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Figure 1.
Illustration of Voronoi diagram, Delaunay triangulation, and Non-Delaunay triangulation. Left chart: The Voronoi diagram and its dual Delaunay triangulation. The points set is $ P $ = {A, B, C, D, E} and the Delaunay is defined as $ \text{DT}(P) $. The blue lines tessellate the plane into Voronoi cells. The red circle are the circumcircles of triangles in $ \text{DT}(P) $. Right chart: A Non-Delaunay triangulation. Vertices E and D are in the green circumcircles, implying the right chart is an example of Non-Delaunay triangulation
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Figure 2.
Illustration of 2D Delaunay triangulation, alpha shapes, and alpha complexes for a set of 6 points A, B, C, D, E, and F. Top left: The 2D Delaunay triangulation. Top right: The alpha shape and alpha complex at filtration value $ \alpha = 0.2 $. Bottom left: The alpha shape and alpha complex at filtration value $ \alpha = 0.6 $. Bottom right: The alpha shape and alpha complex at filtration value $ \alpha = 1.0 $. Here, we use dark blue color to fill the alpha shape
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Figure 3.
The persistent barcode for a set of points as illustrated in Figure 2 that are generated from Gudhi and DioDe
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Figure 4.
The 3D structures of C$ _{20} $ and C$ _{60} $. (a) C$ _{20} $ molecule. A total of 12 pentagon rings can be found in C$ _{20} $. (b) C$ _{60} $ molecule. 12 pentagon rings and 20 hexoagon rings form the structure of C$ _{60} $
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Figure 5.
Illustration of the harmonic spectra (for Rips complex) $ \beta_0^{r, 0.05} $, $ \beta_0^{r, 0.05} $, and $ \beta_2^{r, 0.05} $ (green curves from top chart to bottom chart) and the smallest non-zero eigenvalue $ \lambda_0^{r, 0.05} $, $ \lambda_1^{r, 0.05} $, and $ \lambda_2^{r, 0.05} $ (yellow curves from top chart to bottom chart) of C$ _{20} $ molecule (the bottom left chart in Fig. 9) at different filtration values $ \alpha $ calculated from HERMES. Here, the $ x $-axis represents the radius filtration value $ r $ (unit: Å), the left-$ y $-axes represents the number of zero eigenvalues of $ \mathcal{L}_0^{r, 0.05} $, $ \mathcal{L}_1^{r, 0.05} $, and $ \mathcal{L}_1^{r, 0.05} $ from top to bottom, and the right-$ y $-axes represents the first non-zero eigenvalue of $ \mathcal{L}_0^{r, 0.05} $, $ \mathcal{L}_1^{r, 0.05} $, and $ \mathcal{L}_2^{r, 0.05} $ from top to bottom.
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Figure 6.
Illustration of the harmonic spectra (for alpha complex) $ \beta_0^{\alpha, 0.05} $, $ \beta_0^{\alpha, 0.05} $, and $ \beta_2^{\alpha, 0.05} $ (green curves from top chart to bottom chart) and the smallest non-zero eigenvalue $ \lambda_0^{\alpha, 0.05} $, $ \lambda_1^{\alpha, 0.05} $, and $ \lambda_2^{\alpha, 0.05} $ (yellow curves from top chart to bottom chart) of C$ _{20} $ molecule (the bottom left chart in Fig. 9) at different filtration value $ \alpha $ calculated from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: Å), the left-$ y $-axes represents the number of zero eigenvalues of $ \mathcal{L}_0^{\alpha, 0.05} $, $ \mathcal{L}_1^{\alpha, 0.05} $, and $ \mathcal{L}_1^{\alpha, 0.05} $ from top to bottom, and the right-$ y $-axes represents the first non-zero eigenvalue of $ \mathcal{L}_0^{\alpha, 0.05} $, $ \mathcal{L}_1^{\alpha, 0.05} $, and $ \mathcal{L}_2^{\alpha, 0.05} $ from top to bottom.
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Figure 7.
Illustration of the harmonic spectra $ \beta_0^{r, 0.05} $, $ \beta_0^{r, 0.05} $, and $ \beta_2^{r, 0.05} $ (blue curves from top chart to bottom chart) and the smallest non-zero eigenvalue $ \lambda_0^{r, 0.05} $, $ \lambda_1^{r, 0.05} $, and $ \lambda_2^{r, 0.05} $ (red curves from top chart to bottom chart) of C$ _{60} $ molecule (the bottom left chart in Fig. 9) at different filtration value $ \alpha $ calculated from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axes represents the number of zero eigenvalues of $ \mathcal{L}_0^{r, 0.05} $, $ \mathcal{L}_1^{r, 0.05} $, and $ \mathcal{L}_1^{r, 0.05} $ from top to bottom, and the right-$ y $-axes represents the first non-zero eigenvalue of $ \mathcal{L}_0^{r, 0.05} $, $ \mathcal{L}_1^{r, 0.05} $, and $ \mathcal{L}_2^{r, 0.05} $ from top to bottom.
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Figure 8.
