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

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)