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

Ferromagnetic behaviour of ZnO: the role of grain boundaries

• Boris B. Straumal,
• Svetlana G. Protasova,
• Andrei A. Mazilkin,
• Eberhard Goering,
• Gisela Schütz,
• Petr B. Straumal and
• Brigitte Baretzky

Beilstein J. Nanotechnol. 2016, 7, 1936–1947, doi:10.3762/bjnano.7.185

• the role of GB in ferromagnetic behaviour was supported by our new results on ZnO doped with nickel and iron [6][9][12] as well as by measurements with low-energy muon spin relaxation combined with molecular dynamics modeling and density functional theory calculations [13]. These new results

• in the bulk [13]. The LE-µSR measurements were supported by theoretical studies [13]. Using molecular dynamics the simulations of 4800 atoms in a periodic box were performed for two grain boundaries. They permitted to simulate the atomic disorder in the grain boundary region. The simulation periodic

• box was first equilibrated at 300 K and constant pressure of 105 Pa for 0.5 ns, then heated to 2700 K and equilibrated for 1 ns. Then it was cooled to 300 K and equilibrated for 1 ns. The atomic configurations in GBs obtained by the molecular dynamics formed the basis for the further density

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

• 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

• 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

Fracture behaviors of pre-cracked monolayer molybdenum disulfide: A molecular dynamics study

• Qi-lin Xiong,
• Zhen-huan Li and
• Xiao-geng Tian

Beilstein J. Nanotechnol. 2016, 7, 1411–1420, doi:10.3762/bjnano.7.132

• and Vibration, Xi’an Jiaotong University, Xi’an 710049, China 10.3762/bjnano.7.132 Abstract The fracture strength and crack propagation of monolayer molybdenum disulfide (MoS2) sheets with various pre-existing cracks are investigated using molecular dynamics simulation (MDS). The uniaxial tensions of

• model without finite size effect. Finally, the MDS results of monolayer MoS2 sheets with different angled crack are also analyzed based on the continuum fracture mechanics model. Keywords: crack propagation; fracture strength; molecular dynamics simulation; monolayer molybdenum disulfide; pre-existing

• molecular dynamics modeling To study the fracture behaviors of MoS2 sheets with different pre-existing cracks, the MD model of a defect-free MoS2 sheet composed of 31680 atoms (10560 Mo and 21120 S atoms) was built, with the spatial dimension of 299.5 Å × 297.6 Å as shown in Figure 1 (only part of the model

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

On the pathway of cellular uptake: new insight into the interaction between the cell membrane and very small nanoparticles

• Claudia Messerschmidt,
• Daniel Hofmann,
• Anja Kroeger,
• Katharina Landfester,
• Volker Mailänder and
• Ingo Lieberwirth

Beilstein J. Nanotechnol. 2016, 7, 1296–1311, doi:10.3762/bjnano.7.121

• higher compared to the cell membrane. Nonetheless, it is remarkable that quite a little difference in NP size results in completely different uptake morphologies. From molecular dynamics simulations of two curvature imprinting particles on a lipid bilayer membrane we learn, that the membrane mediates

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

• Michael Klocke Dietrich E. Wolf Department of Physics, University of Duisburg-Essen and CeNIDE, D-47048 Duisburg, Germany 10.3762/bjnano.7.63 Abstract A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM

• 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

• shift is commonly used instead of Δf in order to minimize the dependence on system parameters such as fz or kz. This is helpful in the simulation context, because molecular dynamics simulations are only feasible with exaggerated frequencies fz [32]). As in Figure 4, the dissipated energy ΔE fluctuates

Tight junction between endothelial cells: the interaction between nanoparticles and blood vessels

• Yue Zhang and
• Wan-Xi Yang

Beilstein J. Nanotechnol. 2016, 7, 675–684, doi:10.3762/bjnano.7.60

• equilibrium molecular dynamics simulations [84]. An experimental investigation showed a positive correlation between the concentration of Cu nanoparticles and the viscosity of viscoelastic surfactant solutions [85]. Interestingly, viscoelastic nanofluids containing multiwalled carbon nanotubes also showed non

In situ observation of deformation processes in nanocrystalline face-centered cubic metals

• Aaron Kobler,
• Christian Brandl,
• Horst Hahn and
• Christian Kübel

Beilstein J. Nanotechnol. 2016, 7, 572–580, doi:10.3762/bjnano.7.50

• investigated here. No significantly different behavior (within the statistical limitations) was observed for the different alloy systems, although molecular dynamics simulations suggest different dislocation and stacking fault densities with increasing strain as well as different grain boundary migration

