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

• system per unit time, P divided by temperature difference ΔT throughout the system: Molecular dynamics In Figure 2 we show the thermal conductance of kinked nanowires in MD simulations as they vary with kink angle. The cylindrical nanowires were simulated using a Lennard-Jones potential and built on an

• FCC lattice. Dimensionless Lennard-Jones units are used throughout this work. Further details can be found in the Methodology section. The value of l is 30 lattice constants, with r/l = 1/3. The kink angles range from 0° to 70°. The upper panel shows the thermal conductance for varying angled segment

• 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

Plasmonic nanotechnology for photothermal applications – an evaluation

• A. R. Indhu,
• L. Keerthana and
• Gnanaprakash Dharmalingam

Beilstein J. Nanotechnol. 2023, 14, 380–419, doi:10.3762/bjnano.14.33

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

• pressure, and critical temperature, despite being a simple model [15][53]. The SHAKE algorithm was employed to keep the rigidity of water molecules. The oxygen–carbon Lennard-Jones (LJ) pair-wise non-bonded interaction, εO−C = 0.126 kcal/mol and σO−C = 3.279 Å, was calculated using the Lorentz–Berthelot

• the nanocone. If the nanocone is fully hydrophobic, no water crosses the nanocone. Therefore, hydrophilic rings are necessary for the water to enter and flow through the nanocone. We employ the Lennard-Jones potential to calculate the interaction between the nanocone wall and water. Within this

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

• ) The formation of a TPT SAM on Au(111) was initiated by placing carbon atoms above a surface at positions they would have in the STM image, where the underlying gold substrate was replaced by a repulsive Lennard-Jones wall potential (initialization). (2) Specific starting conditions were imposed by

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

• structural unit (C2H4O) (see Figure 1). The nonbonded interaction is given by a Lennard-Jones 9-6 potential, where ε0 = 0.0179 eV, σ0 = 4.628 Å, and r is the distance between the interacting monomers. The bonded interactions are described by a harmonic potential Vbond = K(r − r0)2, where K = 2.37 eV/Å2 is

• 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

• potential described in the previous section. The hybrid interaction potential consists of a 12-6 Lennard-Jones potential for the non-bonded interactions and a spring potential for the bonded interactions. Once we have reached a melt with the correct interaction, we equilibrate it for 0.25 ns in the NVE

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

• account by, for example, Lennard-Jones potentials [50]. Several works based on MD simulations were performed to study the shear viscosity in either bulk lubricants [51][52][53] or lubricants confined by two surfaces [54][55]. However, to date, MD simulations for the gear–lubricant–gear case are still

• ensure that there are still some lubricant molecules between the gears during rotation. To confine the gear rotation, we define an artificial Lennard-Jones (LJ) plane with parameters given below and an initial distance of 9.3 Å below the gears with periodic boundary conditions in both x- and y-directions

• protocol A, we use (i) AIREBO for carbon interactions within the gears, (ii) AIREBO for gear–lubricant interactions and (iii) a 12-6 Lennard-Jones potential with ε = 2.875 meV, σ = 3.5 Å [60] and cutoff distance 3σ for gear–gear interactions. Note, that the LJ parameters are chosen differently to the ones

A review on slip boundary conditions at the nanoscale: recent development and applications

• Ruifei Wang,
• Jin Chai,
• Bobo Luo,
• Xiong Liu,
• Jianting Zhang,
• Min Wu,
• Mingdan Wei and
• Zhuanyue Ma

Beilstein J. Nanotechnol. 2021, 12, 1237–1251, doi:10.3762/bjnano.12.91

• this conclusion was drawn based on an ideal Lennard–Jones fluid. Its applicability on other Newtonian fluids with properties such as polarity and even on non-Newtonian fluids should be further validated. 2.2 Surface charge effects Investigating electrokinetics phenomena, including electro-osmosis

Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF₃)₄

• Alexey Prosvetov,
• Alexey V. Verkhovtsev,
• Gennady Sushko and
• Andrey V. Solov’yov

