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.

In this paper, we discuss high order finite difference weighted essentially non-oscillatory (WENO) schemes, coupled with total variation diminishing (TVD) Runge-Kutta (RK) temporal integration, for solving the semilinear hyperbolic system of a correlated random walk model describing movement of animals and cells in biology. Since the solutions to this system are non-negative, we discuss a positivity-preserving limiter without compromising accuracy. Analysis is performed to justify the maintanance of third order spatial / temporal accuracy when the limiters are applied to a third order finite difference scheme and third order TVD-RK time discretization for solving this model. Numerical results are also provided to demonstrate these methods up to fifth order accuracy.

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We investigate mirror symmetry for toric Calabi-Yau manifolds from the perspective of the SYZ conjecture. Starting with a non-toric special Lagrangian torus fibration on a toric Calabi-Yau manifold $X$, we construct a complex manifold $\check{X}$ using T-duality modified by quantum corrections. These corrections are encoded by Fourier transforms of generating functions of certain open Gromov-Witten invariants. We conjecture that this complex manifold $\check{X}$, which belongs to the Hori-Iqbal-Vafa mirror family, is inherently written in canonical flat coordinates. In particular, we obtain an enumerative meaning for the (inverse) mirror maps, and this gives a geometric reason for why their Taylor series expansions in terms of the K\"ahler parameters of $X$ have integral coefficients. Applying the results in \cite{Chan10} and \cite{LLW10}, we compute the open Gromov-Witten invariants in terms of local BPS invariants and give evidences of our conjecture for several 3-dimensional examples including $K_{\proj^2}$ and $K_{\proj^1\times\proj^1}$.