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

• force fields are used since the computational cost associated with ab initio methods is too high. The LAMMPS code was used for all calculations [44] along with a combination of several classical force fields. A Buckingham potential was used to describe the interactions inside the KCl slab, as

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

• the Polymer Modeller software [53] with the initial equilibration being carried out at constant number, volume and temperature (NVT) in LAMMPS [54] with the Dreiding force field [55]. The size of the systems is about 3 × 3 × 3 nm3 and the initial density has been set to reflect the real low- (LD) and

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

• implemented in the large-scale atomic/molecular massively parallel simulator (LAMMPS) developed at the Sandia National Laboratory [23], while the OVITO [24] visualization tool is employed to view the atomic configuration of the nanowire. Results and Discussion Morphological evolution We start with 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

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

• 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

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

• case. Therefore, these expressions have been used to provide a qualitative understanding of the problem and have been accompanied by explicit indentation simulations to quantitatively describe the elastic response of a step. Simulation methods All MD runs were carried out with the LAMMPS code [14]. The

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

• . The emphasis will be placed on Young’s modulus, E, yield strength, YS, and yield strain, YP. Computational details In order to acquire the influence of the dopants on the mechanical properties of GNHSs, the large-scale atomic/molecular massively parallel simulator (LAMMPS) [17] is utilized to carry

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

• chosen λ values correspond to concentrated solutions of strong acids. For atomistic molecular dynamics (AMD) simulations we used the LAMMPS software package [64] in its highly optimized form for hybrid CPU/GPU nodes so that the computations scaled almost linearly on a massively parallel supercomputer

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

• , the LAMMPS MD code [52] was used. The input structures were constructed following the Voronoi tessellation method [53], with an average grain size of 10 and 20 nm consisting of 64 and 36 grains, respectively. After initial relaxation at 300 K, in one sample of each grain size, 50% of the grains were

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

• LAMMPS [22], which was extended to perform the MC steps [17]. Initially, we created nc model structures of perfectly (L12) ordered FeNi3 with average grain sizes of 5 and 15 nm consisting of 432 and 54 grains, respectively. The Voronoi tesselation method [16] was used to set up the grain shapes based on

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

• further elucidates how the nanoscale processes differ from the familiar macroscopic counterparts and motivates more studies to understand the possible limits of displacive plasticity. Methods Molecular dynamics (MD) simulations were performed by using a modified version of the LAMMPS [14] simulation

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

• construct long fibrils by replicating the periodic cell along the axis of the filament. For the selected systems, planar straight fibrils 80 β-strands in length (approximately 40 nm) were constructed and subjected to 10 ns MD simulations at T = 300 K. To this end, the LAMMPS simulation package [39], based