36,369 research outputs found
Long-term power-law fluctuation in Internet traffic
Power-law fluctuation in observed Internet packet flow are discussed. The
data is obtained by a multi router traffic grapher (MRTG) system for 9 months.
The internet packet flow is analyzed using the detrended fluctuation analysis.
By extracting the average daily trend, the data shows clear power-law
fluctuations. The exponents of the fluctuation for the incoming and outgoing
flow are almost unity. Internet traffic can be understood as a daily periodic
flow with power-law fluctuations.Comment: 10 pages, 8 figure
Phylogenetic differences in content and intensity of periodic proteins
Many proteins exhibit sequence periodicity, often correlated with a visible structural periodicity. The statistical significance of such periodicity can be assessed by means of a chi-square-based test, with significance thresholds being calculated from shuffled sequences. Comparison of the complete proteomes of 45 species reveals striking differences in the proportion of periodic proteins and the intensity of the most significant periodicities. Eukaryotes tend to have a higher proportion of periodic proteins than eubacteria, which in turn tend to have more than archaea. The intensity of periodicity in the most periodic proteins is also greatest in eukaryotes. By contrast, the relatively small group of periodic proteins in archaea also tend to be weakly periodic compared to those of eukaryotes and eubacteria. Exceptions to this general rule are found in those prokaryotes with multicellular life-cycle phases, e.g. Methanosarcina sps. or Anabaena sps., which have more periodicities than prokaryotes in general, and in unicellular eukaryotes, which have fewer than multicellular eukaryotes. The distribution of significantly periodic proteins in eukaryotes is over a wide range of period lengths, whereas prokaryotic proteins typically have a more limited set of period lengths. This is further investigated by repeating the analysis on the NRL-3D database of proteins of solved structure. Some short range periodicities are explicable in terms of basic secondary structure, e.g. alpha helices, while middle range periodicities are frequently found to consist of known short Pfam domains, e.g. leucine-rich repeats, tetratricopeptides or armadillo domains. However, not all can be explained in this way
The Bacterial Photosynthetic Reaction Center as a Model for Membrane Proteins
Membrane proteins participate in many fundamental cellular processes. Until recently, an understanding of the function and properties of membrane proteins was hampered by an absence of structural information at the atomic level. A landmark achievement toward understanding the structure of membrane proteins was the crystallization (1) and structure determination (2-5) the photosynthetic reaction center (RC) from the purple bacteria Rhodopseudomonas viridis, followed by that of the RC from Rhodobacter sphaeroides (6-17). The RC is an integral membrane protein-pigment complex, which carries out the initial steps of photosynthesis (reviewed in 18). RCs from the purple bacteria Rps. viridis and Rb. sphaeroides are composed of three membrane-associated protein subunits (designated L, M, and H), and the following cofactors: four bacteriochlorophylls (Bchl or B), two bacteriopheophytins (Bphe or [phi]), two quinones, and a nonheme iron. The cofactors are organized into two symmetrical branches that are approximately related by a twofold rotation axis (2, 8). A central feature of the structural organization of the RC is the presence of 11 hydrophobic [alpha]-helixes, approximately 20-30 residues long, which are believed to represent the membrane-spanning portion of the RC (3, 9). Five membrane-spanning helixes are present in both the L and M subunits, while a single helix is in the H subunit. The folding of the L and M subunits is similar, consistent with significant sequence similarity between the two chains (19-25). The L and M subunits are approximately related by the same twofold rotation axis that relates the two cofactor branches.
RCs are the first membrane proteins to be described at atomic resolution; consequently they provide an important model for discussing the folding of membrane proteins. The structure demonstrates that [alpha]-helical structures may be adopted by integral membrane proteins, and provides confirmation of the utility of hydropathy plots in identifying nonpolar membrane-spanning regions from sequence data. An important distinction between the folding environments of water-soluble proteins and membrane proteins is the large difference in water concentration surrounding the proteins. As a result, hydrophobic interactions (26) play very different roles in stabilizing the tertiary structures of these two classes of proteins; this has important structural consequences. There is a striking difference in surface polarity of membrane and water-soluble proteins. However, the characteristic atomic packing and surface area appear quite similar.
A computational method is described for defining the position of the RC in the membrane (10). After localization of the RC structure in the membrane, surface residues in contact with the lipid bilayer were identified. As has been found for soluble globular proteins, surface residues are less well conserved in homologous membrane proteins than the buried, interior residues. Methods based on the variability of residues between homologous proteins are described (13); they are useful (a) in defining surface helical regions of membrane and water-soluble proteins and (b) in assigning the side of these helixes that are exposed to the solvent. A unifying view of protein structure suggests that water-soluble proteins may be considered as modified membrane proteins with covalently attached polar groups that solubilize the proteins in aqueous solution
The Periodic Spectroscopic Variability of FU Orionis
FU Orionis systems are young stars undergoing outbursts of disc accretion and
where the optical spectrum contains lines associated with both the disc
photosphere and a wind component. Previous observations of the prototype FU
Orionis have suggested that the wind lines and the photospheric lines are
modulated with periods of 14.54 and 3.54 days respectively (Herbig et al.
