S. Namilae¹, U. Ch,ra², A Srinivasan³, N. Ch,ra⁴

CMES-Computer Modeling in Engineering & Sciences, Vol.22, No.3, pp. 189-202, 2007, DOI:10.3970/cmes.2007.022.189

Abstract Molecular dynamics (MD) simulations play an important predictive role in understanding the behavior of nanoscale systems. In this paper, parallel MD simulations are used to understand the mechanical behavior of interfaces in CNT based composites. We present an algorithm for parallel implementation of MD simulations of carbon nanotube (CNT) based systems using reactive bond order potentials. We then use that algorithm to model the CNT-polymer interfaces with various levels of interaction as (a) described only by long range Van Der Waals interactions (b) chemically bonded with fixed matrix and (c) chemically bonded with matrix explicitly More >

Wenzhong Tang¹, Suresh G. Advani^1,2

CMES-Computer Modeling in Engineering & Sciences, Vol.22, No.1, pp. 31-40, 2007, DOI:10.3970/cmes.2007.022.031

Abstract In this paper, non-equilibrium molecular dynamics (MD) simulations were performed to investigate water flow around a single-walled carbon nanotube. In the simulation, the nanotube was modeled as a rigid cylinder of carbon atoms. Water molecules were described with the extended simple point charge (SPC/E) model. The nanotube-water interactions were calculated with a Lennard-Jones potential between carbon-oxygen pairs. The water-water interactions comprised a Lennard-Jones potential between the oxygen-oxygen pairs and a Coulomb potential between all charge sites on interactive water molecules. It was shown that classical continuum mechanics does not hold when the drag forces on More >

Yan Liu¹, Xiong Zhang¹, K. Y. Sze², Min Wang¹

CMES-Computer Modeling in Engineering & Sciences, Vol.20, No.3, pp. 177-192, 2007, DOI:10.3970/cmes.2007.020.177

Abstract In molecular simulations, the frequencies of the low-frequency modes are many orders of magnitude lower than those of the high-frequency modes. Compared with the amplitudes of the low-frequency modes, the amplitudes of the high-frequency modes are often negligible and, thus, least interesting. As dictated by the period of the highest frequency mode, the critical time step for stable time integration can be significantly increased by suppressing the negligible high-frequency modes yet the solution remains virtually intact. In this light, a smoothed molecular dynamics (SMD) approach is proposed to eliminate the high-frequency modes from the dynamical… More >

W.H. Chen¹, H.C. Cheng², Y.C. Hsu³

CMES-Computer Modeling in Engineering & Sciences, Vol.20, No.2, pp. 123-146, 2007, DOI:10.3970/cmes.2007.020.123

Abstract The evaluation of the fundamental mechanical properties of single/multi-walled carbon nanotubes(S/MWCNTs) is of great importance for their industrial applications. The present work is thus devoted to the determination of various mechanical properties of S/MWCNTs using molecular dynamics (MD) simulations. The study first focuses on the exploration of the effect of the weak inlayer van der Waals (vdW) atomistic interactions on the mechanical properties of S/MWCNTs. Secondly, in addition to the zig-zag and armchair types of CNTs, the hybrid type of MWCNTs that comprise a zig-zag outer tube and an inner armchair tube is also analyzed.… 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 More >

Yong Gan^*, Zhen Chen^∗,†

Molecular & Cellular Biomechanics, Vol.3, No.3, pp. 89-94, 2006, DOI:10.3970/mcb.2006.003.089

Abstract Due to their nanoscale size and special features, carbon nanotubes could enter the human body via certain way. The growing use of carbon nanotubes in practical applications, hence, prompts a necessity to study the potential health risks of carbon nanotubes. A numerical study is performed in this paper to investigate the size effect of carbon nanotubes on the bulk modulus of a lipid bilayer by using the constant surface tension molecular dynamics simulation procedure. It is found that the size effect is not monotonic with the increase of nanotube length. An explanation is given on More >

Jin Ma, Yang Liu, Hongbing Lu, Ranga Komanduri¹

CMES-Computer Modeling in Engineering & Sciences, Vol.16, No.1, pp. 41-56, 2006, DOI:10.3970/cmes.2006.016.041

Abstract A multiscale simulation technique coupling three scales, namely, the molecular dynamics (MD) at the atomistic scale, the discrete dislocations at the meso scale and the generalized interpolation material point (GIMP) method at the continuum scale is presented. Discrete dislocations are first coupled with GIMP using the principle of superposition (van der Giessen and Needleman (1995)). A detection band seeded in the MD region is used to pass the dislocations to and from the MD simulations (Shilkrot, Miller and Curtin (2004)). A common domain decomposition scheme for each of the three scales was implemented for parallel More >

J. Ma², H. Lu², B. Wang², R. Hornung³, A. Wissink³, R. Komanduri^2,*

CMES-Computer Modeling in Engineering & Sciences, Vol.14, No.2, pp. 101-118, 2006, DOI:10.3970/cmes.2006.014.101

Abstract A new method for multiscale simulation bridging two scales, namely, the continuum scale using the generalized interpolation material point (GIMP) method and the atomistic scale using the molecular dynamics (MD), is presented and verified in 2D. The atomistic strain from the molecular dynamics simulation is determined through interpolation of the displacement field into an Eulerian background grid using the same generalized interpolation functions as that in the GIMP method. The atomistic strain is consistent with that determined from the virial theorem for interior points but provides more accurate values at the boundary of the MD… More >

R. Matsumoto¹, M. Nakagaki¹, A. Nakatani², H. Kitagawa³

CMES-Computer Modeling in Engineering & Sciences, Vol.9, No.1, pp. 75-84, 2005, DOI:10.3970/cmes.2005.009.075

Abstract In this paper, the internal structure-changes around the crack-tip and the pertinent crack growth behavior in an amorphous metal were studied by a molecular dynamics (MD) simulation. In order to perform a large scale calculation, the domain decomposition method was used for parallel calculation. The Finnis-Sinclair potential for$\alpha$-iron was used to describe the interatomic potential. Computed results show that nano-scaled crystalline phase grows around the crack-tip. The distribution of deformation zones and deformation mechanism are significantly altered. While grains are relatively small, they are not deformed, and the most amorphous-crystal interfaces have a large strain More >

Shouqin Lü¹, Mian Long^1,2

Molecular & Cellular Biomechanics, Vol.2, No.4, pp. 161-178, 2005, DOI:10.3970/mcb.2005.002.161

Abstract Selectin-ligand interactions are crucial to such biological processes as inflammatory cascade or tumor metastasis. How transient formation and dissociation of selectin-ligand bonds in blood flow are coupled to molecular conformation at atomic level, however, has not been well understood. In this study, steered molecular dynamics (SMD) simulations were used to elucidate the intramolecular and intermolecular conformational evolutions involved in forced dissociation of three selectin-ligand systems: the construct consisting of P-selectin lectin (Lec) and epidermal growth factor (EGF)-like domains (P-LE) interacting with synthesized sulfoglycopeptide or SGP-3, P-LE with sialyl Lewis X (sLe^X), and E-LE with sLe^X. SMD… More >