Yun Wang¹, Tiantian Wang², Bei Wang¹, Wei Chang³, Jiangli Cao¹, Lihua Hu³, Minxu Lu¹, Lei Zhang^1,*

Journal of Renewable Materials, Vol.10, No.2, pp. 301-327, 2022, DOI:10.32604/jrm.2021.015518

Abstract A novel and effective water-soluble aldehydes (β-HA) as corrosion inhibitor was synthesized for N80 steel corrosion in 15% HCl solution, and the corrosion inhibition performance was evaluated by using weight loss, electrochemical measurements, scanning electron microscope (SEM), quantum chemical calculation and molecular dynamics simulation (MDS). The results show that synthesized β-HA showed excellent corrosion performance compared with MHB and PE for carbon steel in 15% HCl solution compared with MHB and PE, and the inhibition efficiency increased with increasing concentration of the inhibitor. The inhibition efficiency of β-HA at 8 mmol/L reached the maximum value 94.08%. The inhibitor acted as… More >

Gaoge Zhao, Jianzhong Chen, Yong Lv^*, Xiaoyu Zhang, Li Huang

CMES-Computer Modeling in Engineering & Sciences, Vol.128, No.1, pp. 339-357, 2021, DOI:10.32604/cmes.2021.015388

Abstract The influence of different nanoparticle sizes on the elastic modulus and the fatigue properties of epoxy/SiO₂ nanocomposite is studied in this paper. Here, the cross-linked epoxy resins formed by the combination of DGEBA and 1,3-phenylenediamine are used as the matrix phase, and spherical SiO₂ particles are used as the reinforcement phase. In order to simulate the elastic modulus and long-term performance of the composite material at room temperature, the simulated temperature is set to 298 K and the mass fraction of SiO₂ particles is set to 28.9%. The applied strain rate is 10⁹/s during the simulation of the elastic modulus.… More >

BIDYUT MALLICK^1,#, ASHISH RANJAN SHARMA^2,#, MANOJIT BHATTACHARYA³, SANG-SOO LEE^1,*, CHIRANJIB CHAKRABORTY^4,*

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 agonist. The study also shows… More >

Hamidreza Noori¹, Bohayra Mortazavi^{2, 3}, Alessandro Di Pierro⁴, Emad Jomehzadeh⁵, Xiaoying Zhuang^{2, 3}, Zi Goangseup⁶, Kim Sang-Hyun⁷, Timon Rabczuk^{8, 9, *}

CMC-Computers, Materials & Continua, Vol.65, No.3, pp. 2009-2032, 2020, DOI:10.32604/cmc.2020.011256

Abstract In modern physics and fabrication technology, simulation of projectile and target collision is vital to improve design in some critical applications, like; bulletproofing and medical applications. Graphene, the most prominent member of two dimensional materials presents ultrahigh tensile strength and stiffness. Moreover, polydimethylsiloxane (PDMS) is one of the most important elastomeric materials with a high extensive application area, ranging from medical, fabric, and interface material. In this work we considered graphene/PDMS structures to explore the bullet resistance of resulting nanocomposites. To this aim, extensive molecular dynamic simulations were carried out to identify the penetration of bullet through the graphene and… More >

Toshifumi Yui^1,*, Takuya Uto²

Journal of Renewable Materials, Vol.8, No.8, pp. 863-878, 2020, DOI:10.32604/jrm.2020.010830

Abstract We report the systematic survey of the binding free energies at the interface between a carbohydrate binding module (CBM) of Cel7A and the cellulose III_I crystal model using grid docking searches and molecular dynamics simulations. The two hydrophobic crystal surfaces were involved in the distinct energy minima of the binding free energy. The complex models, each with the CBM at the minimum energy position, stably formed in the solution state. The binding free energies of the cellulose III_I complex models, based on both static and dynamics states, were comparable to those of the native cellulose complex models. However, the cellulose… More >

Yun Wang¹, Zhen Wang², Lei Zhang^1,*, Minxu Lu¹

Journal of Renewable Materials, Vol.8, No.7, pp. 819-932, 2020, DOI:10.32604/jrm.2020.09395

