Large-scale molecular dynamics simulations of cluster impact and erosion processes on a diamond surface

Yasutaka Yamaguchi and Jürgen Gspann. Phys. Rev. B 66, 155408, 2002. Copyright 2002 by the American Physical Society

Approximate Spin Projection for Broken-Symmetry Method and Its Application

A broken-(spin) symmetry (BS) method is now widely used for systems that involve (quasi) degenerated frontier orbitals because of their lower cost of computation. The BS method splits up-spin and down-spin electrons into two different special orbitals, so that a singlet spin state of the degenerate system is expressed as a singlet biradical. In the BS solution, therefore, the spin symmetry is no longer retained. Due to such spin-symmetry breaking, the BS method often suffers from a serious problem called a spin contamination error, so that one must eliminate the error by some kind of projection method. An approximate spin projection (AP) method, which is one of the spin projection procedures, can eliminate the error from the BS solutions by assuming the Heisenberg model and can recover the spin symmetry. In this chapter, we illustrate a theoretical background of the BS and AP methods, followed by some examples of their applications, especially for calculations of the exchange interaction and for the geometry optimizations

Equilibrium molecular dynamics evaluation of the solid-liquid friction coefficient: role of timescales

Solid-liquid friction plays a key role in nanofluidic systems. Yet, despite decades of method development to quantify solid-liquid friction using molecular dynamics (MD) simulations, an accurate and widely applicable method is still missing. Here, we propose a method to quantify the solid-liquid friction coefficient (FC) from equilibrium MD simulations of a liquid confined between parallel solid walls. In this method, the FC is evaluated by fitting the Green-Kubo (GK) integral of the S-L shear force autocorrelation for the range of time scales where the GK integral slowly decays with time. The fitting function was derived based on the analytical solution considering the hydrodynamic equations in our previous work [H. Oga et al., Phys. Rev. Research 3, L032019 (2021)], assuming that the timescales related to the friction kernel and to the bulk viscous dissipation can be separated. By comparing the results with those of other equilibrium MD-based methods and those of non-equilibrium MD for a Lennard-Jones liquid between flat crystalline walls with different wettability, we show that the FC is extracted with excellent accuracy by the present method, even in wettability regimes where other methods become innacurate. We then show that the method is also applicable to grooved solid walls, for which the GK integral displays a complex behavior at short times. Overall, the present method extracts efficiently the FC for various systems, with easy implementation and low computational cost.Comment: 22 pages, 6 Figure

Molecular dynamics analysis of the influence of Coulomb and van der Waals interactions on the work of adhesion at the solid-liquid interface

We investigated the solid-liquid work of adhesion of water on a model silica surface by molecular dynamics simulations, where a methodology previously developed to determine the work of adhesion through thermodynamic integration was extended to a system with long-range electrostatic interactions between solid and liquid. In agreement with previous studies, the work of adhesion increased when the magnitude of the surface polarity was increased. On the other hand, we found that when comparing two systems with and without solid-liquid electrostatic interactions, which were set to have approximately the same total solid-liquid interfacial energy, former had a significantly smaller work of adhesion and a broader distribution in the interfacial energies, which has not been previously reported in detail. This was explained by the entropy contribution to the adhesion free energy; i.e., the former with a broader energy distribution had a larger interfacial entropy than the latter. While the entropy contribution to the work of adhesion has already been known, as a work of adhesion itself is free energy, these results indicate that, contrary to common belief, wetting behavior such as the contact angle is not only governed by the interfacial energy but also significantly affected by the interfacial entropy. Finally, a new interpretation of interfacial entropy in the context of solid-liquid energy variance was offered, from which a fast way to qualitatively estimate the work of adhesion was also presented.Donatas Surblys, Frédéric Leroy, Yasutaka Yamaguchi, and Florian Müller-Plathe, "Molecular dynamics analysis of the influence of Coulomb and van der Waals interactions on the work of adhesion at the solid-liquid interface", The Journal of Chemical Physics 148, 134707 (2018) https://doi.org/10.1063/1.5019185

Equilibrium molecular dynamics evaluation of the solid-liquid friction coefficient: Role of timescales

Solid-liquid friction plays a key role in nanofluidic systems. Following the pioneering work of Bocquet and Barrat, who proposed to extract the friction coefficient (FC) from the plateau of the Green-Kubo (GK) integral of the solid-liquid shear force autocorrelation, the so-called plateau problem has been identified when applying the method to finite-sized molecular dynamics simulations, e.g., with a liquid confined between parallel solid walls. A variety of approaches have been developed to overcome this problem. Here, we propose another method that is easy to implement, makes no assumptions about the time dependence of the friction kernel, does not require the hydrodynamic system width as an input, and is applicable to a wide range of interfaces. In this method, the FC is evaluated by fitting the GK integral for the timescale range where it slowly decays with time. The fitting function was derived based on an analytical solution of the hydrodynamics equations [Oga et al., Phys. Rev. Res. 3, L032019 (2021)], assuming that the timescales related to the friction kernel and the bulk viscous dissipation can be separated. By comparing the results with those of other GK-based methods and non-equilibrium molecular dynamics, we show that the FC is extracted with excellent accuracy by the present method, even in wettability regimes where other GK-based methods suffer from the plateau problem. Finally, the method is also applicable to grooved solid walls, where the GK integral displays complex behavior at short times.Oga H., Omori T., Joly L., et al. Equilibrium molecular dynamics evaluation of the solid-liquid friction coefficient: Role of timescales, Journal of Chemical Physics, 159(2), 024701, 14 July 2023, © 2023 American Chemical Society. https://doi.org/10.1063/5.0155628

