nanoporous palladium

• Markus Gößler,
• Eva-Maria Steyskal,
• Markus Stütz,
• Norbert Enzinger and
• Roland Würschum

Beilstein J. Nanotechnol. 2018, 9, 3013–3024, doi:10.3762/bjnano.9.280

• lower surface areas measured after compression tests [47]. Therefore, in our case of nanoporous palladium under compression a coarsening of the structure can be expected, giving rise to the length contraction. It has been shown using molecular dynamics (MD) simulations that plastic deformation at

Recent highlights in nanoscale and mesoscale friction

• Andrea Vanossi,
• Dirk Dietzel,
• Andre Schirmeisen,
• Ernst Meyer,
• Rémy Pawlak,
• Thilo Glatzel,
• Marcin Kisiel,
• Shigeki Kawai and
• Nicola Manini

Beilstein J. Nanotechnol. 2018, 9, 1995–2014, doi:10.3762/bjnano.9.190

• mechanisms of structural lubricity. This crucial importance of the edge was also demonstrated by molecular dynamics (MD) simulations for Kr islands adsorbed on Pb(111). Here, depending on size and shape of the islands, the edge generates a barrier for the unpinning and successive advancement of the edge

Defect formation in multiwalled carbon nanotubes under low-energy He and Ne ion irradiation

• Santhana Eswara,
• Jean-Nicolas Audinot,
• Brahime El Adib,
• Maël Guennou,
• Tom Wirtz and
• Patrick Philipp

Beilstein J. Nanotechnol. 2018, 9, 1951–1963, doi:10.3762/bjnano.9.186

• improved mechanical properties which is similar to the one of collagen found in nature [7]. Vacancy formation and interconnections forming between CNTs have also been observed in molecular dynamics (MD) simulations during the irradiation of SWCNTs supported by silica [8]. MD simulations have been used to

• found in experiments. Molecular dynamics (MD) simulations would be able to provide an atomistic description of the sputter processes, which has already been done for several systems [48], however experimental fluences are beyond their possibilities. BCA-based simulations have already been used for the

Atomic-level characterization and cilostazol affinity of poly(lactic acid) nanoparticles conjugated with differentially charged hydrophilic molecules

• María Francisca Matus,
• Martín Ludueña,
• Cristian Vilos,
• Iván Palomo and
• Marcelo M. Mariscal

Beilstein J. Nanotechnol. 2018, 9, 1328–1338, doi:10.3762/bjnano.9.126

• , cilostazol [32][33]. PEG chains typically create an interface between the NP core (PLA) and the hydrophilic environment, where the drug encapsulation is largely dependent on the intrinsic affinity between the drug and the PLA core [31]. All-atom molecular dynamics (MD) simulations were performed using the

Atomistic modeling of tribological properties of Pd and Al nanoparticles on a graphene surface

• Alexei Khomenko,
• Miroslav Zakharov,
• Denis Boyko and
• Bo N. J. Persson

Beilstein J. Nanotechnol. 2018, 9, 1239–1246, doi:10.3762/bjnano.9.115

• the friction dynamics of metallic nanoparticles [14] makes it virtually impossible to construct a general and reliable analytical theory of the phenomena under consideration. Therefore, computer modeling, in particular molecular dynamics (MD), is a useful tool for the theoretical study of friction and

Fatigue crack growth characteristics of Fe and Ni under cyclic loading using a quasi-continuum method

• Ren-Zheng Qiu,
• Yi-Chen Lin and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2018, 9, 1000–1014, doi:10.3762/bjnano.9.93

• , strong materials. Considerable attention has been focused on the investigation of the fatigue crack growth behavior in single crystals under cyclic loading using molecular dynamics (MD), which is an effective tool for analyzing the mechanical deformation and mechanical properties of materials at the

Dynamics and fragmentation mechanism of (C₅H₄CH₃)Pt(CH₃)₃ on SiO₂ surfaces

• Kaliappan Muthukumar,
• Harald O. Jeschke and
• Roser Valentí

Beilstein J. Nanotechnol. 2018, 9, 711–720, doi:10.3762/bjnano.9.66

• beam pretreated surfaces. Hence, in order to extend the knowledge on the adsorption and to address the open questions in the deposition process, in this study we use DFT and finite temperature DFT-based molecular dynamics (MD) simulations and investigate the adsorption behavior of (C5H4CH3)Pt(CH3)3 on

Interface conditions of roughness-induced superoleophilic and superoleophobic surfaces immersed in hexadecane and ethylene glycol

