Promoter prediction using physico-chemical properties of DNA

The ability to locate promoters within a section of DNA is known to be a very difficult and very important task in DNA analysis. We document an approach that incorporates the concept of DNA as a complex molecule using several models of its physico-chemical properties. A support vector machine is trained to recognise promoters by their distinctive physical and chemical properties. We demonstrate that by combining models, we can improve upon the classification accuracy obtained with a single model. We also show that by examining how the predictive accuracy of these properties varies over the promoter, we can reduce the number of attributes needed. Finally, we apply this method to a real-world problem. The results demonstrate that such an approach has significant merit in its own right. Furthermore, they suggest better results from a planned combined approach to promoter prediction using both physicochemical and sequence based techniques

Magnetohydrodynamical Accretion Flows: Formation of Magnetic Tower Jet and Subsequent Quasi-Steady State

We present three-dimensional (3-D) magnetohydrodynamical (MHD) simulations of radiatively inefficient accretion flow around black holes. General relativistic effects are simulated by using the pseudo-Newtonian potential. We start calculations with a rotating torus threaded by localized poloidal magnetic fields with plasma beta, a ratio of the gas pressure to the magnetic pressure, $\beta =10$ and 100. When the bulk of torus material reaches the innermost region close to a central black hole, a magnetically driven jet emerges. This magnetic jet is derived by vertically inflating toroidal fields (`magnetic tower') and has a two-component structure: low-$\beta$ (\lsim 1) plasmas threaded with poloidal (vertical) fields are surrounded by that with toroidal fields. The collimation width of the jet depends on external pressure, pressure of ambient medium; the weaker the external pressure is, the wider and the longer-lasting becomes the jet. Unless the external pressure is negligible, the bipolar jet phase ceases after several dynamical timescales at the original torus position and a subsequent quasi-steady state starts. The black hole is surrounded by quasi-spherical zone with highly inhomogeneous structure in which toroidal fields are dominant except near the rotation axis. Mass accretion takes place mainly along the equatorial plane. Comparisons with other MHD simulation results and observational implications are discussed.Comment: Accepted for publication in ApJ. 15 pages, 3 tables, 11 figures. A paper with high-resolution figures and movies available at http://www2.yukawa.kyoto-u.ac.jp/~ykato/research

New Panoramic View of 12^{12}CO and 1.1 mm Continuum Emission in the Orion A Molecular Cloud. I. Survey Overview and Possible External Triggers of Star Formation

We present new, wide and deep images in the 1.1 mm continuum and the $^{12}$CO ($J$=1-0) emission toward the northern part of the Orion A Giant Molecular Cloud (Orion-A GMC). The 1.1 mm data were taken with the AzTEC camera mounted on the Atacama Submillimeter Telescope Experiment (ASTE) 10 m telescope in Chile, and the $^{12}$CO ($J$=1-0) data were with the 25 beam receiver (BEARS) on the NRO 45 m telescope in the On-The-Fly (OTF) mode. The present AzTEC observations are the widest (\timeform{1.D7} $\times$ \timeform{2.D3}, corresponding to 12 pc $\times$ 17 pc) and the highest-sensitivity ($\sim$9 mJy beam$^{-1}$) 1.1 mm dust-continuum imaging of the Orion-A GMC with an effective spatial resolution of $\sim$ 40\arcsec. The $^{12}$CO ($J$=1-0) image was taken over the northern \timeform{1D.2} \times\timeform{1D.2} (corresponding 9 pc $\times$ 9 pc) area with a sensitivity of 0.93 K in $T_{\rm MB}$, a velocity resolution of 1.0 km s$^{-1}$, and an effective spatial resolution of 21\arcsec. With these data, together with the MSX 8 $\mu$m, Spitzer 24 $\mu$m and the 2MASS data, we have investigated the detailed structure and kinematics of molecular gas associated with the Orion-A GMC and have found evidence for interactions between molecular clouds and the external forces that may trigger star formation. Two types of possible triggers were revealed; 1) Collision of the diffuse gas on the cloud surface, particularly at the eastern side of the OMC-2/3 region, and 2) Irradiation of UV on the pre-existing filaments and dense molecular cloud cores. Our wide-field and high-sensitivity imaging have provided the first comprehensive view of the potential sites of triggered star formation in the Orion-A GMC.Comment: 32 pages, 20 figures, accepted for publication in PAS

Mass Outflow Rate From Accretion Discs around Compact Objects

We compute mass outflow rates from accretion disks around compact objects, such as neutron stars and black holes. These computations are done using combinations of exact transonic inflow and outflow solutions which may or may not form standing shock waves. Assuming that the bulk of the outflow is from the effective boundary layers of these objects, we find that the ratio of the outflow rate and inflow rate varies anywhere from a few percent to even close to a hundred percent (i.e., close to disk evacuation case) depending on the initial parameters of the disk, the degree of compression of matter near the centrifugal barrier, and the polytropic index of the flow. Our result, in general, matches with the outflow rates obtained through a fully time-dependent numerical simulation. In some region of the parameter space when the standing shock does not form, our results indicate that the disk may be evacuated and may produce quiescence states.Comment: 30 Latex pages and 13 figures. crckapb.sty; Published in Class. Quantum Grav. Vol. 16. No. 12. Pg. 387

