Charged Black Hole in a Canonical Ensemble

We consider the thermodynamics of a charged black hole enclosed in a cavity. The charge in the cavity and the temperature at the walls are fixed so that we have a canonical ensemble. We derive the phase structure and stability of black hole equilibrium states. We compare our results to that of other work which uses asymptotically anti-de Sitter boundary conditions to define the thermodynamics. The thermodynamic properties have extensive similarities which suggest that the idea of AdS holography is more dependent on the existence of the boundary than on the exact details of asymptotically AdS metrics.Comment: 9 pages; 4 multipart figure

Genetics and genetic tools in coral reef management 2011

This report forms a synthesis of current knowledge and future applications of genetics in coral reef management. It is divided up into three parts, (1) the coral host, (2) the Symbiodinium, and (3) other coral associated microbes. Within each of these parts current knowledge is summarised and examples are provided to illustrate how this knowledge may be applicable to the management of the Great Barrier Reef. The synthesis ends with a summary of how it is all linked together and possible future developments, uses and risks associated with the use of genetics in coral reef management. Words in dark blue with a dotted underline are part of the glossary, which can be found at the end of the document

On correlation between protein secondary structure, backbone bond angles, and side-chain orientations

We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to analyze high resolution X-ray structures in Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse grained energy function to describe the ensuing side-chain geometry in terms of the C$_\beta$ carbon orientations. The energy function can model the side-chain geometry with a sub-atomic precision. As an example we construct the C$_\alpha$-C$_\beta$ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 \.A in root-mean-square distance from the experimental X-ray structure

Two-Dimensional Flow Nanometry of Biological Nanoparticles for Accurate Determination of Their Size and Emission Intensity

Biological nanoparticles (BNPs) are of high interest due to their key role in various biological processes and use as biomarkers. BNP size and molecular composition are decisive for their functions, but simultaneous determination of both properties with high accuracy remains challenging, which is a severe limitation. Surface-sensitive microscopy allows one to precisely determine fluorescence or scattering intensity, but not the size of individual BNPs. The latter is better determined by tracking their random motion in bulk, but the limited illumination volume for tracking this motion impedes reliable intensity determination. We here show that attaching BNPs (specifically, vesicles and functionalized gold NPs) to a supported lipid bilayer, subjecting them to a hydrodynamic flow, and tracking their motion via surface-sensitive imaging enable to determine their diffusion coefficients and flow-induced drift velocities and to accurately quantify both BNP size and emission intensity. For vesicles, the high accuracy is demonstrated by resolving the expected radius-squared dependence of their fluorescence intensity.Comment: 28 pages, 5 figure

Elastic Energy and Phase Structure in a Continuous Spin Ising Chain with Applications to the Protein Folding Problem

We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three known nontrivial phases of polymers: At low temperatures the model is in a collapsed phase, at medium temperatures it is in a random walk phase, and at high temperatures it enters the self-avoiding random walk phase. By investigating the temperature dependence of the specific energy we confirm that the transition between the collapsed phase and the random walk phase is a phase transition, while the random walk phase and self-avoiding random walk phase are separated from each other by a cross-over transition. We also compare the predictions of the model to a phenomenological elastic energy formula, proposed by Huang and Lei to describe folded proteins.Comment: 12 pages, 23 figures, RevTeX 4.

Memory and rejuvenation in a spin glass

The temperature dependence of the magnetisation of a Cu(Mn) spin glass ($T_g$ $\approx$ 57 K) has been investigated using weak probing magnetic fields ($H$ = 0.5 or 0 Oe) and specific thermal protocols. The behaviour of the zero-field cooled, thermoremanent and isothermal remanent magnetisation on (re-)cooling the system from a temperature (40 K) where the system has been aged is investigated. It is observed that the measured magnetisation is formed by two parts: (i) a temperature- and observation time-dependent thermally activated relaxational part governed by the age- and temperature-dependent response function and the (latest) field change made at a lower temperature, superposed on (ii) a weakly temperature-dependent frozen-in part. Interestingly we observe that the spin configuration that is imprinted during an elongated halt in the cooling, if it is accompanied by a field induced magnetisation, also includes a unidirectional excess magnetisation that is recovered on returning to the ageing temperature.Comment: EPL style; 7 pages, 5 figure