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 More >

Hai-tao Geng^*, Rui-juan Cao^*, Lei Cheng^†, Chun-yuan Liu^†

Oncology Research, Vol.25, No.7, pp. 1039-1046, 2017, DOI:10.3727/096504016X14813914187138

Abstract Hepatocyte cell adhesion molecule (hepaCAM), a new type of CAM, belongs to the immunoglobulin superfamily. Recently, hepaCAM was reported to be implicated in cancer development, and many researchers investigated its biological function in the tumorigenesis of various cancers. However, what kind of role hepaCAM plays in colorectal cancer (CRC) remains unknown. In this study, we found that hepaCAM was downregulated in CRC tissues and cell lines. Overexpression of hepaCAM inhibited CRC cell proliferation, migration, and invasion in vitro. Furthermore, the tumorigenesis assay showed that increased expression of hepaCAM suppressed CRC tumor growth and metastasis in More >

ZichunYang¹, Gaohui Su^1,2, Bin Chen¹

CMC-Computers, Materials & Continua, Vol.51, No.1, pp. 43-62, 2016, DOI:10.3970/cmc.2016.051.043

Abstract The molecular dynamics (MD) simulations were used to understand the heat transfer process between the gas phase and the solid skeleton in the nanoporous silica aerogels. The amorphous silica nanoparticles were generated by the MD simulations and the energy accommodation coefficient (EAC) between the gases and the nanoparticles was calculated based on the results of the nonequilibrium molecular dynamics (NEMD) simulations. The apparent thermal conductivity (ATC) of the gases between the heat source and heat sink was also obtained. The effects of the temperature, the particle diameter and the molecule type on the EAC and… More >

Hassan P. Modarres^∗, Mohammad R. K. Mofrad^†

Molecular & Cellular Biomechanics, Vol.11, No.1, pp. 39-65, 2014, DOI:10.3970/mcb.2014.011.039

Abstract Focal adhesions are the immediate sites of the cell’s adhesive interaction with the extracellular matrix and as such play a key role in mechanosensing and mechanotransduction at the edge of the cell interface with its surrounding microenvironment. A multitude of proteins orchestrate this mechanochemical communication process between the cell and its outside world. Filamin is a member of focal adhesion protein machinery that also plays a key role in regulating and bundling the acting filament network. A brief review is presented here on filamin and its important protein partners with the aim to shed light More >

F. Maceri¹, M. Marino¹, G. Vairo¹

CMES-Computer Modeling in Engineering & Sciences, Vol.87, No.5, pp. 461-482, 2012, DOI:10.3970/cmes.2012.087.461

Abstract The mechanical behavior of biopolymer mo -le -cu -les is herein addressed and a novel predictive model for their elasto-damage response is proposed. Both entropic and energetic elastic mechanisms are accounted for, and coupled by consistent equilibrium conditions. Moreover, through non-smooth mechanics arguments, molecular damage is modeled accounting for failure due to both mechanical and non-mechanical damage sources. The model is applied to collagen molecules and an excellent agreement with available experimental tests and atomistic computations is shown. The proposed predictive theory can be usefully integrated in hierarchical models of biological structures towards a multiscale More >

Yasuhiro Kajima, Miyabi Hiyama, Shuji Ogata

The International Conference on Computational & Experimental Engineering and Sciences, Vol.18, No.2, pp. 45-46, 2011, DOI:10.3970/icces.2011.018.045

Abstract There has been increased interest to understand through computer simulation the dynamics of micro-droplets; for example, the coalescence and/or disruption of water droplets as a fundamental process of the cloud formation for the earth climate estimation, the formation and size-controlling mechanism of the ink-droplet for advanced ink-jet printer. Since long-time simulations of such water droplets at atomistic scale are required, we often choose the rigid-body type inter-atomic potential as the TIP4P. In the present paper, we propose the improved angular-momentum Verlet (IAMV) method for the time evolution of the rigid molecules, by enforcing complete time-reversibility… More >

T. Zhang^*

Molecular & Cellular Biomechanics, Vol.8, No.3, pp. 169-194, 2011, DOI:10.3970/mcb.2011.008.169

Abstract Cytoplasmic motion assumed as a steady state laminar flow induced by cytoskeleton stretching in a cell is determined and its effect on the mechanical behavior of the cell under externally applied forces is demonstrated. Non-Newtonian fluid is assumed for the multiphase cytoplasmic fluid and the analytical velocity field around the macromolecular chain is obtained by solving the reduced nonlinear momentum equation using homotopy technique. The entropy generation by the fluid internal friction is calculated and incorporated into the entropic elasticity based 8-chain constitutive relations. Numerical examples showed strengthening behavior of cells in response to externally More >

Wen-Hwa Chen^1,2, Chun-Hung Wu¹, Hsien-Chie Cheng^3,4,5

CMC-Computers, Materials & Continua, Vol.25, No.3, pp. 195-214, 2011, DOI:10.3970/cmc.2011.025.195

Abstract The study aims at investigating the linear and volumetric thermal expansion coefficients (CTEs) at temperature below the Debye temperature and phase transformation behaviors at atmospheric pressure of carbon fullerenes, i.e., C₆₀, C₇₀ and C₈₀, through a modified Nosé-Hoover (NH) thermostat method incorporated with molecular dynamics (MD) simulation. The calculated results are compared with those obtained from the standard NH and "massive" NHC (MNHC) thermostats and also with the literature experimental and theoretical data. Results show that at temperature below the Debye temperature, the CTEs of the fullerene molecules would significantly decrease with a decreasing temperature and tend… More >

Fan Song^*

Molecular & Cellular Biomechanics, Vol.7, No.1, pp. 13-24, 2010, DOI:10.3970/mcb.2010.007.013

Abstract The electrostatic interaction effects including the interaction potential, force and torque between the neighboring chondroitin sulfate glycosaminoglycan (CS-GAG) molecular chains in the bottle brush conformation of proteoglycan aggrecan are obtained as the functions of the minimum separation distance and the mutual angle between the molecular chains based on an asymptotic solution of the Poisson-Boltzmann equation that the CS-GAGs satisfy under the normal physiological conditions of articular cartilage. The present study indicates that the electrostatic interactions are not only associated intimately with the separation distance and the mutual angle, which are shown as purely exponential in… More >

Faina Linkov¹, Yian Gu⁴, Alan A. Arslan^2,3,4, Mengling Liu⁴, Roy E. Shore^2,5, Lyudmila Velikokhatnaya¹, Karen L. Koenig^2,4, Paolo Toniolo³, Adele Marrangoni¹, Zoya Yurkovetsky¹, Anne Zeleniuch-Jacquotte^2,4, Anna E. Lokshin^1,6,7

European Cytokine Network, Vol.20, No.1, pp. 21-26, 2009, DOI:10.1684/ecn.2009.0146

Abstract There is a growing interest in the role that cancer biomarkers, metastasis-related molecules, and chemokines may play in the development and progression of various cancers. However, few studies have addressed the reliability of such biomarkers in healthy individuals over time. The objective of this study was to investigate the temporal reliability of multiple proteins in serum samples from healthy women who donated blood over successive years. Thirty five, postmenopausal women with two, repeated annual visits, and thirty, premenopausal women with three, repeated annual visits were randomly selected among eligible subjects from an existing, prospective cohort.… More >