Density waves theory of the capsid structure of small icosahedral viruses

We apply Landau theory of crystallization to explain and to classify the capsid structures of small viruses with spherical topology and icosahedral symmetry. We develop an explicit method which predicts the positions of centers of mass for the proteins constituting viral capsid shell. Corresponding density distribution function which generates the positions has universal form without any fitting parameter. The theory describes in a uniform way both the structures satisfying the well-known Caspar and Klug geometrical model for capsid construction and those violating it. The quasiequivalence of protein environments in viral capsid and peculiarities of the assembly thermodynamics are also discussed.Comment: 8 pages, 3 figur

Discontinuous Change in the Smectic Layer Thickness in Ferrielectric Liquid Crystals

The temperature dependence of the thickness of thick free-standing films is studied using a high-resolution film thickness measurement technique. A small discontinuity in the temperature dependence of the smectic layer thickness at every phase transition between ferro-, ferri-, and antiferroelectric phases is observed. We show that the major contribution to it arises from a change in the smectic tilt angle

Tate blueshift and vanishing for Real oriented cohomology

Ando, Morava, and Sadofsky showed that the Tate construction for a trivial $\mathbb{Z}/p$-action decreases the chromatic height of Johnson-Wilson theory, and Greenlees and Sadofsky proved that the Tate construction for a trivial finite group action vanishes on Morava K-theory. We prove $C_2$-equivariant enrichments of these results using the parametrized Tate construction. The $C_2$-fixed points of our results produce new blueshift and vanishing results for Real Johnson-Wilson theories $ER(n)$ and Real Morava $K$-theories $KR(n)$, respectively, for all $n$. In particular, our blueshift results generalize Greenlees and May's Tate splitting of $KO$ to all chromatic heights.Comment: 38 pages. Revised exposition and expanded some proofs. Comments welcome

Chiral Quasicrystalline Order and Dodecahedral Geometry in Exceptional Families of Viruses

On the example of exceptional families of viruses we i) show the existence of a completely new type of matter organization in nanoparticles, in which the regions with a chiral pentagonal quasicrystalline order of protein positions are arranged in a structure commensurate with the spherical topology and dodecahedral geometry, ii) generalize the classical theory of quasicrystals (QCs) to explain this organization, and iii) establish the relation between local chiral QC order and nonzero curvature of the dodecahedral capsid faces.Comment: 8 pages, 3 figure

Positional, Reorientational and Bond Orientational Order in DNA Mesophases

We investigate the orientational order of transverse polarization vectors of long, stiff polymer molecules and their coupling to bond orientational and positional order in high density mesophases. Homogeneous ordering of transverse polarization vector promotes distortions in the hexatic phase, whereas inhomogeneous ordering precipitates crystalization of the 2D sections with different orientations of the transverse polarization vector on each molecule in the unit cell. We propose possible scenarios for going from the hexatic phase, through the distorted hexatic phase to the crystalline phase with an orthorhombic unit cell observed experimentally for the case of DNA.Comment: 4 pages, 2 figure

Statistical mechanics of columnar DNA assemblies

Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated pair potential [A. A. Kornyshev and S. Leikin, J. Chem. Phys. 107, 3656 (1997)] -- onto an exotic, unknown variant of the XY model on a fixed or restructurable lattice. Here the role of the 'spin' is played by the azimuthal orientation of the molecules. We have solved this model using a Hartree-Fock approximation, ground state calculations, and finite temperature Monte Carlo simulations. We have found peculiar spin order transitions, which may also be accompanied by positional restructuring, from hexagonal to rhombohedric lattices. Some of these have been experimentally observed in dense columnar aggregates. Note that DNA columnar phases are of great interest in biophysical research, not only because they are a useful in vitro tool for the study of DNA condensation, but also since these structures have been detected in living matter. Within the approximations made, our study provides insight into the statistical mechanics of these systems.Comment: 19 pages, 18 figure

Flexoelectricity and piezoelectricity - reason for rich variety of phases in antiferroelectric liquid crystals

The free energy of antiferroelectric liquid crystal which takes into account polar order explicitly is presented. Steric, van der Waals, piezoelectric and flexoelectric interactions to the nearest layers and dipolar electrostatic interactions to the nearest and to the next nearest layers induce indirect tilt interactions with chiral and achiral properties, which extend to the third and to the fourth nearest layers. Chiral indirect interactions between tilts can be large and induce helicoidal modulations even in systems with negligible chiral van der Waals interactions. If indirect chiral interactions compete with chiral van der Waals interactions, the helix unwinding is possible. Although strength of microscopic interactions change monotonically with decreasing temperature, effective interlayer interactions change nonmonotonically and give rise to nonmonotouous change of modulation period through various phases. Increased enatiomeric excess i.e. increased chirality changes the phase sequence.Comment: 4 pages, 1 figur

Digitral Down Conversion Technology for Tevatron Beam Line Tuner at FNAL

Fermilab is presently in Run II collider operations and is developing instrumentation to improve luminosity. Improving the orbit matching between accelerator components using a Beam Line Tuner (BLT) can improve the luminosity. Digital Down Conversion (DDC) has been proposed as a method for making more accurate beam position measurements. Fermilab has implemented a BLT system using a DDC technique to measure orbit oscillations during injections from the Main Injector to the Tevatron. The output of a fast ADC is downconverted and filtered in software. The system measures the x and y positions, the intensity, and the time of arrival for each proton or antiproton bunch, on a turn-by-turn basis, during the first 1024 turns immediately following injection. We present results showing position, intensity, and time of arrival for both injected and coasting beam. Initial results indicate a position resolution of {approx}20 to 40 microns and a phase resolution of {approx}25 ps

Phase Behavior of Columnar DNA Assemblies

The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is investigated, based on the DNA-DNA electrostatic pair potential that takes into account DNA helical symmetry and the amount and distribution of adsorbed counterions. A phase diagram obtained by lattice sum calculations predicts a variety of positionally and azimuthally ordered phases and bundling transitions strongly depending on the counterion adsorption patterns.Comment: 4 pages, 3 figures, submitted to PR

Phase Behavior of Bent-Core Molecules

Recently, a new class of smectic liquid crystal phases (SmCP phases) characterized by the spontaneous formation of macroscopic chiral domains from achiral bent-core molecules has been discovered. We have carried out Monte Carlo simulations of a minimal hard spherocylinder dimer model to investigate the role of excluded volume interations in determining the phase behavior of bent-core materials and to probe the molecular origins of polar and chiral symmetry breaking. We present the phase diagram as a function of pressure or density and dimer opening angle $\psi$. With decreasing $\psi$, a transition from a nonpolar to a polar smectic phase is observed near $\psi = 167^{\circ}$, and the nematic phase becomes thermodynamically unstable for $\psi < 135^{\circ}$. No chiral smectic or biaxial nematic phases were found.Comment: 4 pages Revtex, 3 eps figures (included