Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer

A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters shift and tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general.Comment: 45 pages, 20 figures, published, added Supplementary informatio

Maximum Entropy Estimation of the Galactic Bulge Morphology via the VVV Red Clump

The abundance and narrow magnitude dispersion of Red Clump (RC) stars make them a popular candidate for mapping the morphology of the bulge region of the Milky Way. Using an estimate of the RC's intrinsic luminosity function, we extracted the three-dimensional density distribution of the RC from deep photometric catalogues of the VISTA Variables in the Via Lactea (VVV) survey. We used maximum entropy based deconvolution to extract the spatial distribution of the bulge from Ks-band star counts. We obtained our extrapolated non-parametric model of the bulge over the inner 40 by 40 degrees squared region of the Galactic centre. Our reconstruction also naturally matches onto a parametric fit to the bulge outside the VVV region and inpaints overcrowded and high extinction regions. We found a range of bulge properties consistent with other recent investigations based on the VVV data. In particular, we estimated the bulge mass to be in the range 13 to 17 billion solar masses, the X-component to be between 18% and 25% of the bulge mass, and the bulge angle with respect to the Sun-Galactic centre line to be between 18 and 32 degrees. Studies of the Fermi Large Area Telescope (LAT) gamma-ray Galactic centre excess suggests that the excess may be traced by Galactic bulge distributed sources. We applied our deconvolved density in a template fitting analysis of this Fermi-LAT GeV excess and found an improvement in the fit compared to previous parametric based templates.Comment: 25 pages, 27 figures, minor typo correcte

On higher genus Weierstrass sigma-function

The goal of this paper is to propose a new way to generalize the Weierstrass sigma-function to higher genus Riemann surfaces. Our definition of the odd higher genus sigma-function is based on a generalization of the classical representation of the elliptic sigma-function via Jacobi theta-function. Namely, the odd higher genus sigma-function $\sigma_{\chi}(u)$ (for u\in \C^g) is defined as a product of the theta-function with odd half-integer characteristic $\beta^{\chi}$, associated with a spin line bundle $\chi$, an exponent of a certain bilinear form, the determinant of a period matrix and a power of the product of all even theta-constants which are non-vanishing on a given Riemann surface. We also define an even sigma-function corresponding to an arbitrary even spin structure. Even sigma-functions are constructed as a straightforward analog of a classical formula relating even and odd sigma-functions. In higher genus the even sigma-functions are well-defined on the moduli space of Riemann surfaces outside of a subspace defined by vanishing of the corresponding even theta-constant.Comment: to be published in Physica

Evolution of London penetration depth with scattering in single crystals of K1−x_{1-x}Nax_xFe2_2As2_2

London penetration depth, $\lambda (T)$, was measured in single crystals of K$_{1-x}$Na$_x$Fe$_2$As$_2$, $x$=0 and 0.07, down to temperatures of 50~mK, $\sim T_c/50$. Isovalent substitution of Na for K significantly increases impurity scattering, with $\rho(T_c)$ rising from 0.2 to 2.2 $\mu \Omega$cm, and leads to a suppression of $T_c$ from 3.5~K to 2.8~K. At the same time, a close to $T$-linear $\Delta \lambda (T)$ in pure samples changes to almost $T^2$ in the substituted samples. The behavior never becomes exponential as expected for the accidental nodes, as opposed to $T^2$ dependence in superconductors with symmetry imposed line nodes. The superfluid density in the full temperature range follows a simple clean and dirty $d$-wave dependence, for pure and substituted samples, respectively. This result contradicts suggestions of multi-band scenarios with strongly different gap structure on four sheets of the Fermi surface