Integrating high-performance computing, machine learning, data management workflows, and infrastructures for multiscale simulations and nanomaterials technologies

• Fabio Le Piane,
• Mario Vozza,
• Matteo Baldoni and
• Francesco Mercuri

Beilstein J. Nanotechnol. 2024, 15, 1498–1521, doi:10.3762/bjnano.15.119

• software packages has boosted the field of materials simulations. Advanced tools for the simulation of materials across a broad range of scales, such as Quantum ESPRESSO [33], LAMMPS [34], GROMACS [35], and OpenFOAM [36], implement complex simulation algorithms, making it easier for researchers to perform

Interaction of graphene oxide with tannic acid: computational modeling and toxicity mitigation in C. elegans

• Romana Petry,
• James M. de Almeida,
• Francine Côa,
• Felipe Crasto de Lima,
• Diego Stéfani T. Martinez and
• Adalberto Fazzio

Beilstein J. Nanotechnol. 2024, 15, 1297–1311, doi:10.3762/bjnano.15.105

• temperature; for XPS, the suspensions were dripped on a silicon substrate. Computational methods MD simulations of interactions between TA and the GO surface were performed in LAMMPS, applying ReaxFF reactive force field [72]. MD simulations were conducted under constant pressure (P) and temperature (T), the

Atomistic insights into the morphological dynamics of gold and platinum nanoparticles: MD simulations in vacuum and aqueous media

• Evangelos Voyiatzis,
• Eugenia Valsami-Jones and
• Antreas Afantitis

Beilstein J. Nanotechnol. 2024, 15, 995–1009, doi:10.3762/bjnano.15.81

• LAMMPS format have been obtained from the NIST interatomic potentials repository (https://www.ctcms.nist.gov/potentials/) [59][60]. The initial configurations of the Au (Pt) NPs are constructed as follows: A supercell consisting of 2048 Au (Pt) atoms is obtained by replicating the face-centered cubic

• performed with the LAMMPS code [69], and atomistic configurations are visualized using the Ovito software [70]. The structural modifications occurring in the NPs are identified by monitoring the temperature variation of atomic and cluster parameters. One such atomic quantity is the Berry parameter, δ, which

Effects of cutting tool geometry on material removal of a gradient nanograined CoCrNi medium entropy alloy

• Yu-Sheng Lu,
• Yu-Xuan Hung,
• Thi-Xuyen Bui and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2024, 15, 925–940, doi:10.3762/bjnano.15.76

• /molecularly parallel simulator (LAMMPS) software [16][17], and the GNG model substrates were built from the ATOMSK software [18]. Deformation response, molecular structure, and atomic strain behavior were observed using the Open Visualization Tool (OVITO) software [19][20]. The mechanisms of phase transitions

Heat-induced morphological changes in silver nanowires deposited on a patterned silicon substrate

• Elyad Damerchi,
• Sven Oras,
• Edgars Butanovs,
• Allar Liivlaid,
• Mikk Antsov,
• Boris Polyakov,
• Annamarija Trausa,
• Veronika Zadin,
• Andreas Kyritsakis,
• Loïc Vidal,
• Karine Mougin,
• Siim Pikker and
• Sergei Vlassov

Beilstein J. Nanotechnol. 2024, 15, 435–446, doi:10.3762/bjnano.15.39

•  1. Molecular dynamics simulations were performed with the large-scale atomic/molecular massively parallel simulator (LAMMPS) [40]. Interactions between the atoms were governed by the embedded atom method (EAM) potential [41] for silver atoms. Visualization was performed with the Open Visualization

Ultralow-energy amorphization of contaminated silicon samples investigated by molecular dynamics

• Grégoire R. N. Defoort-Levkov,
• Alan Bahm and
• Patrick Philipp

Beilstein J. Nanotechnol. 2023, 14, 834–849, doi:10.3762/bjnano.14.68

• . Our aim is to determine the optimal conditions to reduce damage formation near the surface while also retaining a high degree of contaminant removal. All bombardments have been simulated using a reactive force field (ReaxFF) [27][28][29] and the molecular dynamics (MD) code LAMMPS [30][31]. While low

• simulations [39]. Molecular dynamics setup The simulation system is made of a box periodic in X and Y dimensions, and aperiodic in the Z dimension. It contains a sample of 5248 atoms (silicon and a thin layer of water molecules). The simulations are performed using the LAMMPS molecular dynamics code on the

