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

• -conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to

• total number of atoms in these systems was limited to about two million because of computer memory and CPU limitations [28]. Significant efforts have been made to take into account quantum effects and chemical reactions within the molecular dynamics models. For this purpose, the so-called Reax force

Deformation-induced grain growth and twinning in nanocrystalline palladium thin films

• Aaron Kobler,
• Jochen Lohmiller,
• Jonathan Schäfer,
• Michael Kerber,
• Anna Castrup,
• Ankush Kashiwar,
• Patric A. Gruber,
• Karsten Albe,
• Horst Hahn and
• Christian Kübel

Beilstein J. Nanotechnol. 2013, 4, 554–566, doi:10.3762/bjnano.4.64

• density was found during straining. On the other hand, starting from a higher twin density, the twins were depleted with increasing strain. The findings from ACOM-TEM were confirmed by results from molecular dynamics (MD) simulations and from conventional and in-situ synchrotron X-ray diffraction (CXRD

• synchrotron X-ray diffraction (SXRD) on equivalent samples. Furthermore, the experimental results for the twin density evolution are qualitatively supported by molecular dynamics (MD) simulations. Results Microstructural characterization of the as deposited Pd films The sputtering parameters were chosen to

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

• atomic scale computer simulations. By using a combination of Monte-Carlo and molecular dynamics methods we find that solutes have an ordering tendency even if grain sizes are in the nanometer regime, where the phase field of the ordered state is widened as compared to larger grain sizes. Tensile testing

• is also found for ordered structures (L12), where dislocation activity is suppressed. Keywords: nanocrystalline materials; grain boundary structure; grain boundary segregation; plastic deformation; molecular dynamics; Introduction In intermetallics grain refinement to the nanometer scale has been

• 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

Nanoglasses: a new kind of noncrystalline materials

• Herbert Gleiter

Beilstein J. Nanotechnol. 2013, 4, 517–533, doi:10.3762/bjnano.4.61

• nanoglass produced by introducing a high density of shear bands, the results of recent studies by molecular dynamics (MD) [12][13] and Mössbauer spectroscopy of a ball-milled melt-quenched Fe90Sc10 glassy ribbon and a Fe90Sc10 nanoglass suggest that the atomic structure of both kinds of nanoglass differ

• NRVS data do not depend on porosity. Structural stability Due to the important role of the structural stability of nanoglasses, this issue is addressed in Figure 14 on application of molecular dynamics (MD). Although already discussed in [28], the essential results obtained so far are briefly repeated

• here in order to provide a complete picture of our present understanding. Figure 14a–g compares the results of a molecular dynamics (MD) simulation of the microstructural evolution of a three-dimensional nanoglass formed by sintering glassy spheres of Ge [27]. The sintering process occurred under a

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

• considered when quantifying the mechanical properties of amyloid fibres containing defects. Keywords: amyloid; fibril fragmentation; steered molecular dynamics (SMD); structural defects; Introduction Amyloid fibrils are biomaterials that are commonly associated with human disease [1]. Over recent years

• fibrils formed from 10-residue fragments of the amylin protein (sequence SNNFGAILSS) as structurally determined by ssNMR [24] are simulated in full atomistic detail using molecular dynamics (MD). These models are classified according to symmetry packing classes, after the Eisenberg steric zipper

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

• , force-field molecular dynamics are used in order to describe the adsorption properties of solvated BTP molecules on graphite. The structure of 3,3′-BTP, which is known for its high versatility in surface structures is shown in Figure 1. There are of course force fields that reproduce structural

• 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

Selective surface modification of lithographic silicon oxide nanostructures by organofunctional silanes

• Thomas Baumgärtel,
• Christian von Borczyskowski and
• Harald Graaf

Beilstein J. Nanotechnol. 2013, 4, 218–226, doi:10.3762/bjnano.4.22

• assumptions about the 3D orientation and bending of the bound FITC molecules would have to be made. Further theoretical considerations (e.g., molecular dynamics simulations) could be employed in order to investigate the molecular orientation on the surface, but it has to be kept in mind that AFM measurements

Plasticity of Cu nanoparticles: Dislocation-dendrite-induced strain hardening and a limit for displacive plasticity

• Antti Tolvanen and
• Karsten Albe

Beilstein J. Nanotechnol. 2013, 4, 173–179, doi:10.3762/bjnano.4.17

• behaviour of individual Cu crystallites under nanoextrusion is studied by molecular dynamics simulations. Single-crystal Cu fcc nanoparticles are embedded in a spherical force field mimicking the effect of a contracting carbon shell, inducing pressure on the system in the range of gigapascals. The material

• radius is reduced below 1.3 Å we observe a transition from displacive plasticity to solid-state amorphisation. Keywords: dislocation interactions; mechanical properties; molecular dynamics; nanoparticle; simulation; Introduction In macroscopic metals, the plastic flow is carried by the continuous

• penetrate the material. Conclusion In summary, we have used molecular dynamics simulations to show how the formation of dislocation dendrites consisting of multiple different types of dislocations leads to strong strain hardening of individual Cu nanocrystallites. We also report a variety of dislocation