2003). We have re-observed the system at higher spectral resolution, by
monitoring variations of optical line profiles over 21 nights in 2007 and have
found periods of 13.48 and 3.6 days in the wind and disc components consistent
with the above: this implies variability mechanisms that are stable over at
least a decade. In addition we have found: i) that the variations in the
photospheric absorption lines are confined to the blue wing of the line (around
-9km/s): we tentatively ascribe this to an orbiting hotspot in the disc which
is obscured by a disc warp during its receding phase. ii) The wind period is
manifested not only in blue-shifted Halpha absorption, but also in red-shifted
emission of Halpha and Hbeta, as well as in blue-shifted absorption of Na I D,
Li I and Fe II. iii) We find that the periodic modulation of blue-shifted
Halpha absorption at around -100km/s, is phase lagged with respect to
variations in the other lines by ~1.8days. This is consistent with a picture in
which variations at the wind base first affect chromospheric emission and then
low velocity blue-shifted absorption, followed - after a lag equal to the
propagation time of disturbances across the wind's acceleration region - by a
response in high velocity blue-shifted absorption. Such arguments constrain the
size of the acceleration region to ~10^12cm. We discuss possible mechanisms for
periodic variations within the innermost 0.1AU of the disc, including the
possibility that these variations indicate the presence of an embedded hot
Jupiter.Comment: 20 pages, 23 figures. Accepted for publication in MNRAS. See
http://www.ast.cam.ac.uk/~slp65/FUOripaperHRes.pdf for a pdf version of the
paper with high-resolution images; footnote added to the titl
Evaluation of nucleosome forming potentials (NFPs) of forensically important STRs
Degraded forensic samples have proved difficult to analyze and interpret. New analysis techniques are constantly being discovered and improved but researchers have overlooked the structural properties that could prevent or slow the process of degradation. In theory, DNA that are bound to histones as nucleosomes are less prone to degradation, because nucleosomes prevent DNA from being exposed to degradative enzymes. In this study we determined the probability of 60 forensic DNA markers to be bound to histones based on their base sequence composition. Two web-based tools - NXSensor and nuScore - were used to analyze four hundred base pairs surrounding each DNA marker for properties that inhibit or promote the binding of DNA to histones. Our results showed that the majority of markers analyzed were likely to be bound as nucleosomes. Selection of the markers that are more protected to form a multiplex could increase the chance of obtaining a better balanced, easier to interpret DNA profile from degraded sample
Diffuse LEED intensities of disordered crystal surfaces : IV. Application of the disorder theory
The principles of the statistical disorder theory are discussed briefly. The theory is applied to a model of the disordered (101)Au surface with the characteristic (1 × 2) supersstructure. A fit procedure is described, by which the experimental angular intensity profiles are used directly to determine the disorder parameters and the interaction energies between the chains of surface atoms
Examining Periodic Solar Wind Density Structures Observed in the SECCHI Heliospheric Imagers
We present an analysis of small-scale, periodic, solar-wind density
enhancements (length-scales as small as \approx 1000 Mm) observed in images
from the Heliospheric Imager (HI) aboard STEREO A. We discuss their possible
relationship to periodic fluctuations of the proton density that have been
identified at 1 AU using in-situ plasma measurements. Specifically, Viall,
Kepko, and Spence (2008) examined 11 years of in-situ solar-wind density
measurements at 1 AU and demonstrated that not only turbulent structures, but
also non-turbulent periodic density structures exist in the solar wind with
scale sizes of hundreds to one thousand Mm. In a subsequent paper, Viall,
Spence, and Kasper (2009) analyzed the {\alpha} to proton solar-wind abundance
ratio measured during one such event of periodic density structures,
demonstrating that the plasma behavior was highly suggestive that either
temporally or spatially varying coronal source plasma created those density
structures. Large periodic density structures observed at 1 AU, which were
generated in the corona, can be observable in coronal and heliospheric
white-light images if they possess sufficiently high density contrast. Indeed,
we identify such periodic density structures as they enter the HI field of view
and follow them as they advect with the solar wind through the images. The
smaller periodic density structures that we identify in the images are
comparable in size to the larger structures analyzed in-situ at 1 AU, yielding
further evidence that periodic density enhancements are a consequence of
coronal activity as the solar wind is formed.Comment: 15 pages, 12 figures. The final publication is available at
http://www.springerlink.co
Information decomposition of symbolic sequences
We developed a non-parametric method of Information Decomposition (ID) of a
content of any symbolical sequence. The method is based on the calculation of
Shannon mutual information between analyzed and artificial symbolical
sequences, and allows the revealing of latent periodicity in any symbolical
sequence. We show the stability of the ID method in the case of a large number
of random letter changes in an analyzed symbolic sequence. We demonstrate the
possibilities of the method, analyzing both poems, and DNA and protein
sequences. In DNA and protein sequences we show the existence of many DNA and
amino acid sequences with different types and lengths of latent periodicity.
The possible origin of latent periodicity for different symbolical sequences is
discussed.Comment: 18 pages, 8 figure
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