Free-radical gases on two-dimensional transition-metal disulfides (XS₂, X = Mo/W): robust half-metallicity for efficient nitrogen oxide sensors

• Chunmei Zhang,
• Yalong Jiao,
• Fengxian Ma,
• Sri Kasi Matta,
• Steven Bottle and
• Aijun Du

Beilstein J. Nanotechnol. 2018, 9, 1641–1646, doi:10.3762/bjnano.9.156

• meV and 3 Å, suggesting that water is physically adsorbed on the surface of the WS2 nanosheet. Monolayer MoS2 [38] and multilayer MoS2 field effect transistors [17] for sensing NO at room temperature have been fabricated experimentally. In this work, the ab initio molecular dynamics simulations at

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

• suggest that the combination of molecular dynamics ReaxFF simulations and blind docking techniques can be used as an explorative tool prior to experiments, which is useful for rational design of new drug delivery systems. Keywords: drug delivery; PEGylated nanoparticle; PLA; polymeric nanoparticle

• , 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

• determine the spatial distribution of cilostazol in polymeric NPs and to explore its potential use in this kind of drug delivery system. Experimental Characterization of copolymer structures by all-atom molecular dynamics simulations The poly(lactic acid) core PLA polymer chains were built in three

Induced smectic phase in binary mixtures of twist-bend nematogens

• Anamarija Knežević,
• Irena Dokli,
• Marin Sapunar,
• Suzana Šegota,
• Ute Baumeister and
• Andreja Lesac

Beilstein J. Nanotechnol. 2018, 9, 1297–1307, doi:10.3762/bjnano.9.122

• investigate how conformational disorder of terminal chains might affect induction of the smectic phase we performed a molecular dynamics simulation of BB at 80 K with a time step of 1 fs for a total duration of 10 ps using the Turbomole program package [48] at the PBE/def2-TZVP level of theory using the RI

• molecular dynamics. Snapshots were taken every 0.2 ps from a 10 ps molecular dynamics simulation at 80 K. To illustrate the motion of the alkyl chain separately from the motion of the remainder of the molecule, the snapshots are shown with the benzene ring of each geometry aligned, and only the alkyl chain

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

• insight into the fundamental origin of sliding friction. Results: Using molecular dynamics we investigate frictional properties of aluminum and palladium nanoparticles deposited on a graphene layer. We study the time evolution of the total momentum of the system, the total and potential energies, the

• 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

• coordinates of metal atoms with maximum and minimum values along the x,y,z-axes. The substrate in our model is a graphene sheet that is parallel to the xy-plane with armchair and zigzag fixed edges along the x- and y-directions (Figure 1). Snapshots in this paper were taken by using the Visual Molecular

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

• molecular dynamics simulations. Fully and partially hydroxylated surfaces represent substrates before and after electron beam treatment and this study examines the role of electron beam pretreatment on the substrates in the initial stages of precursor dissociation and formation of Pt deposits. Our

• 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

• originally bonded to Pt, fragments and bonds to the adjacent vacant site, as observed in the 3 × 3 × 4 cell (see Figure 2d and Figure 3e). These DFT relaxed structures (as shown in Figure 3b–e) are considered as starting point for molecular dynamics simulations. The trajectory of the MD simulations for the

Review: Electrostatically actuated nanobeam-based nanoelectromechanical switches – materials solutions and operational conditions

• Liga Jasulaneca,
• Jelena Kosmaca,
• Raimonds Meija,
• Jana Andzane and
• Donats Erts

Beilstein J. Nanotechnol. 2018, 9, 271–300, doi:10.3762/bjnano.9.29

• switches is mostly focused on developing experimental approaches for device prototype fabrication and testing in laboratory environment and theoretical modelling based on continuum mechanics and molecular dynamics, allowing simulations to be performed on the processes occurring in NEM switching devices and

• experiment was carried out with an AFM in amplitude modulation mode complemented with molecular dynamics simulations. An exponential wear rate dependence on the peak force load was found, suggesting that lower contact forces are needed to reduce the wear rate. It should be noted that for soft materials