Catalytic activity of nanostructured Au: Scale effects versus bimetallic/bifunctional effects in low-temperature CO oxidation on nanoporous Au

• Lu-Cun Wang,
• Yi Zhong,
• Haijun Jin,
• Daniel Widmann,
• Jörg Weissmüller and
• R. Jürgen Behm

Beilstein J. Nanotechnol. 2013, 4, 111–128, doi:10.3762/bjnano.4.13

• density functional theory based calculations and molecular dynamics simulations [76]. (Interestingly, these authors also remarked that there is no clear definition of the surface oxide and subsurface oxide in the literature.) In a recent high-resolution photoelectron spectroscopy study, Schaefer et al

Nanotribology at high temperatures

• Saurav Goel,
• Alexander Stukowski,
• Gaurav Goel,
• Xichun Luo and
• Robert L. Reuben

Beilstein J. Nanotechnol. 2012, 3, 586–588, doi:10.3762/bjnano.3.68

• , Livermore, California, USA School of Engineering and Technology, Sharda University, Greater Noida, 201306, India 10.3762/bjnano.3.68 Abstract Recent molecular dynamics simulation results have increased conceptual understanding of the grazing and the ploughing friction at elevated temperatures, particularly

Graphite, graphene on SiC, and graphene nanoribbons: Calculated images with a numerical FM-AFM

• Fabien Castanié,
• Laurent Nony,
• Sébastien Gauthier and
• Xavier Bouju

Beilstein J. Nanotechnol. 2012, 3, 301–311, doi:10.3762/bjnano.3.34

• their equilibrium position, with dynamic systems, obtained with a molecular dynamics module allowing all the atoms to move freely during the probe oscillations. Conclusion: We found a very good agreement with experimental graphite and graphene images. The imaging process for the deposited nanoribbon

• and a constant-height mode image, whatever the interaction regime is. Moreover, a molecular dynamics (MD) module is added by linking the n-AFM to the MD code DL_POLY [85]. This MD module can be implemented when it is necessary to take temperature conditions and/or deformations of the tip and the

• frequency shift. Moreover, the coupling of a molecular dynamics module allows us to take into account an external temperature as well as the mechanical pressure of the tip during the sample scanning. We have shown three examples on graphitic structures: (i) a flat graphite surface, (ii) smooth corrugated

An NC-AFM and KPFM study of the adsorption of a triphenylene derivative on KBr(001)

• Antoine Hinaut,
• Adeline Pujol,
• Florian Chaumeton,
• David Martrou,
• André Gourdon and
• Sébastien Gauthier

Beilstein J. Nanotechnol. 2012, 3, 221–229, doi:10.3762/bjnano.3.25

• eV, in good agreement with the value obtained for the CN groups of the truxene derivative mentioned previously [10]. Molecular dynamics studies of the diffusion of a HCPTP molecule were performed with the same force field in the NVT ensemble with a Nose–Hoover thermostat. Simulations at 300 K show

Direct monitoring of opto-mechanical switching of self-assembled monolayer films containing the azobenzene group

• Einat Tirosh,
• Enrico Benassi,
• Silvio Pipolo,
• Marcel Mayor,
• Michal Valášek,
• Veronica Frydman,
• Stefano Corni and
• Sidney R. Cohen

Beilstein J. Nanotechnol. 2011, 2, 834–844, doi:10.3762/bjnano.2.93

• show that the modulus of the cis-form is approximately twice that of the trans-isomer. Quantum mechanical and molecular dynamics studies show good agreement with this experimental result, and indicate that the stiffer response in the cis-form comprises contributions both from the individual molecular

• bonds and from intermolecular interactions in the film. These results demonstrate the power and insights gained from cutting-edge AFM technologies, and advanced computational methods. Keywords: AFM; azobenzene; elastic modulus; molecular dynamics; nanomechanics; photoswitch; quantum mechanics

• -containing polymer molecules [5][6]. These elegant measurements were simulated by molecular dynamics [7]. It was shown that the mechanical response arises only partly from the azo moiety, and includes contributions from other constituents of the polymer chain. The ability of azo-containing molecules to self

Current-induced dynamics in carbon atomic contacts

• Jing-Tao Lü,
• Tue Gunst,
• Per Hedegård and
• Mads Brandbyge

Beilstein J. Nanotechnol. 2011, 2, 814–823, doi:10.3762/bjnano.2.90

• , which can be used to explore current-induced vibrational instabilities due the NC/BP forces. Furthermore, using tight-binding and the Brenner potential we illustrate how Langevin-type molecular-dynamics calculations including the Joule heating effect for the carbon-chain systems can be performed

• . Molecular dynamics including current-induced forces enables an energy redistribution mechanism among the modes, mediated by anharmonic interactions, which is found to be vital in the description of the electrical heating. Conclusion: We have developed a semiclassical Langevin equation approach that can be

