THEORETICAL STUDIES OF BILIPROTEIN CHROMOPHORES AND RELATED BILE PIGMENTS BY MOLECULAR ORBITAL AND RAMACHANDRAN TYPE CALCULATIONS

Ramachandran calculations have been used to gain insight into steric hindrance in bile pigments related to biliprotein chromophores. The high optical activity of denatured phycocyanin, as compared to phycoerythrin, has been related to the asymmetric substitution at ring A, which shifts the equilibrium towards the P-helical form of the chromophore. Geometric effects on the electronic structures and transitions have then been studied by molecular orbital calculations for several conjugation systems including the chromophores of phycocyanin. phytochrome P,, cations, cation radicals and tautomeric forms. For these different chromophores some general trends can be deduced. For instance, for a given change in the gross shape (e.g. either unfolding of the molecule from a cyclic-helical to a fully extended geometry, or upon out-of-plane twists of the pyrrole ring A) of the molecules under study, the predicted absorption spectra all change in a simikar way. Nonetheless, there are characteristic distinctions between the different n-systems, both in the transition energies and the charge distribution, which can be related to their known differences in spectroscopic properties and their reactivity

Diffusive spatio-temporal noise in a first-passage time model for intracellular calcium release

The intracellular release of calcium from the endoplasmic reticulum is controlled by ion channels. The resulting calcium signals exhibit a rich spatio-temporal signature, which originates at least partly from microscopic fluctuations. While stochasticity in the gating transition of ion channels has been incorporated into many models, the distribution of calcium is usually described by deterministic reaction-diffusion equations. Here we test the validity of the latter modeling approach by using two different models to calculate the frequency of localized calcium signals (calcium puffs) from clustered IP3 receptor channels. The complexity of the full calcium system is here limited to the basic opening mechanism of the ion channels and, in the mathematical reduction simplifies to the calculation of a first passage time. Two models are then studied: (i) a hybrid model, where channel gating is treated stochastically, while calcium concentration is deterministic and (ii) a fully stochastic model with noisy channel gating and Brownian calcium ion motion. The second model utilises the recently developed two-regime method [M. B. Flegg, S. J. Chapman, and R. Erban, “The two-regime method for optimizing stochastic reaction-diffusion simulations,” J. R. Soc., Interface9, 859–868 (Year: 2012)]10.1098/rsif.2011.0574 in order to simulate a large domain with precision required only near the Ca2+ absorbing channels. The expected time for a first channel opening that results in a calcium puff event is calculated. It is found that for a large diffusion constant, predictions of the interpuff time are significantly overestimated using the model (i) with a deterministic non-spatial calcium variable. It is thus demonstrated that the presence of diffusive noise in local concentrations of intracellular Ca2+ ions can substantially influence the occurrence of calcium signals. The presented approach and results may also be relevant for other cell-physiological first-passage time problems with small ligand concentration and high cooperativity

The inverse cascade and nonlinear alpha-effect in simulations of isotropic helical hydromagnetic turbulence

A numerical model of isotropic homogeneous turbulence with helical forcing is investigated. The resulting flow, which is essentially the prototype of the alpha^2 dynamo of mean-field dynamo theory, produces strong dynamo action with an additional large scale field on the scale of the box (at wavenumber k=1; forcing is at k=5). This large scale field is nearly force-free and exceeds the equipartition value. As the magnetic Reynolds number R_m increases, the saturation field strength and the growth rate of the dynamo increase. However, the time it takes to built up the large scale field from equipartition to its final super-equipartition value increases with magnetic Reynolds number. The large scale field generation can be identified as being due to nonlocal interactions originating from the forcing scale, which is characteristic of the alpha-effect. Both alpha and turbulent magnetic diffusivity eta_t are determined simultaneously using numerical experiments where the mean-field is modified artificially. Both quantities are quenched in a R_m-dependent fashion. The evolution of the energy of the mean field matches that predicted by an alpha^2 dynamo model with similar alpha and eta_t quenchings. For this model an analytic solution is given which matches the results of the simulations. The simulations are numerically robust in that the shape of the spectrum at large scales is unchanged when changing the resolution from 30^3 to 120^3 meshpoints, or when increasing the magnetic Prandtl number (viscosity/magnetic diffusivity) from 1 to 100. Increasing the forcing wavenumber to 30 (i.e. increasing the scale separation) makes the inverse cascade effect more pronounced, although it remains otherwise qualitatively unchanged.Comment: 21 pages, 26 figures, ApJ (accepted