Thermal transport in kinked nanowires through simulation

• Alexander N. Robillard,
• Graham W. Gibson and
• Ralf Meyer

Beilstein J. Nanotechnol. 2023, 14, 586–602, doi:10.3762/bjnano.14.49

• kink effects below room temperature. Methodology Molecular dynamics For this work, a Lennard-Jones potential [43][44][45][46] was used to simulate a solid with a face-centred cubic lattice in the well-known LAMMPS simulation framework [47]. The Lennard-Jones parameters σ and ε, effectively the length

Transferability of interatomic potentials for silicene

• Marcin Maździarz

Beilstein J. Nanotechnol. 2023, 14, 574–585, doi:10.3762/bjnano.14.48

• molecular calculations, the molecular statics (MS) method, T = 0 K [28][29][30], was used by means of the “large-scale atomic/molecular massively parallel simulator” (LAMMPS) [31] and analyzed by means of the “Open Visualization Tool” (OVITO) [32]. As for DFT calculations, the structures here were fully pre

• obtained from the NIST Interatomic Potentials Repository and/or from LAMMPS code sources. Tersoff1988 [33]: the original Tersoff potential for silicon (it is important to remember that this paper proposed a form of potential rather than a specific parametrization for silicon) Tersoff2007 [34]: the Tersoff

The influence of structure and local structural defects on the magnetic properties of cobalt nanofilms

• Alexander Vakhrushev,
• Aleksey Fedotov,
• Olesya Severyukhina and
• Anatolie Sidorenko

Beilstein J. Nanotechnol. 2023, 14, 23–33, doi:10.3762/bjnano.14.3

• ideal structure. In all cases of calculations for cobalt, the ferromagnetic behavior was preserved. Defects in the structure and local arrangement of the atoms cause a deterioration in the magnetic macroscopic parameters, such as a decrease in the magnetization modulus. Keywords: LAMMPS; magnetic

Atmospheric water harvesting using functionalized carbon nanocones

• Fernanda R. Leivas and
• Marcia C. Barbosa

Beilstein J. Nanotechnol. 2023, 14, 1–10, doi:10.3762/bjnano.14.1

• ). Molecular dynamics simulations were performed using the LAMMPS [48] package using an NVT ensemble with a timestep of 0.1 fs. The TIP4P/2005 [49] water model was used since it provides a satisfactory description of self-diffusion coefficient [50], phase diagram, vapor–liquid equilibria [51][52], vapor

Influence of water contamination on the sputtering of silicon with low-energy argon ions investigated by molecular dynamics simulations

• Grégoire R. N. Defoort-Levkov,
• Alan Bahm and
• Patrick Philipp

Beilstein J. Nanotechnol. 2022, 13, 986–1003, doi:10.3762/bjnano.13.86

• carried using the LAMMPS code [52]. A pristine silicon sample containing 5248 atoms was created and used as a reference sample. On top of this sample was added a water layer to study the effect of contaminations. Periodic boundary conditions were applied in x- and y-directions, with some vacuum above and

Comparative molecular dynamics simulations of thermal conductivities of aqueous and hydrocarbon nanofluids

• Adil Loya,
• Antash Najib,
• Fahad Aziz,
• Asif Khan,
• Guogang Ren and
• Kun Luo

Beilstein J. Nanotechnol. 2022, 13, 620–628, doi:10.3762/bjnano.13.54

• alkanes. The large-scale atomic/molecular massively parallel simulator (LAMMPS) molecular dynamic package provided by the Sandia group, created by Plimpton et al. [46][47][48], was used for simulating the dispersion of nanoparticles in water and alkanes. The water/CuO system consisted of 463 transferable

• using the Ovito software. This software is used for simulating molecular dynamics output generated by LAMMPS. Supporting Information File 40: Video of a simulated system of water with CuO nanoparticles. Acknowledgements Authors greatly appreciate and acknowledge the previous work carried out by Dr

Investigation of electron-induced cross-linking of self-assembled monolayers by scanning tunneling microscopy

• Patrick Stohmann,
• Sascha Koch,
• Yang Yang,
• Christopher David Kaiser,
• Julian Ehrens,
• Jürgen Schnack,
• Niklas Biere,
• Dario Anselmetti,
• Armin Gölzhäuser and
• Xianghui Zhang