• computer simulation techniques, such as molecular dynamics (MD), preferably without adjustable parameters, to study in detail the complex current-driven atomic processes. To this end, we recently developed an approach based on the semiclassical Langevin equation, which may form the basis of MD. In this

Femtosecond time-resolved photodissociation dynamics of methyl halide molecules on ultrathin gold films

• Mihai E. Vaida,
• Robert Tchitnga and
• Thorsten M. Bernhardt

Beilstein J. Nanotechnol. 2011, 2, 618–627, doi:10.3762/bjnano.2.65

• organic molecules on metallic substrates. The observed molecular dynamics varies strongly for the three investigated methyl halide molecules and reflects the different electronic structure of the molecules as well as the interaction with the gold substrate surface. The dissociation of methyl iodide on

Surface induced self-organization of comb-like macromolecules

• Konstantin I. Popov,
• Vladimir V. Palyulin,
• Martin Möller,
• Alexei R. Khokhlov and
• Igor I. Potemkin

Beilstein J. Nanotechnol. 2011, 2, 569–584, doi:10.3762/bjnano.2.61

• is selective for A and B chains, spontaneous curvature of the molecule will occur. Recent data obtained from off-lattice molecular dynamics simulations [55] suggest that pearl-necklace type separation is also possible in binary bottle-brushes. This type of separation induced by the decrease in the

Self-organizing bioinspired oligothiophene–oligopeptide hybrids

• Alexey K. Shaytan,
• Eva-Kathrin Schillinger,
• Elena Mena-Osteritz,
• Sylvia Schmid,
• Pavel G. Khalatur,
• Peter Bäuerle and
• Alexei R. Khokhlov

Beilstein J. Nanotechnol. 2011, 2, 525–544, doi:10.3762/bjnano.2.57

• stable fibrils as visualized by AFM and TEM. While the experimental evidence alone is not sufficient to reveal the exact molecular organization of the fibrils, theoretical approaches based on quantum chemistry calculations and large-scale atomistic molecular dynamics simulations are attempted in an

• effort to reveal the structure of the fibrils at the nanoscale. Based on the combined theoretical and experimental analysis, the most likely models of fibril formation and aggregation are suggested. Keywords: amyloid-like fibrils; bioinspired conjugates; molecular dynamics simulations; oligopeptides

• and the fibrillar morphology. When 3-D atomistic structures of microcrystals or oligomeric aggregates are available they may be used to construct computational models of the fibrillar aggregates, and through the application of atomistic molecular dynamics (MD) simulations the structural data can be

Towards a scalable and accurate quantum approach for describing vibrations of molecule–metal interfaces

• David M. Benoit,
• Bruno Madebene,
• Inga Ulusoy,
• Luis Mancera,
• Yohann Scribano and
• Sergey Chulkov

Beilstein J. Nanotechnol. 2011, 2, 427–447, doi:10.3762/bjnano.2.48

• stretching frequencies. As an alternative to the harmonic approximation, two methods for computing anharmonic spectra are of particular interest: Molecular dynamics and the vibrational self-consistent field (VSCF) approach. Both techniques can go beyond the harmonic approximation, and provide a solid basis

• conformationally flexible molecules. Due to its conceptual simplicity and the ready availability of reliable empirical force fields (or forces computed ab initio), molecular dynamics is currently the most popular method for determining anharmonic frequencies of large systems (see [7] for an overview of some

Influence of water on the properties of an Au/Mpy/Pd metal/molecule/metal junction

• Jan Kučera and
• Axel Groß

Beilstein J. Nanotechnol. 2011, 2, 384–393, doi:10.3762/bjnano.2.44

• for the stability in the water complex. Ab initio molecular dynamics simulations showed that at room temperature the hexagonal water bilayer structure on bulk metal surfaces becomes disordered [19], but it may persist on the Au/Mpy/Pd junction because of the higher stability of the H2O layer, which is

Superhydrophobicity in perfection: the outstanding properties of the lotus leaf

• Hans J. Ensikat,
• Petra Ditsche-Kuru,
• Christoph Neinhuis and
• Wilhelm Barthlott

Beilstein J. Nanotechnol. 2011, 2, 152–161, doi:10.3762/bjnano.2.19

• lateral oxygen atoms which inhibit a tight package of the molecules. Thus the resulting layers have a strong curvature and form tubules with a circular cross-section (Figure 13). Today, the progress in molecular dynamics simulations enables the calculation of the behaviour of nano-structured surfaces in

Structure, morphology, and magnetic properties of Fe nanoparticles deposited onto single-crystalline surfaces

• Armin Kleibert,
• Wolfgang Rosellen,
• Mathias Getzlaff and
• Joachim Bansmann

Beilstein J. Nanotechnol. 2011, 2, 47–56, doi:10.3762/bjnano.2.6

• far from thermal equilibrium forming due to the complex landing kinetics of the smaller particles which are connected with the spontaneous reorientation process. Recent molecular-dynamics (MD) simulations give microscopic insight into the processes in nanoparticle deposition experiments [65]. In