On NP-Hardness of the Paired de Bruijn Sound Cycle Problem

The paired de Bruijn graph is an extension of de Bruijn graph incorporating mate pair information for genome assembly proposed by Mevdedev et al. However, unlike in an ordinary de Bruijn graph, not every path or cycle in a paired de Bruijn graph will spell a string, because there is an additional soundness constraint on the path. In this paper we show that the problem of checking if there is a sound cycle in a paired de Bruijn graph is NP-hard in general case. We also explore some of its special cases, as well as a modified version where the cycle must also pass through every edge.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Angular Dependence of Jitter Radiation Spectra from Small-Scale Magnetic Turbulence

Jitter radiation is produced by relativistic electrons moving in turbulent small-scale magnetic fields such as those produced by streaming Weibel-type instabilities at collisionless shocks in weakly magnetized media. Here we present a comprehensive study of the dependence of the jitter radiation spectra on the properties of, in general, anisotropic magnetic turbulence. We have obtained that the radiation spectra do reflect, to some extent, properties of the magnetic field spatial distribution, yet the radiation field is anisotropic and sensitive to the viewing direction with respect to the field anisotropy direction. We explore the parameter space of the magnetic field distribution and its effect on the radiation spectrum. Some important results include: the presence of the harder-than-synchrotron segment below the peak frequency at some viewing angles, the presence of the high-frequency power-law tail even for a monoenergetic distribution of electrons, the dependence of the peak frequency on the field correlation length rather than the field strength, the strong correlation of the spectral parameters with the viewing angle. In general, we have found that even relatively minor changes in the magnetic field properties can produce very significant effects upon the jitter radiation spectra. We consider these results to be important for accurate interpretation of prompt gamma-ray burst spectra and possibly other sources.Comment: 75 pages, 29 figures, submitted to Ap

Radiative diagnostics for sub-Larmor scale magnetic turbulence

Radiative diagnostics of high-energy density plasmas is addressed in this paper. We propose that the radiation produced by energetic particles in small-scale magnetic field turbulence, which can occur in laser-plasma experiments, collisionless shocks, and during magnetic reconnection, can be used to deduce some properties of the turbulent magnetic field. Particles propagating through such turbulence encounter locally strong magnetic fields, but over lengths much shorter than a particle gyroradius. Consequently, the particle is accelerated but not deviated substantially from a straight line path. We develop the general jitter radiation solutions for this case and show that the resulting radiation is directly dependent upon the spectral distribution of the magnetic field through which the particle propagates. We demonstrate the power of this approach in considering the radiation produced by particles moving through a region in which a (Weibel-like) filamentation instability grows magnetic fields randomly oriented in a plane transverse to counterstreaming particle populations. We calculate the spectrum as would be seen from the original particle population and as could be seen by using a quasi-monoenergetic electron beam to probe the turbulent region at various angles to the filamentation axis.Comment: 17 pages, 4 figures, submitted to Phys. Plasma

Jitter radiation images, spectra, and light curves from a relativistic spherical blastwave

We consider radiation emitted by the jitter mechanism in a Blandford-McKee self-similar blastwave. We assume the magnetic field configuration throughout the whole blastwave meets the condition for the emission of jitter radiation and we compute the ensuing images, light curves and spectra. The calculations are performed for both a uniform and a wind environment. We compare our jitter results to synchrotron results. We show that jitter radiation produces slightly different spectra than synchrotron, in particular between the self-absorption and the peak frequency, where the jitter spectrum is flat, while the synchrotron spectrum grows as \nu^{1/3}. The spectral difference is reflected in the early decay slope of the light curves. We conclude that jitter and synchrotron afterglows can be distinguished from each other with good quality observations. However, it is unlikely that the difference can explain the peculiar behavior of several recent observations, such as flat X-ray slopes and uncorrelated optical and X-ray behavior.Comment: 11 pages, 7 postscript figures. Accepted for publication in MNRA