First-principles study of the structure of water layers on flat and stepped Pb electrodes

• Xiaohang Lin,
• Ferdinand Evers and
• Axel Groß

Beilstein J. Nanotechnol. 2016, 7, 533–543, doi:10.3762/bjnano.7.47

• temperatures were addressed using ab initio molecular dynamics (AIMD) simulations [16] yielding good agreement with the experiment [17], and the influence of the presence of ions in aqueous electrolytes on the transport properties of atomic junctions was assessed [18] taking into account an appropriate

• terrace atoms, as confirmed by an analysis of the charge density difference upon water adsorption. The thermal stability of the water layers has been addressed by performing ab initio molecular dynamics simulations at a temperature of 140 K. The minimum-energy structure of the water layers on Pb(111) and

• structure at a coverage of 1 due to the larger lattice constant of Pb. At stepped Pb surfaces, the water layers are pinned at the step edge and form a complex network consisting of rectangles, pentagons and hexagons. The thermal stability of the water layers has been studied by using ab initio molecular

Free vibration of functionally graded carbon-nanotube-reinforced composite plates with cutout

• Mostafa Mirzaei and
• Yaser Kiani

Beilstein J. Nanotechnol. 2016, 7, 511–523, doi:10.3762/bjnano.7.45

• parameters. These parameters compensate for the errors generated due to the conventional rule of mixtures approach for a CNTRC. The values of these constants are obtained by matching the data obtained according to the above formula with those obtained based on the molecular dynamics simulation. It is worth

• present modified rule of mixtures approach and the molecular dynamics simulations of other researchers. A molecular dynamics simulation was performed by Han and Elliott [41]; however, since the condition of maximum thickness for CNTs was not satisfied in this research, their simulations were re-examined

• by Shen [28]. In the simulations of Han and Elliott [41], the effective thickness of the CNTs is set equal to at least 0.34 nm, which is open to criticism since it violates the criteria proposed by Wang and Zhang [42]. The molecular dynamics simulations of Shen [28] result in the following efficiency

Rigid multipodal platforms for metal surfaces

• Michal Valášek,
• Marcin Lindner and
• Marcel Mayor

Beilstein J. Nanotechnol. 2016, 7, 374–405, doi:10.3762/bjnano.7.34

Molecular machines operating on the nanoscale: from classical to quantum

• Igor Goychuk

Beilstein J. Nanotechnol. 2016, 7, 328–350, doi:10.3762/bjnano.7.31

• , friction and noise are intimately related in the microworld, which is nicely seen from a mechanistic derivation of (generalized) Langevin dynamics. It results from hyper-dimensional Hamiltonian dynamics with random initial conditions like in a molecular dynamics approach. For this reason, the thermodynamic

• classical dynamics approach first, we choose initial qi(0) and pi(0) from a canonical, hyper-dimensional, Gaussian distribution, ρ(qi(0),pi(0)), zero-centered in pi(0) subspace and centered around x(0) in qi(0) subspace, and characterized by the thermal bath temperature T, like in a typical molecular

• dynamics setup. Then, each ξ(t) presents a realization of a stationary, zero-mean, Gaussian stochastic process, which can be completely characterized by its autocorrelation function, . Here, denotes statistical averaging done with ρ(qi(0),pi(0)). An elementary calculation yields the fluctuation

Influence of calcium on ceramide-1-phosphate monolayers

• Joana S. L. Oliveira,
• Gerald Brezesinski,
• Alexandra Hill and
• Arne Gericke

Beilstein J. Nanotechnol. 2016, 7, 236–245, doi:10.3762/bjnano.7.22

• between the charged oxygen ions of the phosphomonoester head group. Interestingly, molecular dynamics simulations of dimyristoylphosphatidate (DMPA−) monolayer in water environment (and therefore one-fold deprotonated) reported no difference between the effect of Ca2+ or Na+ ions on the properties of a

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

• copper nanowires using molecular dynamics simulation. We find that the plasticity-mediated structural evolution leads to transformation of the initial hollow structure to a solid wire. The process involves three distinct stages, namely, collapse, recrystallization and slow recovery. We calculate the time

• , which would involve much longer time scales as compared to the plasticity-based mechanism. Keywords: dislocations; molecular dynamics; nanowire; thermal stability; Introduction Nanomaterials, as compared to bulk, are associated with large surfaces and interfaces with respect to their volume. The

• 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