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

Intersections of homogeneous Cantor sets and beta-expansions

Let $\Gamma_{\beta,N}$ be the $N$-part homogeneous Cantor set with $\beta\in(1/(2N-1),1/N)$. Any string $(j_\ell)_{\ell=1}^\N$ with $j_\ell\in\{0,\pm 1,...,\pm(N-1)\}$ such that $t=\sum_{\ell=1}^\N j_\ell\beta^{\ell-1}(1-\beta)/(N-1)$ is called a code of $t$. Let $\mathcal{U}_{\beta,\pm N}$ be the set of $t\in[-1,1]$ having a unique code, and let $\mathcal{S}_{\beta,\pm N}$ be the set of $t\in\mathcal{U}_{\beta,\pm N}$ which make the intersection $\Gamma_{\beta,N}\cap(\Gamma_{\beta,N}+t)$ a self-similar set. We characterize the set $\mathcal{U}_{\beta,\pm N}$ in a geometrical and algebraical way, and give a sufficient and necessary condition for $t\in\mathcal{S}_{\beta,\pm N}$. Using techniques from beta-expansions, we show that there is a critical point $\beta_c\in(1/(2N-1),1/N)$, which is a transcendental number, such that $\mathcal{U}_{\beta,\pm N}$ has positive Hausdorff dimension if $\beta\in(1/(2N-1),\beta_c)$, and contains countably infinite many elements if $\beta\in(\beta_c,1/N)$. Moreover, there exists a second critical point $\alpha_c=\big[N+1-\sqrt{(N-1)(N+3)}\,\big]/2\in(1/(2N-1),\beta_c)$ such that $\mathcal{S}_{\beta,\pm N}$ has positive Hausdorff dimension if $\beta\in(1/(2N-1),\alpha_c)$, and contains countably infinite many elements if $\beta\in[\alpha_c,1/N)$.Comment: 23 pages, 4 figure

A cusp electron gun for millimeter wave gyrodevices

The experimental results of a thermionic cusp electron gun, to drive millimeter and submillimeter wave harmonic gyrodevices, are reported in this paper. Using a "smooth" magnetic field reversal formed by two coils this gun generated an annular-shaped, axis-encircling electron beam with 1.5 A current, and an adjustable velocity ratio alpha of up to 1.56 at a beam voltage of 40 kV. The beam cross-sectional shape and transported beam current were measured by a witness plate technique and Faraday cup, respectively. These measured results were found to be in excellent agreement with the simulated results using the three-dimensional code MAGIC

Plasma fluctuations as Markovian noise

Noise theory is used to study the correlations of stationary Markovian fluctuations that are homogeneous and isotropic in space. The relaxation of the fluctuations is modeled by the diffusion equation. The spatial correlations of random fluctuations are modeled by the exponential decay. Based on these models, the temporal correlations of random fluctuations, such as the correlation function and the power spectrum, are calculated. We find that the diffusion process can give rise to the decay of the correlation function and a broad frequency spectrum of random fluctuations. We also find that the transport coefficients may be estimated by the correlation length and the correlation time. The theoretical results are compared with the observed plasma density fluctuations from the tokamak and helimak experiments.Physic

Space Charge Behaviour in Oil-Paper Insulation with Different Aging Condition

Oil-paper insulation system is widely used in power transformers and cables. The dielectric properties of oilpaper insulation play an important role in the reliable operation of power equipment. Oil-paper insulation degrades under a combined stress of thermal (the most important factor), electrical, mechanical, and chemical stresses during routine operations, which has great effect on the dielectric properties of oil-paper insulation [1]. Space charge in oil-paper insulation has a close relation to its electrical performance [1]. In this paper, space charge behaviour of oil-paper insulation sample with three different ageing conditions (aged for 0, 35 and 77 days) was investigated using the pulsed electroacoustic (PEA) technique. The influence of aging on the space charge dynamics behaviour was analysed. Results show that aging has great effect on the space charge dynamics of oil-paper insulation. The homocharge injection takes place under all three aging conditions above. Positive charges tend to accumulate in the sample, and increase with the oil-paper insulation sample deterioration. The time to achieve the maximum injection charge density is 30s, 2min and 10min for oil-paper insulation sample aged for 0, 35 and 77 days, respectively. The maximum charge density injected in the sample aged for 77 days is more than two times larger than the initial sample. In addition, the charge decay speed becomes much slower with the aging time increase. There is an exponential relationship between the total charge amount and the decay time. The decay time constant ? increases with the increasing deterioration condition of the oil-paper insulation sample. The ? value may be used to reflect the aging status of oil-paper insulation

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.

Exact scaling in the expansion-modification system

This work is devoted to the study of the scaling, and the consequent power-law behavior, of the correlation function in a mutation-replication model known as the expansion-modification system. The latter is a biology inspired random substitution model for the genome evolution, which is defined on a binary alphabet and depends on a parameter interpreted as a \emph{mutation probability}. We prove that the time-evolution of this system is such that any initial measure converges towards a unique stationary one exhibiting decay of correlations not slower than a power-law. We then prove, for a significant range of mutation probabilities, that the decay of correlations indeed follows a power-law with scaling exponent smoothly depending on the mutation probability. Finally we put forward an argument which allows us to give a closed expression for the corresponding scaling exponent for all the values of the mutation probability. Such a scaling exponent turns out to be a piecewise smooth function of the parameter.Comment: 22 pages, 2 figure

Boron nanobelts grown under intensive ion bombardment

High-quality α-tetragonal crystalline boronnanobelts with [001] growth axis were synthesized using a novel method combining e-beam evaporation and plasma ion bombardment techniques. Intensive ion bombardment of the growingboronnanobelts at a high substrate temperature (∼1200°C) was found to be effective in increasing the atomic density, reducing the crystal disorder, and improving the yield of the nanobelts.This work was supported by the Australian Research Council ARC

Inelastic Collisions in an Ultracold quasi-2D Gas

We present a formalism for rigorous calculations of cross sections for inelastic and reactive collisions of ultracold atoms and molecules confined by laser fields in quasi-2D geometry. Our results show that the elastic-to-inelastic ratios of collision cross sections are enhanced in the presence of a laser confinement and that the threshold energy dependence of the collision cross sections can be tuned by varying the confinement strength and external magnetic fields. The enhancement of the elastic-to-inelastic ratios is inversely proportional to $\sqrt{\epsilon/\hbar \omega_0}$, where $\epsilon$ is the kinetic energy and $\omega_0$ is the oscillation frequency of the trapped particles in the confinement potential.Comment: 4 pages, 4 figure