Interstellar Scintillations of Polarization of Compact Sources

We demostrate that the measurement of fluctuations of polarization due to the galactic interstellar scintillations may be used to study the structure of the radiation field at compact radio sources. We develop a mathematical formalism and demonstrate it on a simple analytical model in which the scale of the polarization variation through the source is comparable to the source size. The predicted amplitude of modulation of the polarized radiation flux is ~20% x (pi_s) x (m_sc), where (pi_s) is the characteristic degree of polarization of radiation at the source and (m_sc) is the typical modulation index due to scattering, i.e., (m_sc)~1 for diffractive scintillations and (m_sc)<1 for refractive scintillations.Comment: 5 pages, 2 figures, emilateapj.sty. Submitted to ApJ

The geometry of spontaneous spiking in neuronal networks

The mathematical theory of pattern formation in electrically coupled networks of excitable neurons forced by small noise is presented in this work. Using the Freidlin-Wentzell large deviation theory for randomly perturbed dynamical systems and the elements of the algebraic graph theory, we identify and analyze the main regimes in the network dynamics in terms of the key control parameters: excitability, coupling strength, and network topology. The analysis reveals the geometry of spontaneous dynamics in electrically coupled network. Specifically, we show that the location of the minima of a certain continuous function on the surface of the unit n-cube encodes the most likely activity patterns generated by the network. By studying how the minima of this function evolve under the variation of the coupling strength, we describe the principal transformations in the network dynamics. The minimization problem is also used for the quantitative description of the main dynamical regimes and transitions between them. In particular, for the weak and strong coupling regimes, we present asymptotic formulas for the network activity rate as a function of the coupling strength and the degree of the network. The variational analysis is complemented by the stability analysis of the synchronous state in the strong coupling regime. The stability estimates reveal the contribution of the network connectivity and the properties of the cycle subspace associated with the graph of the network to its synchronization properties. This work is motivated by the experimental and modeling studies of the ensemble of neurons in the Locus Coeruleus, a nucleus in the brainstem involved in the regulation of cognitive performance and behavior

Electric field generation by the electron beam filamentation instability: Filament size effects

The filamentation instability (FI) of counter-propagating beams of electrons is modelled with a particle-in-cell simulation in one spatial dimension and with a high statistical plasma representation. The simulation direction is orthogonal to the beam velocity vector. Both electron beams have initially equal densities, temperatures and moduli of their nonrelativistic mean velocities. The FI is electromagnetic in this case. A previous study of a small filament demonstrated, that the magnetic pressure gradient force (MPGF) results in a nonlinearly driven electrostatic field. The probably small contribution of the thermal pressure gradient to the force balance implied, that the electrostatic field performed undamped oscillations around a background electric field. Here we consider larger filaments, which reach a stronger electrostatic potential when they saturate. The electron heating is enhanced and electrostatic electron phase space holes form. The competition of several smaller filaments, which grow simultaneously with the large filament, also perturbs the balance between the electrostatic and magnetic fields. The oscillations are damped but the final electric field amplitude is still determined by the MPGF.Comment: 14 pages, 10 plots, accepted for publication in Physica Script

Chaos at the border of criticality

The present paper points out to a novel scenario for formation of chaotic attractors in a class of models of excitable cell membranes near an Andronov-Hopf bifurcation (AHB). The mechanism underlying chaotic dynamics admits a simple and visual description in terms of the families of one-dimensional first-return maps, which are constructed using the combination of asymptotic and numerical techniques. The bifurcation structure of the continuous system (specifically, the proximity to a degenerate AHB) endows the Poincare map with distinct qualitative features such as unimodality and the presence of the boundary layer, where the map is strongly expanding. This structure of the map in turn explains the bifurcation scenarios in the continuous system including chaotic mixed-mode oscillations near the border between the regions of sub- and supercritical AHB. The proposed mechanism yields the statistical properties of the mixed-mode oscillations in this regime. The statistics predicted by the analysis of the Poincare map and those observed in the numerical experiments of the continuous system show a very good agreement.Comment: Chaos: An Interdisciplinary Journal of Nonlinear Science (tentatively, Sept 2008