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. Author manuscript; available in PMC: 2016 Jul 30.
Published in final edited form as: J Comput Chem. 2015 May 30;36(20):1502–1520. doi: 10.1002/jcc.23953

Figure 2.

Figure 2

The unfolding of protein 1UBQ and the corresponding multidimensional persistence. a All atom representation of the relaxed structure without hydrogen atoms; b All atom representation of the unfolded structure at the 300th frame; c All atom representation of the unfolded structure at the 500th frame; d 2D β0 persistence; e 2D β1 persistence; f 2D β2 persistence. In subfigures d, e and f, horizontal axises label the filtration radius (Å) and the vertical axises are the configuration index. Color bars denote the natural logarithms of PBNs. We systematically add 1 to all PBNs to avoid the possible logarithm of 0.