545 research outputs found
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
pancreatic cance
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
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