We present a discontinuous Galerkin (DG) scheme with suitable quadrature rules \cite{Tchen2017entropy} for ideal compressible magnetohydrodynamic (MHD) equations on structural meshes. The semi-discrete scheme is analyzed to be entropy stable by using the symmetrizable version of the equations as introduced by Godunov \cite{godunov1972symmetric}, the entropy stable DG framework with suitable quadrature rules \cite{Tchen2017entropy}, the entropy conservative flux in \cite{chandrashekar2016entropy} inside each cell and the entropy dissipative approximate Godunov type numerical flux at cell interfaces to make the scheme entropy stable. {\color{blue}{ The main difficulty in the generalization of the results in \cite{Tchen2017entropy} is the appearance of the non-conservative ``source terms'' added in the modified MHD model introduced by Godunov \cite{godunov1972symmetric}, which do not exist in the general hyperbolic system studied in \cite{Tchen2017entropy}. Special care must be taken to discretize these ``source terms'' adequately so that the resulting DG scheme satisfies entropy stability. }} Total variation diminishing / bounded (TVD/TVB) limiters and bound-preserving limiters are applied to control spurious oscillations. We demonstrate the accuracy and robustness of this new scheme on standard MHD examples.

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.

As V. I. Arnold observed in the 1960s, the Euler equations of incompressible fluid flow correspond formally to geodesic equations in a group of volume-preserving diffeomorphisms. Working in an Eulerian framework, we study incompressible flows of shapes as critical paths for action (kinetic energy) along transport paths constrained to be shape densities (characteristic functions). The formal geodesic equations for this problem are Euler equations for incompressible, inviscid potential flow of fluid with zero pressure and surface tension on the free boundary. The problem of minimizing this action exhibits an instability associated with microdroplet formation, with the following outcomes: Any two shapes of equal volume can be approximately connected by an Euler spray---a countable superposition of ellipsoidal geodesics. The infimum of the action is the Wasserstein distance squared, and is almost never attained except in dimension 1. Every Wasserstein geodesic between bounded densities of compact support provides a solution of the (compressible) pressureless Euler system that is a weak limit of (incompressible) Euler sprays. Each such Wasserstein geodesic is also the unique minimizer of a relaxed least-action principle for a two-fluid mixture theory corresponding to incompressible fluid mixed with vacuum.

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We propose second order accurate discontinuous Galerkin (DG) schemes which satisfy a strict maximum principle for general nonlinear convection-diffusion equations on unstructured triangular meshes. Motivated by genuinely high order maximum-principle-satisfying DG schemes for hyperbolic conservation laws, we prove that under suitable time step restriction for forward Euler time stepping, for general nonlinear convection-diffusion equations, the same scaling limiter coupled with second order DG methods preserves the physical bounds indicated by the initial condition while maintaining uniform second order accuracy. Similar to the purely convection cases, the limiters are mass conservative and easy to implement. Strong stability preserving (SSP) high order time discretizations will keep the maximum principle. Following the idea in earlier work, we extend the schemes to two-dimensional convection-diffusion equations on triangular meshes. There are no geometric constraints on the mesh such as angle acuteness. Numerical results including incompressible Navier-Stokes equations are presented to validate and demonstrate the effectiveness of the numerical methods.