Wei Huang^*

Molecular & Cellular Biomechanics, Vol.4, No.3, pp. 119-132, 2007, DOI:10.3970/mcb.2007.004.119

Abstract This work presents a tensorial description of the geometrical arrangement of the cellular molecules in the vascular endothelial cells. The geometrical arrangement of the molecules is the foundation of the mechanical properties of the molecular aggregates, which are the foundation of the physical behavior of the cells and tissues. For better studying the physical behavior of the cells and tissues, the geometrical arrangement of the cellular molecules has to be described quantitatively. In this paper, a second order molecular configuration tensor P_ij^g for fibrous protein in the cells is defined for quantitative measurement. Here, the subscripts i, j refer… More >

Baohua Ji^*, Yonggang Huang^†

Molecular & Cellular Biomechanics, Vol.3, No.3, pp. 109-120, 2006, DOI:10.3970/mcb.2006.003.109

Abstract The mechanisms governing the self-assembled structure of biomolecules (single chain and bundle of chains) are studied with an AB copolymer model via the coarse grained molecular dynamics simulations. Non-local hydrophobic interaction is found to play a critical role in the pattern formation of the assembled structure of polymer chains. We show that the polymer structure could be controlled by adjusting the balance between local (short range) and non-local (long range) hydrophobic interaction which are influenced by various factors such as the sequences, chain length, stiffness, confinement, and the topology of polymers. In addition, the competition between the intrachain hydrophobic interaction… More >

Cheng Dong^1,2,3, Margaret J. Slattery^2,3, Shile Liang³, Hsin-Hsin Peng²

Molecular & Cellular Biomechanics, Vol.2, No.3, pp. 145-160, 2005, DOI:10.3970/mcb.2005.002.145

Abstract Attachment of tumor cells to the endothelium (EC) under flow conditions is critical for the migration of tumor cells out of the vascular system to establish metastases. Innate immune system processes can potentially promote tumor progression through inflammation dependant mechanisms.\nobreakspace {} White blood cells, neutrophils (PMN) in particular, are being studied to better understand how the host immune system affects cancer cell adhesion and subsequent migration and metastasis. Melanoma cell interaction with the EC is distinct from PMN-EC adhesion in the circulation. We found PMN increased melanoma cell extravasation, which involved initial PMN tethering on the EC, subsequent PMN capture… 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 to become negative… 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 continuum approach. More >

Kilho Eom¹, Jeong-Hee Ahn², Seung-Chul Baek², Jae-In Kim², Sungsoo Na^2,3

CMC-Computers, Materials & Continua, Vol.6, No.1, pp. 35-42, 2007, DOI:10.3970/cmc.2007.006.035

Abstract This paper concerns the application and demonstration of robust reduction methodology for biomolecular structure modeling, which is able to estimate dynamics of large proteins. The understanding of large protein dynamics is germane to gain insight into biological functions related to conformation change that is well described by normal modes. In general, proteins exhibit the complicated potential field and the large degrees of freedom, resulting in the computational prohibition for large protein dynamics. In this article, large protein dynamics is investigated with modeling reduction schemes. The performance of hierarchical condensation methods implemented in the paper is compared with that obtained from… 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 the ATC were investigated. The… More >