Molecular simulations on the chirality preference of single-walled carbon nanotubes upon ductile behavior under tensile stress at high temperature

Molecular dynamics simulations were carried out on the ductile behavior of single-walled carbon nanotubes (SWNTs) under tensile stress by moving both ends at constant velocity at high temperature. The (10,10) armchair-SWNT resulted in plastic elongation through the sequential Stone-Wales (S-W) transformation, and the chirality changed keeping the two indices equal by alternately taking two dislocation directions with Burgers vectors b→=(1,0) and (0,1) instead of choosing only one of them toward zigzag-chirality with one index equal to zero. The comparison in the activation and formation energies for the two directions revealed that the torsional strain induced by the preceding S-W sequence was the main cause of this alternating choice.Hirotoshi Deguchi, Yasutaka Yamaguchi, Kaori Hirahara, Yoshikazu Nakayama. Molecular simulations on the chirality preference of single-walled carbon nanotubes upon ductile behavior under tensile stress at high temperature. Chemical Physics Letters, Volume 503, Issues 4–6, 2011, Pages 272-276, https://doi.org/10.1016/j.cplett.2011.01.023

Quantifying interfacial tensions of surface nanobubbles: How far can Young's equation explain?

Nanobubbles at solid-liquid interfaces play a key role in various physicochemical phenomena and it is crucial to understand their unique properties. However, little is known about their interfacial tensions due to the lack of reliable calculation methods. Based on mechanical and thermodynamic insights, we quantified for the first time the liquid-gas, solid-liquid, and solid-gas interfacial tensions of submicron-sized nitrogen bubbles at graphite-water interfaces using molecular dynamics (MD) analysis. It was revealed that Young's equation holds even for nanobubbles with different radii. We found that the liquid-gas and solid-liquid interfacial tensions were not largely affected by the gas density inside the nanobubbles. In contrast, the size effect on the solid-gas interfacial tension was observed, namely, the value dramatically decreased upon an increase in the gas density due to gas adsorption on the solid surface. However, our quantitative evaluation also revealed that the gas density effect on the contact angles is negligible when the footprint radius is larger than 50 nm, which is a typical range observed in experiments, and thus the flat shape and stabilization of submicron-sized surface bubbles observed in experiments cannot be explained only by the changes in interfacial tensions due to the van der Waals interaction-induced gas adsorption, namely by Young's equation without introducing the pinning effect. Based on our analysis, it was clarified that additional factors such as the differences in the studied systems are needed to explain the unresolved open issues-a satisfactory explanation for the nanobubbles in MD simulations being ultradense, non-flat, and stable without pinning.Teshima H., Kusudo H., Bistafa C., et al. Quantifying interfacial tensions of surface nanobubbles: How far can Young's equation explain?. Nanoscale 14, 2446 (2022); https://doi.org/10.1039/d1nr07428h

Shear force measurement of the hydrodynamic wall position in molecular dynamics

Flows in nanofluidic systems are strongly affected by liquid-solid slip, which is quantified by the slip length and by the position where the slip boundary condition applies. Here, we show that the viscosity, slip length, and hydrodynamic wall position (HWP) can be accurately determined from a single molecular dynamics (MD) simulation of a Poiseuille flow, after identifying a relation between the HWP and the wall shear stress in that configuration. From this relation, we deduce that in gravity-driven flows, the HWP identifies with the Gibbs dividing plane of the liquid-vacuum density profile. Simulations of a generic Lennard-Jones liquid confined between parallel frozen walls show that the HWP for a pressure-driven flow is also close to the Gibbs dividing plane (measured at equilibrium), which therefore provides an inexpensive estimate of the HWP, going beyond the common practice of assuming a given position for the hydrodynamic wall. For instance, we show that the HWP depends on the wettability of the surface, an effect usually neglected in MD studies of liquid-solid slip. Overall, the method introduced in this article is simple, fast, and accurate and could be applied to a large variety of systems of interest for nanofluidic applications.Cecilia Herrero, Takeshi Omori, Yasutaka Yamaguchi, and Laurent Joly, "Shear force measurement of the hydrodynamic wall position in molecular dynamics", The Journal of Chemical Physics 151, 041103 (2019) https://doi.org/10.1063/1.5111966

Growth of sp-sp² nanostructures in a carbon plasma

The growth of sp and sp² nanostructures in a carbon plasma is simulated by tight-binding molecular dynamics. The simulations are arranged so as to mimic the cluster formation conditions typical of a pulsed microplasma cluster source which is used to grow nanostructured sp-sp² carbon films [L. Ravagnan et al., Phys. Rev. Lett. 98, 216103 (2007)]. The formation of linear, ring, and fullerenelike objects in the carbon plasma is found to proceed through a very long multistep process. Therefore, tight-binding simulations of unprecedented duration have been performed by exploiting the disconnected topology of the simulated carbon plasma which made it possible to implement a computationally efficient divide-and-diagonalize procedure. Present simulations prove that topologically different structures can be formed in experiments, depending on the plasma temperature and density. A thorough characterization of the observed structures as well as their evolution (caused both by thermal annealing and by cluster ripening) is provided.Yasutaka Yamaguchi, Luciano Colombo, Paolo Piseri, Luca Ravagnan, and Paolo Milani. Phys. Rev. B 76, 134119, 2007. Copyright 2007 by the American Physical Society