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Search Results (4)
  • Open Access


    PPARγ LBD and its ligand specificity reveal a selection of potential partial agonist: Molecular dynamics based T2D drug discovery initiative


    BIOCELL, Vol.45, No.4, pp. 953-961, 2021, DOI:10.32604/biocell.2021.015530

    Abstract PPARγ is a peroxisome proliferator-activated receptor (PPAR) family protein and is a target for type 2 diabetes (T2D). In this paper, we have performed a molecular docking analysis between ligand molecules (CID9816265, CID11608015, CID20251380, CID20251343, CID20556263, CID624491, CID42609928, and CID86287562) and PPARγ to determine the ligand specificity. It also helps to understand the ligand-binding domain (LBD) activity of PPARγ during the binding of the ligand. Further, a molecular dynamics simulation study was performed to determine the ligand biding stability in the PPARγ LBD. Its ligand specificity informed us about the potentiality of selecting a partial… More >

  • Open Access


    Local Stress Field in Wafer Thinning Simulations with Phase Space Averaging

    Miaocao Wang1, Yuhua Huang1, Jinming Li1, Ling Xu2, Fulong Zhu1,*

    CMC-Computers, Materials & Continua, Vol.68, No.1, pp. 743-759, 2021, DOI:10.32604/cmc.2021.016372

    Abstract From an ingot to a wafer then to a die, wafer thinning plays an important role in the semiconductor industry. To reveal the material removal mechanism of semiconductor at nanoscale, molecular dynamics has been widely used to investigate the grinding process. However, most simulation analyses were conducted with a single phase space trajectory, which is stochastic and subjective. In this paper, the stress field in wafer thinning simulations of 4H-SiC was obtained from 50 trajectories with spatial averaging and phase space averaging. The spatial averaging was conducted on a uniform spatial grid for each trajectory.… More >

  • Open Access


    The Dependence of Diffusio-Phoretic Mobility and Aggregation Properties of Proteins on Intermolecular Interaction in Confined System

    Jiachen Wei1,2,*

    Molecular & Cellular Biomechanics, Vol.16, Suppl.2, pp. 103-104, 2019, DOI:10.32604/mcb.2019.07721

    Abstract Phoretic flow can be generated by different types of gradient (e.g. temperature, concentration, or charge gradient) [1-3]. Within micro-to-nano confined system, the diffusio-phoretic property for proteins differs dramatically from that obtained in bulk condition, due to concentration fluctuation that emerges at microscopic level induced by specific and nonspecific interactions between protein and co-solute [4-5]. The phoretic mobility of protein individuals and complex in solute gradients can be theoretically described by continuum model [1-2] that neglects microscopic heterogeneity and determined experimentally by microfluidics [6], but the underlying mechanism of diffusio-phoretic motion for confined protein still remains… More >

  • Open Access


    Gating mechanisms of a mechanosensitive ion channel: experiments and molecular simulations

    M. Sokabe1,2,3, Sawada Y1

    The International Conference on Computational & Experimental Engineering and Sciences, Vol.12, No.2, pp. 47-48, 2009, DOI:10.3970/icces.2009.012.047

    Abstract Mechanosensing is ubiquitous in our body. Not only specialized mechanoreceptors like inner ear hair cells and visceral baroreceptors, but also ordinary cells can respond to mechanical stimuli, by which cells can regulate their volume, shape and motility properly. The major biophysical issue in this field is to understand the physicochemical mechanisms of mechanotransduction based on the molecular structure of mechanosensors. To date the mechanosesnitive (MS) ion channel is the only identified molecular class of mechanosensors. Among them the bacterial MS channel MscL is the best studied one owing to the resolved 3D structure of its… More >

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