Development of lattice inversion modified embedded atom method and its applications

Xianbao Duan,Bing Zhou,Rong Chen,Huamin Zhou,YanweiWen,Bin Shan 한국물리학회 2014 Current Applied Physics Vol.14 No.12

The modified embedded atom method (MEAM) has been widely used in describing the physical properties of elemental crystals, alloys and compounds with multiple lattice structures. We report here the development of a reliable procedure to reduce the complexity of the MEAM formalism by removing the many-body screening function. In the proposed formulation, the interatomic pair potential is obtained by applying Chen-M€obius lattice inversion up to fifth nearest neighbors, so that the cohesive energy curve can be reproduced faithfully. The newly developed model (Lattice Inversion MEAM, LI-MEAM), which can be viewed as a direct extension of the embedded atom method (EAM), no longer requires the computation of many-body screen functions and has fewer adjustable parameters than MEAM. As an illustration, we optimized the potential parameters of body centered cubic iron (bcc-Fe). The values of the calculated physical properties agree well with experimental results. We further investigated the sizedependent melting behavior of bcc-Fe nanoparticles (NPs) with particle size ranging from 725-atom (~25 Å) to 22899-atom (~80 Å) using replica exchange molecular dynamics (REMD) simulations. Our simulations show advantages of LI-MEAM in modeling of the melting process and quantitatively reveals that the liquid skin melting (LSM) process of bcc-Fe NPs.

Excellent Cycle Stability of Fe3O4 Nanoparticles Decorated Graphene as Anode Material for Lithium-Ion Batteries

Shan-Shan Chen,Xueqing Wang 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2015 NANO Vol.10 No.6

Fe3O4–graphene nanocomposites were prepared via a simple hydrothermal method. Ultrafine Fe3O4 nanoparticles were evenly anchored on graphene substrates. As anode material for Li-ion batteries (LIB), the nanocomposite showed high initial discharge and charge capacities of 1456 mAhg-1 and 739.9 mAhg-1 at high current density of 500 mAg-1. Additionally, the charge capacity was also retained at 698.3 mAhg-1 after 200 cycles, thereby indicating excellent cycling stability. The results suggested that the as-prepared Fe3O4–graphene nanocomposite is a promising candidate for practical application as a Li-ion battery anode material.

Xylitol fermentation by Candida subtropicalis WF79 immobilized in polyacrylic hydrogel films

Chee-Shan Chen,Wen-Chang Liaw,Wen-Shion Chang,Kuan-Pin Chen,Yee-Fan Chen 한국화학공학회 2008 Korean Journal of Chemical Engineering Vol.25 No.5

Polyacrylate hydrogel films were used as immobilization matrices for cell entrapment of the yeast strain, Candida subtropicalis WF79, isolated from sugarcane bagasse. The hydrogel films with immobilized viable yeast cells were employed for the bioconversion from xylose to xylitol. The hydrogel was prepared from the monomers of 2-hydroxyethyl methacrylate (HEMA), methacrylic acid (MAA), and N,N-dimethyl acrylamide (DMA) with polyethylene glycol diacrylate (PEG-DA, weight-average molecular weight Mw=400 and 1,000 g/mol) as the crosslinking agent. The mechanical properties and fermentation yields of the immobilized polyacrylate hydrogel film with different monomeric formulation were investigated. Fermentation was carried out in a medium of 100 mL aqueous solution containing various amount of xylose. The conversion rate of xylose to xylitol conversion reached a maximum value of 80% after 120 h. The bioconversion activity gradually declined, after 720 h, to 65% conversion at 1,080 h

Combination of Tumor Volume and Epstein-Barr Virus DNA Improved Prognostic Stratification of Stage II Nasopharyngeal Carcinoma in the Intensity Modulated Radiotherapy Era: A Large-Scale Cohort Study

Qiu-Yan Chen,Shao-Yan Guo,Lin-Quan Tang,Tong-Yu Lu,Bo-Lin Chen,Qi-Yu Zhong,Meng-Sha Zou,Qing-Nan Tang,Wen-Hui Chen,Shan-Shan Guo,Li-Ting Liu,Yang Li,Ling Guo,Hao-Yuan Mo,Rui Sun,Dong-Hua Luo,Chong Zha 대한암학회 2018 Cancer Research and Treatment Vol.50 No.3

