Ankitkumar Patel¹, Srivathsan Vasudevan^1,*, Satya Bulusu^2,*

CMC-Computers, Materials & Continua, Vol.80, No.3, pp. 3803-3818, 2024, DOI:10.32604/cmc.2024.052851 - 12 September 2024

Abstract Molecular Dynamics (MD) simulation for computing Interatomic Potential (IAP) is a very important High-Performance Computing (HPC) application. MD simulation on particles of experimental relevance takes huge computation time, despite using an expensive high-end server. Heterogeneous computing, a combination of the Field Programmable Gate Array (FPGA) and a computer, is proposed as a solution to compute MD simulation efficiently. In such heterogeneous computation, communication between FPGA and Computer is necessary. One such MD simulation, explained in the paper, is the (Artificial Neural Network) ANN-based IAP computation of gold (Au₁₄₇ & Au₃₀₉) nanoparticles. MD simulation calculates the forces… More >

Dingyi Jin¹, Guo Wei^2,*

CMC-Computers, Materials & Continua, Vol.79, No.3, pp. 3455-3468, 2024, DOI:10.32604/cmc.2024.048644 - 20 June 2024

Abstract To investigate the effects of material combinations and velocity conditions on atomic diffusion behavior near collision interfaces, this study simulates the atomic diffusion behavior near collision interfaces in Cu-Al, Al-Al and Cu-Cu combinations fabricated through collision welding using molecular dynamic (MD) simulation. The atomic diffusion behaviors are compared between similar metal combinations (Al-Al, Cu-Cu) and dissimilar metal combinations (Al-Cu). By combining the simulation results and classical diffusion theory, the diffusion coefficients for similar and dissimilar metal material combinations under different velocity conditions are obtained. The effects of material combinations and collision velocity on diffusion behaviors More >

Xinliang Li¹, Jiangang Guo^1,*

The International Conference on Computational & Experimental Engineering and Sciences, Vol.27, No.1, pp. 1-2, 2023, DOI:10.32604/icces.2023.09484

Abstract As the first two-dimensional (2D) material discovered in experiments, graphene has attracted increasing attention from the scientific community [1]. And it possesses many superb mechanical, electronic and optical properties [2-4] due to its unique atomic structure. Its Young’s modulus and failure strength are 1TPa and 130GPa [5], respectively. Thus, 2D graphene has been extensively used in nanosensors and nanocomposites [6-8], etc. In order to fabricate graphene-based devices which inherit outstanding properties of 2D graphene, materials scientists are trying to use 2D graphene as building blocks to construct three-dimensional (3D) carbon nanomaterials, such as 3D graphene… More >

XINJUN YANG¹, AFTAB ALAM², NAIYAR IQBAL³, KHALID RAZA^4,*

BIOCELL, Vol.45, No.6, pp. 1569-1583, 2021, DOI:10.32604/biocell.2021.017019 - 01 September 2021

Abstract

Tuberculosis (TB) disease has become one of the major public health concerns globally, especially in developing countries. Numerous research studies have already been carried out for TB, but we are still struggling for a complete and quick cure for it. The progress of Mycobacterium tuberculosis (MTB) strains resistant to existing drugs makes its cure and control very complicated. Therefore, it is the need of the hour to search for newer and effective drugs that can inhibit an increasing number of putative drug targets. We applied the drug repurposing concept to identify promising FDA-approved drugs against five key-regulatory

… 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. More >

Wen-Ping Wu^1,2, Zong-Zhuan Yao³

CMES-Computer Modeling in Engineering & Sciences, Vol.93, No.4, pp. 235-252, 2013, DOI:10.3970/cmes.2013.093.235

Abstract The internal microstructure evolution and atomic stress distribution around the crack tip of a pre-cracked single crystal nickel with unequal sample sizes are studied by molecular dynamics (MD) simulation. The simulated results indicate that the crack propagation dynamics and stress distributions around the crack tip are strongly dependent on the microstructure evolution caused by the change of sample size. Unequal sample sizes induce various atomic configurations around the crack tip during the crack propagation. When atomic configuration is invariable around the crack tip, the crack grows rapidly along the crack path, the stress concentration occurs… More >

Chen X.Y.^∗,†, Liu Y.^2,‡, Fu B.M.^§, Fan J.T.^¶, Yang J.M.¹

Molecular & Cellular Biomechanics, Vol.5, No.4, pp. 275-284, 2008, DOI:10.3970/mcb.2008.005.275

Abstract Surface glycocalyx, as a barrier to material exchange between circulating blood and body tissues, can be treated as a periodic square array of cylindrical fibers. Previous study treated the glycocalyx as porous media and simulated by continuum theory. However, it has recently been found that a relatively hexagonal fibre-matrix structure may be responsible for the ultrafiltration properties of microvascular walls. The fibre-matrix is an underlaying three-dimensional meshwork with a fibre diameter of 10$\sim$12 nm and characteristic spacing of about 20 nm. The porous medium model does not consider the particle size, when the particle size… More >