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

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

• dynamics simulations, another setup was tested: TCB molecules will readily form dimers on terraces, in which two molecules will align next to each other (see inset of Figure 5). This process occurs spontaneously in MD simulations at 300 K when two TCB molecules are placed near each other on a KCl terrace

• . Therefore, fully exploring the phase space for complex flexible molecules would require further increasing the MD trajectory time or employing a different method, such as umbrella sampling. Converging entropy calculations In order to illuminate the problem of obtaining converged free energies from molecular

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

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

• 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

• 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

• dynamics simulations (AIMD) at a temperature of 140 K. Whereas the water layer on Pb(111) is already unstable at this temperature, the water layers on Pb(100), Pb(311), Pb(511) and Pb(711) exhibit a higher stability because of stronger water–water interactions. The vibrational spectra of the water layers

• 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

• 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

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

Synthesis and applications of carbon nanomaterials for energy generation and storage

• Marco Notarianni,
• Jinzhang Liu,
• Kristy Vernon and
• Nunzio Motta

Beilstein J. Nanotechnol. 2016, 7, 149–196, doi:10.3762/bjnano.7.17

Metal hydrides: an innovative and challenging conversion reaction anode for lithium-ion batteries

• Luc Aymard,
• Yassine Oumellal and
• Jean-Pierre Bonnet

Beilstein J. Nanotechnol. 2015, 6, 1821–1839, doi:10.3762/bjnano.6.186

• interesting alternatives to help the search and development of materials for hydrogen storage and batteries. The idea is, for instance, to look for materials having high volume capacity, minimal expansion volume and high lithium mobility. A recent study by molecular dynamics simulations has revealed that the

Possibilities and limitations of advanced transmission electron microscopy for carbon-based nanomaterials

• Xiaoxing Ke,
• Carla Bittencourt and
• Gustaaf Van Tendeloo

Beilstein J. Nanotechnol. 2015, 6, 1541–1557, doi:10.3762/bjnano.6.158

• Figure 3a [33]. More recent studies using molecular dynamics simulations based on tight-binding density functional theory [32] and first principle calculations [34] have agreed on a Td of 23 eV and 22 eV, respectively, corresponding to an accelerating voltage of about 110 kV using Equation 2. However

• thus provide a HRTEM image with an acceptable signal to noise ratio with only limited damage to the sample. The introduction of a high-speed detector may also have an impact on increasing the time resolution. In a molecular dynamics simulations on the reconstruction of vacancies, the time scale is

Influence of grain size and composition, topology and excess free volume on the deformation behavior of Cu–Zr nanoglasses

• Daniel Şopu and
• Karsten Albe

Beilstein J. Nanotechnol. 2015, 6, 537–545, doi:10.3762/bjnano.6.56

• properties of Cu–Zr nanoglasses (NGs) is investigated by molecular dynamics simulations using two model glasses of different alloy composition, namely Cu64Zr36 (Cu-rich) and Cu36Zr64 (Zr-rich). When the grain size is increased, or the fraction of interfaces in these NGs is decreased, we find a transition

• on the situation in bulk NGs. In this work, we study the influence of grain size and chemical composition on mechanical properties of Cu–Zr NGs by means of molecular dynamics simulations. First, we investigate whether by varying the grain size the plastic deformation of NGs changes. Second, we

• out in 3D periodic arrangements and thus surface effects are deliberately excluded. Methods Molecular dynamics simulations are carried out with the program package LAMMPS [18]. The modified Finnis–Sinclair type potential for Cu–Zr proposed by Mendelev et al. [19] was applied for describing the atomic

Synthesis of boron nitride nanotubes and their applications

• Saban Kalay,
• Zehra Yilmaz,
• Ozlem Sen,
• Melis Emanet,
• Emine Kazanc and
• Mustafa Çulha

Beilstein J. Nanotechnol. 2015, 6, 84–102, doi:10.3762/bjnano.6.9

• techniques that can generate an abundant amount of hydrogen, its storage and transportation is an obstacle for its widespread use. In this respect, BNNTs were also investigated for their hydrogen adsorption capacity. Molecular dynamics simulations indicated that the collision and adsorption behavior of

Quasi-1D physics in metal-organic frameworks: MIL-47(V) from first principles

• Danny E. P. Vanpoucke,
• Jan W. Jaeken,
• Stijn De Baerdemacker,
• Kurt Lejaeghere and
• Veronique Van Speybroeck

Beilstein J. Nanotechnol. 2014, 5, 1738–1748, doi:10.3762/bjnano.5.184

• based molecular dynamics simulations, which found Pt = 137 MPa [45]. In contrast to these simulations, experimental Hg-intrusion measurements did not give a transition at one specific pressure. Instead, the transition spanned a broader range of pressures: Pt = 85–125 MPa [45]. This is in perfect

Non-covalent and reversible functionalization of carbon nanotubes

• Antonello Di Crescenzo,
• Valeria Ettorre and
• Antonella Fontana

Beilstein J. Nanotechnol. 2014, 5, 1675–1690, doi:10.3762/bjnano.5.178

• ] through molecular dynamics simulations run for 0.4 ns. The nanotube represented the core of a SDS cylindrical micelles were the hydrophobic tails of SDS molecules could adopt a wide range of orientations with respect to the tube (see Figure 3, arrangement B). As no water density was observed in the

