The eukaryotic promoter prediction is one of the most important problems in DNA sequence analysis, but also a very difficult one. Although a number of algorithms have been proposed, their performances are still limited by low sensitivities and high false positives. We present a method for improving the performance of promoter regions prediction. We focus on the selection of most effective features for different functional regions in DNA sequences. Our feature selection algorithm is based on relative entropy or Kullback-Leibler divergence, and a system combined with position-specific information for promoter regions prediction is developed. The results of testing on large genomic sequences and comparisons with the PromoterInspector and Dragon Promoter Finder show that our algorithm is efficient with higher sensitivity and specificity in predicting promoter regions.

Based on cluster desynchronization properties of phase oscillators, we introduce an efficient method for the detection and identification of modules in complex networks. The performance of the algorithm is tested on computer generated and real-world networks whose modular structure is already known or has been studied by means of other methods. The algorithm attains a high level of precision, especially when the modular units are very mixed and hardly detectable by the other methods, with a computational effort $O\left(KN\right)$ on a generic graph with $N$ nodes and $K$ links.

A randomly driven linear filter that synthesizes Lorenz-like, reverse-time chaos is shown also to produce Rössler-like folded band wave forms when driven using a different encoding of the random source. The relationship between the topological entropy of the random source, dissipation in the linear filter, and the positive Lyapunov exponent for the reverse-time wave form is exposed. The two drive encodings are viewed as grammar restrictions on a more general encoding that produces a chaotic superset encompassing both the Lorenz butterfly and Rössler folded band paradigms of nonlinear dynamics.

The effects of the incidence angle of the main pump (MP) pulse in non-normal pumping geometry and the influence of the MP duration are investigated experimentally and theoretically for a transient collisionally pumped (TCE) x-ray laser in Ni-like Zr at 45° and 72° incidence angle on the target. The way they transfer to the x-ray laser output depends on the preplasma conditions, most notably on the average ionization distribution at the arrival of the MP. Moreover, contrary to previous grazing incidence pumping results, it is found that the shortest attainable MP maximizes the output. Modeling of the experimental results is performed with EHYBRID code. The results are important for scaling high repetition-rate non-normal incidence pumped lasers to sub-$10\mathrm{nm}$ wavelengths.

We consider small network models for mutually delay-coupled systems which typically do not exhibit stable isochronally synchronized solutions. We show analytically and numerically that for certain coupling architectures which involve delayed self-feedback to the nodes, the oscillators become isochronally synchronized. Applications are shown for both incoherent pump-coupled lasers and spatiotemporal coupled fiber ring lasers.

We investigate analytically and numerically the effect of inhomogeneities on the nonequilibrium dynamics of wave patterns in the framework of a complex Ginzburg-Landau equation (CGLE) with parametric, nonresonant forcing periodic in space and time. It is found that the forcing results in occurrence of traveling waves with different dispersion properties. In the limiting case of forcing with very large wavelength, the waves have essentially anharmonic spatial structure. We consider the influence of modulations on the development of an intermittent chaos and show that the parametric forcing may completely suppress the appearance of chaotic patterns. The relations between this and other pattern-forming systems are discussed. The results obtained are applied to describe the dynamics of thermal Rossby waves influenced by surface topography.

The direct observation of cavitation bubbles emerging in liquid mercury under the action of mechanical impacts and theoretical investigations on the experimental results have been made. Through a glass wall, the image of cavitation bubbles appearing near or in contact with the wall was captured by high-speed cameras. Discrepancies found between the bubbles’ growth rates determined experimentally and given by a single-bubble theory have been discussed using a theoretical model of Rayleigh-Plesset type that takes into account bubble-bubble and bubble-wall interactions. A theoretical equation for the asymptotic growth rate in a multibubble case has been given and time dependence of the growth rate under a constant negative pressure has been clarified.

After finding the basic solutions of the linearized nonlinear Schrödinger equation by the method of separation of variables, the perturbation theory for the dark soliton solution is constructed by linear Green’s function theory. In application to the self-induced Raman scattering, the adiabatic corrections to the soliton’s parameters are obtained and the remaining correction term is given as a pure integral with respect to the continuous spectral parameter.

A lattice Boltzmann method for double-diffusive natural convection is presented. The model combines a multicomponent lattice Boltzmann scheme with a finite-difference solution of the energy equation to simulate natural convection caused by gradients in temperature and concentration. The model is validated both in two and three dimensions, and the agreement with literature data is satisfactory. A case study of thermosolutal convection of air in a cubical enclosure with horizontal thermal and solutal gradients is presented, exhibiting a rich variety of flow structures.

