An Analytical Approach to the Protein Designability Problem

We present an analytical method for determining the designability of protein structures. We apply our method to the case of two-dimensional lattice structures, and give a systematic solution for the spectrum of any structure. Using this spectrum, the designability of a structure can be estimated. We outline a heirarchy of structures, from most to least designable, and show that this heirarchy depends on the potential that is used.Comment: 16 pages 4 figure

Experimental demonstration of a squeezing enhanced power recycled Michelson interferometer for gravitational wave detection

Interferometric gravitational wave detectors are expected to be limited by shot noise at some frequencies. We experimentally demonstrate that a power recycled Michelson with squeezed light injected into the dark port can overcome this limit. An improvement in the signal-to-noise ratio of 2.3dB is measured and locked stably for long periods of time. The configuration, control and signal readout of our experiment are compatible with current gravitational wave detector designs. We consider the application of our system to long baseline interferometer designs such as LIGO.Comment: 4 pages 4 figure

Unconditional Continuous Variable Dense Coding

We investigate the conditions under which unconditional dense coding can be achieved using continuous variable entanglement. We consider the effect of entanglement impurity and detector efficiency and discuss experimental verification. We conclude that the requirements for a strong demonstration are not as stringent as previously thought and are within the reach of present technology

PHD3 regulates differentiation, tumour growth and angiogenesis in pancreatic cancer

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Geometric and Statistical Properties of the Mean-Field HP Model, the LS Model and Real Protein Sequences

Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a relatively small number of about 500 topological classes of conformations. Here it is shown that on a lattice the most highly designable simulated protein structures are those that have the largest number of surface-core switchbacks. A combination of physical, mathematical and biological reasons that causes the phenomenon is given. By comparing the most foldable model peptides with protein sequences in the Protein Data Bank, it is shown that whereas different models may yield similar designabilities, predicted foldable peptides will simulate natural proteins only when the model incorporates the correct physics and biology, in this case if the main folding force arises from the differing hydrophobicity of the residues, but does not originate, say, from the steric hindrance effect caused by the differing sizes of the residues.Comment: 12 pages, 10 figure

Mean-Field HP Model, Designability and Alpha-Helices in Protein Structures

Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground states. Global comparison of model (binary) peptide sequences with concatenated (binary) protein sequences listed in the Protein Data Bank and the Dali Domain Dictionary indicates that the highest correlation occurs between model peptides choosing the favored structures and those portions of protein sequences containing alpha-helices.Comment: 4 pages, 2 figure

Balanced Homodyne Detection of Optical Quantum States at Audio-Band Frequencies and Below

The advent of stable, highly squeezed states of light has generated great interest in the gravitational wave community as a means for improving the quantumnoise- limited performance of advanced interferometric detectors. To confidently measure these squeezed states, it is first necessary to measure the shot-noise across the frequency band of interest. Technical noise, such as non-stationary events, beam pointing, and parasitic interference, can corrupt shot-noise measurements at low Fourier frequencies, below tens of kilo-Hertz. In this paper we present a qualitative investigation into all of the relevant noise sources and the methods by which they can be identified and mitigated in order to achieve quantum noise limited balanced homodyne detection. Using these techniques, flat shot-noise down to Fourier frequencies below 0.5 Hz is produced. This enables the direct observation of large magnitudes of squeezing across the entire audio-band, of particular interest for ground-based interferometric gravitational wave detectors. 11.6 dB of shot-noise suppression is directly observed, with more than 10 dB down to 10 Hz.Comment: 16 pages, 11 figure

The unusual pulsation spectrum of the cool ZZ Ceti star HS 0507+0434B

We present the analysis of one week of single-site high-speed CCD photometric observations of the cool ZZ Ceti star HS 0507+0434B. Ten independent frequencies are detected in the star's light variations: one singlet and three nearly-equally spaced triplets. We argue that these triplets are due to rotationally split modes of spherical degree l=1. This is the first detection of consistent multiplet structure in the amplitude spectrum of a cool ZZ Ceti star and it allows us to determine the star's rotation period: 1.70 +/- 0.11 d. We report exactly equal frequency, not period, spacings between the detected mode groups. In addition, certain pairs of modes from the four principal groups have frequency ratios which are very close to 3:4 or 4:5; while these ratios are nearly exact (within one part in 10^4), they still lie outside the computed error bars. We speculate that these relationships between different frequencies could be caused by resonances. One of the three triplets may not be constant in amplitude and/or frequency. We compare our frequency solution for the combination frequencies (of which we detected 38) to Wu's (1998, 2001) model thereof. We obtain consistent results when trying to infer the star's convective thermal time and the inclination angle of its rotational axis. Theoretical combination-frequency amplitude spectra also resemble those of the observations well, and direct theoretical predictions of the observed second-order light-curve distortions were also reasonably successful assuming the three triplets are due to l=1 modes. Attempts to reproduce the observed combination frequencies adopting all possible l=2 identifications for the triplets did not provide similarly consistent results, supporting their identification with l=1.Comment: Accepted for publication in MNRAS; 12 pages, 8 figure

Designing sequential transcription logic: a simple genetic circuit for conditional memory

The ability to learn and respond to recurrent events depends on the capacity to remember transient biological signals received in the past. Moreover, it may be desirable to remember or ignore these transient signals conditioned upon other signals that are active at specific points in time or in unique environments. Here, we propose a simple genetic circuit in bacteria that is capable of conditionally memorizing a signal in the form of a transcription factor concentration. The circuit behaves similarly to a "data latch" in an electronic circuit, i.e. it reads and stores an input signal only when conditioned to do so by a "read command". Our circuit is of the same size as the well-known genetic toggle switch (an unconditional latch) which consists of two mutually repressing genes, but is complemented with a "regulatory front end" involving protein heterodimerization as a simple way to implement conditional control. Deterministic and stochastic analysis of the circuit dynamics indicate that an experimental implementation is feasible based on well-characterized genes and proteins. It is not known, to which extent molecular networks are able to conditionally store information in natural contexts for bacteria. However, our results suggest that such sequential logic elements may be readily implemented by cells through the combination of existing protein-protein interactions and simple transcriptional regulation.Comment: 20 pages, 5 figures; supplementary material available upon request from the author

Multi-Periodic Oscillations in Cepheids and RR Lyrae-Type Stars

Classical Cepheids and RR Lyrae-type stars are usually considered to be textbook examples of purely radial, strictly periodic pulsators. Not all the variables, however, conform to this simple picture. In this review I discuss different forms of multi-periodicity observed in Cepheids and RR Lyrae stars, including Blazhko effect and various types of radial and nonradial multi-mode oscillations.Comment: Proceedings of the 20th Stellar Pulsation Conference Series: "Impact of new instrumentation & new insights in stellar pulsations", 5-9 September 2011, Granada, Spai