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

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

CA19-9-Producing early gastric adenocarcinoma arising in hyperplastic foveolar polyp: a very unique resection case

Here we report the first case of carbohydrate antigen (CA) 19-9-producing early gastric adenocarcinoma arising in polyp. A solitary pedunculated polyp lesion of the stomach, measuring 26 × 20 × 20 mm, was noticed in a 76-year-old Japanese woman due to an abdominal disorder, associated with a markedly high serum CA19-9 level (2,172.6 U/ml). After endoscopic mucosal resection was performed, the CA19-9 level was drastically decreased and normalized. The scanning view of immunohistochemical staining of CA19-9 exhibited a focal, not diffuse, positive-expression in the hyperplastic epithelium and, especially, in the irregular and fused tubular glands and the mucinous material secreted into the dilated glands. In particular, microscopic examination of the strongly CA19-9-positive areas showed structurally atypical epithelium containing mildly to focal moderately enlarged nuclei and prominent nucleoli with loss of cellular polarity, estimated as adenocarcinoma. No stromal invasion was evident. Immunohistochemically, distinct nuclear stainings for p53 and Ki-67 were seen, occasionally conforming to the CA19-9-positive atypical cells, respectively, confirmed by double immunostaining. These hyperplastic and atypical cells were classified into the pure gastric phenotype by mucin histochemical methods. Based on these features, we finally made a conclusive diagnosis of CA19-9-producing in situ well differentiated adenocarcinoma of gastric type arising in hyperplastic foveolar polyp. We suggest that the markedly high serum CA 19-9 level could be indicative of carcinoma in polyp at the very least

Theoretical framework for the atomistic modeling of frequency-dependent liquid-solid friction

Oga Haruki, Omori Takeshi, Herrero Cecilia, et al. Theoretical framework for the atomistic modeling of frequency-dependent liquid-solid friction. Physical Review Research, 3(3). https://doi.org/10.1103/physrevresearch.3.l032019. 2021. Copyright 2021 by the American Physical Society

Green-Kubo measurement of liquid-solid friction in finite-size systems

International audienceTo characterize liquid-solid friction using molecular dynamics simulations, Bocquet and Barrat (BB) [Phys. Rev. E 49, 3079–3092 (1994)] proposed to use the plateau value of a Green-Kubo (GK) integral of the friction force. The BB method is delicate to apply in finite-size simulations, where the GK integral vanishes at long times. Here, we derive an expression for the GK integral in finite-size systems, based on a Langevin description of a coarse-grained system effectively involving a certain thickness of liquid close to the wall. Fitting this expression to GK integrals obtained from simulations of a liquid slab provides the friction coefficient and the effective thickness of the coarse-grained system. We show that the coarse-grained system for a Lennard-Jones fluid between flat and smooth solid surfaces is 2–3 molecules thick, which provides a criterion for measuring the friction coefficient independently of confinement. As compared to nonequilibrium simulations, the new approach is more accurate and removes some ambiguities of nonequilibrium measurements. Overall, we hope that this new method can be used to characterize efficiently liquid-solid friction in a variety of systems of interest, e.g., for nanofluidic applications

Large effect of lateral box size in molecular dynamics simulations of liquid-solid friction

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