We give two different, statistically consistent definitions of the length $l$ of a prime knot tied into a polymer ring. In the good solvent regime the polymer is modeled by a self avoiding polygon of $N$ steps on cubic lattice and $l$ is the number of steps over which the knot “spreads” in a given configuration. An analysis of extensive Monte Carlo data in equilibrium shows that the probability distribution of $l$ as a function of $N$ obeys a scaling of the form $p(l,N)\sim l^{-c}f(l∕N^D)$, with $c\simeq 1.25$ and $D\simeq 1$. Both $D$ and $c$ could be independent of knot type. As a consequence, the knot is weakly localized, i.e., $⟨l⟩\sim N^t$, with $t=2-c\simeq 0.75$. For a ring with fixed knot type, weak localization implies the existence of a peculiar characteristic length $l^{\nu }\sim N^{t\nu }$. In the scaling $\sim N^{\nu }$ $(\nu \simeq 0.58)$ of the radius of gyration of the whole ring, this length determines a leading power law correction which is much stronger than that found in the case of unrestricted topology. The existence of this correction is confirmed by an analysis of extensive Monte Carlo data for the radius of gyration. The collapsed regime is studied by introducing in the model sufficiently strong attractive interactions for nearest neighbor sites visited by the self-avoiding polygon. In this regime knot length determinations can be based on the entropic competition between two knotted loops separated by a slip link. These measurements enable us to conclude that each knot is delocalized $(t\simeq 1)$.

There have been many attempts to derive continuum models for dense granular flow, but a general theory is still lacking. Here, we start with Mohr-Coulomb plasticity for quasi-two-dimensional granular materials to calculate (average) stresses and slip planes, but we propose a “stochastic flow rule” (SFR) to replace the principle of coaxiality in classical plasticity. The SFR takes into account two crucial features of granular materials—discreteness and randomness—via diffusing “spots” of local fluidization, which act as carriers of plasticity. We postulate that spots perform random walks biased along slip lines with a drift direction determined by the stress imbalance upon a local switch from static to dynamic friction. In the continuum limit (based on a Fokker-Planck equation for the spot concentration), this simple model is able to predict a variety of granular flow profiles in flat-bottom silos, annular Couette cells, flowing heaps, and plate-dragging experiments—with essentially no fitting parameters—although it is only expected to function where material is at incipient failure and slip lines are inadmissible. For special cases of admissible slip lines, such as plate dragging under a heavy load or flow down an inclined plane, we postulate a transition to rate-dependent Bagnold rheology, where flow occurs by sliding shear planes. With different yield criteria, the SFR provides a general framework for multiscale modeling of plasticity in amorphous materials, cycling between continuum limit-state stress calculations, mesoscale spot random walks, and microscopic particle relaxation.

We introduce a Mittag-Leffler correlated random force leading to anomalous diffusion. Starting from a generalized Langevin equation, and using Laplace analysis we derive exact expressions for the mean values, variances and diffusion coefficient for a free particle in terms of generalized Mittag-Leffler functions and its derivatives. The asymptotic behavior of these quantities are obtained, from which the anomalous diffusion behavior of the particle is displayed.

The spatial invasion of a stable into an unstable phase is studied for the branching-coalescence process with nonlocal competition. Numerical experiments show that the threshold at the front leading edge, introduced by the discreteness of the reactants, allows for the nonlocal competition to affect the front velocity. However, the front still moves ballistically after a short transient period for any finite range competition length.

It is shown that the numerical results of Skoge et al. [Phys. Rev. E 74, 041127 (2006)] are in very good agreement with the theoretical predictions of Parisi and Zamponi [J. Stat. Mech.: Theory Exp. (2006) P03017].

Stable dynamic bound states of dissipative localized structures are found. It is characterized by chaotic oscillations of distance between the localized structures, their phase difference, and the center of mass velocity.

Recent numerical and heuristic arguments have revealed that the average phase-synchronization time between the input and the output associated with stochastic resonance is highly sensitive to noise variation. In particular there is evidence that this average time exhibits a cusplike behavior as the noise strength varies through the optimal value. Here we present an explicit formula for the average phase-synchronization time in terms of the phase diffusion coefficient and the average frequency difference between the input and the output signals. We also provide experimental evidence for the cusplike behavior by using a bistable microelectronic-circuit system.

We propose a control method with time delayed coupling which makes it possible to convert the stability features of systems close to a Hopf bifurcation. We consider two delay-coupled normal forms for Hopf bifurcation and demonstrate the conversion of stability, i.e., an interchange between the sub- and supercritical Hopf bifurcation. The control system provides us with an unified method for stabilizing both the unstable periodic orbit and the unstable steady state and reveals typical effects like amplitude death and phase locking. The main method and the results are applicable to a wide class of systems showing Hopf bifurcations, for example, the Van der Pol oscillator. The analytical theory is supported by numerical simulations of two delay-coupled Van der Pol oscillators, which show good agreement with the theory.

We propose a hybrid model, coupling lattice Boltzmann (LB) and molecular dynamics (MD) models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of two- and three-dimensional flows of liquid argon past and through a carbon nanotube. Comparisons with existing hybrid algorithms and with reference MD solutions demonstrate the validity of the present approach.

The axisymmetric linear stability of dissipative Taylor-Couette flow with an azimuthal magnetic field is considered. The magnetic field can be unstable without a rotation. This is the well-known pinch type instability. The stable rotation stabilizes the unstable azimuthal magnetic field. The dissipative flow stability can be classified according to Michael’s stability condition for an ideal flow. The dissipative effects stabilize the flow and an ideally unstable flow becomes really unstable only when both the angular velocity and the magnetic field exceed some critical values.

We propose a lattice model for the co-evolution of a virus population and an adaptive immune system. We show that, under some natural assumptions, both probability distribution of the virus population and the distribution of activity of the immune system tend during the evolution to a self-organized critical state.