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In earlier work, two of the authors developed a high order accurate numerical boundary condition procedure for hyperbolic conservation laws, which allows the computation using high order finite difference schemes on Cartesian meshes to solve problems in arbitrary physical domains whose boundaries do not coincide with grid lines. This procedure is based on the so-called inverse Lax-Wendroff (ILW) procedure for inflow boundary conditions and high order extrapolation for outflow boundary conditions. However, the algebra of the ILW procedure is quite heavy for two dimensional (2D) hyperbolic systems, which makes it difficult to implement the procedure for order of accuracy higher than three. In this paper, we first discuss a simplified and improved implementation for this procedure, which uses the relatively complicated ILW procedure only for the evaluation of the first order normal derivatives. Fifth order WENO type extrapolation is used for all other derivatives, regardless of the direction of the local characteristics and the smoothness of the solution. This makes the implementation of a fifth order boundary treatment practical for 2D systems with source terms. For no-penetration boundary condition of compressible inviscid flows, a further simplification is discussed, in which the evaluation of the tangential derivatives involved in the ILW procedure is avoided. We test our simplified and improved boundary treatment for Euler equations with or without source terms representing chemical reactions in detonations. The results demonstrate the designed fifth order accuracy, stability, and good performance for problems involving complicated interactions between detonation/shock waves and solid boundaries.

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Current methods cannot tell us what the nature of the protein universe is concretely. They are based on different models of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requires manual intervention. Protein structural analysis also gives a direction for mapping the protein universe. Unfortunately, now only a minuscule fraction of proteins' 3-dimensional structures are known. Furthermore, the phylogenetic tree representations are not unique for any existing tree construction methods. Here we develop a novel method to realize the nature of protein universe. We show the protein universe can be realized as a protein space in 60-dimensional Euclidean space using a distance based on a normalized distribution of amino acids. Every protein is in one-to-one correspondence with a point in protein space, where proteins with similar properties stay close together. Thus the distance between two points in protein space represents the biological distance of the corresponding two proteins. We also propose a natural graphical representation for inferring phylogenies. The representation is natural and unique based on the biological distances of proteins in protein space. This will solve the fundamental question of how proteins are distributed in the protein universe.

We study homogenization of G-equation with a ow straining term (or the strain G-equation) in two dimensional periodic cellular ow. The strain G-equation is a highly non-coercive and non-convex level set Hamilton-Jacobi equation. The main objective is to investigate how the ow induced straining (the nonconvex term) in uences front propagation as the ow intensity A increases. Three distinct regimes are identified. When A is below the critical level, homogenization holds and the turbulent ame speed sT (effective Hamiltonian) is well-defined for any periodic ow with small divergence and is enhanced by the cellular ow as $s_T \ge O(A/logA)$. In the second regime where A is slightly above the critical value, homogenization breaks down, and $s_T$ is not well defined along any direction. Solutions become a mixture of fast moving part and a stagnant part. When $A$ is sufficiently large, the whole ame front ceases to propagate forward due to the flow induced straining. In particular, along directions $p = (1; 0)$ and $(0;1)$, $s_T$ is well-defined again with a value of zero (trapping). A partial homogenization result is also proved. If we consider a similar but relatively simpler Hamiltonian, the trapping occurs along all directions. The analysis is based on the two-player dierential game representation of solutions, selection of game strategies and trapping regions, and construction of connecting trajectories.