Comparing DNA and protein sequence groups plays an important role in biological evolutionary relationship research. Despite many methods available for sequence comparison, only a few can be used for group comparison. In this study, we propose a novel approach using convex hulls. We use statistical information contained within the sequences to represent each sequence as a point in high dimensional space. We find that the points belonging to one biological group are located in a different region of space than points belonging to other biological groups. To be more precise, the convex hull of the points from one group are disjoint from the convex hulls of points from other groups. This finding allows us to do phylogenetic analysis for groups in an efficient way. Five different theorems are presented for checking whether two convex hulls intersect or are disjoint. Test results for datasets related to HRV, HPV, Ebolavirus, PKC and protein phosphatase domains demonstrate that our method performs well and provides a new tool for studying group phylogeny. More significantly, the convex analysis presents a new way to search for sequences belonging to a biological group by examining points within the group’s convex hull.

Let M be a complete non-compact Riemannian manifold whose sectional curvature is bounded between two constants-k and K. Then one expects that the heat diffusion in such a manifold behaves like the heat diffusion in Euclidean space. The purpose of this paper is to give a justi-fication of such a statement.

This article focuses on the discrete double-curl operator arising in the Maxwell equation that models three dimensional photonic crystals with face centered cubic lattice. The discrete double-curl operator is the degenerate coefficient matrix of the generalized eigenvalue problems (GEVP) due to the Maxwell equation. We derive an eigendecomposition of the degenerate coefficient matrix and explore an explicit form of orthogonal basis for the range and null spaces of this matrix. To solve the GEVP, we apply these theoretical results to project the GEVP to a standard eigenvalue problem (SEVP), which involves only the eigenspace associated with the nonzero eigenvalues of the GEVP and therefore the zero eigenvalues are excluded and will not degrade the computational efficiency. This projected SEVP can be solved efficiently by the inverse Lanczos method. The linear systems within the inverse Lanczos method are well-conditioned and can be solved efficiently by the conjugate gradient method without using a preconditioner. We also demonstrate how two forms of matrix-vector multiplications, which are the most costly part of the inverse Lanczos method, can be computed by fast Fourier transformation due to the eigendecomposition to significantly reduce the computation cost. Integrating all of these findings and techniques, we obtain a fast eigenvalue solver. The solver has been implemented by MATLAB and successfully solves each of a set of $5.184$ million dimension eigenvalue problems within $50$ to $104$ minutes on a workstation with two Intel Quad-C ore Xeon X5687 3.6 GHz CPUs.

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