Combined energy -- diffraction data refinement of decagonal AlNiCo

We incorporate realistic pair potential energies directly into a non-linear least-square fit of diffraction data to quantitatively compare structure models with experiment for the Ni-rich $d$(AlNiCo) quasicrystal. The initial structure models are derived from a few {\it a priori} assumptions (gross features of the Patterson function) and the pair potentials. In place of the common hyperspace approach to the structure refinement of quasicrystals, we use a real-space tile decoration scheme, which does not rely on strict quasiperiodicity, and makes it easy to enforce sensible local arrangements of the atoms. Inclusion of the energies provides information complementary to the diffraction data and protects the fit procedure from converging on spurious solutions. The method pinpoints sites which are likely to break the symmetry of their local environment.Comment: 7 pages, 5 figures, proceedings of the Internation Conference on Quasicrystals, Bangalore, India, August 200

Repton model of gel electrophoresis in the long chain limit

Reptation governs motion of long polymers through a confining environment. Slack enters at the ends and diffuses along the polymer as stored length. The rate at which stored length diffuses limits the speed at which the chain can drift. This paper relates the rate of stored length diffusion to the conformation of the tube within which the polymer is confined. In the scaling limit of long polymer chains and weak applied electric fields, holding the product of polymer length times field finite, the tube length and stored length density take on their zero-field values. The drift velocity then depends only on the the polymer's end-to-end separation in the direction of the field.Comment: 14 pages,4 figure

Vitrification of a monatomic 2D simple liquid

A monatomic simple liquid in two dimensions, where atoms interact isotropically through the Lennard-Jones-Gauss potential [M. Engel and H.-R. Trebin, Phys. Rev. Lett. 98, 225505 (2007)], is vitrified by the use of a rapid cooling technique in a molecular dynamics simulation. Transformation to a crystalline state is investigated at various temperatures and the time-temperature-transformation (TTT) curve is determined. It is found that the transformation time to a crystalline state is the shortest at a temerature 14% below the melting temperature Tm and that at temperatures below Tv = 0.6 Tm the transformation time is much longer than the available CPU time. This indicates that a long-lived glassy state is realized for T < Tv.Comment: 5pages,5figures,accepted for publication in CEJ

Clusters, phason elasticity, and entropic stabilisation: a theory perspective

Personal comments are made about the title subjects, including: the relation of Friedel oscillations to Hume-Rothery stabilisation; how calculations may resolve the random-tiling versus ideal pictures of quasicrystals; and the role of entropies apart from tile-configurational.Comment: IOP macros; 8pp, 1 figure. In press, Phil. Mag. A (Proc. Intl. Conf. on Quasicrystals 9, Ames Iowa, May 2005

Total-energy-based prediction of a quasicrystal structure

Quasicrystals are metal alloys whose noncrystallographic symmetry and lack of structural periodicity challenge methods of experimental structure determination. Here we employ quantum-based total-energy calculations to predict the structure of a decagonal quasicrystal from first principles considerations. We employ Monte Carlo simulations, taking as input the knowledge that a decagonal phase occurs in Al-Ni-Co near a given composition, and using a few features of the experimental Patterson function. The resulting structure obeys a nearly deterministic decoration of tiles on a hierarchy of length scales related by powers of $\tau$, the golden mean.Comment: 9 pages, 3 figure

Coarse-grained simulation of transmembrane peptides in the gel phase

We use Dissipative Particle Dynamics simulations, combined with parallel tempering and umbrella sampling, to investigate the potential of mean force between model transmembrane peptides in the various phases of a lipid bilayer, including the low-temperature gel phase. The observed oscillations in the effective interaction between peptides are consistent with the different structures of the surrounding lipid phases