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Due to vast sequence divergence among different viral groups, sequence alignment is not directly applicable to genome-wide comparative analysis of viruses. More and more attention has been paid to alignment-free methods for whole genome comparison and phylogenetic tree reconstruction. Among alignment-free methods, the recently proposed ‘‘Natural Vector (NV) representation” has successfully been used to study the phylogeny of multi-segmented viruses based on a 12-dimensional genome space derived from the nucleotide sequence structure. But the preference of proteomes over genomes for the determination of viral phylogeny was not deeply investigated. As the translated products of genes, proteins directly form the shape of viral structure and are vital for all metabolic pathways. In this study, using the NV representation of a protein sequence along with the Hausdorff distance suitable to compare point sets, we construct a 60-dimensional protein space to analyze the evolutionary relationships of 4021 viruses by whole-proteomes in the current NCBI Reference Sequence Database (RefSeq). We also take advantage of the previously developed natural graphical representation to recover viral phylogeny. Our results demonstrate that the proposed method is efficient and accurate for classifying viruses. The accuracy rates of our predictions such as for Baltimore II viruses are as high as 95.9% for family labels, 95.7% for subfamily labels and 96.5% for genus labels. Finally, we discover that proteomes lead to better viral classification when reliable protein sequences are abundant. In other cases, the accuracy rates using proteomes are still comparable to that of genomes.

Robustness of numerical methods has attracted an increasing interest in the community of computational fluid dynamics. One mathematical aspect of robustness for numerical methods is the positivity-preserving property. At high Mach numbers or for flows near vacuum, solving the conservative Euler equations may generate negative density or internal energy numerically, which may lead to nonlinear instability and crash of the code. This difficulty is particularly profound for high order methods, for multi-material flows and for problems with moving meshes, such as the Lagrangian methods. In this paper, we construct both first order and uniformly high order accurate conservative Lagrangian schemes which preserve positivity of physically positive variables such as density and internal energy in the simulation of compressible multi-material flows with general equations of state (EOS). We first develop a positivity-preserving approximate Riemann solver for the Lagrangian scheme solving compressible Euler equations with both ideal and non ideal EOS. Then we design a class of high order positivity-preserving and conservative Lagrangian schemes by using the essentially non-oscillatory (ENO) reconstruction, the strong stability preserving (SSP) high order time discretizations and the positivity-preserving scaling limiter which can be proven to maintain conservation and uniformly high order accuracy and is easy to implement. One-dimensional and two-dimensional numerical tests for the positivity-preserving Lagrangian schemes are provided to demonstrate the effectiveness of these methods.

We prove rigidity results for a class of non-uniformly hyperbolic holomorphic maps. If a holomorphic Collet-Eckmann map$f$is topologically conjugate to a holomorphic map$g$, then the conjugacy can be improved to be quasiconformal. If there is only one critical point in the repeller, then$g$is Collet-Eckmann, too.