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

• dynamics simulations, in contrast, suggest that the glass–glass boundaries would delocalize in a few nanoseconds at 100 K.) These observations emphasize that detailed computations will be necessary in order to determine the interatomic forces in solids with modified structures/basic units and reduced

• melt-quenched variants) even at temperatures close to the crystallization temperature. To date, the width of the glass–glass boundaries has not increased by a factor of more than two even after annealing the specimens close to the glass transition temperature for several hours. (Usual molecular

Magnesium batteries: Current state of the art, issues and future perspectives

• Rana Mohtadi and
• Fuminori Mizuno

Beilstein J. Nanotechnol. 2014, 5, 1291–1311, doi:10.3762/bjnano.5.143

• . [53] studied the possibility of magnesium ion conduction in the high temperature phase of magnesium borohydride using first-principles molecular dynamics simulations FPMD [53][54]. The magnesium ions, present in the center of a tetrahedral cage surrounded by the BH4− anions, were found to have limited

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

• each of four studied systems 800–1000 trajectories of a discharging proton were integrated by molecular dynamics simulations until discharge occurred. The results show significant influences of ion presence on the average behavior of protons prior to the discharge event. Rationalization of the observed

Classical molecular dynamics investigations of biphenyl-based carbon nanomembranes

• Andreas Mrugalla and
• Jürgen Schnack

Beilstein J. Nanotechnol. 2014, 5, 865–871, doi:10.3762/bjnano.5.98

• ., a lattice structure as in solids cannot be assumed, a quantum mechanical simulation is virtually impossible. In this article we therefore resort to classical molecular dynamics simulations, which allow to simulate up to several millions of carbon atoms. In order to account for the very flexible spn

• configuration that is laterally linked through carbon bonds of broken phenyls. We show that such structures indeed form in our simulations. The article is organized as follows. In the next two sections we shortly repeat the essentials of our classical molecular dynamics simulations. The main section discusses

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

• Pavel V. Komarov,
• Pavel G. Khalatur and
• Alexei R. Khokhlov

Beilstein J. Nanotechnol. 2013, 4, 567–587, doi:10.3762/bjnano.4.65

• Department, Moscow State University, Moscow 119991, Russia 10.3762/bjnano.4.65 Abstract Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the

• PEFCs [54][55][56][57][58][59]. There are excellent reviews that cover this subject in considerable detail [5][12][60]. In this paper, the atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in hydrated Nafion membrane and the solvation and

Plasticity of nanocrystalline alloys with chemical order: on the strength and ductility of nanocrystalline Ni–Fe

• Jonathan Schäfer and
• Karsten Albe

Beilstein J. Nanotechnol. 2013, 4, 542–553, doi:10.3762/bjnano.4.63

• while at large strains dislocation motion becomes dominant [12]. Computational attempts such as molecular dynamics simulations (MD) can help to understand the macroscopic properties by means of the atomistic processes. For intermetallic phases, MD simulations have been successfully employed, to

Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects

• Hlengisizwe Ndlovu,
• Alison E. Ashcroft,
• Sheena E. Radford and
• Sarah A. Harris

Beilstein J. Nanotechnol. 2013, 4, 429–440, doi:10.3762/bjnano.4.50

• , Leeds LS2 9JT, UK 10.3762/bjnano.4.50 Abstract We examine how the different steric packing arrangements found in amyloid fibril polymorphs can modulate their mechanical properties using steered molecular dynamics simulations. Our calculations demonstrate that for fibrils containing structural defects

• modifications. Molecular dynamics simulations Molecular dynamics simulations were run using AMBER9 [35] and NAMD2.7b1 [36] simulation packages, with the all atom AMBER99SB [37] and the CHARMM22/CMAP [38] force fields used, respectively. All models were explicitly solvated in a periodic water-box of TIP3

Kelvin probe force microscopy of nanocrystalline TiO₂ photoelectrodes

• Alex Henning,
• Gino Günzburger,
• Res Jöhr,
• Yossi Rosenwaks,
• Biljana Bozic-Weber,
• Catherine E. Housecroft,
• Edwin C. Constable,
• Ernst Meyer and
• Thilo Glatzel

Beilstein J. Nanotechnol. 2013, 4, 418–428, doi:10.3762/bjnano.4.49

• that the N719 is chemisorbed either through two or three carboxylic acid groups. Results by Lee et al. support that an additional hydrogen bonding (physisorption) is present [60]. Molecular dynamics simulations by DeAngelis et al. show that the binding occurs through three carboxylic acid groups and

Influence of the solvent on the stability of bis(terpyridine) structures on graphite

• Daniela Künzel and
• Axel Groß

Beilstein J. Nanotechnol. 2013, 4, 269–277, doi:10.3762/bjnano.4.29

• Daniela Kunzel Axel Gross Institute of Theoretical Chemistry, Ulm University, D-89069 Ulm, Germany 10.3762/bjnano.4.29 Abstract The effect of solvation on the adsorption of organic molecules on graphite at room temperature has been addressed with force-field molecular dynamics simulations. As a

• scheme, such as the recently developed enveloping distribution sampling (EDS) method [30]. However, using one of these schemes often requires a series of molecular dynamics simulations. In order to derive the adsorption energy of the BTP molecules from solution at finite temperatures, we rather take

• to improve by using the solvent model. The free enthalpies are derived as the energy average through the molecular dynamics simulations, which were performed within the NPT ensemble at 298 K (Nosé thermostat) and at 0.0001 GPa (Berendsen barostat) after initial geometry optimization steps of the