Topology‐based Visualization of Transformation Pathways in Complex Chemical Systems |
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Authors: | K Beketayev GH Weber M Haranczyk P‐T Bremer M Hlawitschka B Hamann |
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Affiliation: | 1. Computational Research Division, Lawrence Berkeley National Laboratory;2. Institute for Data Analysis and Visualization, Department of Computer Science, University of California, Davis;3. Center for Applied Scientific Computing, Lawrence Livermore National Laboratory |
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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. |
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Keywords: | J 2 4 [Computer Applications]: Physical Sciences and Engineering Chemistry I 3 8 [Computing Methodologies]: Computer Graphics Applications |
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