Purpose Little is known about combination of the circulating Epstein-Barr viral (EBV) DNA and tumor volume in prognosis of stage II nasopharyngeal carcinoma (NPC) patients in the intensity modulated radiotherapy (IMRT) era. We conducted this cohort study to evaluate the prognostic values of combining these two factors. Materials and Methods By Kaplan-Meier, we compare the differences of survival curves between 385 patients with different EBV DNA or tumor volume levels, or with the combination of two biomarkers mentioned above. Results Gross tumor volume of cervical lymph nodes (GTVnd, p < 0.001) and total tumor volume (GTVtotal, p < 0.001) were both closely related to pretreatment EBV DNA, while gross tumor volume of nasopharynx (GTVnx, p=0.047) was weakly related to EBV DNA. EBV DNA was significantly correlated with progress-free survival (PFS, p=0.005), locoregional-free survival (LRFS, p=0.039), and distant metastasis-free survival (DMFS, p=0.017), while GTVtotal, regardless of GTVnx and GTVnd, had a significant correlation with PFS and LRFS. The p-values of GTVtotal for PFS and LRFS were 0.008 and 0.001, respectively. According to GTVtotal and pretreatment EBV DNA level, patients were divided into a low-risk group (EBV DNA 0 copy/mL, GTVtotal < 30 cm3; EBV DNA 0 copy/mL, GTVtotal  30 cm3; or EBV DNA > 0 copy/mL, GTVtotal < 30 cm3) and a high-risk group (EBV DNA > 0 copy/mL, GTVtotal  30 cm3). When patients in the low-risk group were compared with those in the high-risk group, 3-year PFS (p=0.003), LRFS (p=0.010), and DMFS (p=0.031) rates were statistically significant. Conclusion Pretreatment plasma EBV DNA and tumor volume were both closely correlated with prognosis of stage II NPC patients in the IMRT era. Combination of EBV DNA and tumor volume can refine prognosis and indicate for clinical therapy.

Contact toxicity and transcriptomic analysis of terpinen-4-ol exposure in Tribolium castaneum

Shan-shan Gao,Yong-lei Zhang,Kun-peng Zhang,Wang Xing-yun,Qing-bo Tang,Yuan-chen Zhang 한국응용곤충학회 2022 Journal of Asia-Pacific Entomology Vol.25 No.3

The terpene, terpinen-4-ol (T4ol), exhibits contact toxicity in Tribolium castaneum. However, the molecular mechanisms underlying this toxicity have not been elucidated. This study examined changes in the expression of four classic enzymes after exposure of T. castaneum to T4ol. Acetylcholinesterase and glutathione S-transferase activities were markedly inhibited after exposure to T4ol, while that of the detoxifying enzyme cytochrome oxidase P450 increased markedly. Carboxylesterase activity did not show significant changes. Furthermore, RNA sequencing revealed 260 differentially expressed genes (DEG) between the T4ol-treated and control samples, and qRT-PCR was used to validate the RNA-Seq data. The Gene Ontology analysis classified the DEGs into 36 functional groups, including the immune system processes, response to stimulus, and developmental processes. T4ol altered the response to stimulus and the immune system process of beetles by inducing the expression of the genes Stabilin-1, Attacin 1, and Defensin 1. Furthermore, the DEGs receptor tyrosine kinase Torso-like protein (RTKTsl), Frizzled 4 (Fz4), Protein Wnt-5b, Ecdysone-induced protein 78C (E78), Zinc finger protein GLIS1 (ZFPGLIS1) were classified as participating in beetle development, and Fz4 and Protein Wnt-5b also mapped to the Wnt signaling pathway. This indicated that pathways associated with development are inhibited after exposure to T4ol. T4ol also induced CYP9Z6/GSTs7 overexpression, and RNAi targeting these genes significantly increased larvae mortality on T4ol exposure, supporting the participation of CYP9Z6/GSTs7 in the response to T4ol in T. castaneum. The results of this study will facilitate understanding of the toxic mechanisms of T4ol and provide a basis for controlling the pests of stored products.

