30-Issue 3

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Topology-based Visualization of Transformation Pathways in Complex Chemical Systems
(The Eurographics Association and Blackwell Publishing Ltd., 2011) Beketayev, Kenes; Weber, G. H.; Haranczyk, M.; Bremer, P.-T.; Hlawitschka, M.; Hamann, B.; H. Hauser, H. Pfister, and J. J. van Wijk
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.