Abstract The adsorption process of new nicotinic derivatives on Fe (110) surface and diffusion of corrosive particles in inhibition film were studied by quantum chemistry and molecular dynamics simulation, and inhibition mechanism of inhibitor was discussed. The results indicated that the main active sites of three inhibitors are located in N atoms on the five membered ring. The inhibitor YM-1 has the strongest activity of electrophilic reaction, and the adsorption process of inhibitor molecules is polycentric chemisorption. The adsorption energy for inhibitors followed the order of YM-1 > YM-2 > YM-3. The adsorption film YM-1 more effectively impedes the diffusion and… More >

Yue Jia¹, Chun Li^{1, *}, Jinwu Jiang², Ning Wei³, Yang Chen⁴, Yongjie Jessica Zhang⁵

CMC-Computers, Materials & Continua, Vol.63, No.2, pp. 813-823, 2020, DOI:10.32604/cmc.2020.07801

Abstract The present work carries out molecular dynamics simulations to compute the thermal conductivity of the borophene nanoribbon and the borophene nanotube using the Muller-Plathe approach. We investigate the thermal conductivity of the armchair and zigzag borophenes, and show the strong anisotropic thermal conductivity property of borophene. We compare results of the borophene nanoribbon and the borophene nanotube, and find the thermal conductivity of the borophene is orientation dependent. The thermal conductivity of the borophene does not vary as changing the width of the borophene nanoribbon and the perimeter of the borophene nanotube. In addition, the thermal conductivity of the borophene… More >

R. R. Valisetty¹, A. M. Dongare², A. M. Rajendran³, R. R. Namburu¹

CMC-Computers, Materials & Continua, Vol.44, No.1, pp. 23-57, 2014, DOI:10.3970/cmc.2014.044.023

Abstract Materials used in soldier protective structures, such as armor, vehicles and civil infrastructures, are being improved for performance in extreme dynamic environments. Accordingly, atomistic molecular dynamics simulations were performed to study the spall response in a single crystal aluminum atom system. A planar 9.6 picoseconds (ps) shock pulse was generated through impacts with a shock piston at velocities ranging from 0.6 km/s to 1.5 km/s in three <1,0,0>, <1,1,0>, and <1,1,1> crystal orientations. In addition to characterizing the transient spall region width and duration, the spall response was characterized interms of the traditional axial stress vs. axial strain response for… More >

Ning Li^{1, 2, 3}, Xiao Zhang^{1, 2}, Peiwen Li^{1, 2}, Hao Yang^{1, 2}, Chunfang Tong^{1, 2}, Shouqin Lü^{1, 2}, Yan Zhang^{1, 2}, Zhiyi Ye³, Jun Pan^{3, *}, Mian Long^{1, 2, *}

CMES-Computer Modeling in Engineering & Sciences, Vol.116, No.2, pp. 263-279, 2018, DOI:10.31614/cmes.2018.04079

Abstract Neutrophil (PMN) accumulation on liver sinusoidal endothelial cells (LSECs) is crucial to pathogen clearance and tissue damage in the liver sinusoids and controlled by a series of adhesion molecules expressed on the surface of PMNs and LSECs. The role of lymphocyte function-associated antigen-1 (LFA-1) and macrophage-1 antigen (Mac-1) in this process is still contentious. Here we compared the dynamic force spectra of the binding of β2 integrin to intercellular adhesion molecule-1 (ICAM-1) on LSECs using atomic force microscopy (AFM) and performed free and steered molecular dynamics (MD) simulations to analyze their structural bases of LFA-1- or Mac-1-I-domain and ICAM-1-D1 or… More >

Muhammad H. Zaman¹, Mohammad R. Kaazempur-Mofrad²

Molecular & Cellular Biomechanics, Vol.1, No.4, pp. 291-302, 2004, DOI:10.3970/mcb.2004.001.291

Abstract α-actinin, an actin binding protein, plays a key role in cell migration, cross-links actin filaments in the Z-disk, and is a major component of contractile muscle apparatus. The flexibility of the molecule is critical to its function. The flexibility of various regions of the molecule, including the linker connecting central subunits is studied using constant force steered molecular dynamics simulations. The linker, whose structure has been a subject of debate, is predicted to be semi-flexible. The flexibility of the linker is compared to all possible segments of equal length throughout the molecule. The stretching profile of the molecule at different… More >