Structure and dynamics of topological defects in a glassy liquid on a negatively curved manifold

We study the low-temperature regime of an atomic liquid on the hyperbolic plane by means of molecular dynamics simulation and we compare the results to a continuum theory of defects in a negatively curved hexagonal background. In agreement with the theory and previous results on positively curved (spherical) surfaces, we find that the atomic configurations consist of isolated defect structures, dubbed "grain boundary scars", that form around an irreducible density of curvature-induced disclinations in an otherwise hexagonal background. We investigate the structure and the dynamics of these grain boundary scars

Critical parameters for efficient sonication and improved chromatin immunoprecipitation of high molecular weight proteins

Solubilization of cross-linked cells followed by chromatin shearing is essential for successful chromatin immunoprecipitation (ChIP). However, this task, typically accomplished by ultrasound treatment, may often become a pitfall of the process, due to inconsistent results obtained between different experiments under seemingly identical conditions. To address this issue we systematically studied ultrasound-mediated cell lysis and chromatin shearing, identified critical parameters of the process and formulated a generic strategy for rational optimization of ultrasound treatment. We also demonstrated that whereas ultrasound treatment required to shear chromatin to within a range of 100–400 bp typically degrades large proteins, a combination of brief sonication and benzonase digestion allows for the generation of similarly sized chromatin fragments while preserving the integrity of associated proteins. This approach should drastically improve ChIP efficiency for this class of proteins

Free Energies of Isolated 5- and 7-fold Disclinations in Hexatic Membranes

We examine the shapes and energies of 5- and 7-fold disclinations in low-temperature hexatic membranes. These defects buckle at different values of the ratio of the bending rigidity, $\kappa$, to the hexatic stiffness constant, $K_A$, suggesting {\em two} distinct Kosterlitz-Thouless defect proliferation temperatures. Seven-fold disclinations are studied in detail numerically for arbitrary $\kappa/K_A$. We argue that thermal fluctuations always drive $\kappa/K_A$ into an ``unbuckled'' regime at long wavelengths, so that disclinations should, in fact, proliferate at the {\em same} critical temperature. We show analytically that both types of defects have power law shapes with continuously variable exponents in the ``unbuckled'' regime. Thermal fluctuations then lock in specific power laws at long wavelengths, which we calculate for 5- and 7-fold defects at low temperatures.Comment: LaTeX format. 17 pages. To appear in Phys. Rev.

Localization transitions in non-Hermitian quantum mechanics

We study the localization transitions which arise in both one and two dimensions when quantum mechanical particles described by a random Schr\"odinger equation are subjected to a constant imaginary vector potential. A path-integral formulation relates the transition to flux lines depinned from columnar defects by a transverse magnetic field in superconductors. The theory predicts that the transverse Meissner effect is accompanied by stretched exponential relaxation of the field into the bulk and a diverging penetration depth at the transition.Comment: 4 pages (latex) with 3 figures (epsf) embedded in the text using the style file epsf.st

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

A tool to aid redesign of flexible transport services to increase efficiency in rural transport service provision

This research was supported by the Research Councils UK Digital Economy programme award (reference: EP/G066051/1) to the dot.rural Digital Economy Hub, at the University of Aberdeen.Peer reviewedPublisher PD

Thermodynamics and the Global Optimization of Lennard-Jones clusters

Theoretical design of global optimization algorithms can profitably utilize recent statistical mechanical treatments of potential energy surfaces (PES's). Here we analyze the basin-hopping algorithm to explain its success in locating the global minima of Lennard-Jones (LJ) clusters, even those such as \LJ{38} for which the PES has a multiple-funnel topography, where trapping in local minima with different morphologies is expected. We find that a key factor in overcoming trapping is the transformation applied to the PES which broadens the thermodynamic transitions. The global minimum then has a significant probability of occupation at temperatures where the free energy barriers between funnels are surmountable.Comment: 13 pages, 13 figures, revte

The double-funnel energy landscape of the 38-atom Lennard-Jones cluster

The 38-atom Lennard-Jones cluster has a paradigmatic double-funnel energy landscape. One funnel ends in the global minimum, a face-centred-cubic (fcc) truncated octahedron. At the bottom of the other funnel is the second lowest energy minimum which is an incomplete Mackay icosahedron. We characterize the energy landscape in two ways. Firstly, from a large sample of minima and transition states we construct a disconnectivity tree showing which minima are connected below certain energy thresholds. Secondly we compute the free energy as a function of a bond-order parameter. The free energy profile has two minima, one which corresponds to the fcc funnel and the other which at low temperature corresponds to the icosahedral funnel and at higher temperatures to the liquid-like state. These two approaches show that the greater width of the icosahedral funnel, and the greater structural similarity between the icosahedral structures and those associated with the liquid-like state, are the cause of the smaller free energy barrier for entering the icosahedral funnel from the liquid-like state and therefore of the cluster's preferential entry into this funnel on relaxation down the energy landscape. Furthermore, the large free energy barrier between the fcc and icosahedral funnels, which is energetic in origin, causes the cluster to be trapped in one of the funnels at low temperature. These results explain in detail the link between the double-funnel energy landscape and the difficulty of global optimization for this cluster.Comment: 12 pages, 11 figures, revte