Jiangguo Lin¹, Botao Xiao^1,2, Quhuan Li¹, Ying Fang¹, Jianhua Wu^1,*

Molecular & Cellular Biomechanics, Vol.15, No.1, pp. 37-49, 2018, DOI:10.3970/mcb.2018.015.037

Abstract The protein structure-function paradigm implies that the structure of a protein defines its function. Crystallization techniques such as X-ray, electron microscopy (EM) and nuclear magnetic resonance (NMR) have been applied to resolve the crystal structure of numerous proteins, provided beautiful and informative models of proteins. However, proteins are not intrinsically in static state but in dynamic state, which is lack in crystal models. The protein flexibility, a key mechanical property of proteins, plays important roles in various biological processes, such as ligand-receptor interaction, signaling transduction, substrate recognition and post-translational modifications. Advanced time-resolved crystallography has been developed recent years to visualize… More >

Jizeng Wang^1,2, Xiaojun Fan², Huajian Gao²

Molecular & Cellular Biomechanics, Vol.3, No.1, pp. 13-20, 2006, DOI:10.3970/mcb.2006.003.013

Abstract This paper is aimed at a combined theoretical and numerical study of the force-extension relation of a short DNA molecule stretched in an electrolyte. A theoretical formula based on a recent discrete wormlike chain (WLC) model of Kierfeld et al. (Eur. Phys. J. E, Vol. 14, pp.17-34, 2004) and the classical OSF mean-field theory on electrostatic stiffening of a charged polymer is numerically verified by a set of Brownian dynamics simulations based on a generalized bead-rod (GBR) model incorporating long-ranged electrostatic interactions via the Debye-Hueckel potential (DH). The analysis indicates that the stretching of a short DNA can be well… More >

Itsuo Hanasaki, Hirofumi Shintaku, Satoshi Matsunami, Satoyuki Kawano¹

CMES-Computer Modeling in Engineering & Sciences, Vol.46, No.2, pp. 191-208, 2009, DOI:10.3970/cmes.2009.046.191

Abstract Self-assembly is one of the physical phenomena that are promising for the manufacturing process of the devices on which DNA molecules are mounted as the components. We have conducted a structural study of self-assembled poly(dA)\discretionary poly(dT) DNA networks on mica surface to discuss the design requirements. The results indicate that the network formation process consists of the adsorption and the subsequent coarsening. The final form of the component filaments are roughly straight. These characteristics imply the possible tensile loads during the network formation. Therefore, we have conducted molecular dynamics simulations of tensile tests of a short DNA fragment to elucidate… More >

Yugai Huang ^{1, 2, *}

CMC-Computers, Materials & Continua, Vol.57, No.3, pp. 485-494, 2018, DOI:10.32604/cmc.2018.03112

Abstract It has been demonstrated that low energy electrons (LEEs) can induce serious DNA damages including bases loss and even single and double strand breaks. Experiments also showed that LEE induced DNA damages will be reduced with the presence of amino acids. For understanding of the protection of amino acids to DNA, the stability of 6 kinds of thymine and glycine (T-g) dimers with planar configurations with an excess electron were studied with density functional theory (DFT) method. The results show that, when the excess electron is vertically attached, all the dimers become more active with higher energy. After re-optimization, 4… More >