Patterning of supported gold monolayers via chemical lift-off lithography

• Liane S. Slaughter,
• Kevin M. Cheung,
• Sami Kaappa,
• Huan H. Cao,
• Qing Yang,
• Thomas D. Young,
• Andrew C. Serino,
• Sami Malola,
• Jana M. Olson,
• Stephan Link,
• Hannu Häkkinen,
• Anne M. Andrews and
• Paul S. Weiss

Beilstein J. Nanotechnol. 2017, 8, 2648–2661, doi:10.3762/bjnano.8.265

• found to be consistent with molecular dynamics simulations that predicted the removal of no more than 1.5 Au atoms per thiol, thus presenting a monolayer-like structure. Keywords: chemical patterning; hybrid material; monolayer; soft lithography; two-dimensional material; Introduction Chemical lift

• into lift-off lithography removal mechanisms and outcomes of the lift-off process at the atomic scale, we simulated lift-off using molecular dynamics and density functional theory. We determined the energetics of this complex system during lift-off. The simulations were used to predict the

• assumptions made above regarding the structure of Au–alkanethiolate monolayers on PDMS are in agreement with estimates of the stoichiometry of the Au–alkanethiolate monolayer calculated through molecular dynamics simulations. Atomic rearrangement during the CLL process was modeled using density functional

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

Robust procedure for creating and characterizing the atomic structure of scanning tunneling microscope tips

• Sumit Tewari,
• Koen M. Bastiaans,
• Milan P. Allan and
• Jan M. van Ruitenbeek

Beilstein J. Nanotechnol. 2017, 8, 2389–2395, doi:10.3762/bjnano.8.238

• repeatable cycles, which is interpreted as evidence for a crystalline tip structure. This work on mechanical annealing was inspired by earlier break junction and STM experiments, supported by molecular dynamics simulations [25][27][28]. A first application of this approach for a Au STM tip over a graphene

• imaged, and we find that the shape of the STM tip evolves surprisingly smoothly and reproducibly towards an atomically sharp and symmetric structure of the second layer from the tip apex atom, starting from any random and poorly defined tip shapes. As has been illustrated by molecular dynamics

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

• nanoindentation results (i.e., indentation on the upper area) of the vertical grain boundary showed that the force was translated along the grain boundary, thereby producing intergranular fractures. Keywords: indentation; molecular dynamics; nanograin boundary; nanoscratch; Introduction The recent developments

• ][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

Au₅₅, a stable glassy cluster: results of ab initio calculations

• Dieter Vollath,
• David Holec and
• Franz Dieter Fischer

Beilstein J. Nanotechnol. 2017, 8, 2221–2229, doi:10.3762/bjnano.8.222

• means of molecular dynamics or ab initio modeling. These studies resulted in puzzling and often contradictory conclusions regarding the nanoparticle structure: crystalline vs non-crystalline, icosahedral vs cuboctahedral or even unspecific shapes. Doye and Wales [16] described their resulting Au55

Comprehensive investigation of the electronic excitation of W(CO)₆ by photoabsorption and theoretical analysis in the energy region from 3.9 to 10.8 eV

• Mónica Mendes,
• Khrystyna Regeta,
• Filipe Ferreira da Silva,
• Nykola C. Jones,
• Søren Vrønning Hoffmann,
• Gustavo García,
• Chantal Daniel and
• Paulo Limão-Vieira

Beilstein J. Nanotechnol. 2017, 8, 2208–2218, doi:10.3762/bjnano.8.220

• initio molecular dynamics simulations of focused electron beam induced deposition (FEBID) precursor molecules adsorbed on fully and partially hydroxylated SiO2 surfaces [24]. Electron-induced reactions in FEBID processes are initiated by low-energy secondary electrons rather than the high-energy primary

