Universality of Long-Range Correlations in Expansion-Randomization Systems

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 $\chi$ 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 $\chi$, 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

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.

Interdot Coulomb repulsion effect on the charge transport of parallel double single electron transistors

The charge transport behaviors of parallel double single electron transistors (SETs) are investigated by the Anderson model with two impurity levels. The nonequilibrium Keldysh Green's technique is used to calculate the current-voltage characteristics of system. For SETs implemented by quantum dots (QDs) embedded into a thin $SiO_2$ layer, the interdot Coulomb repulsion is more important than the interdot electron hopping as a result of high potential barrier height between QDs and $SiO_2$. We found that the interdot Coulomb repulsion not onlyleads to new resonant levels, but also creates negative differential conductances.Comment: 12 pages, 7 figure

On the efficiency of estimating penetrating rank on large graphs

P-Rank (Penetrating Rank) has been suggested as a useful measure of structural similarity that takes account of both incoming and outgoing edges in ubiquitous networks. Existing work often utilizes memoization to compute P-Rank similarity in an iterative fashion, which requires cubic time in the worst case. Besides, previous methods mainly focus on the deterministic computation of P-Rank, but lack the probabilistic framework that scales well for large graphs. In this paper, we propose two efficient algorithms for computing P-Rank on large graphs. The first observation is that a large body of objects in a real graph usually share similar neighborhood structures. By merging such objects with an explicit low-rank factorization, we devise a deterministic algorithm to compute P-Rank in quadratic time. The second observation is that by converting the iterative form of P-Rank into a matrix power series form, we can leverage the random sampling approach to probabilistically compute P-Rank in linear time with provable accuracy guarantees. The empirical results on both real and synthetic datasets show that our approaches achieve high time efficiency with controlled error and outperform the baseline algorithms by at least one order of magnitude

Cusp Summations and Cusp Relations of Simple Quad Lenses

We review five often used quad lens models, each of which has analytical solutions and can produce four images at most. Each lens model has two parameters, including one that describes the intensity of non-dimensional mass density, and the other one that describes the deviation from the circular lens. In our recent work, we have found that the cusp and the fold summations are not equal to 0, when a point source infinitely approaches a cusp or a fold from inner side of the caustic. Based on the magnification invariant theory, which states that the sum of signed magnifications of the total images of a given source is a constant, we calculate the cusp summations for the five lens models. We find that the cusp summations are always larger than 0 for source on the major cusps, while can be larger or smaller than 0 for source on the minor cusps. We also find that if these lenses tend to the circular lens, the major and minor cusp summations will have infinite values, and with positive and negative signs respectively. The cusp summations do not change significantly if the sources are slightly deviated from the cusps. In addition, through the magnification invariants, we also derive the analytical signed cusp relations on the axes for three lens models. We find that both on the major and the minor axes the larger the lenses deviated from the circular lens, the larger the signed cusp relations. The major cusp relations are usually larger than the absolute minor cusp relations, but for some lens models with very large deviation from circular lens, the minor cusp relations can be larger than the major cusp relations.Comment: 8 pages, 4 figures, accepted for publication in MNRA

New stopping criteria for segmenting DNA sequences

We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns. This new stopping criterion is based on Bayesian Information Criterion (BIC) in the model selection framework. When this stopping criterion is applied to a left telomere sequence of yeast Saccharomyces cerevisiae and the complete genome sequence of bacterium Escherichia coli, borders of biologically meaningful units were identified (e.g. subtelomeric units, replication origin, and replication terminus), and a more reasonable number of domains was obtained. We also introduce a measure called segmentation strength which can be used to control the delineation of large domains. The relationship between the average domain size and the threshold of segmentation strength is determined for several genome sequences.Comment: 4 pages, 4 figures, Physical Review Letters, to appea

New parametrization for the nuclear covariant energy density functional with point-coupling interaction

A new parametrization PC-PK1 for the nuclear covariant energy density functional with nonlinear point-coupling interaction is proposed by fitting to observables for 60 selected spherical nuclei, including the binding energies, charge radii and empirical pairing gaps. The success of PC-PK1 is illustrated in its description for infinite nuclear matter and finite nuclei including the ground-state and low-lying excited states. Particularly, PC-PK1 improves the description for isospin dependence of binding energy along either the isotopic or the isotonic chains, which makes it more reliable for application in exotic nuclei. The predictive power of PC-PK1 is also illustrated for the nuclear low-lying excitation states in a five-dimensional collective Hamiltonian in which the parameters are determined by constrained calculations for triaxial shapes.Comment: 32 pages, 12 figures, 4 tables, accepted by Phys. Rev.

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