355,317 research outputs found

    Simplifying the mosaic description of DNA sequences

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    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.

    Rectifying "nanohomo" contacts of W-Ga-C composite pad and nanowire fabricated by focused-ion-beam induced chemical vapour deposition

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    We prepared W-Ga-C composite contacts on W-Ga-C composite nanowires by focused-ion-beam-induced chemical vapor deposition using a dual-beam scanning electron microscope/focused-ion-beam system. The current-voltage (I-V) characteristics of wires were found to change from nonlinear to linear with increasing wire thickness. For wires with small dimensions, which result in strong nonlinear I-V behavior at room temperature, pairs of contacts were fabricated along the wire under different ion energies and scanning modes. Nonlinear and asymmetric rectifying I-V characteristics were observed. The results suggest that nanoscaled W-Ga-C nanowires may behave similarly to semiconductors and that the contact characteristics may be modified using different deposition conditions. Furthermore, ohmiclike junctions could be formed through the use of specific deposition conditions for the contact pads and nanowires

    Dutch agricultural development and its importance to China : a comparative analysis

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    Automatic loop-shaping in quantitative feedback theory using genetic algorithms

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    Design automation in Quantitative Feedback Theory (QFT) is addressed in this paper. An automatic loop shaping procedure based on Genetic Algorithms (GAs) is developed, where a robust controller for uncertain plants can be designed automatically such that the cost of feedback is minimised and all robust stability and performance specifcations are satisfed. The developed approach can improve the current QFT design in at least two aspects. One is in the design of an initial controller for complicated plants, which might be difficult even to find a stabilising controller manually. The other is in improving the initial manual design by optimisation of the performance index under the prescribed requirements within the neighbourhood of the manual design. An illustrative example which compares manual loop shaping with automatic loop shaping is presented

    Universality of Long-Range Correlations in Expansion-Randomization Systems

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    We study the stochastic dynamics of sequences evolving by single site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of non-equilibrium 1D expansion-randomization systems with generic stationary long-range correlations in a regime of growing sequence length. We obtain explicitly the two-point correlation function of the sequence composition and the distribution function of the composition bias in sequences of finite length. The characteristic exponent χ\chi of these quantities is determined by the ratio of two effective rates, which are explicitly calculated for several specific sequence evolution dynamics of the universality class. Depending on the value of χ\chi, we find two different scaling regimes, which are distinguished by the detectability of the initial composition bias. All analytic results are accurately verified by numerical simulations. We also discuss the non-stationary build-up and decay of correlations, as well as more complex evolutionary scenarios, where the rates of the processes vary in time. Our findings provide a possible example for the emergence of universality in molecular biology.Comment: 23 pages, 15 figure
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