Chih-Wei Hsieh¹, Chien-Li Wu¹, Cheng-Kuo Sung^1,2

The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.2, pp. 33-34, 2009, DOI:10.3970/icces.2009.013.033

Abstract Molecular dynamics (MD) simulation has been demonstrated as a promising method to analyze formation and friction mechanisms of the nanoimprint process. Especially, it provides a useful tool for investigating critical issues that are generally difficult to be examined by the experiment because of cross talks among influential factors or attainability of direct measurement. This study utilized the friction mechanism to explore the factors that would affect the quality of mold replication in the direct nanoimprint. Those factors included mechanical properties of thin films, interaction force between mold and thin-film materials, and surface roughness of the mold, etc. First, we set… More >

N. J. Lee, C.R. Welch¹

The International Conference on Computational & Experimental Engineering and Sciences, Vol.13, No.1, pp. 11-12, 2009, DOI:10.3970/icces.2009.013.011

Abstract Carbon nanotubes have significant potential as the basis for super infrastructure material. The shear modulus of carbon nanotube ensembles is relatively low, comparable to graphite, as the carbon nanotubes interact via weak van der Waals forces. Unmodified, their intermolecular interactions are insufficient to take full advantage of the extraordinarily high strengths predicted for carbon nanotube-based fibers. Thus, a key to their use in high-strength materials is developing strong bonds between these molecules. In this study, we examine the potential development of covalent bonds between carbon nanotube pairs cross-bonded by proton bombardment using molecular dynamics simulation. Covalent bond formation between aligned… More >

Tei-Chen Chen^1,2, Heng-Chieh Wang¹, Shu-Fan Wu¹, Yen-Hung Lin¹

The International Conference on Computational & Experimental Engineering and Sciences, Vol.9, No.4, pp. 247-262, 2009, DOI:10.3970/icces.2009.009.247

Abstract Mechanical properties of materials in the micro- and nano-meter scale have been successfully obtained by using the indentation technique. Up to now, large-scale atomistic models to simulate the experimental condition, however, still remain computationally demanding. In this article, a simple and accurate method is proposed to derive the intermolecular potential functions of coarse-grained molecular dynamics (CGMD) suitable for various single crystalline materials. This CGMD technique is then provided to simulate nano-indentation process to verify its accuracy and reliability. Simulation results evaluated by CGMD approach are obtained and compared to those predicted by MD. It is found that the results predicted… More >

Chun-Lang Yeh¹

The International Conference on Computational & Experimental Engineering and Sciences, Vol.9, No.2, pp. 81-94, 2009, DOI:10.3970/icces.2009.009.081

Abstract In this study, the vaporization process of a nanojet is investigated by molecular dynamics simulation. Liquid argon nanojet made of 44000 Lennard-Jones molecules is investigated under various simulation parameters to examine their influence on the nanojet vaporization process. Snapshots of the molecules, evolution of the density field, and evolution of the intermolecular force are analyzed. The present simulation results can provide insight into the fundamental mechanism of the atomization process and will be helpful for the design of nanojet devices such as nano-printer or nano-sprayer. 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 >

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 the basis of the atomic… 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 simulations were based on… More >

Zhiyi Han¹, Yugai Huang^2,3, Xiaoqiang Xie¹, Ying Mei¹, Bin Gu^1,*

CMC-Computers, Materials & Continua, Vol.59, No.3, pp. 995-1003, 2019, DOI:10.32604/cmc.2019.02181

Abstract In ab initio molecular dynamics (AIMD) simulations of chemical reactions, it is important but difficult to identify the chemical species in the trajectory automatically and quickly. In this paper, based on the chemical graph theory, an algorithm for molecular species identification, according to the molecular coordinates and empirical bond length database, is presented. As an example, the chemical species in condensed glycine at room temperature are investigated with our algorithm in detail. The chemical species, including canonical and zwitterionic glycine, their protonated and de-protonated states, and the free protons, are all identified, counted and recorded correctly. Potential applications and further… More >

Guojian Li¹, Qiang Wang¹, Yongze Cao¹, Kai Wang¹, Jiaojiao Du¹, Jicheng He¹

CMC-Computers, Materials & Continua, Vol.30, No.3, pp. 195-206, 2012, DOI:10.3970/cmc.2012.030.195

Abstract This paper studies the influence of Ag atomic segregation on the structural evolutions of the mixed (PdAg)₃₀₉ clusters during the heating processes by using molecular dynamics with a general embedded atom method. The results show that the Ag atomic segregation makes the cluster exhibit a segregate-melting stage in which the energy does not monotonic increase with the increase of temperature. In this stage, the cluster first transforms to form a disorder structure from the initial icosahedron and then a decahedron. By comparing with the cases in the pure Pd₃₀₉, Ag₃₀₉, and core-shell (PdAg)₃₀₉, it is found that the icosahedral-decahedral transformation… More >

Qing Song Tu¹, Michelle Lee², Samuel Zhang², Shaofan Li¹

CMES-Computer Modeling in Engineering & Sciences, Vol.98, No.3, pp. 247-259, 2014, DOI:10.32604/cmes.2014.098.247

Abstract In this paper, we present molecular dynamics simulations of diffusion of Na⁺, K⁺, and Cl^- ions through the single-walled carbon nanotubes(SWCNTs) that are embedded into the membrane of cells in aqueous solutions. A simplified atomic cell model that considers bilayer membranes is employed to study the transportation of ions inside CNTs. The simulated results indicate that the diffusion properties of ions and selectivity of CNT with respect to ions are affected by biological complexity of the cell membrane. We have found that the ion diffusion only occurs in the CNTs with chirality higher than (8, 8), which is bigger than… More >