DeePMD-kit v2: A software package for Deep Potential models

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments.Comment: 51 pages, 2 figure

Mechanistic study of the anti-cancer effect of gynostemma pentaphyllum saponins in rat 6 fibroblast cell system

The medicinal herb, Gynostemma pentaphyllum (Gp) has been shown to have anticancer effects. However, the precise mechanism is not known. The key active components of Gp are a group of saponins, structurally related to ginsenosides. In the present study, the anticancer effect of Gp saponins was assessed by testing their abilities to prevent the formation of foci induced by an activated c-Ha-ras oncogene in normal Rat 6 fibroblasts. The results indicated that the Gp saponins inhibited ras-induced foci in dosage and time dependent manners. To facilitate the investigation of the mode of inhibition of Gp in living cells, a green fluorescent protein-ras fusion construct (pGFP-ras) was used to substitute ras in the focus formation assay. Using this approach, the pGFP-ras transfected cells can be identified within 24 hours upon transfection under a fluorescent microscope. Cells acquired GFP-ras gene grew into green fluorescent foci with striking transforming morphology in the absence of Gp, whereas the GFP-ras transfected cell, in most of cases, remained as single green fluorescent cell with Gp saponins present in the medium. Based on cell proliferation, colony formation and cell cycle analysis, Gp saponins exhibited non-cytotoxic effect on either normal or the transformed R6 cells. However, Gp saponins posted a strong inhibition against the growth of the ras-transformed cells that were co-cultivated with normal R6 cells. Thus, the data strongly suggest that the inhibitory effect of Gp saponins is not due to a direct killing of transformed cells, rather, Gp might stimulate R6 cells to secret factor(s) that presumably has growth inhibitory effect against the transformed cells. Indeed, an active fraction against the transformed cells has been identified from the conditioned medium collected from Gp-treated R6 cultures. The bioactive component(s) seems to be heat-labile, with molecular weight larger than 14,000. Column purification of the active component(s) will be one of the immediate tasks. The potential gene targets of Gp were investigated. Based on the results obtained from the Western, Northern blot analysis and protein expression in situ, the addition of Gp does not affect the transforming ability, subcellular localization, or the level of expression of Ras protein. Instead, the level of Raf-1 protein was sharply down-regulated within 2 days of Gp treatment. Further investigation indicated that Gp treatment induced instability, instead of transcriptional inactivation of the Raf-1 expression. Besides Raf-1, the immediate downstream gene, Erk seemed to be dephosphorylated upon Gp treatment, while the total protein remained unchanged. To further understand the effect of Gp on R6 cells, a cDNA microarray containing 1176 rat cDNAs was used to examine the gene profilings between Gp-treated and -untreated R6 cells. The result showed that four genes: β2-microglobulin, GST7-7, gelatinase A and cathepsin L were up-regulated, while three genes: Erk-1, γIGFBP-6, and 14-3-3 zeta were down-regulated upon treatment with Gp saponins. The possible impact of the altered genes on ras-transformation is under evaluation. In order to identify the potential active glycosides in Gp, column chromatography, NMR and TLC were performed. Out of seventeen isolated saponins, five of which have retained the anti-cancer effect against ras-transformed cells. Ras proteins play a pivotal role in regulating cell growth and the development of cancer. The finding that an anti-cancer effect of a non-toxic drug may be mediated through the surrounding normal cells is conceptually novel and should have a broad implication in the future development of drugs or dietary supplements with cancer prevention function

Permeability and Disintegration Characteristics of Composite Improved Phyllite Soil by Red Clay and Cement

The bearing capacity of the phyllite soil subgrade can be greatly improved by red clay, but the water stability of the modified soil is still poor. Hence, the blended soil has been found to be unsuitable for the construction of high-speed railways. This paper proposes an innovative scheme, by adding appropriate amounts of cement and red clay concurrently, to improve phyllite soil, which achieves a higher bearing capacity of the subgrade immediately after compaction, while also solving the problem of insufficient water stability. Laboratory tests of the permeability and disintegration characteristics of phyllite soils improved by cement, red clay, and both were carried out. The test results show that the permeability coefficient and maximum disintegration rate of soil can be improved effectively by using both red clay and cement. It was found that the optimal combination scheme is to add 3% cement and 40% red clay to phyllite soil by mass. Under the optimal scheme, the permeability coefficient, maximum disintegration rate, and disintegration rate of the improved soil decreased by 90.02%, 90.30%, and 99.02%, respectively, compared with the phyllite soil. The microscopic study shows that the mechanism of red clay blending with phyllite is that the finer particles of red clay infill the pores among the phyllite particles, thus reducing its permeability coefficient. The mechanism of adding cement to the blending soil mainly results from the production of hard-setting new materials and the formation of a cementation network among the soil particles, which not only increases the shear strength of the soil, but also reduces the permeability coefficient and the maximum disintegration ratio of the soil. This work makes full use of the complementary characteristics of red clay and phyllite soil and the advantages of hard-setting new materials, which will provide a new idea for soil improvement of the phyllite soil in the future

Preparation of Lung-Targeting, Emodin-Loaded Polylactic Acid Microspheres and Their Properties

Emodin (1,3,8-trihydroxy-6-methylanthraquinone) has been identified to have the potential to improve lung fibrosis and lung cancer. To avoid the liver and kidney toxicities and the fast metabolism of emodin, emodin-loaded polylactic acid microspheres (ED-PLA-MS) were prepared and their characteristics were studied. ED-PLA-MS were prepared by the organic phase dispersion-solvent diffusion method. By applying an orthogonal design, our results indicated that the optimal formulation was 12 mg/mL PLA, 0.5% gelatin, and an organic phase:glycerol ratio of 1:20. Using the optimal experimental conditions, the drug loading and encapsulation efficiencies were (19.0 ± 1.8)% and (62.2 ± 2.6)%, respectively. The average particle size was 9.7 ± 0.7 μm. In vitro studies indicated that the ED-PLA-MS demonstrated a well-sustained release efficacy. The microspheres delivered emodin, primarily to the lungs of mice, upon intravenous injection. It was also detected by microscopy that partial lung inflammation was observed in lung tissues and no pathological changes were found in other tissues of the ED-PLA-MS-treated animals. These results suggested that ED-PLA-MS are of potential value in treating lung diseases in animals