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

• distance between a step edge and the COM of a molecule. Averages were taken from 50 ns MD simulations at each separation R. The MD simulation time was then increased to 80 ns and 100 ns in order to check for convergence. Zero entropy was defined to be at a configuration where the force along the reaction

• state is more favourable than the other. However, the convergence of thermodynamic integration calculations must be checked thoroughly. When increasing the MD simulation time at each step along the reaction coordinate from 50 ns to 80 ns the calculated values for change in entropy differed only

• curves. Increasing the MD trajectory from 50 ns to 100 ns leads to a drop in the free energy of step adhesion from 0.5 eV to 0.35 eV. As MD simulation times are increased, the free energy continues to decrease as more and more of the higher-energy, low-probability configurational space is sampled. This

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

• previous studies [15][16][17]. The MD simulation technique described in the existing study [11] is applied in the present work and the periodic boundary condition is applied in all directions of model to remove the effect of finite size and the time steps selected are 1.0 fs for all the MD simulations in

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 results can already be obtained for the first cycle of the cantilever oscillation. Focussing on the first cycle allows for a microcanonical approach that is complementary to the common MD simulations, which couple the system to a thermostat. A microcanonical MD simulation has advantages in our

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

• stages considering the representative case at a temperature of 700 K, which is about 150 K below the melting point of the studied wire as computed through MD simulation [6]. Stage 1 Figure 1 shows the initial stage of the simulation. The hollow structure shows an almost immediate collapse, within the

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

• ). The length of the simulation cell in the axial direction fluctuates during the MD simulation (Figure 1b). A derivative of the third-order polynomial fit to the thermal strain vs temperature results is used to obtain the coefficient of thermal expansion, α. The open source MD codes LAMMPS [27] and MD

• modulus is computed by obtaining the strain energy as a function of longitudinal strain. The cross-sectional view of a typical CSNW is also shown. (b) The thermal expansion is obtained from the thermal strain in a direct MD simulation. At higher temperatures, the thermal fluctuations increase, thereby

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

• . Nevertheless, the stress-induced softening, observed when using one-atom indentation, and the hardening, observed in the FEM simulation, seem to nearly compensate in the MD simulation for this contact radius (Figure 4). The decrease of M for y > 0 towards the step looks quite similar in Figure 4 and Figure 6

Tensile properties of a boron/nitrogen-doped carbon nanotube–graphene hybrid structure

• Kang Xia,
• Haifei Zhan,
• Ye Wei and
• Yuantong Gu

Beilstein J. Nanotechnol. 2014, 5, 329–336, doi:10.3762/bjnano.5.37

• reduction of the Young’s modulus, while the other considered cases exhibit Young’s moduli around 0.29 TPa. Conclusion Basing on the large-scale MD simulation, the tensile properties of a graphene–carbon nanotube hybrid structure with different dopants have been investigated. It is found that with the

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

• . The force field has a significant effect on the results of any atomistic MD simulation. In this work, a class II (second-generation) polymer-consistent force field (PCFF) [65] was employed. PCFF is an ab-initio based force field in which the total potential energy of an atomistic system is represented

• boundary conditions. The initial distribution of molecules in the box was random. Model II. The model of an ion-conducting channel was based on the data obtained from our classical MD simulation at λ = 10 and T = 298 K. The channel was modeled as a slit whose two opposite walls separated by a distance of

Nanoglasses: a new kind of noncrystalline materials

• Herbert Gleiter

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

• 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

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

• characteristics. The indenter is an incompressible Lennard–Jones sphere. Whereas the QM model is focused on the single-molecule properties, the MD simulation allows for steric interactions between neighboring molecules. Comparison of experiment with computation As shown in Table 2, the results of the two

• and the procedural settings were the same as the previous protocol, except that two series of simulations were run for each isomer (instead of four), and the MD simulation for each distance was shorter (5 ns instead of 10 ns). Furthermore, the reference distance for penetration was calculated between

• replicated to generate the starting conformation of the SAM is also shown as a black rectangle. It reproduces the periodicity of bright spots in the STM images of [3]. Only the Au atoms of the first surface layer are shown. (b) Snapshot from the MD simulation with the spherical probe (in green) upon the thio

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

• -dynamics simulations based on the full anharmonic potential. Our simple, approximate MD simulation indicates that anharmonic couplings play an important role for the energy redistribution and effective heat dissipation to the electrode reservoirs. However, the MD is computationally very demanding beyond