Compton Scattering in Static and Moving Media. II. System-Frame Solutions for Spherically Symmetric Flows

I study the formation of Comptonization spectra in spherically symmetric, fast moving media in a flat spacetime. I analyze the mathematical character of the moments of the transfer equation in the system-frame and describe a numerical method that provides fast solutions of the time-independent radiative transfer problem that are accurate in both the diffusion and free-streaming regimes. I show that even if the flows are mildly relativistic (V~0.1, where V is the electron bulk velocity in units of the speed of light), terms that are second-order in V alter the emerging spectrum both quantitatively and qualitatively. In particular, terms that are second-order in V produce power-law spectral tails, which are the dominant feature at high energies, and therefore cannot be neglected. I further show that photons from a static source are upscattered by the bulk motion of the medium even if the velocity field does not converge. Finally, I discuss these results in the context of radial accretion onto and outflows from compact objects.Comment: 28 pages, 9 figures; minor changes, to appear in the Astrophysical Journa

Compton Scattering by Static and Moving Media I. The Transfer Equation and Its Moments

Compton scattering of photons by nonrelativistic particles is thought to play an important role in forming the radiation spectrum of many astrophysical systems. Here we derive the time-dependent photon kinetic equation that describes spontaneous and induced Compton scattering as well as absorption and emission by static and moving media, the corresponding radiative transfer equation, and their zeroth and first moments, in both the system frame and in the frame comoving with the medium. We show that it is necessary to use the correct relativistic differential scattering cross section in order to obtain a photon kinetic equation that is correct to first order in epsilon/m_e, T_e/m_e, and V, where epsilon is the photon energy, T_e and m_e are the electron temperature and rest mass, and V is the electron bulk velocity in units of the speed of light. We also demonstrate that the terms in the radiative transfer equation that are second-order in V usually should be retained, because if the radiation energy density is sufficiently large compared to the radiation flux, the effects of bulk Comptonization described by the terms that are second-order in V are at least as important as the effects described by the terms that are first-order in V, even when V is small. Our equations are valid for systems of arbitrary optical depth and can therefore be used in both the free-streaming and the diffusion regimes. We demonstrate that Comptonization by the electron bulk motion occurs whether or not the radiation field is isotropic or the bulk flow converges and that it is more important than thermal Comptonization if V^2 > 3 T_e/m_e.Comment: 31 pages, accepted for publication in The Astrophysical Journa

Mass-losing accretion discs around supermassive black holes

We study the effects of outflow/wind on the gravitational stability of accretion discs around supermassive black holes using a set of analytical steady-state solutions. Mass-loss rate by the outflow from the disc is assumed to be a power-law of the radial distance and the amount of the energy and the angular momentum which are carried away by the wind are parameterized phenomenologically. We show that the mass of the first clumps at the self-gravitating radius linearly decreases with the total mass-loss rate of the outflow. Except for the case of small viscosity and high accretion rate, generally, the self-gravitating radius increases as the amount of mass-loss by the outflow increases. Our solutions show that as more angular momentum is lost by the outflow, then reduction to the mass of the first clumps is more significant.Comment: Accepted for publication in Astrophysics & Space Scienc

Self-Collimation and Magnetic Field Generation of Astrophysical Jets

A novel model for collimation and transport of electron-positron-ion jets is presented. Analytical results show that the filamentary structures can be sustained by self-induced toroidal magnetic fields permeating through the filaments, whose widths significantly expand in the pair-dominant regimes. The magnetic field strength reflects a characteristic of equipartition of excess kinetic energy of the jets. It is also shown that growth of the hoselike instability is strongly suppressed. Essential features derived from this model are consistent with recent results observed by using very long baseline telescopes.Comment: 10 pages including 2 eps figures, to be published in 10 April 2002, ApJ

Kinematics of classical Cepheids in the Nuclear Stellar Disk

Classical Cepheids are useful tracers of the Galactic young stellar population because their distances and ages can be determined from their period-luminosity and period-age relations. In addition, the radial velocities and chemical abundance of the Cepheids can be derived from spectroscopic observations, providing further insights into the structure and evolution of the Galaxy. Here, we report the radial velocities of classical Cepheids near the Galactic Center, three of which were reported in 2011, the other reported for the first time. The velocities of these Cepheids suggest that the stars orbit within the Nuclear Stellar Disk, a group of stars and interstellar matter occupying a region of 200 pc around the Center, although the three-dimensional velocities cannot be determined until the proper motions are known. According to our simulation, these four Cepheids formed within the Nuclear Stellar Disk like younger stars and stellar clusters therein.Comment: Accepted for publication in ApJ; 8 pages, 7 figures, 6 table