Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation

In this paper, a new model of self-organized criticality is introduced. This model, called the gene expression paradigm, is motivated by the problem of gene expression initiation in the newly-born daughter cells after mitosis. The model is fundamentally different in dynamics and properties from the well known sand-pile paradigm. Simulation experiments demonstrate that a critical total number of proteins exists below which transcription is impossible. Above this critical threshold, the system enters the regime of self-sustained oscillations with standard deviations and periods proportional to the genes’ complexities with probability one. The borderline between these two regimes is very sharp. Importantly, such a self-organization emerges without any deterministic feedback loops or external supervision, and is a result of completely random redistribution of proteins between inactive genes. Given the size of the genome, the domain of self-organized oscillatory motion is also limited by the genes’ maximal complexities. Below the critical complexity, all the regimes of self-organized oscillations are self-similar and largely independent of the genes’ complexities. Above the level of critical complexity, the whole-genome transcription is impossible. Again, the borderline between the domains of oscillations and quiescence is very sharp. The gene expression paradigm is an example of cellular automata with the domain of application potentially far beyond its biological context. The model seems to be simple enough for staging an experiment for verification of its remarkable properties

Pattern recognition. v- samp - a computer program for estimating surface area from contour maps

Fortran computer program for computing linear approximation of surface area for any given portion of digitized contour ma

A new approach to the inverse problem for current mapping in thin-film superconductors

A novel mathematical approach has been developed to complete the inversion of the Biot-Savart law in one- and two-dimensional cases from measurements of the perpendicular component of the magnetic field using the well-developed Magneto-Optical Imaging technique. Our approach, especially in the 2D case, is provided in great detail to allow a straightforward implementation as opposed to those found in the literature. Our new approach also refines our previous results for the 1D case [Johansen et al., Phys. Rev. B 54, 16264 (1996)], and streamlines the method developed by Jooss et al. [Physica C 299, 215 (1998)] deemed as the most accurate if compared to that of Roth et al. [J. Appl. Phys. 65, 361 (1989)]. We also verify and streamline the iterative technique, which was developed following Laviano et al. [Supercond. Sci. Technol. 16, 71 (2002)] to account for in-plane magnetic fields caused by the bending of the applied magnetic field due to the demagnetising effect. After testing on magneto-optical images of a high quality YBa2Cu3O7 superconducting thin film, we show that the procedure employed is effective

The High Eccentricity of the Planet Around 16 Cyg B

We consider the high eccentricity, 0.66, of the newly discovered planet around 16 Cyg B, using the fact that the parent star is part of a wide binary. We show that the high eccentricity of the planet could be the result of tidal forces exerted on 16 Cyg B and its planet by 16 Cyg A, the distant companion in the system. By following stellar triple systems with parameters similar to those of 16 Cyg, we have established that the orbital eccentricity of the planet could have gone through strong modulation, with an amplitude of 0.8 or even larger, with typical timescale of tens of millions years. The amplitude of the planet eccentricity strongly depends on the relative inclination between the plane of motion of the planet and that of the wide binary 16 Cyg AB. To account for the present eccentricity of the planet we have to assume that the angle between the two planes of motion is large, at least 60 deg. We argue that this assumption is reasonable for wide binaries like 16 Cyg AB.Comment: 2 Figures, Latex, submitted for publication to ApJ

Lattice density-functional theory of surface melting: the effect of a square-gradient correction

I use the method of classical density-functional theory in the weighted-density approximation of Tarazona to investigate the phase diagram and the interface structure of a two-dimensional lattice-gas model with three phases -- vapour, liquid, and triangular solid. While a straightforward mean-field treatment of the interparticle attraction is unable to give a stable liquid phase, the correct phase diagram is obtained when including a suitably chosen square-gradient term in the system grand potential. Taken this theory for granted, I further examine the structure of the solid-vapour interface as the triple point is approached from low temperature. Surprisingly, a novel phase (rather than the liquid) is found to grow at the interface, exhibiting an unusually long modulation along the interface normal. The conventional surface-melting behaviour is recovered only by artificially restricting the symmetries being available to the density field.Comment: 16 pages, 6 figure

Dimerization and low-dimensional magnetism in nanocrystalline TiO2 semiconductors doped by Fe and Co

The report is devoted to an analysis of the structural and magnetic state of the nanocrystalline diluted magnetic semiconductors based on TiO2 doped with Fe and Co atoms. Structural and magnetic characterization of samples was carried out using X-ray diffraction (XRD) analysis, transmission electron microscopy (TEM), X-ray absorption spectroscopy (XAS), electron paramagnetic resonance (EPR) spectroscopy, SQUID magnetometry, and the density functional theory (DFT) calculations. Analysis of the experimental data suggests the presence of non-interacting paramagnetic Fe3+ and Co2+ ions in the high-spin state and negative exchange interactions between them. The important conclusions is that the distribution of dopants in the TiO2 matrix, even at low concentrations of 3d-metal dopant (less than one percent), is not random, but the 3d ions localization and dimerization is observed both on the surface and in the nanoparticles core. Thus, in the paper the quantum mechanical model for describing the magnetic properties of TiO2:(Fe, Co) was suggested. The model operates only with two parameters: paramagnetic contribution of non-interacting 3d-ions and dimers having different exchange interactions between 3d magnetic carriers. © Published under licence by IOP Publishing Ltd

A new signature for color octet pseudoscalars at the LHC

Color octet (pseudo)scalars, if they exist, will be copiously produced at the CERN Large Hadron Collider (LHC). However, their detection can become a very challenging task. In particular, if their decay into a pair of top quarks is kinematically forbidden, the main decay channel would be into two jets, with a very large background. In this Brief Report we explore the possibility of using anomaly-induced decays of the color octet pseudoscalars into gauge bosons to find them at the LHC.Comment: 4 pages, 2 figures. New references adde

Entropic torque

Quantitative predictions are presented of a depletion-induced torque and force acting on a single colloidal hard rod immersed in a solvent of hard spheres close to a planar hard wall. This torque and force, which are entirely of entropic origin, may play an important role for the key-lock principle, where a biological macromolecule (the key) is only functional in a particular orientation with respect to a cavity (the lock)