• Yifan Li,
• Yunlu Pan and
• Xuezeng Zhao

Beilstein J. Nanotechnol. 2017, 8, 2504–2514, doi:10.3762/bjnano.8.250

• of roughness by using AFM. Results show that the slip length enhanced with larger RMS roughness, as the increasing roughness could magnify the intrinsic wetting properties of surface. In addition, the published studies based on LB simulation and molecular dynamics (MD) also show that roughness could

Molecular dynamics simulations of nanoindentation and scratch in Cu grain boundaries

• Shih-Wei Liang,
• Ren-Zheng Qiu and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2017, 8, 2283–2295, doi:10.3762/bjnano.8.228

• scratch conditions were studied by molecular dynamics (MD) simulations. The type of grain boundary is the main factor in the control of the substrate atoms with respect to the size of dislocations since the existence of the grain boundary itself restricts the movement associated with dislocations. In this

• ][18][19][20][21]. Molecular dynamics (MD) simulation is an effective tool for studying material behavior and system design at the nanometer scale while avoiding experimental noise and turbulence issues. Landman et al. [7] studied the interactional properties (i.e., the characteristics of deformation

Velocity dependence of sliding friction on a crystalline surface

• Christian Apostoli,
• Giovanni Giusti,
• Jacopo Ciccoianni,
• Gabriele Riva,
• Rosario Capozza,
• Rosalie Laure Woulaché,
• Andrea Vanossi,
• Emanuele Panizon and
• Nicola Manini

Beilstein J. Nanotechnol. 2017, 8, 2186–2199, doi:10.3762/bjnano.8.218

• of the atomic force microscope (AFM) and its friction force microscope (FFM) variant [6][7][8], as well as the extensive usage of atomistic molecular dynamics (MD) simulations and modeling made possible by the vastly increased computing power availability [9][10][11][12][13][14][15][16]. Despite this

Calculating free energies of organic molecules on insulating substrates

• Julian Gaberle,
• David Z. Gao and
• Alexander L. Shluger

Beilstein J. Nanotechnol. 2017, 8, 667–674, doi:10.3762/bjnano.8.71

• molecular dynamics (MD) simulations have been developed for many years and the most popular ones are summarised in [31]. Instead of calculating free energies directly, they can be expressed as averages over ensembles of atomic configurations. Such ensembles can be obtained from Monte Carlo (MC) or MD

Numerical investigation of depth profiling capabilities of helium and neon ions in ion microscopy

• Patrick Philipp,
• Lukasz Rzeznik and
• Tom Wirtz

Beilstein J. Nanotechnol. 2016, 7, 1749–1760, doi:10.3762/bjnano.7.168

• dynamics (MD) simulations, possible changes in the sample upon irradiation due to chemical reactions, as they are included in reactive force fields [27][28][29], are not contained in the model, but SD_TRIM_SP has the advantage to allow for the simulation of high fluences up in the 1018 ions/cm2 range, i.e

• chemical species present in the different layers, the influence of atomic mass on atomic mixing and the sputtering processes can be studied for different primary ion species. For this reason, layers of polytetrafluoroethylene (PTFE), PS or PMMA have been embedded into PE layers. Compared to molecular

Three-gradient regular solution model for simple liquids wetting complex surface topologies

• Sabine Akerboom,
• Marleen Kamperman and
• Frans A. M. Leermakers

Beilstein J. Nanotechnol. 2016, 7, 1377–1396, doi:10.3762/bjnano.7.129

• methods [29], molecular dynamics (MD) [23][30][31][32], and mesoscopic lattice-Boltzmann (LB) models [33][34][35][36][37] are a viable option for this problem, but are challenging because wetting on complex structures involves multiple length scales [38] and the time needed to converge to a solution can

Experimental and simulation-based investigation of He, Ne and Ar irradiation of polymers for ion microscopy

• Lukasz Rzeznik,
• Yves Fleming,
• Tom Wirtz and
• Patrick Philipp

Beilstein J. Nanotechnol. 2016, 7, 1113–1128, doi:10.3762/bjnano.7.104

• + bombardment influences roughness formation and preferential sputtering for polymer samples and how they compare to Ar+ primary ions used in classical SIMS by combining experimental techniques with Molecular Dynamics (MD) simulations and SD_TRIM_SP modelling. The results show that diffusion coefficients for He

• of the sample under ion bombardment is obtained. As an example, one may cite molecular dynamics (MD) simulations of Ar+ irradiation on a benzene overlayer on a Ni(001) surface [17] and on an ethylidyne (C2H3) overlayer on a Pt(111) substrate [18]. Ion bombardment on polymers was reported first for 1

