Magnetic fields in barred galaxies. IV. NGC 1097 and NGC 1365

We present 3.5cm and 6.2cm radio continuum maps in total and polarized intensity of the barred galaxies NGC 1097 and NGC 1365. Both galaxies exhibit radio ridges roughly overlapping with the massive dust lanes in the bar region. The contrast in total intensity across the radio ridges is compatible with compression and shear of an isotropic random magnetic field. The contrast in polarized intensity is significantly smaller than that expected from compression and shearing of the regular magnetic field; this could be the result of decoupling of the regular field from the dense molecular clouds. The regular field in the ridge is probably strong enough to reduce significantly shear in the diffuse gas (to which it is coupled) and hence to reduce magnetic field amplification by shearing. This contributes to the misalignment of the observed field orientation with respect to the velocity vectors of the dense gas. Our observations, for the first time, indicate that magnetic forces can control the flow of the diffuse interstellar gas at kiloparsec scales. The total radio intensity reaches its maximum in the circumnuclear starburst regions, where the equipartition field strength is about 60\mu G, amongst the strongest fields detected in spiral galaxies so far. The regular field in the inner region has a spiral shape with large pitch angle, indicating the action of a dynamo. Magnetic stress leads to mass inflow towards the centre, sufficient to feed the active nucleus in NGC 1097. We detected diffuse X-ray emission, possibly forming a halo of hot gas around NGC 1097.Comment: 32 pages with 45 PostScript figures. Accepted for publication in A&A; Typos corrected 12/10/200

Magnetic fields in barred galaxies. V. Modelling NGC 1365

We present a model of the global magnetic field in the barred galaxy NGC 1365 based jointly on the large-scale velocity field of interstellar gas fitted to HI and CO observations of this galaxy and on mean-field dynamo theory. The aim of the paper is to present a detailed quantitative comparison of a galactic dynamo model with independent radio observations. We consider several gas dynamical and nonlinear dynamo models that include plausible variations of parameters that are poorly known. Models of cosmic ray distribution in the galaxy are introduced to produce synthetic radio polarization maps allowing direct comparison with those observed at 3.5cm and 6.2cm. We show that the dynamo model is robust in that the most important magnetic features are controlled by the relatively well established properties of the density distribution and gas velocity field. The optimal agreement between the synthetic polarization maps and observations is obtained when a uniform cosmic ray distribution is adopted. We find some indirect evidence for enhanced turbulence in the regions of strong velocity shear and within 1-2kpc of the galactic centre. We confirm that magnetic stresses can drive an inflow of gas into the inner 1kpc of the galaxy at a rate of a few solar masses per year. The dynamo models are successful to some extent in modelling the large scale regular magnetic field in this galaxy. Our results demonstrate that dynamo models and synthetic polarization maps can provide information about both the gas dynamical models and conditions in the interstellar medium. We demonstrate that the dynamical effects of magnetic fields cannot be everywhere ignored in galaxy modelling.Comment: 14 pages, 25 figures, Accepted for publication in A&

Simulations of galactic dynamos

We review our current understanding of galactic dynamo theory, paying particular attention to numerical simulations both of the mean-field equations and the original three-dimensional equations relevant to describing the magnetic field evolution for a turbulent flow. We emphasize the theoretical difficulties in explaining non-axisymmetric magnetic fields in galaxies and discuss the observational basis for such results in terms of rotation measure analysis. Next, we discuss nonlinear theory, the role of magnetic helicity conservation and magnetic helicity fluxes. This leads to the possibility that galactic magnetic fields may be bi-helical, with opposite signs of helicity and large and small length scales. We discuss their observational signatures and close by discussing the possibilities of explaining the origin of primordial magnetic fields.Comment: 28 pages, 15 figure, to appear in Lecture Notes in Physics "Magnetic fields in diffuse media", Eds. E. de Gouveia Dal Pino and A. Lazaria

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na +] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA

An untargeted multi-technique metabolomics approach to studying intracellular metabolites of HepG2 cells exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin

<p>Abstract</p> <p>Background</p> <p><it>In vitro </it>cell systems together with omics methods represent promising alternatives to conventional animal models for toxicity testing. Transcriptomic and proteomic approaches have been widely applied <it>in vitro </it>but relatively few studies have used metabolomics. Therefore, the goal of the present study was to develop an untargeted methodology for performing reproducible metabolomics on <it>in vitro </it>systems. The human liver cell line HepG2, and the well-known hepatotoxic and non-genotoxic carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), were used as the <it>in vitro </it>model system and model toxicant, respectively.</p> <p>Results</p> <p>The study focused on the analysis of intracellular metabolites using NMR, LC-MS and GC-MS, with emphasis on the reproducibility and repeatability of the data. State of the art pre-processing and alignment tools and multivariate statistics were used to detect significantly altered levels of metabolites after exposing HepG2 cells to TCDD. Several metabolites identified using databases, literature and LC-nanomate-Orbitrap analysis were affected by the treatment. The observed changes in metabolite levels are discussed in relation to the reported effects of TCDD.</p> <p>Conclusions</p> <p>Untargeted profiling of the polar and apolar metabolites of <it>in vitro </it>cultured HepG2 cells is a valid approach to studying the effects of TCDD on the cell metabolome. The approach described in this research demonstrates that highly reproducible experiments and correct normalization of the datasets are essential for obtaining reliable results. The effects of TCDD on HepG2 cells reported herein are in agreement with previous studies and serve to validate the procedures used in the present work.</p

A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA

The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules -- up to a million base pairs -- for time-scales which are relevant to physiological processes. This is made possible by an efficient and highly-parallelised implementation of the model which we discuss here. We compare the behaviour of our model with single molecule experiments where dsDNA is manipulated by external forces or torques. We also present some results on the kinetics of denaturation of linear DNA