Electrically monitoring DNA repair by photolyase

Cyclobutane pyrimidine dimers are the major DNA photoproducts produced upon exposure to UV radiation. If left unrepaired, these lesions can lead to replication errors, mutation, and cell death. Photolyase is a light-activated flavoenzyme that binds to pyrimidine dimers in DNA and repairs them in a reaction triggered by electron transfer from the photoexcited flavin cofactor to the dimer. Using gold electrodes modified with DNA duplexes containing a cyclobutane thymine dimer (T T), here we probe the electrochemistry of the flavin cofactor in Escherichia coli photolyase. Cyclic and square-wave voltammograms of photolyase deposited on these electrodes show a redox signal at 40 mV versus normal hydrogen electrode, consistent with electron transfer to and from the flavin in the DNA-bound protein. This signal is dramatically attenuated on surfaces where the pi-stacking of the DNA bases is perturbed by the presence of an abasic site below the T T, an indication that the redox pathway is DNA-mediated. DNA repair can, moreover, be monitored electrically. Exposure of photolyase on T T-damaged DNA films to near-UV/blue light leads to changes in the flavin signal consistent with repair, as confirmed by parallel HPLC experiments. These results demonstrate the exquisite sensitivity of DNA electrochemistry to perturbations in base pair stacking and the applicability of this chemistry to probe reactions of proteins with DNA

Nonlinear force-free field modeling of a solar active region using SDO/HMI and SOLIS/VSM data

We use SDO/HMI and SOLIS/VSM photospheric magnetic field measurements to model the force-free coronal field above a solar active region, assuming magnetic forces to dominate. We take measurement uncertainties caused by, e.g., noise and the particular inversion technique into account. After searching for the optimum modeling parameters for the particular data sets, we compare the resulting nonlinear force-free model fields. We show the degree of agreement of the coronal field reconstructions from the different data sources by comparing the relative free energy content, the vertical distribution of the magnetic pressure and the vertically integrated current density. Though the longitudinal and transverse magnetic flux measured by the VSM and HMI is clearly different, we find considerable similarities in the modeled fields. This indicates the robustness of the algorithm we use to calculate the nonlinear force-free fields against differences and deficiencies of the photospheric vector maps used as an input. We also depict how much the absolute values of the total force-free, virial and the free magnetic energy differ and how the orientation of the longitudinal and transverse components of the HMI- and VSM-based model volumes compares to each other.Comment: 9 pages, 5 figure

Structure and Evolution of Giant Cells in Global Models of Solar Convection

The global scales of solar convection are studied through three-dimensional simulations of compressible convection carried out in spherical shells of rotating fluid which extend from the base of the convection zone to within 15 Mm of the photosphere. Such modelling at the highest spatial resolution to date allows study of distinctly turbulent convection, revealing that coherent downflow structures associated with giant cells continue to play a significant role in maintaining the strong differential rotation that is achieved. These giant cells at lower latitudes exhibit prograde propagation relative to the mean zonal flow, or differential rotation, that they establish, and retrograde propagation of more isotropic structures with vortical character at mid and high latitudes. The interstices of the downflow networks often possess strong and compact cyclonic flows. The evolving giant-cell downflow systems can be partly masked by the intense smaller scales of convection driven closer to the surface, yet they are likely to be detectable with the helioseismic probing that is now becoming available. Indeed, the meandering streams and varying cellular subsurface flows revealed by helioseismology must be sampling contributions from the giant cells, yet it is difficult to separate out these signals from those attributed to the faster horizontal flows of supergranulation. To aid in such detection, we use our simulations to describe how the properties of giant cells may be expected to vary with depth, how their patterns evolve in time, and analyze the statistical features of correlations within these complex flow fields.Comment: 22 pages, 16 figures (color figures are low res), uses emulateapj.cls Latex class file, Results shown during a Press release at the AAS meeting in June 2007. Submitted to Ap

The Influence of Spatial Resolution on Nonlinear Force-Free Modeling

The nonlinear force-free field (NLFFF) model is often used to describe the solar coronal magnetic field, however a series of earlier studies revealed difficulties in the numerical solution of the model in application to photospheric boundary data. We investigate the sensitivity of the modeling to the spatial resolution of the boundary data, by applying multiple codes that numerically solve the NLFFF model to a sequence of vector magnetogram data at different resolutions, prepared from a single Hinode/SOT-SP scan of NOAA Active Region 10978 on 2007 December 13. We analyze the resulting energies and relative magnetic helicities, employ a Helmholtz decomposition to characterize divergence errors, and quantify changes made by the codes to the vector magnetogram boundary data in order to be compatible with the force-free model. This study shows that NLFFF modeling results depend quantitatively on the spatial resolution of the input boundary data, and that using more highly resolved boundary data yields more self-consistent results. The free energies of the resulting solutions generally trend higher with increasing resolution, while relative magnetic helicity values vary significantly between resolutions for all methods. All methods require changing the horizontal components, and for some methods also the vertical components, of the vector magnetogram boundary field in excess of nominal uncertainties in the data. The solutions produced by the various methods are significantly different at each resolution level. We continue to recommend verifying agreement between the modeled field lines and corresponding coronal loop images before any NLFFF model is used in a scientific setting.Comment: Accepted to ApJ; comments/corrections to this article are welcome via e-mail, even after publicatio

Quantum Transport through Organic Molecules

We explore electron transport properties for the model of benzene-1, 4-dithiolate (BDT) molecule and for some other geometric models of benzene molecule attached to two semi-infinite one-dimensional metallic electrodes using the Green's function formalism. An analytic approach, based on a simple tight-binding framework, is presented to describe electron transport through the molecular wires. Electronic transport in such molecular systems is strongly affected by the geometry of the molecules as well as their coupling to the side-attached electrodes. Conductance reveals resonant peaks associated with the molecular energy eigenstates providing several complex spectra. Current passing through the molecules shows staircase-like behavior with sharp steps in the weak molecule-to-electrode coupling limit, while it varies quite continuously with the applied bias voltage in the limit of strong molecular coupling. In the presence of transverse magnetic field, conductance exhibits oscillatory behavior with flux $\phi$, threaded by the molecular ring, showing $\phi_0$ ($=ch/e$) flux-quantum periodicity. Though, conductance changes in the presence of transverse magnetic field, but the current-voltage characteristics are not significantly affected by this field.Comment: 11 pages, 8 figure

Tuning of electron transport through a moebius strip: shot noise

We explore electron transport through a moebius strip attached to two metallic electrodes by the use of Green's function technique. A parametric approach is used based on the tight-binding model to characterize the electron transport through such a bridge system and it is observed that the transport properties are significantly affected by (a) the transverse hopping strength between the two channels and (b) the strip-to-electrode coupling strength. In this context we also describe the noise power of the current fluctuations that provides a key information about the electron correlation which is obtained by calculating the Fano factor ($F$). The knowledge of this current fluctuations gives important ideas for fabrication of efficient electronic devices.Comment: 9 pages, 8 figure

Optimising non-Newtonian fluids for impact protection of laminates

Non-Newtonian fluids can be used for the protection of flexible laminates. Understanding the coupling between the flow of the protecting fluid and the deformation of the protected solids is necessary in order to optimize this functionality. We present a scaling analysis of the problem based on a single coupling variable, the effective width of a squeeze flow between flat rigid plates, and predict that impact protection for laminates is optimized by using shear-thinning, and not shear-thickening, fluids. The prediction is verified experimentally by measuring the velocity and pressure in impact experiments. Our scaling analysis should be generically applicable for non-Newtonian fluid-solid interactions in diverse applications.</p