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

Modelling focused electron beam induced deposition beyond Langmuir adsorption

• Dédalo Sanz-Hernández and
• Amalio Fernández-Pacheco

Beilstein J. Nanotechnol. 2017, 8, 2151–2161, doi:10.3762/bjnano.8.214

• model to simulate gas flow surface distribution when delivered from an injector [24], code that analytically and numerically solves FEBID continuum models [25], a hybrid Monte Carlo-continuum model to predict and guide the growth of 3D nanostructures [26], and a molecular dynamics model to give an

A nanocomplex of C₆₀ fullerene with cisplatin: design, characterization and toxicity

• Svitlana Prylutska,
• Svitlana Politenkova,
• Kateryna Afanasieva,
• Volodymyr Korolovych,
• Kateryna Bogutska,
• Andriy Sivolob,
• Larysa Skivka,
• Maxim Evstigneev,
• Viktor Kostjukov,
• Yuriy Prylutskyy and
• Uwe Ritter

Beilstein J. Nanotechnol. 2017, 8, 1494–1501, doi:10.3762/bjnano.8.149

• complexation were investigated by calculating the energy-minimized spatial structure of their complex, shown in Figure 3. The initial location coordinates of Cis above the C60 fullerene surface were taken from the ab initio structure [39]. Then we performed the molecular dynamics simulation of this nanocomplex

Atomic structure of Mg-based metallic glass investigated with neutron diffraction, reverse Monte Carlo modeling and electron microscopy

• Rafał Babilas,
• Dariusz Łukowiec and
• Laszlo Temleitner

Beilstein J. Nanotechnol. 2017, 8, 1174–1182, doi:10.3762/bjnano.8.119

• the ternary Mg–Cu–Y glasses. Gao et al. [11] performed ab initio molecular dynamics simulations of the structural evolution of a Mg65Cu25Y10 alloy from liquid to glass state. Moreover, Laws et al. [12] provided an analysis of the dynamic crystallization in Mg65Cu25Y10 bulk metallic glass using

• samples was characterized by high-energy X-ray and neutron diffraction as well as the EXAFS method. The obtained experimental data were fitted by RMC modeling. Also, Gao et al. [11] used ab initio molecular dynamics to describe the atomic structure of a Mg65Cu25Y10 alloy during transformation from the

Bio-inspired micro-to-nanoporous polymers with tunable stiffness

• Julia Syurik,
• Ruth Schwaiger,
• Prerna Sudera,
• Stephan Weyand,
• Siegbert Johnsen,
• Gabriele Wiegand and
• Hendrik Hölscher

Beilstein J. Nanotechnol. 2017, 8, 906–914, doi:10.3762/bjnano.8.92

• polymeric walls as predicted from the point of discontinuous molecular dynamics [22]. Therefore, in addition to the wide range of applications, the size-dependent viscoelastic properties of polymers with a morphological gradient, especially in the nanometre-range, are a very interesting phenomena. Here, we

• of the elastic modulus in comparison to its bulk value was predicted from the point of discontinuous molecular dynamics [22]. We have estimated this critical value for PMMA as 30 nm, taking into account a Kuhn length of 1.53 nm [41]. Thus, in our study, the mean wall thickness is 8–13 times greater

The role of 2D/3D spin-polarization interactions in hybrid copper hydroxide acetate: new insights from first-principles molecular dynamics

• Ziyad Chaker,
• Guido Ori,
• Mauro Boero and
• Carlo Massobrio

Beilstein J. Nanotechnol. 2017, 8, 857–860, doi:10.3762/bjnano.8.86

• Cu2(OH)3CH3COO·H2O is studied as a function of the applied pressure within first-principles molecular dynamics. We are able to elucidate the interplay between the structural properties of this material and its magnetic character, both at the local (atomic) level and at the bulk level. We performed a

• between the spin polarizations pertaining to each layer. Therefore, at high pressure, copper hydroxide acetate is a ferromagnet with no changes of spin polarization in the direction perpendicular to the inorganic layers. Keywords: first-principles molecular dynamics; hybrid material; magnetic properties

• (within each layer) a weak ferromagnetic (F) intralayer (2D) character. The use of pressure is a valuable and practical tool to tune the magnetic behavior of this lamellar hybrid material [4]. In our previous studies, first-principles molecular dynamics (FPMD) approaches combined with density functional

