895 research outputs found
Jet engine powers large, high-temperature wind tunnel
Wind tunnel for large component testing uses a jet engine with afterburner to provide high temperatures /1200 degrees to 2000 degrees F/ and controlled high velocity gas. This economical wind tunnel can accommodate parts ten feet by ten feet or larger, and is a useful technique for qualitative information
Pulsation period variations in the RRc Lyrae star KIC 5520878
Learned et. al. proposed that a sufficiently advanced extra-terrestrial
civilization may tickle Cepheid and RR Lyrae variable stars with a neutrino
beam at the right time, thus causing them to trigger early and jogging the
otherwise very regular phase of their expansion and contraction. This would
turn these stars into beacons to transmit information throughout the galaxy and
beyond. The idea is to search for signs of phase modulation (in the regime of
short pulse duration) and patterns, which could be indicative of intentional,
omnidirectional signaling.
We have performed such a search among variable stars using photometric data
from the Kepler space telescope. In the RRc Lyrae star KIC 5520878, we have
found two such regimes of long and short pulse durations. The sequence of
period lengths, expressed as time series data, is strongly auto correlated,
with correlation coefficients of prime numbers being significantly higher
(\%). Our analysis of this candidate star shows that the prime number
oddity originates from two simultaneous pulsation periods and is likely of
natural origin.
Simple physical models elucidate the frequency content and asymmetries of the
KIC 5520878 light curve.
Despite this SETI null result, we encourage testing other archival and future
time-series photometry for signs of modulated stars. This can be done as a
by-product to the standard analysis, and even partly automated.Comment: Accepted for publication in ApJ. 49 pages, 16 figure
Nonlinear Mechanical Response of DNA due to Anisotropic Bending Elasticity
The response of a short DNA segment to bending is studied, taking into
account the anisotropy in the bending rigidities caused by the double-helical
structure. It is shown that the anisotropy introduces an effective nonlinear
twist-bend coupling that can lead to the formation of kinks and modulations in
the curvature and/or in the twist, depending on the values of the elastic
constants and the imposed deflection angle. The typical wavelength for the
modulations, or the distance between the neighboring kinks is found to be set
by half of the DNA pitch.Comment: 4 pages, 3 encapsulated EPS figure
Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA
We present a method to calculate the propensities of regions within a DNA molecule to transition from B-form to Z-form under negative superhelical stresses. We use statistical mechanics to analyze the competition that occurs among all susceptible Z-forming regions at thermodynamic equilibrium in a superhelically stressed DNA of specified sequence. This method, which we call SIBZ, is similar to the SIDD algorithm that was previously developed to analyze superhelical duplex destabilization. A state of the system is determined by assigning to each base pair either the B- or the Z-conformation, accounting for the dinucleotide repeat unit of Z-DNA. The free energy of a state is comprised of the nucleation energy, the sequence-dependent B-Z transition energy, and the energy associated with the residual superhelicity remaining after the change of twist due to transition. Using this information, SIBZ calculates the equilibrium B-Z transition probability of each base pair in the sequence. This can be done at any physiologically reasonable level of negative superhelicity. We use SIBZ to analyze a variety of representative genomic DNA sequences. We show that the dominant Z-DNA forming regions in a sequence can compete in highly complex ways as the superhelicity level changes. Despite having no tunable parameters, the predictions of SIBZ agree precisely with experimental results, both for the onset of transition in plasmids containing introduced Z-forming sequences and for the locations of Z-forming regions in genomic sequences. We calculate the transition profiles of 5 kb regions taken from each of 12,841 mouse genes and centered on the transcription start site (TSS). We find a substantial increase in the frequency of Z-forming regions immediately upstream from the TSS. The approach developed here has the potential to illuminate the occurrence of Z-form regions in vivo, and the possible roles this transition may play in biological processes
A stitch in time: Efficient computation of genomic DNA melting bubbles
Background: It is of biological interest to make genome-wide predictions of
the locations of DNA melting bubbles using statistical mechanics models.
Computationally, this poses the challenge that a generic search through all
combinations of bubble starts and ends is quadratic.
Results: An efficient algorithm is described, which shows that the time
complexity of the task is O(NlogN) rather than quadratic. The algorithm
exploits that bubble lengths may be limited, but without a prior assumption of
a maximal bubble length. No approximations, such as windowing, have been
introduced to reduce the time complexity. More than just finding the bubbles,
the algorithm produces a stitch profile, which is a probabilistic graphical
model of bubbles and helical regions. The algorithm applies a probability peak
finding method based on a hierarchical analysis of the energy barriers in the
Poland-Scheraga model.
