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. More >

Ning Li^{1, 2, 3}, Xiao Zhang^{1, 2}, Peiwen Li^{1, 2}, Hao Yang^{1, 2}, Chunfang Tong^{1, 2}, Shouqin Lü^{1, 2}, Yan Zhang^{1, 2}, Zhiyi Ye³, Jun Pan^{3, *}, Mian Long^{1, 2, *}

CMES-Computer Modeling in Engineering & Sciences, Vol.116, No.2, pp. 263-279, 2018, DOI:10.31614/cmes.2018.04079

Abstract Neutrophil (PMN) accumulation on liver sinusoidal endothelial cells (LSECs) is crucial to pathogen clearance and tissue damage in the liver sinusoids and controlled by a series of adhesion molecules expressed on the surface of PMNs and LSECs. The role of lymphocyte function-associated antigen-1 (LFA-1) and macrophage-1 antigen (Mac-1) in this process is still contentious. Here we compared the dynamic force spectra of the binding of β2 integrin to intercellular adhesion molecule-1 (ICAM-1) on LSECs using atomic force microscopy (AFM) and performed free and steered molecular dynamics (MD) simulations to analyze their structural bases of LFA-1-… 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 More >

Xiaozhi Tang, Yafang Guo, Yu Gao

The International Conference on Computational & Experimental Engineering and Sciences, Vol.20, No.1, pp. 25-26, 2011, DOI:10.3970/icces.2011.020.025

Abstract Atomistic simulations were performed to study the nano-indentation for two kinds of FCC metals, aluminum and copper. Two different deformation mechanisms were observed in our simulation under exactly the same simulation condition. An embedded atom method potential was employed for copper and a generalized form of EAM potential due to Finnis and Sinclair for aluminum. In the simulation model, the substrate was constructed with 78408 atoms in an 8I?*40I?*60I? cell, here I? means the lattice constant. The indenter was modeled by a cubic with its side length of 8a.During the simulation, the period boundary condition… More >

Aiichiro Nakano, Rajiv K. Kalia, Priya Vashishta

The International Conference on Computational & Experimental Engineering and Sciences, Vol.16, No.4, pp. 125-126, 2011, DOI:10.3970/icces.2011.016.125

Abstract We have developed a metascalable (or "design once, scale on new architectures") parallelization scheme to perform large spatiotemporal-scale molecular dynamics (MD) simulations of materials on peta-to-exaflops computers based on embedded divide-and-conquer algorithms. The scheme has achieved parallel efficiency well over 0.95 on 212,992 IBM BlueGene/L processors for 218 billion-atom MD and 1.68 trillion electronic degrees-of-freedom quantum-mechanical MD in the framework of density functional theory. Simulation results reveal intricate interplay between photoexcitation, mechanics, flow, and chemical reactions at the nanoscale. Specifically, we will discuss atomistic mechanisms of: (1) mechanically enhanced reaction kinetics in nanobubbles and nanojets; More >

Xiaozhi Tang¹, Yafang Guo¹, Yu Gao¹

CMC-Computers, Materials & Continua, Vol.23, No.1, pp. 1-8, 2011, DOI:10.3970/cmc.2011.023.001

Abstract Atomistic simulations were performed to study the nanoindentation for two kinds of FCC metals, aluminum and copper. Due to the higher stacking faults in aluminum than in copper, two different deformation mechanisms were observed in our simulation under exactly the same simulation condition. Aluminum and copper also showed different mechanical properties in the unloading stage. The influence of stacking sequence along the loading direction on deformation mechanism was also investigated in this paper. More >

L. Dai¹, V.B.C. Tan^1,2, C.H. Sow^1,3, C.T. Lim^1,2,4, W.C.D. Cheong⁵

The International Conference on Computational & Experimental Engineering and Sciences, Vol.9, No.3, pp. 151-162, 2009, DOI:10.3970/icces.2009.009.151

Abstract The mechanisms governing the tensile response of TiO₂ nanowires were studied by molecular dynamics simulations. The free side surfaces of the nanowires were found to be undulating because atoms near the free surface were relaxed into a disordered state during thermodynamic equilibration. For wires below a threshold diameter of around 10 Å, this free surface effect extends throughout the entire wire, resulting in a complete lack of ordered structure. For thick nanowires, the core of the wire retains a crystalline structure. The thicker the wire, the larger the crystalline core and the more dominant is its 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. More >

Yeau-Ren Jeng¹,Ping-Chi Tsai¹,Guo-Zhe Huang¹, I-Ling Chang¹

CMC-Computers, Materials & Continua, Vol.11, No.2, pp. 109-126, 2009, DOI:10.3970/cmc.2009.011.109

Abstract This study performs a series of Molecular Dynamics (MD) and Molecular Statics (MS) simulations to investigate the mechanical properties of single-walled carbon nanotubes (SWCNTs) under a uniaxial tensile strain. The simulations focus specifically on the effects of the nanotube helicity, the nanotube diameter and the percentage of vacancy defects on the bond length, bond angle and tensile strength of zigzag and armchair SWCNTs. In this study, a good agreement is observed between the MD and MS simulation results for the stress-strain response of the SWCNTs in both the elastic and the plastic deformation regimes. The… More >

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 >