Beilstein J. Nanotechnol. 2021, 12, 1151–1172, doi:10.3762/bjnano.12.86

• with the results of [31]. The van der Waals forces between the atoms of the substrate and the adsorbed molecules are described by means of the Lennard-Jones potential: where and . Note that partial hydroxylation, surface defects, and broken O–H bonds may lead to a stronger interaction between Pt and

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

• interactions between C and Cu atoms are calculated by Lennard-Jones (LJ) potentials, using parameters of 0.019996 eV and 3.225 Å [35]. The simulation system uses an isothermal–isobaric (NPT) ensemble to reach equilibrium by a Nose–Hoover thermostat for 100000 time steps. The shear loading is performed by

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

• Lennard–Jones (LJ) potential is used to describe the interaction between the graphene layers and the tip substrate. The LJ parameters for C–C are εC–C = 2.84 meV, σC–C = 0.34 nm and for Si–C the parameters are εSi–C = 8.909 meV, σSi–C = 0.3326 nm (ε is the depth of the potential well, σ is the finite

Protruding hydrogen atoms as markers for the molecular orientation of a metallocene

• Linda Laflör,
• Michael Reichling and
• Philipp Rahe

Beilstein J. Nanotechnol. 2020, 11, 1432–1438, doi:10.3762/bjnano.11.127

• shown in Figure 2o,p. We use Lennard-Jones parameters for CO and Xe tips, a neutral probe particle, and stiffness values of (kx, ky, kz) = (0.5, 0.5, 20) N/m, yielding the results for CO reproduced in Figure 2f–i and for Xe in Figure 2k–n at the same heights. Both series of images exhibit a remarkable

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

• used the harmonic binding potentials and The same approach has been used to maintain small fluctuations of the angles: The interparticle potential used was the Lennard-Jones 12,6 potential, which was shifted in such way that potential and forces are continuous at the cut-off distance [41]: where ULJ(r

• ) = 4εkl[(σkl/r)12 − (σkl/r)6], and U′LJ(rcut) is the first derivative of ULJ(r) at r = rcut. The backbone Lennard-Jones parameters σ = σb and ε = εbb have been set to be the units of length and energy, respectively. Reduced temperature and timestep have been defined as T* = kT/ε and , respectively. The

Quantitative determination of the interaction potential between two surfaces using frequency-modulated atomic force microscopy

• Nicholas Chan,
• Carrie Lin,
• Tevis Jacobs,
• Robert W. Carpick and
• Philip Egberts

Beilstein J. Nanotechnol. 2020, 11, 729–739, doi:10.3762/bjnano.11.60

• then compared to experimental results. The method is demonstrated here using a silicon AFM probe with its native oxide and a diamond sample. Assuming the 6-12 Lennard-Jones potential form, best-fit values for the work of adhesion (Wadh) and range of adhesion (z0) parameters were determined to be 80

• ± 20 mJ/m2 and 0.6 ± 0.2 nm, respectively. Furthermore, the shape of the experimentally extracted force curves was shown to deviate from that calculated using the 6-12 Lennard-Jones potential, having weaker attraction at larger tip–sample separation distances and weaker repulsion at smaller tip–sample

• AFM; interaction potential; Lennard-Jones; surfaces; Introduction Knowledge of material interface interaction behavior is crucial to the design of nanometer-scale devices and processes, such as high-density hard disk storage [1], digital light processing (DLP) projectors [2][3], atomic force

Effects of surface charge and boundary slip on time-periodic pressure-driven flow and electrokinetic energy conversion in a nanotube

• Mandula Buren,
• Yongjun Jian,
• Yingchun Zhao,
• Long Chang and
• Quansheng Liu

Beilstein J. Nanotechnol. 2019, 10, 1628–1635, doi:10.3762/bjnano.10.158

• is the equilibrium distance of the Lennard–Jones potential, e is the elementary charge, lB = e2/(4πεkBT), kB is the Boltzmann constant, ε is the permittivity of the electrolyte solution and T is the absolute temperature [19][25]. The electric potential distribution φ in EDL satisfies the Poisson

