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The free-living SAR11 clade is a globally abundant group of oceanic Alphaproteobacteria, with small genome sizes and rich genomic A+T content. However, the taxonomy of SAR11 has become controversial recently. Some researchers argue that the position of SAR11 is a sister group to Rickettsiales. Other researchers advocate that SAR11 is located within free-living lineages of Alphaproteobacteria. Here, we use the natural vector representation method to identify the evolutionary origin of the SAR11 clade. This alignment-free method does not depend on any model assumptions. With this approach, the correspondence between proteome sequences and their natural vectors is one-to-one. After fixing a set of proteins, each bacterium is represented by a set of vectors. The Hausdorff distance is then used to compute the dissimilarity distance between two bacteria. The phylogenetic tree can be reconstructed based on these distances. Using our method, we systematically analyze four data sets of alphaproteobacterial proteomes in order to reconstruct the phylogeny of Alphaproteobacteria. From this we can see that the phylogenetic position of the SAR11 group is within a group of other free-living lineages of Alphaproteobacteria.

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In this paper we propose a time-domain finite element method for modeling of electromagnetic cloaks. The permittivity and permeability of the cloak model are described by the Drude dispersion model. The model to be solved is quite challenging in that we have to solve a coupled problem with different partial differential equations given in different regions. Our method is based on a mixed finite element method using edge elements with different types of meshes in different regions. Numerical results demonstrate that our algorithm is quite effective for simulating cloaks in time-domain. To our knowledge, this is the first cloak simulation carried out by the time-domain finite element method.

The paper aims at analytically exhibiting for the first time the fundamental mechanisms underlying the fact that effective biological tissue electrical properties and their frequency dependence reflect the tissue composition and physiology. For doing so, a homogenization theory is derived to describe the effective admittivity of cell suspensions. A new formula is reported for dilute cases that gives the frequency-dependent effective admittivity with re- spect to the membrane polarization. Different microstructures are shown to be distinguish- able via spectroscopic measurements of the overall admittivity using the spectral properties of the membrane polarization. The Debye relaxation times associated with the membrane polarization tensor are shown to be able to give the microscopic structure of the medium. A natural measure of the admittivity anisotropy is introduced and its dependence on the frequency of applied current is derived. A Maxwell-Wagner-Fricke formula is given for concentric circular cells, and the results can be extended to the random cases. A randomly deformed periodic medium is also considered and a new formula is derived for the overall admittivity of a dilute suspension of randomly deformed cells.