Conclusions: Exact and fast computation of genomic stitch profiles is thus
feasible. Sequences of several megabases have been computed, only limited by
computer memory. Possible applications are the genome-wide comparisons of
bubbles with promotors, TSS, viral integration sites, and other melting-related
regions.Comment: 16 pages, 10 figure
Conformations of closed DNA
We examine the conformations of a model for a short segment of closed DNA.
The molecule is represented as a cylindrically symmetric elastic rod with a
constraint corresponding to a specification of the linking number. We obtain
analytic expressions leading to the spatial configuration of a family of
solutions representing distortions that interpolate between the circular form
of DNA and a figure-eight form that represents the onset of interwinding. We
are also able to generate knotted loops. We suggest ways to use our approach to
produce other configurations relevant to studies of DNA structure. The
stability of the distorted configurations is assessed, along with the effects
of fluctuations on the free energy of the various configurations.Comment: 39 pages in REVTEX with 14 eps figures. Submitted to Phys. Rev. E.
This manuscript updates, expands and revises, to a considerable extent, a
previously posted manuscript, entitled "Conformations of Circular DNA," which
appeared as cond-mat/970104
Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA
We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence. Since DNA superhelicity topologically couples together the transition behaviors of all base pairs, a unified model is required to analyze all the transitions to which the DNA sequence is susceptible. Here we present a first model of this type. Our numerical approach generalizes the strategy of previously developed algorithms, which studied superhelical transitions to a single alternate conformation. We apply our multi-state model to study the competition between strand separation and B-Z transitions in superhelical DNA. We show this competition to be highly sensitive to temperature and to the imposed level of supercoiling. Comparison of our results with experimental data shows that, when the energetics appropriate to the experimental conditions are used, the competition between these two transitions is accurately captured by our algorithm. We analyze the superhelical competition between B-Z transitions and denaturation around the c-myc oncogene, where both transitions are known to occur when this gene is transcribing. We apply our model to explore the correlation between stress-induced transitions and transcriptional activity in various organisms. In higher eukaryotes we find a strong enhancement of Z-forming regions immediately 5′ to their transcription start sites (TSS), and a depletion of strand separating sites in a broad region around the TSS. The opposite patterns occur around transcript end locations. We also show that susceptibility to each type of transition is different in eukaryotes and prokaryotes. By analyzing a set of untranscribed pseudogenes we show that the Z-susceptibility just downstream of the TSS is not preserved, suggesting it may be under selection pressure
Superhelical Duplex Destabilization and the Recombination Position Effect
The susceptibility to recombination of a plasmid inserted into a chromosome
varies with its genomic position. This recombination position effect is known to
correlate with the average G+C content of the flanking sequences. Here we
propose that this effect could be mediated by changes in the susceptibility to
superhelical duplex destabilization that would occur. We use standard
nonparametric statistical tests, regression analysis and principal component
analysis to identify statistically significant differences in the
destabilization profiles calculated for the plasmid in different contexts, and
correlate the results with their measured recombination rates. We show that the
flanking sequences significantly affect the free energy of denaturation at
specific sites interior to the plasmid. These changes correlate well with
experimentally measured variations of the recombination rates within the
plasmid. This correlation of recombination rate with superhelical
destabilization properties of the inserted plasmid DNA is stronger than that
with average G+C content of the flanking sequences. This model suggests a
possible mechanism by which flanking sequence base composition, which is not
itself a context-dependent attribute, can affect recombination rates at
positions within the plasmid
Minerals information GIS for regional development and inward investment in Northern Highlands of Scotland
The principal aim of this project, funded by the Department of Trade and Industry (DTI), is to stimulate exploration for metalliferous minerals in the Northern Highlands of Scotland, thereby promoting inward investment, job creation and the development of infrastructure in the region. The Northern Highlands study area occupies about 27,000 km2 located to the north and west of the Great Glen, including the Hebrides, Orkney and Shetland. The regional geology is highly varied, comprising mainly Archaean and Proterozoic metamorphic rocks and Palaeozoic sedimentary rocks. Intrusive igneous rocks are also widely developed. This geological diversity enhances the potential of the region for the occurrence of a wide range of mineral deposit types. The Northern Highlands are under-explored, relative to other parts of Scotland; nevertheless, this study has documented more than 350 recorded mineral occurrences
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