Mechanical and thermodynamic properties of Aβ₄₂, Aβ₄₀, and α-synuclein fibrils: a coarse-grained method to complement experimental studies

• Adolfo B. Poma,
• Horacio V. Guzman,
• Mai Suan Li and
• Panagiotis E. Theodorakis

Beilstein J. Nanotechnol. 2019, 10, 500–513, doi:10.3762/bjnano.10.51

• , described by the Lennard-Jones potential. Here, we take εij to be uniform and equal to ε = 1.5 kcal/mol, which was also derived from all-atom simulations [45]. Our approach has shown very good agreement with experimental data on stretching [46][47] and nanoindentation of biological fibrils, such as virus

The inhibition effect of water on the purification of natural gas with nanoporous graphene membranes

• Krzysztof Nieszporek,
• Tomasz Pańczyk and
• Jolanta Nieszporek

Beilstein J. Nanotechnol. 2018, 9, 1906–1916, doi:10.3762/bjnano.9.182

• fixed. Cutoff distances for Lennard-Jones and Columbic interactions were set to 1 nm and equations of motion were integrated using the velocity Verlet algorithm with a time step of 0.5 fs. Each simulation was equilibrated for 1 ps and then run for 10 ns. In practice, it is very challenging to produce

Atomistic modeling of tribological properties of Pd and Al nanoparticles on a graphene surface

• Alexei Khomenko,
• Miroslav Zakharov,
• Denis Boyko and
• Bo N. J. Persson

Beilstein J. Nanotechnol. 2018, 9, 1239–1246, doi:10.3762/bjnano.9.115

• potential, and the interactions between the nanoparticle and the graphene carbon atoms are taken as a Lennard-Jones potential, which was chosen the same for the Al and Pd atoms [10][11]. The MD method differs from most experimental studies in that usually the total energy E and volume V are fixed, while the

Molecular dynamics simulations of nanoindentation and scratch in Cu grain boundaries

• Shih-Wei Liang,
• Ren-Zheng Qiu and
• Te-Hua Fang

Beilstein J. Nanotechnol. 2017, 8, 2283–2295, doi:10.3762/bjnano.8.228

• [23]. Moreover, the Lennard–Jones (LJ) potential [24] was used to describe the interaction between the indenter and the substrate. The parameters of the LJ potential used in this study are based on the previous literature [25][26][27][28][29], which was expressed as Φ(γ) = 4ε[(σ/r)12 − (σ/r)6]. The

Velocity dependence of sliding friction on a crystalline surface

• Christian Apostoli,
• Giovanni Giusti,
• Jacopo Ciccoianni,
• Gabriele Riva,
• Rosario Capozza,
• Rosalie Laure Woulaché,
• Andrea Vanossi,
• Emanuele Panizon and
• Nicola Manini

Beilstein J. Nanotechnol. 2017, 8, 2186–2199, doi:10.3762/bjnano.8.218

• through a Lennard–Jones (LJ) term. Indicating with Rj = [d2 + (xSL − xj)2]1/2 the distance between the slider and the j-th particle, the total slider-chain interaction energy is where VLJ is the LJ potential with equilibrium distance σ. The total potential energy Vharm + VSL−C combined with the

• interacts via Lennard–Jones forces with all atoms in the harmonic chain (smaller spheres). The potential-energy profile experienced by the slider as it moves along a hypothetical chain with atoms frozen at positions xj = ja (big circles), for a LJ parameter σ = 0.5a. Dashed curve: as obtained with d

Modelling of ‘sub-atomic’ contrast resulting from back-bonding on Si(111)-7×7

• Adam Sweetman,
• Samuel P. Jarvis and
• Mohammad A. Rashid

Beilstein J. Nanotechnol. 2016, 7, 937–945, doi:10.3762/bjnano.7.85

• detailed explanation for ‘sub-atomic’ contrast observed on Si(111)-7×7 using a simple model based on Lennard-Jones potentials, coupled with a flexible tip, as proposed by Hapala et al. [Phys. Rev. B 2014, 90, 085421] in the context of interpreting sub-molecular contrast. Our results show a striking

