A Solvable Sequence Evolution Model and Genomic Correlations

We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations in the composition of letters as long as the sequence length is growing, i.e., the combined rates of duplications and insertions are higher than the deletion rate. For constant sequence length, on the other hand, all initial correlations decay exponentially. These results are obtained analytically and by simulations. They are compared with the long-range correlations observed in genomic DNA, and the implications for genome evolution are discussed.Comment: 4 pages, 4 figure

Characteristic Length Scale of Electric Transport Properties of Genomes

A tight-binding model together with a novel statistical method are used to investigate the relation between the sequence-dependent electric transport properties and the sequences of protein-coding regions of complete genomes. A correlation parameter $\Omega$ is defined to analyze the relation. For some particular propagation length $w_{max}$, the transport behaviors of the coding and non-coding sequences are very different and the correlation reaches its maximal value $\Omega_{max}$. $w_{max}$ and \omax are characteristic values for each species. The possible reason of the difference between the features of transport properties in the coding and non-coding regions is the mechanism of DNA damage repair processes together with the natural selection.Comment: 4 pages, 4 figure

Adsorption/desorption and electrically controlled flipping of ammonia molecules on graphene

In this paper, we evaluate of the adsorption/ desorption of ammonia molecules on a graphene surface by studying the Fermi level shift. Based on a physically plausible model, the adsorption and desorption rates of ammonia molecules on graphene have been extracted from the measured Fermi level shift as a function of exposure time. An electric field-induced flipping behavior of ammonia molecules on graphene is suggested, based on field effect transistor (FET) measurements

An optical fibre dynamic instrumented palpation sensor for the characterisation of biological tissue

AbstractThe diagnosis of prostate cancer using invasive techniques (such as biopsy and blood tests for prostate-specific antigen) and non-invasive techniques (such as digital rectal examination and trans-rectal ultrasonography) may be enhanced by using an additional dynamic instrumented palpation approach to prostate tissue classification. A dynamically actuated membrane sensor/actuator has been developed that incorporates an optical fibre Fabry–Pérot interferometer to record the displacement of the membrane when it is pressed on to different tissue samples. The membrane sensor was tested on a silicon elastomer prostate model with enlarged and stiffer material on one side to simulate early stage prostate cancer. The interferometer measurement was found to have high dynamic range and accuracy, with a minimum displacement resolution of ±0.4μm over a 721μm measurement range. The dynamic response of the membrane sensor when applied to different tissue types changed depending on the stiffness of the tissue being measured. This demonstrates the feasibility of an optically tracked dynamic palpation technique for classifying tissue type based on the dynamic response of the sensor/actuator

Generalized Induced Norms

Let ||.|| be a norm on the algebra M_n of all n-by-n matrices over the complex field C. An interesting problem in matrix theory is that "are there two norms ||.||_1 and ||.||_2 on C^n such that ||A||=max{||Ax||_2: ||x||_1=1} for all A in M_n. We will investigate this problem and its various aspects and will discuss under which conditions ||.||_1=||.||_2.Comment: 8 page

Picoheterotroph (Bacteria and Archaea) biomass distribution in the global ocean

We compiled a database of 39 766 data points consisting of flow cytometric and microscopical measurements of picoheterotroph abundance, including both Bacteria and Archaea. After gridding with 1° spacing, the database covers 1.3% of the ocean surface. There are data covering all ocean basins and depths except the Southern Hemisphere below 350m or from April until June. The average picoheterotroph biomass is 3.9 ± 3.6 µg Cl-1 with a 20-fold decrease between the surface and the deep sea. We estimate a total ocean inventory of about 1.3 × 1029 picoheterotroph cells. Surprisingly, the abundance in the coastal regions is the same as at the same depths in the open ocean. Using an average of published open ocean measurements for the conversion from abundance to carbon biomass of 9.1 fg cell-1, we calculate a picoheterotroph carbon inventory of about 1.2 Pg C. The main source of uncertainty in this inventory is the conversion factor from abundance to biomass. Picoheterotroph biomass is ? 2 times higher in the tropics than in the polar oceans

Simplifying the mosaic description of DNA sequences

By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share compositional similarity with one or more distant (non--neighbouring) domains. We thus obtain a coarse--grained description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly reducing its organizational complexity. This procedure gives a new means of evaluating genomic complexity as one examines organisms ranging from bacteria to human. The mosaic organization of DNA sequences could have originated from the insertion of fragments of one genome (the parasite) inside another (the host), and we present numerical experiments that are suggestive of this scenario.Comment: 16 pages, 1 figure, Accepted for publication in Phys. Rev.

Entropy of the FRW universe based on the generalized uncertainty principle

The statistical entropy of the FRW universe described by time-dependent metric is newly calculated using the brick wall method based on the general uncertainty principle with the minimal length. We can determine the minimal length with the Plank scale to obtain the entropy proportional to the area of the cosmological apparent horizon.Comment: 10 pages, accepted in Modern Physics Letters