Genome organization and interaction with capsid protein in a multipartite RNA virus.

We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a sample consisting exclusively of particles with the same RNA content-specifically, RNAs 3 and 4-assembled in planta by agrobacterium-mediated transient expression. We find that the interior of the particle is nearly empty, with most of the RNA genome situated at the capsid shell. However, this density is disordered in the sense that the RNA is not associated with any particular structure but rather, with an ensemble of secondary/tertiary structures that interact with the capsid protein. Our results illustrate a fundamental difference between the ssRNA organization in the multipartite BMV viral capsid and the monopartite bacteriophages MS2 and Qβ for which a dominant RNA conformation is found inside the assembled viral capsids, with RNA density conserved even at the center of the particle. This can be understood in the context of the differing demands on their respective lifecycles: BMV must package separately each of several different RNA molecules and has been shown to replicate and package them in isolated, membrane-bound, cytoplasmic complexes, whereas the bacteriophages exploit sequence-specific "packaging signals" throughout the viral RNA to package their monopartite genomes

Charge reversal of colloidal particles

A theory is presented for the effective charge of colloidal particles in suspensions containing multivalent counterions. It is shown that if colloids are sufficiently strongly charged, the number of condensed multivalent counterion can exceed the bare colloidal charge leading to charge reversal. Charge renormalization in suspensions with multivalent counterions depends on a subtle interplay between the solvation energies of the multivalent counterions in the bulk and near the colloidal surface. We find that the effective charge is {\it not} a monotonically decreasing function of the multivalent salt concentration. Furthermore, contrary to the previous theories, it is found that except at very low concentrations, monovalent salt hinders the charge reversal. This conclusion is in agreement with the recent experiments and simulations

Bounding sup-norms of cusp forms of large level

Let f be an $L^2$-normalized weight zero Hecke-Maass cusp form of square-free level N, character $\chi$ and Laplacian eigenvalue $\lambda\geq 1/4$. It is shown that $\| f \|_{\infty} \ll_{\lambda} N^{-1/37}$, from which the hybrid bound $\|f \|_{\infty} \ll \lambda^{1/4} (N\lambda)^{-\delta}$ (for some $\delta > 0$) is derived. The first bound holds also for $f = y^{k/2}F$ where F is a holomorphic cusp form of weight k with the implied constant now depending on k.Comment: version 3: substantially revised versio

Torsional fluctuations in columnar DNA assemblies

In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy between neighbouring molecules explicitly depends on their relative azimuthal orientations. For DNA this leads to a rich variety of mesophases for columnar assemblies, each categorized by a specific azimuthal ordering. In a preceding paper [A. Wynveen, D. J. Lee, and A. A. Kornyshev, Eur. Phys. J. E, 16, 303 (2005)] a statistical mechanical theory was developed for the assemblies of torsionally rigid molecues in order to determine how thermal fluctuations influence the structure of these mesophases. Here we extend this theory by including torsional fluctuations of the molecules, where a DNA molecule may twist about its long axis at the cost of torsional elastic energy. Comparing this with the previous study, we find that inclusion of torsional fluctuations further increases the density at which the transition between the hexagonal structure and the predicted rhombic phase occurs and reduces the level of distortion in the rhombic phase. As X-ray diffraction may probe the 2-D lattice structure of such assemblies and provide information concerning the underlying interaction between molecules, we have also calculated correlation functions for the azimuthal ordering which are manifest in an x-ray scattering intensity profiles.Comment: 33 pages, 8 figure

Mass equidistribution of Hilbert modular eigenforms

Let F be a totally real number field, and let f traverse a sequence of non-dihedral holomorphic eigencuspforms on GL(2)/F of weight (k_1,...,k_n), trivial central character and full level. We show that the mass of f equidistributes on the Hilbert modular variety as max(k_1,...,k_n) tends to infinity. Our result answers affirmatively a natural analogue of a conjecture of Rudnick and Sarnak (1994). Our proof generalizes the argument of Holowinsky-Soundararajan (2008) who established the case F = Q. The essential difficulty in doing so is to adapt Holowinsky's bounds for the Weyl periods of the equidistribution problem in terms of manageable shifted convolution sums of Fourier coefficients to the case of a number field with nontrivial unit group.Comment: 40 pages; typos corrected, nearly accepted for

Light scattering spectra of supercooled molecular liquids

The light scattering spectra of molecular liquids are derived within a generalized hydrodynamics. The wave vector and scattering angle dependences are given in the most general case and the change of the spectral features from liquid to solidlike is discussed without phenomenological model assumptions for (general) dielectric systems without long-ranged order. Exact microscopic expressions are derived for the frequency-dependent transport kernels, generalized thermodynamic derivatives and the background spectra.Comment: 12 page

Stripe glasses: self generated randomness in a uniformly frustrated system

We show that a system with competing interactions on different length scales, as relevant for the formation of stripes in doped Mott insulators, undergoes a self-generated glass transition which is caused by the frustrated nature of the interactions and not related to the presence of quenched disorder. An exponentially large number of metastable configurations is found, leading to a slow, landscape dominated long time relaxation and a break up of the system into a disordered inhomogeneous state.Comment: 5 pages, 2 figure