An improved spectral graph partitioning algorithm for mapping parallel computations
SIAM Journal on Scientific Computing
Clustering in large graphs and matrices
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
Visualization of the Molecular Dynamics of Polymers and Carbon Nanotubes
ISVC '09 Proceedings of the 5th International Symposium on Advances in Visual Computing: Part II
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Simulating the dynamics of complex biomolecules produces trajectories comprising a large number of different configurations of the molecule. These configurations must be classified into a small number of conformational ensembles representing essential changes in the molecule's shape. Using a conformational distance measure based on the changes in intramolecular atom distances, we show that a planar map can help us visualize these trajectories efficiently such that different conformational ensembles appear as well-separated point sets. We then use statistical cluster analysis to identify clusters that represent different conformational ensembles.