Investigation of growth dynamics of carbon nanotubes

• Marianna V. Kharlamova

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

• growth of carbon filaments on liquid catalysts [24][25][26]. Later on, the VLS model was applied to describe the growth of MWCNTs [27] and SWCNTs [28][29] on liquid-metal particles. The atomic-level description of the VLS growth process of SWCNTs was performed by molecular dynamics simulations [29][30

• would lead to an unphysically large heat flow [30][32]. Molecular dynamics simulations performed in [30][32] showed that the carbon concentration gradient within the catalytic particle is important for the VLS growth of SWCNTs, whereas the temperature gradient is not necessary. Thermodynamic

• carbon atoms was the growth rate-limiting process. The surface diffusion mechanism of the growth of carbon nanofibers and nanotubes on metallic catalysts was also revealed by theoretical methods [41][42][44]. In [44], Raty with co-authors reported ab initio molecular dynamics simulations of the formation

First examples of organosilica-based ionogels: synthesis and electrochemical behavior

• Andreas Taubert,
• Ruben Löbbicke,
• Barbara Kirchner and
• Fabrice Leroux

Beilstein J. Nanotechnol. 2017, 8, 736–751, doi:10.3762/bjnano.8.77

• molecular dynamics (AIMD) simulations in which the forces are calculated from the electronic structure on the fly were carried out as described previously [41] using the cp2k program packages [42]. AIMD simulation was started from a classical molecular dynamics simulation snapshot of 32 ion pairs of

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. Both molecules contain the same anchoring groups and benzene ring structures, yet differ in their flexibility. Therefore, the entropic contributions to their free energy differ, which affects surface processes. Using potential of mean force and thermodynamic integration techniques, free

• understanding dynamic processes of organic molecules on insulating substrates. Keywords: entropy; free energy; molecular dynamics; organic molecules; potential of mean force; thermodynamic integration surface step; Introduction In recent years molecular films and self-assembled monolayers have attracted a lot

• 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

Dispersion of single-wall carbon nanotubes with supramolecular Congo red – properties of the complexes and mechanism of the interaction

• Anna Jagusiak,
• Barbara Piekarska,
• Tomasz Pańczyk,
• Małgorzata Jemioła-Rzemińska,
• Elżbieta Bielańska,
• Barbara Stopa,
• Grzegorz Zemanek,
• Janina Rybarska,
• Irena Roterman and
• Leszek Konieczny

Beilstein J. Nanotechnol. 2017, 8, 636–648, doi:10.3762/bjnano.8.68

• therapy. The aim of our studies is to explain whether CR-functionalized SWNTs could be used as drug delivery systems. Molecular dynamics study of SWNT–CR interactions has already been published [39]. These authors studied several combinations of parameters in order to assess how the SWNT diameter and CR

Fundamental properties of high-quality carbon nanofoam: from low to high density

• Natalie Frese,
• Shelby Taylor Mitchell,
• Christof Neumann,
• Amanda Bowers,
• Armin Gölzhäuser and
• Klaus Sattler

Beilstein J. Nanotechnol. 2016, 7, 2065–2073, doi:10.3762/bjnano.7.197

• cellular structures, other scaffolds have been suggested in some cases, for example, for gold. Foams of connected gold nanowires have been designed in molecular dynamics computer simulations [8]. Also, for materials such as glass compounds, nanofoam with a three-dimensional scaffold of interconnected

The difference in the thermal conductivity of nanofluids measured by different methods and its rationalization

• Aparna Zagabathuni,
• Sudipto Ghosh and
• Shyamal Kumar Pabi

Beilstein J. Nanotechnol. 2016, 7, 2037–2044, doi:10.3762/bjnano.7.194

• phononic heat exchange during the collision. In order to do so Karthik et al. [23] used a continuum approach rather than classical molecular dynamics (CMD) approach to estimate the energy exchange between the nanoparticles and wall, because in the CMD approach the movement of electrons cannot be considered