Topology-based visualization of transformation pathways in complex chemical systems

Authors:
K. Beketayev;G. H. Weber;M. Haranczyk;P.-T. Bremer;M. Hlawitschka;B. Hamann
Affiliations:
Lawrence Berkeley National Laboratory and Institute for Data Analysis and Visualization, Department of Computer Science, University of California, Davis;-;Computational Research Division, Lawrence Berkeley National Laboratory, University of California, Davis;Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, University of California, Davis;Institute for Data Analysis and Visualization, Department of Computer Science, University of California, Davis;Institute for Data Analysis and Visualization, Department of Computer Science, University of California, Davis
Venue:
EuroVis'11 Proceedings of the 13th Eurographics / IEEE - VGTC conference on Visualization
Year:
2011

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Abstract

Studying transformation in a chemical system by considering its energy as a function of coordinates of the system's components provides insight and changes our understanding of this process. Currently, a lack of effective visualization techniques for high-dimensional energy functions limits chemists to plot energy with respect to one or two coordinates at a time. In some complex systems, developing a comprehensive understanding requires new visualization techniques that show relationships between all coordinates at the same time. We propose a new visualization technique that combines concepts from topological analysis, multi-dimensional scaling, and graph layout to enable the analysis of energy functions for a wide range of molecular structures. We demonstrate our technique by studying the energy function of a dimer of formic and acetic acids and a LTA zeolite structure, in which we consider diffusion of methane.