Beilstein J. Nanotechnol. 2022, 13, 462–471, doi:10.3762/bjnano.13.39

• molecular dynamics. The LAMMPS package was employed and the EDIP as well as AIREBO carbon potentials were used depending on more technical simulation-specific parameters. As reported in the reference [71], the simulations included only carbon atoms. The modelling was achieved through the following steps: (1

• atoms with subnanometer-sized voids. (d) Example wireframe structure of a TPT-based CNM calculated via LAMMPS using the EDIP potential: the colors denote height (blue to red). Several voids are visible here. The simulation box contains 20 × 20 × 18 carbon atoms. Figure 5d was adapted with permission

Nanoscale friction and wear of a polymer coated with graphene

• Robin Vacher and
• Astrid S. de Wijn

Beilstein J. Nanotechnol. 2022, 13, 63–73, doi:10.3762/bjnano.13.4

• using LAMMPS [29]. We use the same simulation setup for the polymer as in our previous work [23]. We summarise this setup below. Interaction potentials PVA is described using a united-atom force field developed by Müller-Plathe and co-workers [30]. Each polymer particle represents a monomer of one

• implemented in LAMMPS: The interaction between PVA and graphene is modelled using a Lennard-Jones 12-6 potential and the Lorentz–Berlot mixing rule, so that σ1 = 4.025 Å, and ε1 = 0.015066 eV. We model the interaction between the silicon tip and graphene using a Lennard-Jones 12-6 with the same parameters

Effect of lubricants on the rotational transmission between solid-state gears

• Huang-Hsiang Lin,
• Jonathan Heinze,
• Alexander Croy,
• Rafael Gutiérrez and
• Gianaurelio Cuniberti

Beilstein J. Nanotechnol. 2022, 13, 54–62, doi:10.3762/bjnano.13.3

• only for better visibility since the actual thickness of the lubricant layer is 5.0–5.5 nm to ensure that the gears are immersed. Finally, the whole system is optimized by using the conjugate gradient method implemented within LAMMPS [58]. Molecular dynamics In this study, we use LAMMPS to perform the

• obtained by integrating the z-component of angular velocity vectors over time, where the angular velocity vectors can be calculated by LAMMPS. The blue dashed lines are denoting trajectories |θ1(t)| of the first gear and all the other lines represent |θ2(t)| for different dCM. One can immediately see that

Effects of temperature and repeat layer spacing on mechanical properties of graphene/polycrystalline copper nanolaminated composites under shear loading

• Chia-Wei Huang,
• Man-Ping Chang and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2021, 12, 863–877, doi:10.3762/bjnano.12.65

• [001] along the x-, y-, and z-directions, respectively. According to a previous report, the C–C bond length in the graphene monolayer was set to 0.143 nm [34], as shown in Figure 2. The simulations were carried out using the large-scale atomic/molecular mass parallel simulator (LAMMPS), with a time

Reducing molecular simulation time for AFM images based on super-resolution methods

• Zhipeng Dou,
• Jianqiang Qian,
• Yingzi Li,
• Rui Lin,
• Jianhai Wang,
• Peng Cheng and
• Zeyu Xu

Beilstein J. Nanotechnol. 2021, 12, 775–785, doi:10.3762/bjnano.12.61

• small cut-off distance, the effect of the boundary could be ignored. The NVT ensemble (the number of atoms, volume, and temperature are conserved) is employed to the free atoms in the system. All simulations are performed using the LAMMPS simulation software with a time step of 1 fs. In AM mode, a

Molecular dynamics modeling of the influence forming process parameters on the structure and morphology of a superconducting spin valve

• Alexander Vakhrushev,
• Aleksey Fedotov,
• Vladimir Boian,
• Roman Morari and
• Anatolie Sidorenko

Beilstein J. Nanotechnol. 2020, 11, 1776–1788, doi:10.3762/bjnano.11.160

• deposited atoms per unit time; substrate temperature; and spraying flux density, which was determined by the area of the evaporation zone. As the computational module of the program for theoretical research, the large-scale atomic/molecular massively parallel simulator (LAMMPS) computing complex was used

• [41]. This software and tool package is freely distributed, contains the ability to perform parallel computing and supports multilevel mathematical models, including molecular dynamics. The results analysis algorithms were described in TCL and C++. Based on LAMMPS, scripts and algorithms were

Three-dimensional solvation structure of ethanol on carbonate minerals

• Hagen Söngen,
• Ygor Morais Jaques,
• Peter Spijker,
• Christoph Marutschke,
• Stefanie Klassen,
• Ilka Hermes,
• Ralf Bechstein,
• Lidija Zivanovic,
• John Tracey,
• Adam S. Foster and
• Angelika Kühnle

