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

Parameter space metric for 3.5 post-Newtonian gravitational-waves from compact binary inspirals

We derive the metric on the parameter space of 3.5 post-Newtonian (3.5PN) stationary phase compact binary inspiral waveforms for a single detector, neglecting spin, eccentricity, and finite-body effects. We demonstrate that this leads to better template placement than the current practice of using the 2PN metric to place 3.5PN templates: The recovered event rate is improved by about 10% at a cost of nearly doubling the number of templates. The cross-correlations between mass parameters are also more accurate, which will result in better coincidence tests.Comment: 10 pages, 7 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.

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