• average roughness measurement is based on the roughness from 6 different linescans covering different areas of the scanned image. Numerical methods Diffusion of rare gas atoms To study the mobility of noble gas atoms in a polymer matrix molecular dynamics (MD) simulations have been used to track the time

Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy

• Michael Klocke and
• Dietrich E. Wolf

Beilstein J. Nanotechnol. 2016, 7, 708–720, doi:10.3762/bjnano.7.63

• these models use ab initio molecular dynamics or DFT methods [2][18][19], which represent the material properties most reliably. Their computational demand is very high, though, so that the force between tip and sample surface is usually calculated for a quasistatic tip. Molecular dynamics (MD

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

• still needs to be probed through rigorous atomistic simulation without relying on the preconceived notion of diffusive transport of vacancies. In this article, we study the above-mentioned issue by performing molecular dynamics (MD) simulation of ultra-thin single crystalline copper nanowire (NW) with

Electroviscous effect on fluid drag in a microchannel with large zeta potential

• Dalei Jing and
• Bharat Bhushan

Beilstein J. Nanotechnol. 2015, 6, 2207–2216, doi:10.3762/bjnano.6.226

• molecular dynamics (MD) simulations. They found that a large surface charge density results in a smaller slip. Jing and Bhushan [13] experimentally studied the coupling relationship between the surface charge and the slip of a smooth and hydrophobic octadecyltrichlorosilane (OTS) sample immersed in

Simulation of thermal stress and buckling instability in Si/Ge and Ge/Si core/shell nanowires

• Suvankar Das,
• Amitava Moitra,
• Mishreyee Bhattacharya and
• Amlan Dutta

Beilstein J. Nanotechnol. 2015, 6, 1970–1977, doi:10.3762/bjnano.6.201

• stress for elastic instability of the nanowire, which furnishes the safe limits of designing and operating parameters of these nanowire devices. Results and Discussion Simulation scheme The present study involves a series of molecular statics (MS) and molecular dynamics (MD) simulations of core/shell

Multiscale modeling of lithium ion batteries: thermal aspects

• Arnulf Latz and
• Jochen Zausch

Beilstein J. Nanotechnol. 2015, 6, 987–1007, doi:10.3762/bjnano.6.102

• energy barriers caused by the local environment of the Li ions. They may depend in solids on vacancy distributions as well as on the local lithium-ion concentration itself [9][11][12][13]. The diffusion coefficients for liquid electrolytes might more easily obtained from molecular dynamics (MD

Nanometer-resolved mechanical properties around GaN crystal surface steps

• Jörg Buchwald,
• Marina Sarmanova,
• Bernd Rauschenbach and
• Stefan G. Mayr

Beilstein J. Nanotechnol. 2014, 5, 2164–2170, doi:10.3762/bjnano.5.225

• more advanced surface features, including steps, are unclear at this point. The present work addresses the mechanical behavior around a gallium nitride (GaN) step employing a combination of classical molecular dynamics (MD) simulations with a finite element (FEM) approach and CR-AFM experiments. GaN is

Sequence-dependent electrical response of ssDNA-decorated carbon nanotube, field-effect transistors to dopamine

• Hari Krishna Salila Vijayalal Mohan,
• Jianing An and
• Lianxi Zheng

Beilstein J. Nanotechnol. 2014, 5, 2113–2121, doi:10.3762/bjnano.5.220

• devices, suggesting carrier scattering by molecular coating [16]. There were no major changes observed for gmp or H. According to molecular dynamics (MD) simulations [28][29], ssDNA interacts with the SWCNT sidewall through its DNA bases [30][31], with a significant number of the bases being desorbed [32

On the structure of grain/interphase boundaries and interfaces

• K. Anantha Padmanabhan and
• Herbert Gleiter

Beilstein J. Nanotechnol. 2014, 5, 1603–1615, doi:10.3762/bjnano.5.172

• weaker than the grain interior because of the larger interatomic distances.) Therefore, for this class of materials molecular dynamics (MD) simulations may be used to determine the structure of grain/interphase boundaries/interfaces. (As these involve the use of empirical potentials, their relevance has

Double layer effects in a model of proton discharge on charged electrodes

• Johannes Wiebe and
• Eckhard Spohr

Beilstein J. Nanotechnol. 2014, 5, 973–982, doi:10.3762/bjnano.5.111

• proton transfer and discharge at charged electrodes on the basis of reactive force field molecular dynamics (MD), which allows us at present to incorporate for a given model the first four of these requirements into a molecular model. As a starting system we chose a simple platinum (111) surface, because