RNA polymerase I subunit D activated by Yin Yang 1 transcription promote cell proliferation and angiogenesis of colorectal cancer cells

Shan Jianfeng,Liang Yuanxiao,Yang Zhili,Chen Wenshan,Chen Yun,Sun Ke 대한약리학회 2024 The Korean Journal of Physiology & Pharmacology Vol.28 No.3

This study aims to explore possible effect of RNA polymerase I subunit D (POLR1D) on proliferation and angiogenesis ability of colorectal cancer (CRC) cells and mechanism herein. The correlation of POLR1D and Yin Yang 1 (YY1) expressions with prognosis of CRC patients in TCGA database was analyzed. Quantitative realtime polymerase chain reaction (qRT-PCR) and Western blot were applied to detect expression levels of POLR1D and YY1 in CRC cell lines and CRC tissues. SW480 and HT- 29 cells were transfected with si-POLR1D or pcDNA3.1-POLR1D to achieve POLR1D suppression or overexpression before cell migration, angiogenesis of human umbilical vein endothelial cells were assessed. Western blot was used to detect expressions of p38 MAPK signal pathway related proteins and interaction of YY1 with POLR1D was confirmed by dual luciferase reporter gene assay and chromatin immunoprecipitation (ChIP). TCGA data showed that both POLR1D and YY1 expressions were up-regulated in CRC patients. High expression of POLR1D was associated with poor prognosis of CRC patients. The results showed that POLR1D and YY1 were highly expressed in CRC cell lines. Inhibition or overexpression of POLR1D can respectively suppress or enhance proliferation and angiogenesis of CRC cells. YY1 inhibition can suppress CRC progression and deactivate p38 MAPK signal pathway, which can be counteracted by POLR1D overexpression. JASPAR predicted YY1 can bind with POLR1D promoter, which was confirmed by dual luciferase reporter gene assay and ChIP. YY1 transcription can up-regulate POLR1D expression to activate p38 MAPK signal pathway, thus promoting proliferation and angiogenesis ability of CRC cells

IQGAP1 is overexpressed in hepatocellular carcinoma and promotes cell proliferation by Akt activation

Chen, Feng,Zhu, Hai-Hong,Zhou, Lin-Fu,Wu, Shan-Shan,Wang, Jing,Chen, Zhi Korean Society for Biochemistry and Molecular Bion 2010 Experimental and molecular medicine Vol.42 No.7

The scaffold protein IQGAP1 shows elevated levels in several cancer types, but its expression in hepatocellular carcinoma is unknown. We found that 58% of human hepatocellular carcinoma tissue samples had increased IQGAP1 expression compared to adjacent normal tissue. Overexpressing IQGAP1 raised the in vivo tumorigenicity of hepatocellular carcinoma cells, and forced overexpression of IQGAP1 in vitro stimulated cell proliferation. Cell growth was reduced by knockdown or mutation of IQGAP1, or by treatment of cells with a phosphotidylinositol 3-kinase inhibitor. To determine the mechanism by which IQGAP1 overexpression affected hepatocellular carcinoma cells, we confirmed its interaction in these cells with mammalian target of rapamycin (mTOR), a serine/threonine kinase that integrates signals about nutrient and energy status with downstream effectors that influence cell division. In addition, we discovered a new interaction involving IQGAP1, mTOR and Akt, which is a downstream target of mTOR. Akt phosphorylation on Ser-473, which is catalyzed by mTOR and required for Akt activation, increased with increasing amounts of IQGAP1, and decreased with IQGAP1 mutation. We hypothesize that IQGAP1 is a scaffold that facilitates mTOR and Akt interaction.

Overexpression of RUNX3 Inhibits Malignant Behaviour of Eca109 Cells in Vitro and Vivo

Chen, Hua-Xia,Wang, Shuai,Wang, Zhou,Zhang, Zhi-Ping,Shi, Shan-Shan Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.4