Illustration of the harmonic spectra $ \beta_0^{\alpha, 0.05} $, $ \beta_0^{\alpha, 0.05} $, and $ \beta_2^{\alpha, 0.05} $ (green curves from top chart to bottom chart) and the smallest non-zero eigenvalue $ \lambda_0^{\alpha, 0.05} $, $ \lambda_1^{\alpha, 0.05} $, and $ \lambda_2^{\alpha, 0.05} $ (yellow curves from top chart to bottom chart) of C$ _{60} $ molecule (the bottom left chart in Fig. 9) at different filtration value $ \alpha $ calculated from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axes represents the number of zero eigenvalues of $ \mathcal{L}_0^{\alpha, 0.05} $, $ \mathcal{L}_1^{\alpha, 0.05} $, and $ \mathcal{L}_1^{\alpha, 0.05} $ from top to bottom, and the right-$ y $-axes represents the first non-zero eigenvalue of $ \mathcal{L}_0^{\alpha, 0.05} $, $ \mathcal{L}_1^{\alpha, 0.05} $, and $ \mathcal{L}_2^{\alpha, 0.05} $ from top to bottom.
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Figure 9.
The alpha carbon network plots of 15 proteins: PDB IDs 1CCR, 1NKO, 1O08, 1OPD, 1QTO, 1R7J, 1V70, 1W2L, 1WHI, 2CG7, 2FQ3, 2HQK, 2PKT, 2VIM, and 5CYT from left to right and top to bottom. The color represents the normalized diagonal element of the accumulated Laplacian at each alpha carbon atom
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Figure 10.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 5CYT (the bottom left chart in Fig. 9) at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 11.
Illustration of the harmonic spectra $ \beta_0^{\alpha, 0.5} $, $ \beta_0^{\alpha, 0.5} $, and $ \beta_2^{\alpha, 0.5} $ (green curves from top chart to bottom chart) and the smallest non-zero eigenvalue $ \lambda_0^{\alpha, 0.5} $, $ \lambda_1^{\alpha, 0.5} $, and $ \lambda_2^{\alpha, 0.5} $ (yellow curves from top chart to bottom chart) of PDB ID 5CYT (the bottom left chart in Fig. 9) at different filtration value $ \alpha $ calculated from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axes represents the number of zero eigenvalues of $ \mathcal{L}_0^{\alpha, 0.5} $, $ \mathcal{L}_1^{\alpha, 0.5} $, and $ \mathcal{L}_1^{\alpha, 0.5} $ from top to bottom, and the right-$ y $-axes represents the first non-zero eigenvalue of $ \mathcal{L}_0^{\alpha, 0.5} $, $ \mathcal{L}_1^{\alpha, 0.5} $, and $ \mathcal{L}_2^{\alpha, 0.5} $ from top to bottom
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Figure 12.
(a) The 3D secondary structure of PDB ID 1O08. The blue, purple, and orange colors represent helix, sheet, and random coils of PDB ID 1O08. The ball represents the alpha carbon of PDB ID 1O08. (b) Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 1O08 at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are calculated only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents for the number of zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents for the non-zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 13.
Illustration of the harmonic spectra $ \beta_0^{r, 0} $, $ \beta_0^{r, 0} $, and $ \beta_2^{r, 0} $ (blue curves from top chart to bottom chart) and the smallest non-zero eigenvalue $ \lambda_0^{r, 0} $, $ \lambda_1^{r, 0} $, and $ \lambda_2^{r, 0} $ (red curves from top chart to bottom chart) of C$ _{60} $ molecule with one atom shifted (the bottom left chart in Fig. 9) at different filtration value $ \alpha $ calculated from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axes represents the number of zero eigenvalues of $ \mathcal{L}_0^{r, 0} $, $ \mathcal{L}_1^{r, 0} $, and $ \mathcal{L}_1^{r, 0} $ from top to bottom, and the right-$ y $-axes represents the first non-zero eigenvalue of $ \mathcal{L}_0^{r, 0} $, $ \mathcal{L}_1^{r, 0} $, and $ \mathcal{L}_2^{r, 0} $ from top to bottom.
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Figure 14.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 1CCR at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 15.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 1NKO at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 16.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 1OPD at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 17.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 1QTO at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 18.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 1R7J at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 19.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 1V70 at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 20.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 1W2L at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 21.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 1WHI at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 22.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 2CG7 at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 23.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 2FQ3 at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 24.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 2HQK at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 25.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 2PKT at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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Figure 26.
Illustration of the harmonic spectra $ \beta_q^{\alpha, 0} $ (blue curve) and the smallest non-zero eigenvalue $ \lambda_q^{\alpha, 0} $ (red curve) of PDB ID 2VIM at different filtration value $ \alpha $ when $ q = 0, 1, 2 $. The $ \beta_q^{\alpha, 0} $ are calculated from Gudhi, DioDe, and HERMES, and $ \lambda_q^{\alpha, 0} $ are obtained only from HERMES. Here, the $ x $-axis represents the radius filtration value $ \alpha $ (unit: $Å $), the left-$ y $-axis represents the number of zero eigenvalues of $ \mathcal{L}_q^{\alpha, 0} $, and the right-$ y $-axis represents the first non-zero eigenvalue of $ \mathcal{L}_q^{\alpha, 0} $. Note that the harmonic spectra from three methods are indistinguishable
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