Beilstein J. Nanotechnol. 2020, 11, 891–898, doi:10.3762/bjnano.11.74

• conservation. The output data was collected every 1 ps during the production run, providing enough statistics for all required analysis. MD simulations were performed in Lammps code [33]. The analysis was performed using the Python library MDAnalysis [34][35]. Calcite and magnesite were described by the force

Simulations of the 2D self-assembly of tripod-shaped building blocks

• Łukasz Baran,
• Wojciech Rżysko and
• Edyta Słyk

Beilstein J. Nanotechnol. 2020, 11, 884–890, doi:10.3762/bjnano.11.73

• latter means that the only attraction in the system is due to the interactions between active sites. The harmonic potential constants are equal to kbb ≡ kab = 1000ε/σ2 and kθ = 1000ε/rad2. All MD simulations have been performed in the NVT ensemble with the LAMMPS simulation package [42][43]. The standard

Formation of metal/semiconductor Cu–Si composite nanostructures

• Natalya V. Yumozhapova,
• Andrey V. Nomoev,
• Vyacheslav V. Syzrantsev and
• Erzhena C. Khartaeva

Beilstein J. Nanotechnol. 2019, 10, 2497–2504, doi:10.3762/bjnano.10.240

• study, the simulation of thermal effects on CuSi nanoclusters was carried out using the modified immersion atom potentials (MEAM) [24]. For the numerical integration of the motion equations, the Verlet algorithm was used, and the time step was τ = 1 fs. The simulation was carried out in the LAMMPS

Abrupt elastic-to-plastic transition in pentagonal nanowires under bending

• Sergei Vlassov,
• Magnus Mets,
• Boris Polyakov,
• Jianjun Bian,
• Leonid Dorogin and
• Vahur Zadin

Beilstein J. Nanotechnol. 2019, 10, 2468–2476, doi:10.3762/bjnano.10.237

• : Classical molecular dynamics (MD) simulations were conducted to investigate the atomic deformation behavior of the penta-twinned Ag NW under bending. The large-scale open-source molecular dynamics simulator, LAMMPS, developed by Sandia National Laboratories, was adopted [35]. The interatomic interactions

Graphynes: an alternative lightweight solution for shock protection

• Kang Xia,
• Haifei Zhan,
• Aimin Ji,
• Jianli Shao,
• Yuantong Gu and
• Zhiyong Li

Beilstein J. Nanotechnol. 2019, 10, 1588–1595, doi:10.3762/bjnano.10.154

• performance as well as the number of broken bonds. Results and Discussion The fracture behavior and mechanical performance of GYs, including α-, β-, γ- and 6612-GY under supersonic-velocity impact were assessed through a series of large-scale MD simulations performed using the open-source package LAMMPS [30

Accurate control of the covalent functionalization of single-walled carbon nanotubes for the electro-enzymatically controlled oxidation of biomolecules

• Naoual Allali,
• Veronika Urbanova,
• Mathieu Etienne,
• Xavier Devaux,
• Martine Mallet,
• Brigitte Vigolo,
• Jean-Joseph Adjizian,
• Chris P. Ewels,
• Sven Oberg,
• Alexander V. Soldatov,
• Edward McRae,
• Yves Fort,
• Manuel Dossot and
• Victor Mamane

Beilstein J. Nanotechnol. 2018, 9, 2750–2762, doi:10.3762/bjnano.9.257

• the PEG linker via molecular dynamics calculations The influence of the linker length on the resultant enzymatic reactivity of the ferrocene unit was explored using the molecular dynamics package LAMMPS [32][33] to simulate both FcETG2 and FcETG8 when covalently attached to the surface of a (10,0

Atomic-level characterization and cilostazol affinity of poly(lactic acid) nanoparticles conjugated with differentially charged hydrophilic molecules

• María Francisca Matus,
• Martín Ludueña,
• Cristian Vilos,
• Iván Palomo and
• Marcelo M. Mariscal

Beilstein J. Nanotechnol. 2018, 9, 1328–1338, doi:10.3762/bjnano.9.126

• , the length of the PLA polymer was defined as 20 monomers (Figure 1B). All MD simulations described in this study were performed using the molecular dynamics simulator, large-scale atomic/molecular massively parallel simulator (LAMMPS) [35][36]. The interactions between atomic species were represented