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

One Model Fits All: Cross-Region Taxi-Demand Forecasting

The growing demand for ride-hailing services has led to an increasing need for accurate taxi demand prediction. Existing systems are limited to specific regions, lacking generalizability to unseen areas. This paper presents a novel taxi demand forecasting system that leverages a graph neural network to capture spatial dependencies and patterns in urban environments. Additionally, the proposed system employs a region-neutral approach, enabling it to train a model that can be applied to any region, including unseen regions. To achieve this, the framework incorporates the power of Variational Autoencoder to disentangle the input features into region-specific and region-neutral components. The region-neutral features facilitate cross-region taxi demand predictions, allowing the model to generalize well across different urban areas. Experimental results demonstrate the effectiveness of the proposed system in accurately forecasting taxi demand, even in previously unobserved regions, thus showcasing its potential for optimizing taxi services and improving transportation efficiency on a broader scale.Comment: Accepted to The 31st ACM International Conference on Advances in Geographic Information Systems(SIGSPATIAL '23) as a short paper in the Research, Systems and Industrial Experience Papers trac

Improved Path Planning of the Blade for an Automatic Spinach Harvester

ArticleIFAC-PapersOnLine. 53(2): 15816-15823. (2020)journal articl

Laparoscopy-assisted distal gastrectomy for early gastric cancer and laparoscopic cholecystectomy for gallstone with situs inversus totalis: a case report

We report our case of laparoscopy-assisted distal gastrectomy with D1 + β lymph node dissection for a patient with early gastric cancer and laparoscopic cholecystectomy for gallstone with situs inversus totalis. A superficial elevated lesion was found on the lesser curvature of the antrum. The preoperative diagnosis was cStage IA (cT1, cN0, cH0, cP0, cM0). A 1 cm-sized gallstone was found in the fundus through upper abdominal ultrasound. A laparoscopy-assisted distal gastrectomy with standard D2 lymph node dissection for early gastric cancer and laparoscopic cholecystectomy was successfully performed by not shifting the monitor to the left and right and not changing operator's position without additional blood loss and time. The number of retrieved lymph nodes was 36. We have not found any abnormal course of blood vessels except for the right/left inversion. Billroth I reconstruction was performed through end-to-side anastomosis. Based on a histopathological examination, a 1.5 × 1.5 cm, submucosal (sm3), moderately differentiated adenocarcinoma (pT1, pN0, sH0, sP0, sM0, stage IA) was diagnosed. The postoperative course was favorable and the patient was discharged on postoperative day 7

Anterior Pituitary Progenitor Cells Express Costimulatory Molecule 4Ig-B7-H31

Abstract Stem/Progenitor cells in the postnatal pituitary gland are embedded in a marginal cell layer around Rathke’s pouch. However, the nature and behavior of anterior pituitary progenitor cells remain unclear. We established bovine anterior pituitary progenitor cell line (BAPC)-1 from the anterior pituitary gland, which expressed stem/progenitor cell-related genes and several inflammatory cytokines. To characterize and localize these pituitary progenitor cells, we produced a mAb (12B mAb) against BAPC-1. The 12B mAb recognized the 4Ig-B7-H3 molecule, which is a costimulatory molecule and negative regulator in T cell activation. WC1+ γδ T cells in young bovine PBMC express the 4Ig-B7-H3 molecule, but few or no 4Ig-B7-H3-immunoreactive cells are expressed in PBMC in adult cattle. The 12B-immunoreactive cells in the bovine anterior pituitary gland were localized around Rathke’s pouch and expressed IL-18 and MHC class II. However, the number of 12B-immunoreactive cells was lower in adult than in young cattle. BAPC-1 expressed IL-18 and MHC class II, and demonstrated phagocytotic activity. BAPC-1 also had the ability to promote CD25 expression in PBMC after 5 days of coculture, and blocking 4Ig-B7-H3 × 12B mAb enhanced their expression of CD25. In addition, the 12B-immunoreactive cells were observed around the pars tuberalis closely bordering the median eminence and in the blood vessels of the primary portal plexus in the anterior pituitary gland. These results suggest that an established BAPC-1 may originate from these progenitor cells, and that the progenitor cells with 4Ig-B7-H3 may play a critical role in the immunoendocrine network.</jats:p

Cellular and viral chromatin proteins are positive factors in the regulation of adenovirus gene expression

The adenovirus genome forms chromatin-like structure with viral core proteins. This complex supports only a low level of transcription in a cell-free system, and thus core proteins have been thought to be negative factors for transcription. The mechanism how the transcription from the viral DNA complexed with core proteins is activated in infected cells remains unclear. Here, we found that both core proteins and histones are bound with the viral DNA in early phases of infection. We also found that acetylation of histone H3 occurs at the promoter regions of viral active genes in a transcription-independent manner. In addition, when a plasmid DNA complexed with core proteins was introduced into cells, core proteins enhanced transcription. Knockdown of TAF-I, a remodeling factor for viral core protein–DNA complexes, reduces the enhancement effect by core proteins, indicating that core proteins positively regulate viral transcription through the interaction with TAF-I. We would propose a possible mechanism that core proteins ensure transcription by regulating viral chromatin structure through the interaction with TAF-I