Extracting the Atomic Coordinates and Connectivity of Zirconia Nanotubes from PDB Files for Modelling in ANSYS

DOI: 10.4236/anp.2014.33013, PP. 92-98

Keywords: Zirconia Nanotubes, Molecular Modelling, Python, ANSYS

Full-Text   Cite this paper   Add to My Lib

Abstract:

Zirconia in the form of nanotubes has potential for application in various areas. However, information on structural and mechanical properties of zirconia nanotubes is not easily available and/ or limited in scope. This challenge requires multi-scale numerical modeling and simulation. As a way out, the structure of (10, 10) zirconia nanotube is modeled using available crystal and molecular software (Material Studio^© and CrystalMaker^©). The output in the form of PDB file is exported into ANSYS by using a script developed in Python. The output contains only the atomic coordinates and connectivity pattern, which make the conversion process faster and more efficient compared to manual option used when performing similar task.

References

[1]	Kijima, T. (2010) Introduction to Inorganic and Metallic Nanotubes. In: Kijima, T., Ed., Inorganic and Metallic Nanotubular Materials: Recent Technologies and Applications, Springer, Berlin, 5-16. http://dx.doi.org/10.1007/978-3-642-03622-4
[2]	Tenne, R. and Seifert, G. (2009) Progress in the Study of Inorganic Nanotubes and Fullerene-Like Structures. Annual Review of Materials Research, 39, 387-413. http://dx.doi.org/10.1146/annurev-matsci-082908-145429
[3]	Yan, C., Liu, J., Liu, F., Wu, J., Gao, K. and Xue, D. (2008) Tube Formation in Nanoscale Materials. Nanoscale Research Letters, 3, 473-480. http://dx.doi.org/10.1007/s11671-008-9193-6
[4]	Lockman, Z., Ismail, S., Kawamura, G. and Matsuda, A. (2011) Formation of Zirconia and Titania Nanotubes in Fluorine Contained Glycerol Electrochemical Bath. Defect and Diffusion Forum, 76, 312-315.
[5]	Li, L., Yan, D., Lei, J., He, J., Wu, S. and Pan, F. (2011) Fast Fabrication of Highly Regular and Ordered ZrO2 Nanotubes. Materials Letters, 65, 1434-1437. http://dx.doi.org/10.1016/j.matlet.2011.02.025
[6]	Xia, R.O. and Catlow, R. (2009) Computational Modelling Study of Bulk and Surface of Yttria-Stabilized Cubic Zirconia. Chemistry of Materials, 21, 3576-358. http://dx.doi.org/10.1021/cm900417g
[7]	Evarestov, R.A., Zhukovskii, Y.F., Bandura, A.V. and Piskunov, S. (2010) Symmetry and Models of Single-Wall BN and TiO2 Nanotubes with Hexagonal Morphology. The Journal of Physical Chemistry C, 114, 21061-21069. http://dx.doi.org/10.1021/jp106929f
[8]	Guimaraes, L., Enyashin, A.N., Seifert, G. and Duarte, H.A. (2010) Structural, Electronic, and Mechanical Properties of Single-Walled Halloysite Nanotube Models. The Journal of Physical Chemistry C, 26, 11358-11363. http://dx.doi.org/10.1021/jp100902e
[9]	Bandura, A.V. and Evarestov, R.A. (2012) Ab Initio Structural Modelling of ZrO2 Nanosheets and Single-Wall Nanotubes. Computational Materials Science, 65, 395-405. http://dx.doi.org/10.1016/j.commatsci.2012.08.001
[10]	Nulaka, S., Allam, A.R. and Kopparthi, S. (2012) Python Program to Generate Atom Records from PDB Protein Files for Drug Design Studies. Journal of Bioinformatics & Research, 1, 36-40.
[11]	Enyashin, A.N., Gemming, S. and Seifert, G. (2010) Simulation of Inorganic Nanotubes. In: Gemming, S., Schreiber, M. and Suck, J.-B. (Eds.), Materials for Tomorrow: Theory, Experiments and Modelling, Springer, Berlin, 33-57.

Full-Text