Decoherence of the Superconducting Persistent Current Qubit

Decoherence of a solid state based qubit can be caused by coupling to microscopic degrees of freedom in the solid. We lay out a simple theory and use it to estimate decoherence for a recently proposed superconducting persistent current design. All considered sources of decoherence are found to be quite weak, leading to a high quality factor for this qubit.Comment: 10 pages, 1 figure, Latex/revtex.To appear in proceedings of the NATO-ASI on "Quantum Mesoscopic Phenomena and Mesoscopic Devices in Microelectronics"; Corrections were made on Oct. 29th, 199

Simulations of Two-Dimensional Melting on the Surface of a Sphere

We have simulated a system of classical particles confined on the surface of a sphere interacting with a repulsive $r^{-12}$ potential. The same system simulated on a plane with periodic boundary conditions has van der Waals loops in pressure-density plots which are usually interpreted as evidence for a first order melting transition, but on the sphere such loops are absent. We also investigated the structure factor and from the width of the first peak as a function of density we can show that the growth of the correlation length is consistent with KTHNY theory. This suggests that simulations of two dimensional melting phenomena are best performed on the surface of a sphere.Comment: 4 eps figure

Simulation studies of a phenomenological model for elongated virus capsid formation

We study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation approach combines the traditional Monte Carlo method with a modified method of random sampling on an ellipsoidal surface and a convex hull searching algorithm. Using this approach we identify the minimum physical requirements for non-icosahedral, elongated virus capsids, such as two aberrant flock house virus (FHV) particles and the prolate prohead of bacteriophage $\phi_{29}$, and discuss the implication of our simulation results in the context of recent experimental findings. Our predicted structures may also be experimentally realized by evaporation-driven assembly of colloidal spheres

Anomalous coupling between topological defects and curvature

We investigate a counterintuitive geometric interaction between defects and curvature in thin layers of superfluids, superconductors and liquid crystals deposited on curved surfaces. Each defect feels a geometric potential whose functional form is determined only by the shape of the surface, but whose sign and strength depend on the transformation properties of the order parameter. For superfluids and superconductors, the strength of this interaction is proportional to the square of the charge and causes all defects to be repelled (attracted) by regions of positive (negative) Gaussian curvature. For liquid crystals in the one elastic constant approximation, charges between 0 and $4\pi$ are attracted by regions of positive curvature while all other charges are repelled.Comment: 5 pages, 4 figures, minor changes, accepted for publication in Phys. Rev. Let

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

Crystalline Order on a Sphere and the Generalized Thomson Problem

We attack generalized Thomson problems with a continuum formalism which exploits a universal long range interaction between defects depending on the Young modulus of the underlying lattice. Our predictions for the ground state energy agree with simulations of long range power law interactions of the form 1/r^{gamma} (0 < gamma < 2) to four significant digits. The regime of grain boundaries is studied in the context of tilted crystalline order and the generality of our approach is illustrated with new results for square tilings on the sphere.Comment: 4 pages, 5 eps figures Fig. 2 revised, improved Fig. 3, reference typo fixe

Self-assembly, modularity and physical complexity

We present a quantitative measure of physical complexity, based on the amount of information required to build a given physical structure through self-assembly. Our procedure can be adapted to any given geometry, and thus to any given type of physical system. We illustrate our approach using self-assembling polyominoes, and demonstrate the breadth of its potential applications by quantifying the physical complexity of molecules and protein complexes. This measure is particularly well suited for the detection of symmetry and modularity in the underlying structure, and allows for a quantitative definition of structural modularity. Furthermore we use our approach to show that symmetric and modular structures are favoured in biological self-assembly, for example of protein complexes. Lastly, we also introduce the notions of joint, mutual and conditional complexity, which provide a useful distance measure between physical structures.Comment: 9 pages, submitted for publicatio

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