AI Chat Paper
Note: Please note that the following content is generated by AMiner AI. SciOpen does not take any responsibility related to this content.
{{lang === 'zh_CN' ? '文章概述' : 'Summary'}}
{{lang === 'en_US' ? '中' : 'Eng'}}
Chat more with AI
Powered by AMiner. Clicking this button will take you away from SciOpen.
Home Tsinghua Science and Technology Article
PDF (2.4 MB)
Cite
EndNote(RIS) BibTeX
Collect
Submit Manuscript AI Chat Paper
Show Outline
Outline
Show full outline
Hide outline
Outline
Show full outline
Hide outline
Open Access

Similarity-Based 3-D Atmospheric Nucleation Data Visualization and Analysis

Department of Computer Science, University of The Pacific, Stockton, CA 95211, USA
Department of Computer Science, University of California, Davis, CA 95616, USA
Show Author Information

Abstract

Atmospheric nucleation is a process of phase transformation, which serves a significant role in many atmospheric and technological processes. To simulate atmospheric nucleation activities, certain molecular models with three-dimensional (3-D) structures are generated. Analyzing these 3-D molecular models can help promote understanding of nucleation processes. Unfortunately, the ability to understand atmospheric nucleation processes is greatly restricted due to lack of efficient visual data exploration tools. In this paper, we present a data visualization solution to visualize and classify 3-D molecular crystals. We developed a novel algorithm for calculating similarity between the 3-D molecular crystals, and further improved the overall system performance with GPU (graphics processing unit) acceleration.

Keywords

atmospheric nucleationsimilarity calculationGPU3-D molecular models

References

[1]
B. Chen, J. I. Siepmann, and M. Klein, Simulating vapor-liquid nucleation of water: A combined histogram-reweighting and aggregation-volumebias monte carlo investigation for fixed-charge and polarizable models, J. Phys. Chem. A,vol. 109, no. 6, pp. 1137-1145, 2005.
Crossref Google Scholar
[2]
M. E. McKenzie and B. Chen, Unravelling the peculiar nucleation mechanisms for non-ideal binary mixtures with atomistic simulations, The Journal of Physical Chemistry B,vol. 110, no. 8, pp. 3511-3516, 2006.
Crossref Google Scholar
[3]
J. Braun, A. Kerber, M. Meringer, and C. Rcker, Similarity of molecular descriptors: The equivalence of Zagreb indices and walk counts, MATCH Commun. Math. Comput. Chem.,vol. 54, pp. 163-176, 2005.
Google Scholar
[4]
A. Bender and R. C. Glen, Molecular similarity: A key technique in molecular informatics, Organic and Biomolecular Chemistry,vol. 2, no. 22, pp. 3204-3218, 2004.
Crossref Google Scholar
[5]
A. S. Mian, M. Bennamoun, and R. Owens, Three-dimensional model-based object recognition and segmentation in cluttered scenes, IEEE Transactions on Pattern Analysis and Machine Intelligence,vol. 28, no. 10, pp. 1584-1601, 2006.
Crossref Google Scholar
[6]
O. Ursu, M. V. Diudea, and S. Nakayama, 3D molecular similarity: Method and algorithms, Journal of Computer Chemistry, Japan,vol. 5, no. 1, pp. 39-46, 2006.
Crossref Google Scholar
[7]
E. J. Gardiner, P. J. Artymiuk, and P. Willett, Clique-detection algorithms for matching three-dimensional molecular structures, Journal of Molecular Graphics and Modelling,vol. 15, no. 4, pp. 245-253, 1997.
Crossref Google Scholar
[8]
O. Kreylos, N. L. Max, B. Hamann, S. N. Crivell, and E. Bethel, Interactive protein manipulation, in Proc. 14th IEEE Visualization 2003, IEEE Computer Society, 2003, pp. 77.
[9]
R. B. Nellas, B. Chen, and J. I. Siepmann, Similarity recognition of molecular structures by optimal atomic matching and rotational superposition, Phys. Chem. Chem. Phys.,vol. 9, no. 22, pp. 2779-2781, 2007.
Google Scholar
[10]
B. Helmich and M. Sierka, Dumbbells and onions in ternary nucleation, Journal of Computational Chemistry,vol. 33, no. 22, pp. 134-140, 2012.
Crossref Google Scholar
[11]
M. Sukekawa and A. Nakayama, Application of molecular similarity analysis in 3D-QSAR of neonicotinoid insecticides, Nippon Noyaku Gakkaishi,vol. 24, no. 1, pp. 38-43, 1999.
Crossref Google Scholar
[12]
X. Liu, H. Jiang, and H. Li, SHAFTS: A hybrid approach for 3D molecular similarity calculation. 1. Method and assessment of virtual screening, Journal of Chemical Information and Modeling,vol. 51, no. 9, pp. 2372-2385, 2011.
Crossref Google Scholar
[13]
A. C. Good and W. G. Richards, Explicit calculation of 3D molecular similarity, 3D QSAR in Drug Design,vol. 2, pp. 321-338, 2002.
Crossref Google Scholar
[14]
H. Eckert and J. Bajorath, Molecular similarity analysis in virtual screening: Foundations, limitations and novel approaches, Drug Discovery Today,vol. 12, no. 5-6, pp. 225-223, 2007.
Crossref Google Scholar
[15]
Y. Yan, M. Grossman, and V. Sarkar, JCUDA: A programmer-friendly interface for accelerating Java programs with CUDA, in Euro-Par 2009 Parallel Processing, 2009, pp. 887-899.
Crossref
[16]
R. Ding, J. Gao, B. Chen, and J. I. Siepmann, Web-based visualization of atmospheric nucleation processes using Java3D, in the 9th IEEE/ACM International Symposium on Cluster Computing and the Grid, 2009.
Crossref
[17]
R. Haenni and N. Lehmann, Efficient Hypertree Contruction, Washington, DC: American Psychological Association, 1999.
[18]
K. Elshafey, A 2D-mesh hypertree interconnection network, in the 20th International Conference on Microelectronics, 2008.
[19]
J. R. Goodman and C. H. Sequin, Clique-detection algorithms for matching three-dimensional molecular structures, Journal of Molecular Graphics and Modelling,vol. 15, no. 4, pp. 245-253, 1997.
Crossref Google Scholar
Tsinghua Science and Technology
Volume 18 Issue 2,
April 2013
Pages 137-144
DOI: 10.1109/TST.2013.6509097
Cite this article:
Zhu K, Liu Y, Aboagye AG, et al. Similarity-Based 3-D Atmospheric Nucleation Data Visualization and Analysis. Tsinghua Science and Technology, 2013, 18(2): 137-144. https://doi.org/10.1109/TST.2013.6509097

554

Views

9

Downloads

0

Crossref

N/A

Web of Science

1

Scopus

0

CSCD

Altmetrics
Received: 04 March 2013
Accepted: 11 March 2013
Published: 30 April 2013
© The author(s) 2013
Return