• experiment, which is essential for meaningful qualitative comparisons. In this paper we explore the application of a simple Lennard-Jones model with a flexible tip probe [5][7][8] to a case of ‘sub-atomic’ imaging on the Si(111)-7×7 surface [11][12]. We show that the triangular features observed

• constant height force images, we used the method proposed by Hapala et al. [7][13] to model the interaction between a functionalized probe and the Si(111)-7×7 unit cell, using simple Lennard-Jones (L-J) potentials. In this model the functionalized tip is assumed to consist of a tip base, representing the

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

• separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism

• the center of mass. The stiffness ks should generally be much larger than kz and kx. Prior to the simulation, the initial configuration is obtained in the following way: First, we set up a system that consists only of the substrate atoms. For the Lennard-Jones crystal, these were placed on regular fcc

• than for the Lennard-Jones crystal. Therefore, a different procedure turned out to be more favorable. For the ionic crystals the substrate ions were placed on a regular NaCl lattice with a lattice constant characteristic for the finite crystal size. Then the positions of all surface atoms apart from

Electroviscous effect on fluid drag in a microchannel with large zeta potential

• Dalei Jing and
• Bharat Bhushan

Beilstein J. Nanotechnol. 2015, 6, 2207–2216, doi:10.3762/bjnano.6.226

• surface charge on the slip length of the solid–liquid interface can be expressed as [32], where b0 is the original slip length without the effect of surface charge, α is a numerical factor, d is the equilibrium distance of Lennard-Jones potential, and lB is the Bjerrum length. Because the zeta potential

Accurate, explicit formulae for higher harmonic force spectroscopy by frequency modulation-AFM

• Kfir Kuchuk and
• Uri Sivan

Beilstein J. Nanotechnol. 2015, 6, 149–156, doi:10.3762/bjnano.6.14

• inversion formulae, we insert a known conservative force into Equation 6, a generalized damping coefficient into Equation 17, and then recover them with second harmonic analysis, namely with Equation 15 and Equation 20. For the conservative interaction, we employ a Lennard–Jones force law Where F0 is

• with the range of the Lennard–Jones potential, the Sader–Jarvis formula grows inaccurate, while reconstruction using the second harmonic maintains its accuracy. When the amplitude is increased (Figure 1c), the accuracy of the Sader–Jarvis formula improves and for large amplitudes (Figure 1d) both

• analysis compared with the fundamental harmonic one. Lennard–Jones interaction (solid red line) and reconstructed forces. Blue circles depict reconstruction using the second harmonic. Green diamonds depict reconstruction using the Sader–Jarvis formula for the fundamental harmonic. Amplitudes of oscillation

Experimental techniques for the characterization of carbon nanoparticles – a brief overview

• Wojciech Kempiński,
• Szymon Łoś,
• Mateusz Kempiński and
• Damian Markowski

Beilstein J. Nanotechnol. 2014, 5, 1760–1766, doi:10.3762/bjnano.5.186

• interplay between the interactions within the liquid and of the liquid within the pore walls. The wetting parameter is given as: where c is a constant that comprises the parameters related to the structure of the pore walls and ε is the energy parameter in the Lennard–Jones potential, where the index fw

The study of surface wetting, nanobubbles and boundary slip with an applied voltage: A review

• Yunlu Pan,
• Bharat Bhushan and
• Xuezeng Zhao

Beilstein J. Nanotechnol. 2014, 5, 1042–1065, doi:10.3762/bjnano.5.117

• molecules of solid and liquid beside the Lennard-Jones potential, so the boundary slip will be affected by the surface charge. Barrat and Bocquet give a Green–Kubo expression for the interfacial friction coefficient [13]: where μ is the viscosity of the liquid, A = LxLy is the area of the solid surface