International Journal of Modern Physics C

The complexity of DNA sequences is evaluated in order to differentiate between protein-coding and noncoding RNA segments. The method is based on computing the Shannon entropy of the sequences. By comparing the entropy of the original sequence with that of its shuffled one, we identify the source of the difference between the two segments and their relative contributions to the sequence. To demonstrate the method, the DNA sequences of the bacterium Clostridium difficile 630(G + C = 29.1%) and Bdellovibrio bacteriovorus(G + C = 50.6%) are analyzed, which are representatives of bacteria with unbalanced and balanced nucleotide content, respectively. It is shown that in both bacteria, regardless of nucleotide content, Δ_rS — the relative difference of the two entropies — is significantly greater in protein-coding regions, when compared with noncoding RNA segments.

Electromagnetic waves, solving the full set of Maxwell equations in vacuum, are numerically computed. These waves occupy a fixed bounded region of the three-dimensional space, topologically equivalent to a toroid. Thus, their fluid dynamics analogs are vortex rings. An analysis of the shape of the sections of the rings, depending on the angular speed of rotation and the major diameter, is carried out. Successively, spherical electromagnetic vortex rings of Hill's type are taken into consideration. For some interesting peculiar configurations, explicit numerical solutions are exhibited.

In the frame of inviscid and incompressible fluids without taking into consideration of surface tension effects, the axisymmetric evolution of two buoyancy-driven bubbles in an infinite and initially stationary liquid are investigated numerically by VOF method. The numerical experiments are performed for two bubbles with same size, with the following one being half of the leading one, and with the leading one being half of the following one, and for different bubble distances. The ratio of gas density to liquid density is 0.001. It is found by numerical experiment that when the distance between the two bubbles is greater than or equal to one and half of the bigger bubble radius, the interaction is very weak and the two bubbles evolute like isolated ones rising in an infinite liquid. When the two bubbles come closer, the leading bubble itself evolutes like an isolated one rising in an infinite liquid. However, due to the smaller distance between the two bubbles, large pressure gradient forms in the liquid region near the top of the following bubble, which causes the upward stretch of its top part no matter what sizes of the two bubbles are. When the distance between the two bubbles is less than or equal to three-tenth of the bigger bubble radius, before the liquid jet behind the leading bubble fully developed, the top part of the following bubble has already been sucked into the leading one, giving a pear-like shape. Soon after the following bubble merges with the leading one. It is also found that for the smaller bubble, its transition to toroidal is always faster than that of the bigger one because of its smaller size. The mechanism of the above phenomena has been analyzed numerically.

Contentious political debates regarding the issues on population and family planning have been perennial over the past four decades especially in developing countries. While its prominence in the public agenda varies depending on other national issues vying for public attention, its presence in policy and political agendas is constant. Here, a computational approach to framing analysis is developed that examines the pattern of media coverage on the population issue in the Philippines. The content of 146 articles sampled from 1988 to 2007 in Manila Bulletin (one of the leading newspapers in the Philippines) is analyzed by creating a syntactic network of concept co-occurrences. The topological properties of the network indicates that the discussion of an article revolves around few central ideas. Moreover, cluster analysis of the network suggests three well-defined frame themes, namely:

(1) Development Frame;

(2) Maternal Health Frame; and

(3) Framing by the Catholic Church.

Our results support the thesis that the inability to fruitfully discuss points of contention to reach agreement about suitable population policies in the Philippines is due to the mismatched frames within which it is discussed.

To efficiently enhance the synchronizability of a scale-free network by adding some edges, we numerically study the effect of edge-adding on the spectrum of the network Laplacian matrix. Based on the relation between the largest eigenvalue of the Laplacian matrix and the largest degree of the scale-free network, we show that adding a new edge to the node of largest degree will generally weaken the synchronizability of a scale-free network. We consequently propose a method to effectively enhance the network synchronizability by attaching the new edge to a node whose nearest-neighbors have small degrees. The effect of the new method is analyzed and demonstrated with comparisons.

Applying the statistical hypothesis testing, we investigate several nonlinear properties embedded in the return series of the Chinese Fund Market (CFM), which suggests the series is non-normal, auto-correlative and heteroskedastic. We hereby analyze the Hurst exponent of the return series in different timescales on the basis of the detrended fluctuation analysis (DFA) algorithm, and discuss the fractal behavior of the CFM. Furthermore, by studying the correlation of different weights in the volatility, we find the persistent long-range power-law correlation exists in the time series. We also provide hints that the above statistical properties are insensitive to the funds kind, and may be irrelevant to the market phases. Our work may reveal the self-similarity characteristics of the financial market and show a better understanding of the CFM.

The adsorption of alanine dipeptide on a Si(100)-2 × 1 asymmetric surface is studied by using pseudopotential plane wave approach based on Density Functional Theory (DFT). Adsorption energies for different surface sites of various conformations are calculated and the groove site is found to be energetically most favorable. We observed that the molecule-surface interactions might modify surface reconstruction: asymmetric surface dimers reconstruct to asymmetric dimers in opposite directions doubling the surface periodicity, which in turn gives the surface metallic properties.

The role of irregularity in intercellular connections is studied in the first natural human pacemaker called the sinoatrial node by modeling with the Greenberg–Hastings cellular automata. Facts from modern physiology about the sinoatrial node drive modeling. Heterogeneity between cell connections is reproduced by a rewiring procedure applied to a square lattice. The Greenberg–Hastings rule, representing the intrinsic cellular dynamics, is modified to imitate self-excitation of each pacemaker cell. Moreover, interactions with nearest neighbors are changed to heterogeneous ones by enhancing horizontal connections. Stationary states of the modeled system emerge as self-organized robust oscillatory states. Since the sinoatrial node role relies on a single cell cyclic activity, properties of single cells are studied. It appears that the strength and diversity of cellular oscillations depend directly on properties of intrinsic cellular dynamics. But these oscillations also depend on the underlying topology. Moderate nonuniformity of intercellular connections are found vital for proper function of the sinoatrial node, namely, for producing robust oscillatory states that are able to respond effectively to the autonomic system control.

We propose a new mechanism leading to scale-free networks which is based on the presence of an intrinsic character of a vertex called fitness. In our model, a vertex i is assigned a fitness x_i, drawn from a given probability distribution function f(x). During network evolution, with rate p we add a vertex j of fitness x_j and connect to an existing vertex i of fitness x_i selected preferentially to a linking probability function g(x_i, x_j) which depends on the fitnesses of the two vertices involved and, with rate 1 - p we create an edge between two already existed vertices with fitnesses x_i and x_j, with a probability also preferential to the connection function g(x_i, x_j). For the proper choice of g, the resulting networks have generalized power-laws, irrespective of the fitness distribution of vertices.

In this paper, the statistical property, namely degree correlation between users and objects, is taken into account and be embedded into the similarity index of collaborative filtering (CF) algorithm to improve the algorithmic performance. The numerical simulation on a benchmark data set shows that the algorithmic accuracy of the presented algorithm, measured by the average ranking score, is improved by 18.19% in the optimal case. The statistical analysis on the product distribution of the user and object degrees indicate that, in the optimal case, the distribution obeys the power-law and the exponential is equal to -2.33. Numerical results show that the presented algorithm can provide more diverse and less popular recommendations, for example, when the recommendation list contains 10 objects, the diversity, measured by the hamming distance, is improved by 21.90%. Since all of the real recommendation data evolving with time, this work may shed some light on the adaptive recommendation algorithm which could change its parameter automatically according to the statistical properties of the user-object bipartite network.