A biological sequence comparison algorithm using quantum computers

Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas of biology and medicine. Careful monitoring of virulence-enhancing mutations is essential. However, an enormous amount of classical computing power is required to analyze genetic sequences of this size. Inspired by human perception of vision and pixel representation of images on quantum computers, we leverage these techniques to implement a pairwise sequence analysis. The methodology has a potential advantage over classical approaches and can be further applied to identify mutations and other modifications in genetic sequences. We present a method to display and analyze the similarity between two genome sequences on a quantum computer where a similarity score is calculated to determine the similarity between nucleotides.Comment: 14 pages, 8 figures, 3 tables New version: typo in figure 7 New version because of a missing information in affiliations in footer, page

Magnetic field generation in fully convective rotating spheres

Magnetohydrodynamic simulations of fully convective, rotating spheres with volume heating near the center and cooling at the surface are presented. The dynamo-generated magnetic field saturates at equipartition field strength near the surface. In the interior, the field is dominated by small-scale structures, but outside the sphere by the global scale. Azimuthal averages of the field reveal a large-scale field of smaller amplitude also inside the star. The internal angular velocity shows some tendency to be constant along cylinders and is ``anti-solar'' (fastest at the poles and slowest at the equator).Comment: 12 pages, 11 figures, 2 tables, to appear in the 10 Feb issue of Ap

The Accretion Rates and Spectral Energy Distributions of BL Lacertae Objects

We investigate the relationship between accretion rates and the spectral energy distributions (SEDs) of BL Lac objects, using a sample of objects for which published information on the host galaxies, emission-line luminosities, and peak frequencies and luminosities of their SEDs are available. The sample is composed of 43 BL Lac objects which have a relatively continuous distribution of peak frequencies. Under the assumption that the observed emission lines are photoionized by the central accretion disk, we use the line luminosities to estimate the accretion luminosities and hence accretion rates. We find that low frequency-peaked BL Lac objects (LBLs) span a wide range of accretion rates, whereas high frequency-peaked BL Lac objects (HBLs) cover a more restricted range of lower values. There appears to be a continuous distribution of accretion rates between the two subclasses of BL Lac objects. We find that the peak frequency of the SED, \pknu, correlates with the accretion rate, approximately with the form \pknu\propto \Lambda^{-3} in HBLs and \pknu \propto \Lambda^{-0.25} in LBLs, where $\Lambda \equiv L_{\rm lines}/c^2$. The peak luminosity of the SED is also correlated with $\Lambda$. These results suggest that the accretion rate influences the shape of the SED in BL Lac objects. They also support models which couple the jet and the accretion disk. We present a physical scenario to account for the empirical trends.Comment: 6 pages in emulateapj.sty, 3 figures 1 table. The Astrophysical Journal (in press

The alpha-effect and current helicity for fast sheared rotators

We explore the alpha-effect and the small-scale current helicity, for the case of weakly compressible magnetically driven turbulence that is subjected to the differential rotation. No restriction is applied to the amplitude of angular velocity, i.e., the derivations presented are valid for an arbitrary Coriolis number, though the differential rotation itself is assumed to be weak. The expressions obtained are used to explore the possible distributions of alpha-effect and current helicity in convection zones (CZ) of the solar-type stars. The implications of the obtained results to the mean-field dynamo models are discussed.Comment: 20 pages, 6 figure

The role of Hall diffusion in the magnetically threaded thin accretion discs

We study role of the Hall diffusion in the magnetic star-disc interaction. In a simplified steady state configuration, the total torque is calculated in terms of the fastness parameter and a new term because of the Hall diffusion. We show the total torque reduces as the Hall term becomes more significant. Also, the critical fastness parameter (at which the total torque is zero) reduces because of the Hall diffusion.Comment: Accepted for publication in Astrophysics and Space Scienc