Runt-related transcription factor 3 (RUNX3) is a tumor suppressor gene whose reduced expression may play an important role in the development and progression of esophageal squamous cell cancer (ESCC). The aim of this study was to investigate the clinical relevance of RUNX3 in ESCC patients and effects of overexpression on biological behaviour of Eca109 cells in vitro and in vivo. Immunohistochemistry was performed to detect the clinical relevance of RUNX3 and lymph node metastasis in 80 ESCC tissues and 40 non-cancerous tissues using the SP method. RT-PCR and Western blotting were applied to assess the RUNX3 level and verify the Eca109 cell line with stable overexpression. Localization of RUNX3 proteins was performed by cell immunofluorescence. CCK-8 and Scrape motility assays were used to determine proliferation and migration and the TUNEL assay to analyze cell apoptosis. Invasive potential was assessed in cell transwell invasion experiments. In nude mice, tumorigenesis in vivo was determined. Results showed decreased expression of RUNX3 in esophageal tissue to be significantly related to lymph node metastasis (LNM) (P<0.01). In addition, construction of a recombinant lentiviral vector and transfection into the human ESCC cell line Eca109 demonstrated that overexpression could inhibit cell proliferation, migration and invasion, and induce apoptosis. The in vivo experiments in mice showed tumorigenicity and invasiveness to be significantly reduced. Taken together, our studies indicate that underexpression of RUNX3 in human ESCC tissue is significantly correlated with progression. Restoration of RUNX3 expression significantly inhibits ESCC cells proliferation, migration, invasion and tumorigenesis.

Detoxification, antioxidant, and digestive enzyme activities and gene expression analysis of Lymantria dispar larvae under carvacrol

Chen Yun-ze,Zhang Bo-wen,Yang Jing,Zou Chuan-shan,Li Tao,Zhang Guo-cai,Chen Guang-sheng 한국응용곤충학회 2021 Journal of Asia-Pacific Entomology Vol.24 No.1

Carvacrol is a terpene compound with various biological activities. However, few studies have specifically focused on its insecticidal activity and mechanism of carvacrol. The larvae of Lymantria dispar are seriously harmful herbivorous insect. This study measured the antifeedant, growth-inhibitory, and toxic effects of carvacrol on L. dispar larvae. To further clarify the insecticidal mechanism of carvacrol, the effects of carvacrol on detoxifying enzymes, antioxidative enzymes, digestive enzyme activities, and the mRNA expression of the abovementioned enzyme genes were investigated. The results of the study showed that the median lethal concentration (LC 50 ) and the sublethal concentration (LC 20 ) of carvacrol were 1.120 mg/mL and 0.297 mg/mL, respectively, at 72 h. After LC 20 treatment of L. dispar larvae for 72 h, food intake and weight gain were significantly lower compared with the control. Enzyme activity assays showed that carvacrol significantly inhibited the activities of carboxylesterase (CarE), glutathione S-transferase (GST), and acetylcholinesterase (AchE), and the inhibition rate of AchE activity was highest (66.51%). Carvacrol also activated the activities of superoxide dismutase (SOD) and catalase (CAT), while it inhibited the activities of lipase (LIP) and amylase (AMS), and first inhibited and then activated protease. In addition, qRT-PCR tests showed that carvacrol affected the mRNA expression levels of CarE, GST, AchE, SOD, CAT, LIP, AMS, and protease. This study helps to clarify the insecticidal mechanism of carvacrol on L. dispar larvae.

Bulk Synthesis of Fe3Al Intermetallic Compound Nanoparticles by Flow-Levitation Method

Shan-Jun Chen,Song Li,Yang-En Wang,Hui Zeng,Yong-Jian Tang,Wei-Guo Sun,Yan Chen 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2015 NANO Vol.10 No.1

Metallic nanopowders have an increasing application in magnetic materials, catalysts and chemical and metallic industries. In this research, a novel bulk synthesis method for preparing high pure intermetallic Fe3Al nanoparticles was developed by flow-levitation (FL) method. The Fe and Al vapors ascending from the high-temperature levitated droplet were condensed by cryogenic argon gas under atmospheric pressure. X-ray diffraction (XRD) and selected-area electron diffraction (SAED) were used to identify and characterize the prepared nanopowders exhibiting a Fe3Al phase. Measurement of transmission electron microscopy (TEM) indicated that the Fe3Al particles are nearly spherical, and the particle size of the compound ranges from 10 nm to 200 nm in diameter. The chemical composition of the nanoparticles were determined with energy dispersive spectrometer. The magnetic properties of the nanopowder indicate that Fe3Al intermetallic compound is a soft magnet at room temperature, with coercivity of 24.2 Oe and saturation magnetization of 173.2 emu/g. The production rate of Fe3Al nanoparticles was estimated to be about 4 g/h in a continuous manner, by using the FL method. This method as great potential in mass production of Fe3Al nanoparticles.